# Patent

## Title
Heparan sulfate D-glucosaminyl 3-O-sulfotransferases, and uses therefor

## Abstract

Disclosed are novel isolated nucleic acids and substantially pure protein preparations for naturally occurring and synthetic or chimeric heparan sulfate D-glicosaminyl 3-O-sulfo-transferases (3-OSTs). Also disclosed are uses for these genes and proteins, including uses for the modification and sequencing of glycosaminoglycans.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application is a Continuation of PCT International Patent Application Serial No. PCT/US98/22597, filed on Oct. 23, 1998, which claims priority of U.S. Provisional Patent Application Ser. No. 60/062,762, filed on Oct. 24, 1997 and U.S. Provisional Patent Application Ser. No. 60/065,437, filed on Oct. 31, 1997.


FIELD OF THE INVENTION
The present invention is related to the field of biochemistry and molecular biology, and in particular to the field of enzymology and heparan sulfate biosynthesis.
BACKGROUND OF THE INVENTION
The serine proteases of the intrinsic blood coagulation cascade art slowly neutralized by antithrombin (AT) (reviewed in (1)). This inhibition is secondary to the generation of 1:1 enzyme-AT complexes whose formation is dramatically enhanced by the mast cell product, heparin (2). Damus et al. (3) hypothesized that endothelial cell surface heparan sulfate proteoglycans (HSPGs) function in a similar fashion to accelerate coagulation enzyme inactivation by AT, and therefore are responsible for the non-thrombogenic properties of blood vessels. It was initially demonstrated that profusion of the hindlimbs of normal rodents and rodents deficient in mast cells with purified thrombin (T) and AT leads to a greatly elevated rate of T-AT complex formation and that the enzyme heparitinase as well as the natural heparin antagonist platelet factor 4 suppress the above acceleration (4, 5). It was subsequently showed that cultured cloned bovine macrovascular and rodent microvascular endothelial cells synthesize both anticoagulant HSPG (HSPGact) as well as nonanticoagulant HSPG (HSPGinact) (6-14 8). HSPGact bear glycosaminoglycan (GAG) chains that bind tightly to AT and accelerate T-AT complex generation (6-8).
The biosynthesis of HSPGact requires generation of a core protein, assembly of a linkage region of four neutral sugars on specific serine attachment sites of the core protein, elongation of a GAG backbone composed of alternating N-acetylglucosamine and glucuronic acid residues, and modification of this homogenous copolymer by partial N-deacetylation with coupled N-sulfation of glucosamine residues, partial epimerization of glucuronic acid to iduronic acid residues, partial 2-O-sulfation of uronic acid residues, and partial 6-O-sulfation and partial 3-O-sulfation of glucosamine residues (reviewed in 9)). This multienzyme pathway generates HSPGact with regions of defined structure that contain the primary AT binding domain sequence found in anticoagulant heparin: uronic acid→glucosamine (N-acetyl/N-sulfate) 6-O-sulfate→glucuronic acid→glucosamine N-sulfate 3-O-sulfate (6-O-sulfate)→iduronic acid 2-O-sulfate→glucosamine N-sulfate 6-O-sulfate (10-17). These reactions also produce HSPGinact with regions of varying monosaccharide sequence that lack the primary AT-binding domain. The structure-function relationships of the AT binding domain have been elucidated with heparin/heparan sulfate oligosaccharides in association with fast reaction kinetics and equilibrium binding assays. The 6-O-sulfate group on residue 2 and the 3-O-sulfate group on residue 4 function in a thermodynamically linked fashion to supply half of the binding energy for interaction with AT, and trigger a conformational event that accelerates neutralization of specific coagulation proteases (11, 12). The amino and ester sulfate groups at residues 5 and 6, as well as carboxyl groups at other sites, provide the other half of the binding energy for interaction with protease inhibitor (10, 11). Furthermore, monosaccharide sequences outside the primary AT binding domain are essential in facilitating inhibition of coagulation proteases other than factor Xa (18, 19).
During the past eight years, several biosynthetic enzymes that generate HSPGact and HSPGinact have been purified. These proteins include an N-acetylglucosamine/glucuronic acid copolymerase (20), N-deacetylase/N-sulfotransferases (NST-1 and NST-2) (21, 22), a glucuronic acid/iduronic acid epimerase (23), an iduronic acid/glucuronic acid 2-O-sulfotransferase (2-OST) (24), a glucosamine 6-O-sulfotransferase (6-OST) (25) and a glucosamine 3-O-sulfotransferase (3-OST) (26, 35). However, the only enzymes that have also been molecularly cloned are two structurally and functionally distinct isoforms of N-deacetylase/N-sulfotransferase (NST-1 from liver and NST-2 from mastocytoma) (27-31), and the 2-OST and epimerase. The above enzymes must function in a coordinated manner to produce the AT binding domain because the abundance of this sequence is much greater than predicted from a random assembly of constituents (32). The postulated regulatory mechanism must direct the biosynthetic enzymes to carry out the appropriate sequence of epimerization/sulfation reactions to generate the AT binding domain (33, 34).
SUMMARY OF THE INVENTION
The present invention depends, in part, upon the identification and molecular cloning of novel genes encoding mammalian heparan sulfate D-glucosaminyl 3-O-sulfotransferases (3-OSTs). In particular, as disclosed herein, the present invention provides nucleic acid (SEQ ID NO: 1) and amino acid (SEQ ID NO: 2) sequences for murine 3-OST-1; nucleic acid (SEQ ID NO: 3) and amino acid (SEQ ID NO: 4) sequences for human 3-OST-1; nucleic acid (SEQ ID NO: 5) and amino acid (SEQ ID NO: 6) sequences for human 3-OST-2; nucleic acid (SEQ ID NO: 7) and amino acid (SEQ ID NO: 8) sequences for human 3-OST-3A; nucleic acid (SEQ ID NO: 9) and amino acid (SEQ ID NO: 10) sequences for human 3-OST-3B; and nucleic acid (SEQ ID NO: 11) and amino acid (SEQ ID NO: 12) sequences for human 3-OST-4. In addition, the invention provides amino acid (SEQ ID NO: 15) sequences for a C. elegans homologue, ce3-OST.
Thus, in one aspect, the present invention provides isolated nucleic acids encoding at least a functional fragment of a 3-OST protein. In preferred embodiments, the nucleic acid encodes a 3-OST protein comprising a mature murine or human 3-OST-1. In other embodiments, the nucleic acid encodes a 3-OST protein selected from 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4, and ce3-OST. In other preferred embodiments, the nucleic acid encodes a 3-O-sulfotransferase domain of a 3-OST protein selected from 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4, and ce3-OST. In particular embodiments, the nucleic acid comprises a nucleotide sequence selected from nucleotide sequences within: (a) SEQ ID NO: 1; (b) SEQ ID NO: 3; (c) SEQ ID NO: 5; (d) SEQ ID NO: 7; (e) SEQ ID NO: 9; (f) SEQ ID NO: 11; (g) a sequence having at least 60% nucleotide sequence identity with at least one of (a)-(f) and encoding a functional fragment having sequence-specific HS binding affinity or 3-O-sulfotransferase activity; and (h) a sequence differing from a sequence of (a)-(g) only by the substitution of synonymous codons. In other particular embodiments, the present invention provides an isolated nucleic acid encoding a polypeptide selected from: (a) residues 21-52, 260-269, 250-276, 53-311, or 21-307 of SEQ ID NO: 2; (b) residues 21-48, 256-265, 246-272, 49-307, or 21-303 of SEQ ID NO: 4; (c) residues 42-109, 313-325, 303-332, or 110-367 of SEQ ID NO: 6; (d) residues 44-147, 351-363, 341-370, or 148-406 of SEQ ID NO: 8; (e) residues 66-132, 336-348, 326-355, or 133-390 of SEQ ID NO: 10; (f) residues 396-408, 386-415, or 207-456 of SEQ ID NO: 12; (g) residues 240-250, 230-257, 23-291 of SEQ ID NO: 15, (h) a sequence having at least 60% amino acid sequence similarity with at least one of (a)-(g) and encoding a functional fragment having sequence-specific HS binding affinity or 3-O-sulfotransferase activity; and (i) a sequence comprising a chimera of at least two of sequences (a)-(h).
In another aspect, the present invention provides isolated nucleic acids comprising at least 16 consecutive nucleotides of a nucleotide sequence selected from SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, and SEQ ID NO: 11.
In another aspect, the present invention provides for cells and cell lines transformed with the nucleic acids of the present invention. Thus, the invention provides host cells transformed with any of the above-described nucleic acids. The transformed host cells may be bacterial, yeast, or insect cells. Preferably, however, the host cells are mammalian cells, including endothelial cells, mast cells, fibroblasts, hybridomas, oocytes, and embryonic stem cells. Examples of preferred mammalian cells include COS-7 cells, murine primary cardiac microvascular endothelial cells (CME), murine mast cell line C57.1, primary human endothelial cells of umbilical vein (HUVEC), F9 embryonal carcinoma cells, rat fat pad endothelial cells (RFPEC), L cells (e.g., murine LTA tk− cells), and cells derived from the transgenic animals of the invention. The transformed host cells may also be fetal cells, embryonic stem cells, zygotes, gametes, or germ line cells. Transformed embryonic stem cells, zygotes, gametes, and germ line cells, as well as other mammalian cells, may be used to produce transgenic animals in which the expression of 3-OST genes have been altered (e.g., knock-outs, enhanced expression, ectopic expression).
In another aspect, the present invention provides substantially pure protein preparations comprising at least a functional fragment of a 3-OST protein. Thus, in one embodiment, the present invention provides a substantially pure protein preparation comprising mature murine 3-OST-1 or mature human 3-OST-1. In another embodiment, the 3-OST protein is selected from the group consisting of 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4, and ce3-OST. In another embodiment, the fragment comprises a 3-O-sulfotransferase domain of a 3-OST protein selected from the group consisting of 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4; and ce3-OST. In particular embodiments, the present invention provides a substantially pure protein preparation in which the 3-OST protein comprises an amino acid sequence selected from: (a) SEQ ID NO: 2; (b) SEQ ID NO: 4; (c) SEQ ID NO: 6; (d) SEQ ID NO: 8; (e) SEQ ID NO: 10; (f) SEQ ID NO: 12; (g) SEQ ID NO 15; and (h) a sequence having at least 60% amino acid similarity with at least one of (a)-(g) and having sequence-specific HS binding affinity or 3-O-sulfotransferase activity. In other particular embodiments, the present invention provides a substantially pure protein preparation in which the 3-OST protein comprises an amino acid sequence selected from: (a) residues 21-52, 260-269, 250-276, 53-311, or 21-307 of SEQ ID NO: 2; (b) residues 21-48, 256-265, 246-272, 49-307, or 21-303 of SEQ ID NO: 4; (c) residues 42-109, 313-325, 303-332, or 110-367 of SEQ ID NO: 6; (d) residues 44-147, 351-363, 341-370, or 148-406 of SEQ ID NO: 8; (e) residues 66-132, 336-348, 326-355, or 133-390 of SEQ ID NO: 10; (f) residues 396-408, 386-415, or 207-456 of SEQ ID NO: 12; (g) residues 240-250, 230-257, 23-291 of SEQ ID NO: 15; (h) a sequence having at least 60% amino acid sequence similarity with at least one of (a)-(g) and encoding a functional fragment having sequence-specific HS binding affinity or 3-O-sulfotransferase activity; and (i) a sequence comprising a chimera of at least two of sequences (a)-(h).
In another aspect, the present invention provides for antibodies and methods for making antibodies which selectively bind with the 3-OST proteins. These antibodies include monoclonal and polyclonal antibodies, as well as functional antibody fragments such as F(ab) and Fc.
In another aspect, the present invention provides for methods for producing the above-described proteins. Thus, in one set of embodiments, the isolated nucleic acids of the invention may be used to transform host cells or create transgenic animals which express the proteins of the invention. The proteins may then be substantially purified from the cells or animals by standard methods. Alternatively, the isolated nucleic acids of the invention may be used in cell-free in vitro translation systems to produce the proteins of the invention.
In another aspect, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides by contacting the preparation with at least a 3-O-sulfotransferase domain of a 3-OST protein in the presence of a sulfate donor under conditions which permit sulfation of the residues, and wherein the 3-OST protein is selected from 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4, and ce3-OST proteins, as well as conservative substitution variants and/or chimeras thereof. In particular embodiments, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides in which the polysaccharides include a polysaccharide sequence of GlcA→GlcNS±6S. These methods comprise contacting the GlcA→GlcNS±6S-containing polysaccharide preparation with a 3-OST-1 protein in the presence of a sulfate donor under conditions which permit the 3-OST-1 to convert the GlcA→GlcNS±6S sequence to GlcA→GlcNS 3S±6S. In particular embodiments, the GlcA→GlcNS±6S sequence comprises a part of an HSact precursor sequence (i.e., IdoA→GlcNAc 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S or IdoA→GlcNS 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S) or a part of an HSinact precursor sequence (i.e., IdoA→GlcNAc→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S; IdoA→GlcNS→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S; IdoA→GlcNAc 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS; or IdoA→GlcNS 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS). Conversion of the HSact precursor pool to HSact increases the fraction with AT-binding activity and is particularly useful in the production of anticoagulant heparan sulfate products. Thus, in another embodiment, the present invention provides for means of enriching the AT-binding fraction of a heparan sulfate pool by contacting the polysaccharide preparation with 3-OST-1 protein in the presence of a sulfate donor under conditions which permit the 3-OST HSact conversion activity. The 3-OST-1 protein for use in these methods is selected from murine 3-OST-1, human 3-OST-1, mature murine 3-OST-1, mature human 3-OST-1, a functional fragment of a 3-OST-1 having 3-O-sulfotransferase activity, a conservative substitution variant of 3-OST-1 having 3-O-sulfotransferase activity, and a chimeric 3-OST-1 having 3-O-sulfotransferase activity. In preferred embodiments, the sulfate donor is 3′-phospho-adenosine 5′-phosphosulfate (PAPS).
Similarly, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides by contacting the preparation with at least a 3-O-sulfotransferase domain of a 3-OST protein in the presence of a sulfate donor under conditions which permit sulfation of the residues, and wherein the 3-OST protein is selected from 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4, ce3-OST and conservative substitution variants or chimeras thereof. In particular embodiments, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides in which the polysaccharides include a polysaccharide sequence of GlcA 2S→GlcNS. These methods comprise contacting the GlcA 2S→GlcNS-containing polysaccharide preparation with a 3-OST-2 protein in the presence of a sulfate donor under conditions which permit the 3-OST-2 protein to convert the GlcA 2S→GlcNS sequence to GlcA 2S→GlcNS 3S. In particular embodiments, the GicA 2S→GlcNS sequence comprises a part of a GlcNS→GlcA 2S→GlcNS sequence. In other particular embodiments, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides in which the polysaccharides include a polysaccharide sequence of IdoA 2S→GlcNS. These methods comprise contacting the IdoA 2S→GlcNS-containing polysaccharide preparation with a 3-OST-3 protein in the presence of a sulfate donor under conditions which permit the 3-OST-3 protein to convert the IdoA 2S→GlcNS sequence to IdoA 2S→GlcNS 3S. In particular embodiments, the IdoA 2S→GlcNS sequence comprises a part of a GlcNS→IdoA 2S→GlcNS sequence. The 3-OST proteins for use in these methods are selected from 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4ce3-OST, functional fragments of these 3-OSTs having 3-O-sulfotransferase activity, conservative substitution variants of these 3-OSTs having 3-O-sulfotransferase activity, and chimeric 3-OSTs having 3-O-sulfotransferase activity. In preferred embodiments, the sulfate donor is 3′-phospho-adenosine 5′-phosphosulfate (PAPS).
In another aspect, the present invention provides methods for partially sequencing complex polysaccharides such as heparan sulfates or other glycosaminoglycans (GAGs). In these methods, a pool of polysaccharides which includes sequences which may be 3-O-sulfated is contacted with a 3-OST protein in the presence of a sulfate donor (e.g., PAPS) under conditions which permit sulfation by the 3-OST. The treated polysaccharides are then subjected to degradation by enzymes which degrade polysaccharides in a sequence-specific manner (e.g., polysaccharide lyases; heparinase I, II or III; heparitinase) and the size profile of the resulting fragments is determined. An identical pool which has not been treated with 3-OST is similarly cleaved by the same enzymes and a size profile determined. Changes in the size profiles indicate that 3-OST activity has modified the saccharide units so as to prevent (or permit) cleavage at sites which previously were (or were not) cleaved. Thus, comparison of the profiles will indicate positions at which the target sequences for 3-OST activity are present and provide a partial polysaccharide sequence.
In another embodiment, the sequence of complex polysaccharides such as HS or GAGs may be partially determined using sequence specific polysaccharide affinity fractionation. To this end, 3-OST proteins which lack enzymatic function but retain sequence-specific HS or GAG binding capacity can be identified or produced (e.g., altering or deleting a portion of the catalytic ST domain by site-directed mutagenesis or deletion mutagenesis). These inactive forms will bind HS or GAGs in a sequence dependent manner and allow sequence-specific saccharide affinity fractionation from complex mixtures of GAGs. The purified structures may be degraded in a step-wise fashion with exolytic, endolytic enzymes and/or nitrous acid, and the resulting degradation products can be compared to standard compounds of known structure. This method will allow the quantitation and characterization of known structures contained within unknown complex polysaccharide samples.
In another embodiment, partial sequence information can be obtained using the 3-OSTs of the invention or other heparan sulfate sequence specific binding ligands as protective groups prior to treating the HS or GAG with modifying agents that detectably alter the HS or GAG. Useful protective groups include catalytically inactive enzymes, chimeric enzymes and small molecule ligands with identified sequence binding specificities. The protecting group is contacted with the heparan or other glycosaminoglycans (GAGs), and the resultant complex is treated with one or more modifying agents. Useful modifying agents include catalytically active heparan lyases, sulfotransferases, N-deacetylases, N-acetyltransferases, epimerases, or chimeric proteins of the invention. In embodiments where multiple protecting groups and/or modifying reagents are used in combination, the sample is first contacted with the protective group, then one or more modifying reagents may be with contacted with the protected polysaccharide, either simultaneously or in turn. The protective group(s) will interfere with the ability of a modifying agent to interact with, attach to and/or cleave specific GAG sequence motifs. The sample can then be analyzed for ligand-specific protection and/or cleavage to elucidate the sequence of the original GAG using separation and/or quantitation using methods known in the art.
In another aspect, the present invention also provides methods for diagnosing individuals with disorders involving heparan sulfate biosynthesis comprising assaying such individuals for the presence of mutations in 3-OST genes/proteins. Such assays include nucleic acid based assays (employing the nucleic acids of the present invention), protein based assays (employing the antibodies of the present invention), and HS based assays employing the glycosaminoglycan sequencing methods of the present invention.
These and other aspects of the present invention will be apparent to one of ordinary skill in the art from the following detailed description.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is an alignment of the amino acid sequences of murine and human 3-OST-1 proteins (SEQ ID NO: 2 and 4, respectively), showing the degree of homology. Vertical bars (|) between residues indicate identical residues.
FIG. 2 is an alignment of the sulfotransferase domains of human NST-1 (SEQ ID NO: 13), human NST-2 (SEQ ID NO: 14), C. elegans (residues 23-291 of SEQ ID NO: 15), human 3-OST-4 (residues 193-456 of SEQ ID NO: 12), human 3-OST-3A (residues 148-406 of SEQ ID NO: 8), human 3-OST-2 (residues 110-367 of SEQ ID NO: 6) and human 3-OST-1 (residues 49-307 of SEQ ID NO: 4).
FIG. 3 is a schematic depiction of the structures of the 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B and 3-OST-4 proteins.



DETAILED DESCRIPTION OF THE INVENTION
Definitions
In order to more clearly and distinctly point out and describe the subject matter that applicants regard as the invention, the following definitions are provided for certain terms used in the following written description and the appended claims.
Isolated nucleic acids. As used herein with respect to nucleic acids derived from naturally-occurring sequences, the term “isolated nucleic acid” means a ribonucleic or deoxyribonucleic acid which comprises a naturally-occurring nucleotide sequence and which is manipulable by standard recombinant DNA techniques, but which is not covalently joined to the nucleotide sequences that are immediately contiguous on its 5′ and 3′ ends in the naturally-occurring genome of the organism from which it is derived. As used herein with respect to synthetic nucleic acids, the term “isolated nucleic acid” means a ribonucleic or deoxyribonucleic acid which comprises a nucleotide sequence which does not occur in nature and which is manipulable by standard recombinant DNA techniques. An isolated nucleic acid is manipulable by standard recombinant DNA techniques when it may be used in, for example, amplification by polymerase chain reaction (PCR), in vitro translation, ligation to other nucleic acids (e.g., cloning or expression vectors), restriction from other nucleic acids (e.g., cloning or expression vectors), transformation of cells, hybridization screening assays, or the like. The term “isolated nucleic acids” is also intended to embrace synthetic oligonucleotides such as peptide nucleic acids (PNAs), nucleotides joined by phosphorothioate or other non-phosphodiester linkages, nucleic acids incorporating functionally equivalent nucleotide analogs, and the like.
Transformation As used herein, means any method of introducing exogenous a nucleic acid into a cell including, but not limited to, transformation, transfection, electroporation, microinjection, direct injection of naked nucleic acid, particle-mediated delivery, viral-mediated transduction or any other means of delivering a nucleic acid into a host cell which results in transient or stable expression of said nucleic acid or integration of said nucleic acid into the genome of said host cell or descendant thereof.
Substantially pure. As used herein with respect to protein preparations, the term “substantially pure” means a preparation which contains at least 60% (by dry weight) the protein of interest, exclusive of the weight of other intentionally included compounds. Preferably the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by dry weight the protein of interest, exclusive of the weight of other intentionally included compounds. Purity can be measured by any appropriate method, e.g., column chromatography, gel electrophoresis, or HPLC analysis. If a preparation intentionally includes two or more different proteins of the invention, a “substantially pure” preparation means a preparation in which the total dry weight of the proteins of the invention is at least 60% of the total dry weight, exclusive of the weight of other intentionally included compounds. Preferably, for such preparations containing two or more proteins of the invention, the total weight of the proteins of the invention be at least 75%, more preferably at least 90%, and most preferably at least 99%, of the total dry weight of the preparation, exclusive of the weight of other intentionally included compounds. Thus, if the proteins of the invention are mixed with one or more other proteins (e.g., serum albumin, 6-OST) or compounds (e.g., diluents, detergents, excipients, salts, polysaccharides, sugars, lipids) for purposes of administration, stability, storage, and the like, the weight of such other proteins or compounds is ignored in the calculation of the purity of the preparation.
Similarity. As used herein with respect to amino acid sequences, the “similarity” between two sequences means the percentage of amino acid residue positions, after aligning the sequences according to standard techniques, at which the two sequences have identical or similar residues. In general, “similar” residues include those which are regarded in the art as “conservative substitutions” (see, e.g., Dayhoff et al. (1978), Atlas of Protein Sequence and Structure Vol. 5 (Suppl. 3), pp. 354-352, Natl. Biomed. Res. Found., Washington, D.C.); which fall within the groups (a) methionine, leucine, isoleucine and valine, (b) phenylalanine, tyrosine and tryptophan, (c) lysine, arginine and histidine, (d) alanine and glycine. (e) serine and threonine, (f) glutamine and asparagine. and (g) glutamate an aspartate; or which are otherwise shown to have no substantial effect on the biological activity of the protein. Numerical values for similarity were determined using the PileUp program. This program performed multiple sequence alignments based on methods of Feng and Doolittle (1987) J. Mol. Evol. 35: 351-360, and Higgins and Sharp (1998), CABIOS 5:151-153. Using these methods for each sequence alignment, the gap weight was set at 3.0 and the gap length was set at 0.10. Percentages of similarity recited in the appended claims may be determined by these methods.
Chimeric protein. As used herein, the term “chimeric protein” means a protein having an amino acid sequence which is a positionally conserved combination of the amino acid sequences of two or more other proteins. Thus, for a chimera of two or more reference proteins, the amino acid sequences of the reference proteins are aligned by standard techniques to identify residues which correspond at each position, allowing for relative insertions/deletions as necessary. Then, for each amino acid position of the chimeric protein, an amino acid residue is selected from the residues present at corresponding positions in the two or more reference proteins (allowing for no residue in the chimera when deletions are present amongst the reference proteins). The resultant chimera has an amino acid sequence which is a combination of the reference amino acid sequences, in which the relative position of each residue selected from the reference sequences is conserved within the chimera.
Heparan sulfate. As used herein, the term “heparan sulfate” or the abbreviation “HS” means a polysaccharide of the form ([→4-D-GlcApβ1 or →4-L-IdoApα1]→4-D-GlcNp[Ac or S]α1→)n which is modified to a variable extent by sulfation of the 2-O-position of Glc and Ido residues, and the 6-O- and 3-O-positions of GlcN[Ac or S] residues. Therefore, this definition encompasses all glycosaminoglycan compounds referred to as heparan(s), heparan sulfate(s), heparin(s), heparin sulfate(s), heparitin(s), heparitin sulfate(s), heparanoid(s), heparosan(s). The heparan molecules may be pure glycosaminoglycans or can be linked to other molecules including other polymers such as proteins, and lipids, or small molecules such as biotin.
The Heparan Sulfate D-Glucosaminyl 3-O-Sulfotransferaseses. The present invention depends, in part, upon the identification and molecular cloning of cDNAs encoding mammalian heparan sulfate D-glucosaminyl 3-O-sulfotransferases (3-OSTs). These proteins have been designated 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, and 3-OST-4. In addition, a nematode 3-OST from C. elegans, ce3-OST, has been identified.
3-OST-1s. Disclosed herein are the isolation and identification of murine and human 3-OST-1 cDNAs (SEQ ID NO: 1 and SEQ ID NO: 3, respectively). The coding regions of these cDNAs extend from, respectively, nucleotide positions 323-1255 of SEQ ID NO: 1 and positions 119-1039 of SEQ ID NO: 3. The protein coding portions of the cDNAs are 85% identical and encode proteins of 311 and 307 amino acids (SEQ ID NO: 2 and SEQ ID NO: 4, respectively) which are 93% similar. The murine and human protein sequences are aligned in FIG. 1. Each protein includes a twenty residue presumptive signal peptide (residues 1-20 of SEQ ID NO: 2 and SEQ ID NO: 4) which is cleaved off to form the mature form of these proteins. The mouse 3-OST-1 contains an extra four residues (Ala24-Pro25-Gly26-Pro27) not found in the human form. Each protein has five potential N-glycosylation sites (at residues 52-54, 141-143, 196-198, 246-248 and 253-255 of SEQ ID NO: 2, and residues 48-50, 137-139, 192-194, 242-244, 249-251 of SEQ ID NO: 4). N-glycosylation of at least some of these sites appears important to 3-OST protein stability, specificity and/or activity. After the 3-OST-1 signal peptide, there is a domain rich in the residues S, P, L, A, and G (SPLAG-rich domain) (residues 21-52 of SEQ ID NO: 2 and residues 21-48 of SEQ ID NO: 4). 3-OST-1 and all known NST species possess a homologous carboxy terminal sulfotransferase (ST) domain of  ̃260 amino acids (residues 53-311 of SEQ ID NO: 2 and residues 49-307 of SEQ ID NO: 4) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. FIG. 2 shows a sequence alignment of the ST domains of the sulfotransferases NST-1 (SEQ ID NO: 13), NST-2 (SEQ ID NO: 14), OST-1, OST-2, OST-3A/B, and OST-4. Within this region is a conserved sequence (at residues 260-269 of SEQ ID NO: 2, and 256-265 of SEQ ID NO: 4) which is a presumptive cysteine-bridged peptide loop thought to be involved in heparan sulfate substrate specificity. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 250-276 of SEQ ID NO: 2 and 246-272 of SEQ ID NO: 4). A conserved lysine residue (residue 68 of SEQ ID NO: 2, and 64 of SEQ ID NO: 4) is presumptively catalytic.
The 3-OST-1 proteins have 3-O-sulfotransferase activity on polysaccharide sequences including the sequence GlcA→GlcNS±6S, and convert this polysaccharide sequence to the sequence to GlcA→GlcNS 3S±6S. Of particular importance, the 3-OST-1 proteins are useful in converting HSact precursor sequences (i.e., IdoA→GlcNAc 6S→GlcAGlcNS±6S→IdoA 2S→GlcNS 6S; or IdoA→GlcNS 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S) to HSact. The 3-OST-1 proteins are highly expressed in endothelial cells, brain and kidney tissues, and to a lesser extent in heart, lung, skeletal muscle and placenta. The human 3-OST-1 gene has been syntactically localized to chromosome 4, and more particularly to chromosome segment 4p 15-16.
3-OST-2s. Also disclosed herein are the isolation and identification of a human 3-OST-2 cDNA (SEQ ID NO: 5). The coding region of this cDNA extends from nucleotide positions 73-1173 of SEQ ID NO: 5. The cDNA encodes a protein of 367 amino acids (SEQ ID NO: 6). The protein has four potential N-glycosylation sites (at residues 102-104, 193-195, 235-237 and 306-308 of SEQ ID NO: 6). N-glycosylation of at least some of these sites appears important to 3-OST protein stability, specificity and/or activity. The 3-OST-2 protein has a putative N-terminal cytoplasmic domain (residues 1-19 of SEQ ID NO: 6), followed by a putative transmembrane domain (residues 20-41 of SEQ ID NO: 6), followed by a SPLAG-rich domain (residues 42-109 of SEQ ID NO: 6). This is followed by the characteristic carboxy terminal ST domain of  ̃260 amino acids (residues 110-367 of SEQ ID NO: 6) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. Within this region is a conserved sequence (at residues 313-325 of SEQ ID NO: 6) which is a presumptive cysteine-bridged peptide loop thought to be involved in heparan sulfate substrate specificity. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 303-332 of SEQ ID NO: 6). A conserved lysine residue (residue 24 of SEQ ID NO: 6) is presumptively catalytic. A cDNA of an allelic variant has also been identified, which includes four silent nucleotide substitutions (G→A at bp 804, T→G at bp 1249, T→C at bp 1350, and C→T at bp 1507 of SEQ ID NO: 5) which do not affect the encoded protein.
The 3-OST-2 proteins have 3-O-sulfotransferase activity on polysaccharide sequences including the sequences GlcA 2S→GlcNS or GlcNS→GlcA 2S→GlcNS, and convert these polysaccharide sequences to GlcA 2S→GlcNS 3S or GlcNS→GlcA 2S→GlcNS 3S, respectively. The 3-OST-2 proteins are not expressed in endothelial cells, but are highly expressed in brain tissues, and to a lesser extent in heart, lung, skeletal muscle and placenta. The human 3-OST-2 gene has been localized to chromosome 16, and more particularly to chromosome segment 16p12.3.
3-OST-3As. Also disclosed herein are the isolation and identification of a human 3-OST-3A cDNA (SEQ ID NO: 7). The coding region of this cDNA extends from nucleotide positions 799-2016 of SEQ ID NO: 7. The cDNA encodes a protein of 406 amino acids (SEQ ID NO: 8). The protein has two potential N-glycosylation sites (at residues 273-275 and 344-346 of SEQ ID NO: 8). N-glycosylation of one or more of these sites appears important to 3-OST protein stability, specificity and/or activity. The 3-OST-3A protein has a putative N-terminal cytoplasmic domain (residues 1-24 of SEQ IDNO: 8), followed by a putative transmembrane domain (residues 25-43 of SEQ ID NO: 8), followed by a SPLAG-rich domain (residues 44-147 of SEQ ID NO: 8). This is followed by the characteristic carboxy terminal ST domain of  ̃260 amino acids (residues 148-406 of SEQ ID NO: 8) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. Within this region is a conserved sequence (at residues 351-363 of SEQ ID NO: 8) which is a presumptive cysteine-bridged peptide loop thought to be involved in heparan sulfate substrate specificity. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 341-370 of SEQ ID NO: 8). A conserved lysine residue (residue 162 of SEQ ID NO: 8) is presumptively catalytic.
The 3-OST-3A proteins have 3-O-sulfotransferase activity on polysaccharide sequences including the sequences IdoA 2S→GlcNS or GlcNS→IdoA 2S→GlcNS, and convert these polysaccharide sequences to IdoA 2S→GlcNS 3S or GlcNS→IdoA 2S→GlcNS 3S, respectively. The 3-OST-3A proteins are not expressed in endothelial cells, but are highly expressed in kidney, placenta and liver tissues, and to a lesser extent in brain, heart, lung, and skeletal muscle.
3-OST-3Bs. Also disclosed herein are the isolation and identification of a human 3-OST-3B cDNA (SEQ ID NO: 9). The coding region of this cDNA extends from nucleotide positions 331-1500 of SEQ ID NO: 9. The cDNA encodes a protein of 390 amino acids (SEQ ID NO: 10). The protein has two potential N-glycosylation sites (at residues 258-260 and 329-331 of SEQ ID NO: 10). N-glycosylation of one or more of these sites appears important to 3-OST protein stability, specificity and/or activity. The 3-OST-3B protein has a putative N-terminal cytoplasmic domain (residues 1-32 of SEQ ID NO: 10), followed by a putative transmembrane domain (residues 33-65 of SEQ ID NO: 10), followed by a SPLAG-rich domain (residues 66-132 of SEQ ID NO: 10). This is followed by the characteristic carboxy terminal ST domain of  ̃260 amino acids (residues 133-390 of SEQ ID NO: 10) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. Within this region is a conserved sequence (at residues 336-348 of SEQ ID NO: 10) which is a presumptive cysteine-bridged peptide loop thought to be involved in heparan sulfate substrate specificity. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 326-355 of SEQ ID NO: 10). A conserved lysine residue (residue 147 of SEQ ID NO: 10) is presumptively catalytic.
The 3-OST-3B proteins have 3-O-sulfotransferase activity on polysaccharide sequences including the sequences IdoA 2S→GlcNS or GlcNS→IdoA 2S→GlcNS, and convert these polysaccharide sequences to IdoA 2S→GlcNS 3S or GlcNS→IdoA 2S→GlcNS 3S, respectively. The 3-OST-3A proteins are not expressed in endothelial cells, but are highly expressed in kidney, placenta and liver tissues, and to a lesser extent in brain, heart, lung, and skeletal muscle.
3-OST-4s. Also disclosed herein are the isolation and identification of a human 3-OST-4 nucleic acid sequence (SEQ ID NO: 11). This sequence represents is a possible or predicted heteronuclear RNA species, and is a composite of 5′ genomic sequences information and an overlapping partial cDNA. The coding region of this sequence extends from nucleotide positions 847-2214 of SEQ ID NO: 11, and encodes a protein of 456 amino acids (SEQ ID NO: 12). The protein has two potential N-glycosylation sites (at residues 318-320 and 389-391 of SEQ ID NO: 12). N-glycosylation of one or more of these sites appears important to 3-OST protein stability, specificity and/or activity. The 3-OST-4 includes the characteristic carboxy terminal ST domain of  ̃260 residues (residues 207-456 of SEQ ID NO: 12) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. Within this region is a conserved sequence (at residues 396-408 of SEQ ID NO: 12) which is a presumptive cysteine-bridged peptide loop thought to be positioned near the active site. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 386-415 of SEQ ID NO: 12). A conserved lysine residue (residue 207 of SEQ ID NO: 12) is presumptively catalytic.
The 3-OST-4 proteins have sulfotransferase activity, but the sequence specificity of this activity has not yet been determined. The 3-OST-4 proteins appear to be expressed at detectable levels only in the brain. The human 3-OST-4 gene has been localized to chromosome 16, and more particularly to chromosome segment 16p11.
C. elegans 3-OSTs. Also disclosed herein is the identification of a C. elegans homologue of the human 3-OSTs, ce3-OST. This protein is disclosed as SEQ ID NO: 15, and includes the characteristic carboxy terminal ST domain of  ̃260 residues (residues 23-291 of SEQ ID NO: 15) that exhibits homology to all known sulfotransferases and which includes the minimal fragment necessary for sulfation activity. Within this region is a conserved sequence (at residues 240-250 of SEQ ID NO: 15) which is a presumptive cysteine-bridged peptide loop thought to be positioned near the active site. This cysteine-bridged peptide loop is part of the larger HS-binding domain (residues 230-257 of SEQ ID NO: 15). A conserved lysine residue (residue 38 of SEQ ID NO: 15) is presumptively catalytic.
The C. elegans 3-OST proteins have sulfotransferase activity, but the sequence specificity of this activity has not yet been determined. BLAST and Genefinder anaysis of genomic cosmids predicts that ce3-OST is an intraluminal resident protein of 291 residues encoded by 4 exons (clone F52B10, Gban U41990; residues 26317-26090, 21886-21732, 21682-21395, and 21345-21140).
The homology between the sulfotransferase domain of the ce3-OST and the human 3-OST and NST proteins is illustrated in FIG. 2. BAsed on this sequence alignment, one may also produce chimeric proteins between and the C elegans protein and its human homologues.
Isolated Nucleic Acids
In one aspect, the present invention provides isolated nucleic acids encoding 3-OST proteins or functional fragments thereof. In preferred embodiments, the 3-OST proteins are 3-OST-1 proteins, 3-OST-2 proteins, 3-OST-3A proteins, 3-OST-3B proteins, 3-OST-4 proteins, or ce3-OST proteins. In particularly preferred embodiments, the 3-OST proteins are those disclosed as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 15. As shown in the examples below, the isolated nucleic acids encoding all or a portion of one mammalian 3-OST protein may be used to isolate homologues in other species by standard techniques known to those of ordinary skill in the art. Thus, the present invention also enables isolated nucleic acids encoding the 3-OST proteins of other mammalian species including, for example, rats, goats, sheep, cows, pigs, and non-human primates. Similarly, the isolated nucleic acids disclosed herein may be used to screen additional human or other mammalian genetic libraries (e.g., genomic or cDNA libraries) to identify allelic variants of the particularly disclosed sequences. Thus, the present invention also enables isolated nucleic acids encoding human and other mammalian 3-OST allelic variants.
In another aspect, the present invention provides isolated nucleic acids encoding functional fragments of 3-OST proteins, 3-OST protein variants in which conservative substitutions have been made for certain residues, or encoding chimeric 3-OST proteins in which the sequences of two or more 3-OST proteins have been mixed, to produce non-naturally occurring variants which retain sequence-specific HS binding affinity and/or 3-O-sulfotransferase activity. The preferred amino acid sequences of such variants are described below.
In preferred embodiments, the isolated nucleic acids encoding a mammalian 3-OST or functional fragment thereof have at least 60%, preferably at least 70%, and more preferably at least 80% nucleotide sequence identity to the coding regions of the mammalian 3-OST sequences particularly disclosed herein (SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9 and SEQ ID NO: 11), and encode at least a functional fragment having sequence-specific HS binding affinity and/or 3-O-sulfotransferase activity. Most preferably, the sequences have at least 90% or 95% nucleotide sequence identity to the disclosed reference sequences.
As will be apparent to one of ordinary skill in the art, the degeneracy of the genetic code allows for numerous nucleotide substitutions in a given coding sequence which do not affect the amino acid sequence of the encoded protein. Thus, the present invention also provides for isolated nucleic acids which differ from any of the above-described sequences only by the substitution of such synonymous codons.
The isolated nucleic acids of the present invention may be joined to other nucleic acid sequences for use in various applications. Thus, for example, the isolated nucleic acids of the invention may be ligated into cloning or expression vectors, as are commonly known in the art and as described in the examples below. In addition, the nucleic acids of the invention may be joined in-frame to sequences encoding another polypeptide so as to form a fusion protein, as is commonly known in the art and as described in the examples below. Thus, in certain embodiments, the present invention provides cloning, expression and fusion vectors comprising any of the above-described nucleic acids.
In another aspect, the isolated nucleic acids of the present invention may comprise only a portion of a nucleotide sequence encoding a complete mammalian 3-OST protein. For example, and as described more fully below, the 3-OST-1 proteins comprise a signal sequence which is removed post-translationally to yield the mature proteins. In some instances (e.g., when translating 3-OST-1 proteins in vitro), it may be preferable to employ an isolated nucleic acid which encodes only the mature protein. In addition, the four C-terminal residues of 3-OST-1 are believed to be involved in localization of the protein within the Golgi apparatus. In some instances (e.g., when encoding 3-OST-1 proteins for use in vitro), it may be preferable to employ an isolated nucleic acid which does not encode these residues, as they will be unnecessary for in vitro function. As described above, an approximately 260 residue portion of the 3-OST proteins includes the catalytically active region (ST domain) and, therefore, it may be preferable to employ an isolated nucleic acid which encodes only this functional fragment which retains 3-O-sulfotransferase activity. Thus, in certain preferred embodiments, the present invention provides isolated nucleic acid sequences encoding mature forms of a mammalian 3-OST-1 protein, C-terminally truncated forms of the 3-OST proteins, or minimal functional fragments of the 3-OST proteins. In addition, as described above, these sequences may also encode conservative substitution variants or chimeras of 3-OST proteins, and may include synonymous codon substitutions.
In another aspect, the present invention provides for nucleic acids which comprise a sequence of at least 16-18, preferably 18-20 consecutive nucleotides from any one of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9 and SEQ ID NO: 11. Such nucleic acid sequences have utility for determining the levels of expression of 3-OST transcripts in cells or tissues, for identifying tissues in which the 3-OST genes are differentially expressed (see above), for encoding peptide fragments which may be used to raise antibodies to corresponding regions of the 3-OST proteins, identifying chromosomes bearing the corresponding 3-OST sequences (see above), for priming polymerase chain reaction amplification of 3-OST sequences (e.g., prior to in vitro translation, see below), and for various other utilities which will be apparent to those skilled in the art. Particularly preferred sequences for PCR amplification include those which are 5′ to and/or include the initiation codon, which are 5′ to and/or include the codons encoding the signal peptide cleavage site, or which are 3′ to and/or include the termination codon. Sequences useful for encoding peptide fragments include those which are located within the coding region.
Cell Lines and Transgenic Animals
The present invention also provides for cells or cell lines, both prokaryotic and eukaryotic, into which have been introduced the nucleic acids of the present invention so as to cause clonal propagation of those nucleic acids and/or expression of the proteins or peptides encoded thereby. Such cells or cell lines have utility in the propagation and production of the nucleic acids of the invention, as well as the production of the proteins of the present invention. As used herein, the term “transformed cell” is intended to embrace any cell, or the descendant of any cell, into which has been introduced any of the nucleic acids of the invention, whether by transformation, transfection, transduction, infection, or other means. Methods of producing appropriate vectors, transforming cells with those vectors, and identifying transformants are well known in the art and are only briefly reviewed here (see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
Prokaryotic cells useful for producing the transformed cells of the invention include members of the bacterial genera Escherichia (e.g., E. coli), Pseudomonas (e.g., P. aeruginosa), and Bacillus (e.g., B. subtiilus, B. stearolhermophilus), as well as many others well known and frequently used in the art. Prokaryotic cells are particularly useful for the production of large quantities of the proteins or peptides of the invention (e.g., naturally occurring or synthetic 3-OSTs, fragments of the 3-OSTs, fusion proteins of the 3-OSTs). Bacterial cells (e.g., E. coli) may be used with a variety of expression vector systems including, for example, plasmids with the T7 RNA polymerase/promoter system, bacteriophage λ regulatory sequences, or M13 Phage regulatory elements. Bacterial hosts may also be transformed with fusion protein vectors which create, for example, Protein A, lacZ, trpE, maltose-binding protein, poly-His tag, or glutathione-S-transferase fusion proteins. All of these, as well as many other prokaryotic expression systems, are well known in the art and widely available commercially (e.g., pGEX-27 (Amrad, USA) for GST fusions).
Eukaryotic cells and cell lines useful for producing the transformed cells of the invention include mammalian cells (e.g., endothelial cells, mast cells, COS cells, CHO cells, fibroblasts, hybridomas, oocytes, embryonic stem cells), insect cells lines (e.g., Drosophila Schneider cells), yeast, and fungi. Eukaryotic cells are particularly useful for embodiments in which it is necessary that the 3-OST proteins, or functional fragments thereof, be properly post-translationally modified (e.g., N-glycosylated) because N-glycosylation of these proteins appears to be important to their stability and/or activity. Currently preferred cells are mammalian cells and, in particular, COS-7 cells, CHO, cells, murine primary cardiac microvascular endothelial cells (CME), murine mast cell line C57.1, human primary endothelial cells of umbilical vein (HUVEC), F9 embryonal carcinoma cells, rat fat pad endothelial cells (RFPEC), L cells (e.g., murine LTA tk− cells), and cells derived from the transgenic animals of the invention.
To accomplish expression in eukaryotic cells, a wide variety of vectors have been developed and are commercially available which allow inducible (e.g., LacSwitch expression vectors, Stratagene, La Jolla, Calif.) or constitutive (e.g., pcDNA3 vectors, Invitrogen, Chatsworth, Calif.) expression of 3-OST nucleotide sequences under the regulation of an artificial promoter element. Such promoter elements are often derived from CMV or SV40 viral genes, although other strong promoter elements which are active in eukaryotic cells can also be employed to induce transcription of 3-OST nucleotide sequences. Typically, these vectors also contain an artificial polyadenylation sequence and 3′ UTR which can also be derived from exogenous viral gene sequences or from other eukaryotic genes. These expression systems are commonly available from commercial sources and are typified by vectors such as pcDNA3 and pZeoSV (Invitrogen, San Diego, Calif.). As described below, the vector pcDNA3 has been successfully used to cause expression of 3-OST-1 proteins in transfected COS-7 cells. Numerous expression vectors are available from commercial sources to allow expression of any desired 3-OST transcript in more or less any desired cell type, either constitutively or after exposure to a certain exogenous stimulus (e.g., withdrawal of tetracycline or exposure to IPTG).
Vectors may be introduced into the recipient or “host” cells by various methods well known in the art including, but not limited to, calcium phosphate transfection, strontium phosphate transfection, DEAE dextran transfection, electroporation, lipofection, microinjection, ballistic insertion on micro-beads, protoplast fusion or, for viral or phage vectors, by infection with the recombinant virus or phage.
Transgenic Animal Models
The present invention also provides for the production of transgenic non-human animal models in which wild type, allelic variant, chimeric, or antisense 3-OST sequences are expressed, or in which 3-OST sequences have been inactivated or deleted (e.g., “knock-out” constructs) or replaced with reporter or marker genes (e.g., “knock-in reporter construct”). The 3-OST sequences may be conspecific to the transgenic animal (e.g., murine sequences in a transgenic mouse) or transpacific to the transgenic animal (e.g. human sequence in a transgenic mouse). In such a transgenic animal, the trangenic sequences may be expressed inducibly, constitutively or ectopically. Expression may be tissue-specific or organism-wide. Engineered expression of 3-OST sequences in tissues and cells not normally containing 3-OST gene products may cause novel alterations of heparan polysaccharide structure and lead to novel cell or tissue phenotypes. Ectopic or altered levels of expression of 3-OST sequences may alter cell, tissue and/or developmental phenotypes. Transgenic animals are useful as models of thromboembolic and other disorders arising from defects in heparan sulfate biosynthesis or metabolism. Transgenic animals are also useful for screening compounds for their effects on HS biosynthesis mediated by 3-OSTs. Transgenic animals transformed with reporter constructs may be used to measure the transcriptional effects of small molecules, drugs, protein physiological mediators, carbohydrate effectors, mimetic compounds or physical perturbations on the expression of 3-OST loci in vivo. The transgenic animals of the invention, may be used to screen such compounds for therapeutic utility.
Animal species suitable for use in the animal models of the present invention include, but are not limited to, rats, mice, hamsters, guinea pigs, rabbits, dogs, cats, goats, sheep, pigs, and non-human primates (e.g., Rhesus monkeys, chimpanzees). For initial studies, transgenic rodents (e.g., mice) are preferred due to their relative ease of maintenance and shorter life spans. Transgenic non-human primates may be preferred for longer term studies due to their greater similarity to humans and their higher cognitive abilities.
Using the a nucleic acid disclosed and otherwise enabled herein, there are now several available approaches for the creation of a transgenic animal. Thus, the enabled animal models include: (1) animals in which sequences encoding at least a functional fragment of a wild type 3-OST gene has been recombinantly introduced into the genome of the animal as an additional gene, under the regulation of either an exogenous or an endogenous promoter element, and as either a minigene (i.e., a genetic construct of the 3-OST with the introns, if any, removed) or a large genomic fragment; (2) animals in which sequences encoding at least a functional fragment of a normal 3-OST gene have been recombinantly substituted for one or both copies of the animal's homologous 3-OST gene by homologous recombination or gene targeting; (3) animals in which one or both copies of one of the animal's homologous 3-OST genes have been recombinantly “humanized” by the partial substitution of sequences encoding the human homologue by homologous recombination or gene targeting; (4) animals in which sequences encoding 3-OST transcriptional elements linked to a reporter gene have replaced the endogenous 3-OST gene and transcriptional elements; (5) “knock-out” animals in which one or both copies of the animal's 3-OST sequences have been partially or completely deleted or have been inactivated by the insertion or substitution by homologous recombination or gene targeting of exogenous sequences (e.g., stop codons,); (6) animals in which additional genes related to the biosynthesis or metabolism of heparan sulfates have been altered (e.g., a murine transgenic in which all of the genes in the HS pathway have been humanized). These and other transgenic animals of the invention are useful as models of thromboembolic and other disorders arising from defects in heparan sulfate biosynthesis or metabolism. These animals are also useful for screening compounds for their effects on HS biosynthesis mediated by 3-OSTs.
To produce an animal model (e.g., a transgenic mouse), a wild type or allelic variant 3-OST sequence or a wild type or allelic variant of a recombinant nucleic acid encoding at least a functional fragment of a 3-OST is preferably inserted into a germ line or stem cell using standard techniques of oocyte or embryonic stem cell microinjection, or other form of transformation of such cells. Alternatively, other cells from adult organism may be employed. Animals produced by these or similar processes are referred to as transgenic. Similarly, if it is desired to inactivate or replace an endogenous 3-OST sequence, homologous recombination using oocytes, embryonic stem or other cells may be employed. Animals produced by these or similar processes are referred to as “knock-out” (inactivation) or “knock-in” (replacement) models.
For oocyte injection, one or more copies of the recombinant DNA constructs of the present invention may be inserted into the pronucleus of a just-fertilized oocyte. This oocyte is then reimplanted into a pseudo-pregnant foster mother. The liveborn animals are screened for integrants using analysis of DNA (e.g., from the tail veins of offspring mice) for the presence of the inserted recombinant transgene sequences. The transgene may be either a complete genomic sequence introduced into a host as a YAC, BAC or other chromosome DNA fragment, a cDNA with either the natural promoter or a heterologous promoter, or a minigene containing all of the coding region and other elements found to be necessary for optimum expression.
To create a transgene, the target sequence of interest (e.g., wild type or allelic variant 3-OST sequences) are typically ligated into a cloning site located downstream of some promoter element which will regulate the expression of RNA from the sequence. Downstream of the coding sequence, there is typically an artificial polyadenylation sequence. An alternative approach to creating a transgene is to use an exogenous promoter and regulatory sequences to drive expression of the transgene. Finally, it is possible to create transgenes using large genomic DNA fragments such as YACs which contain the entire desired gene as well as its appropriate regulatory sequences.
Animal models may be created by targeting endogenous 3-OST sequence in order to alter the endogenous sequence by homologous recombination. These targeting events can have the effect of removing endogenous sequence (knock-out) or altering the endogenous sequence to create an amino acid change associated with human disease or an otherwise abnormal sequence (e.g., a sequence which is more like the human sequence than the original animal sequence) (knock-in animal models). A large number of vectors are available to accomplish this and appropriate sources of genomic DNA for mouse and other animal genomes to be targeted are commercially available from companies such as GenomeSystems Inc. (St. Louis, Mo., USA). The typical feature of these targeting vector constructs is that 2 to 4 kb of genomic DNA is ligated 5′ to a selectable marker (e.g., a bacterial neomycin resistance gene under its own promoter element termed a “neomycin cassette”). A second DNA fragment from the gene of interest is then ligated downstream of the neomycin cassette but upstream of a second selectable marker (e.g., thymidine kinase). The DNA fragments are chosen such that mutant sequences can be introduced into the germ line of the targeted animal by homologous replacement of the endogenous sequences by either one of the sequences included in the vector. Alternatively, the sequences can be chosen to cause deletion of sequences that would normally reside between the left and right arms of the vector surrounding the neomycin cassette. The former is known as a knock-in, the latter is known as a knock-out.
Retroviral infection of early embryos can also be done to insert the recombinant DNA constructs of the invention. In this method, the transgene (e.g., a wild type or allelic variant 3-OST sequence) is inserted into a retroviral vector which is used to directly infect embryos (e.g., mouse or non-human primate embryos) during the early stages of development to generate partially transgenic animals, some of which bear the transgenes in germline cells.
Alternatively, homologous recombination using a population of stem cells allows for the screening of the population for successful transformants. Once identified, these can be injected into blastocysts, and a proportion of the resulting animals will show germline transmission of the transgene.
Techniques of generating transgenic animals, as well as techniques for homologous recombination or gene targeting, are now widely accepted and practiced. A laboratory manual on the manipulation of the mouse embryo, for example, is available detailing standard laboratory techniques for the production of transgenic mice (69).
Finally, equivalents of transgenic animals, including animals with mutated or inactivated 3-OST sequences may be produced using chemical or x-ray mutagenesis of gametes, followed by fertilization. Using the isolated a nucleic acid disclosed or otherwise enabled herein, one of ordinary skill may more rapidly screen the resulting offspring by, for example, direct sequencing, SSCP, RFLP, PCR, or hybridization analysis to detect mutants, or Southern blotting to demonstrate loss of one allele by dosage.
Substantially Pure Proteins
In one aspect, the present invention provides substantially pure preparations of 3-OST proteins. In preferred embodiments, the 3-OST proteins are 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B, 3-OST-4 or ce3-OST proteins. In particularly preferred embodiments, the 3-OST proteins are those disclosed as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO 15. As shown in the examples below, nucleic acids encoding all or a portion of one mammalian 3-OST protein may be used to isolate homologues in other species by standard techniques known to those of ordinary skill in the art. Thus, the present invention also enables substantially pure protein preparations of 3-OST proteins of other mammalian species including, for example, rats, goats, sheep, cows, pigs, and non-human primates. Similarly, the isolated nucleic acids disclosed herein may be used to screen additional human or other mammalian genetic libraries (e.g., genomic or cDNA libraries) to identify allelic variants of the particularly disclosed sequences. Thus, the present invention also enables substantially pure protein preparations of human and other mammalian 3-OST allelic variants.
In another aspect, the present invention provides 3-OST protein variants in which conservative substitutions have been made for certain residues, or chimeric 3-OST proteins in which the sequences of various 3-OST proteins have been mixed, to produce non-naturally occurring variants which retain 3-O-sulfotransferase activity. Conservative substitutions are preferably made in those regions of the proteins which are already known to vary amongst the human and murine sequences (see FIG. 1) or between the 3-OST-1, 3-OST-2, 3-OST-3A, 3-OST-3B 3-OST-4, and ce3-OST proteins (see, e.g., FIG. 2). Substitutions are to be avoided in those areas which have been implicated in catalysis (see above). Chimeric 3-OST proteins may be made using the disclosed sequences as reference sequences, and these chimeras may also be subjected to conservative substitutions as described above. In addition, based upon the homologies of the 3-OST proteins to other glucosaminyl sulfotransferases (e.g., 2-OST, NST-1, NST-2), one of ordinary skill in the art may produce chimeric 3-OSTs using those proteins as reference sequences (see, e.g., FIG. 2).
In preferred embodiments, the 3-OST proteins have at least 60%, preferably at least 70%, and more preferably at least 80% amino acid sequence similarity to the mammalian 3-OST sequences particularly disclosed herein, and retain 3-O-sulfotransferase activity. Most preferably, the sequences have at least 90% or 95% amino acid sequence similarity to the disclosed reference sequences. Such sequences may be routinely produced by those of ordinary skill in the art, and 3-O-sulfotransferase activity may be tested by routine methods such as those disclosed herein.
The substantially pure proteins of the present invention may be joined to other polypeptide sequences for use in various applications. Thus, for example, the proteins of the invention may be joined to one or more additional polypeptides so as to form a fusion protein, as is commonly known in the art and as described in the examples below. The additional polypeptides may be joined to the N-terminus, C-terminus or both termini of the 3-OST protein. Such fusion proteins may be particularly useful if the additional polypeptide sequences are easily identified (e.g., by providing an antigenic determinant) or easily purified (e.g., by providing a ligand for affinity purification).
In another aspect, the substantially pure 3-OST proteins of the present invention may comprise only a portion or fragment of the amino acid sequence of a complete mammalian 3-OST protein. For example, as described above, the 3-OST-1 proteins comprise a twenty amino acid signal sequence which is removed post-translationally to yield the mature proteins. In some instances (e.g., when employing 3-OST-1 proteins in vitro), it may be preferable to employ only the mature protein or a minimal fragment retaining 3-O-sulfotransferase activity. In addition, the four C-terminal residues of 3-OST-1 may be involved in localization of the protein within the Golgi apparatus. In some instances (e.g., when employing 3-OST-1 proteins in vitro), it may be preferable to employ a 3-OST-1 protein which does not include these residues, as they will be unnecessary for in vitro function. As described above, an approximately 260 amino acid portion of the 3-OST proteins includes the catalytically active region and, therefore, it may be preferable to employ a 3-OST protein which includes only this functional fragment which retains 3-O-sulfotransferase activity. Thus, in certain preferred embodiments, the present invention provides substantially pure 3-OST proteins including mature forms of a mammalian 3-OST-1 protein, C-terminally truncated forms, or minimal functional fragments thereof. In addition, as described above, these proteins may also comprise conservative substitution variants or chimeras of 3-OST proteins.
In another aspect, the present invention provides for substantially pure protein preparations which comprise a sequence of at least 6-12, preferably 10-16, more preferably 16-22 consecutive amino acid residues from any one of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, and SEQ ID NO: 15. Such polypeptides have utility to raise antibodies to corresponding regions of the 3-OST proteins. In particular, an analysis of the amino acid sequences of the 3-OST proteins suggests that there are regions which will have particular utility in generating antibodies. Thus, in preferred embodiments, the inventions provides antigenic 3-OST polypeptides selected from the group consisting of (a) residues 4-29, 144-152, 208-222, 31-42, 155-181, 72-94, 195-205, 278-293, 113-136, 56-66, 230-245, 257-263, 301-306, 267-272 and 101 -107 of SEQ ID NO 2; (b) residues 4-22, 140-148, 205-218, 68-90, 191-201, 274-289, 110-133, 51-62, 226-241, 253-259, 151-163, 168-181, 297-302, 27-34, 97-107 and 263-268 of SEQ ID NO: 4; (c) residues 18-44, 199-207, 114-123, 319-328, 250-275, 238-246, 128-143, 47-59, 83-98, 332-349, 178-186, 289-295, 310-316, 63-76, 4-9, 209-218, 170-176 and 300-305 of SEQ ID NO: 6; (d) residues 22-57, 236-256, 166-186, 151-161, 138-147, 77-85, 348-354, 87-94, 323-335, 360-366, 284-314, 217-224, 376-383, 4-20, 130-136, 67-73, 389-395 and 338-343 of SEQ ID NO: 8; (e) residues 221-241, 8-66, 151-171, 135-146, 333-339, 308-320, 345-351, 269-299, 202-209, 361-368, 86-100, 71-80, 115-129, 374-380 and 323-328 of SEQ ID NO: 10; and (f) residues 280-290, 321-364, 371-388, 211-231, 393-399, 310-316, 421-438, 405-411, 262-268 and 292-301 of SEQ ID NO: 12. Note that these polypeptides are listed in decreasing order of preference within in group (a) to (f). Preferred antigenic peptide sequences also include residues 218-231, 87-100, 167-180 and 275-288 of SEQ ID NO: 2, which have been successfully used to generate antibodies to m3-OST-1.
Thus, in another aspect, the present invention provides for antibodies and methods for making antibodies which selectively bind with the 3-OST proteins.
These antibodies include monoclonal and polyclonal antibodies, as well as functional antibody fragments such as F(ab) and Fc.
The proteins or peptides of the invention may be substantially purified by any of a variety of methods selected on the basis of the properties revealed by their protein sequences. As shown in the examples below, and previously described (26), cells naturally expressing 3-OST-1 proteins secrete the protein when grown in culture, and the proteins may be isolated from the cell culture medium. The 3-OST-2, 3-OST-3A, 3-OST-3B and 3-OST-4 proteins, however, appear to include transmembrane domains. Thus, these proteins are not expected to be secreted at high levels. Because the 3-OSTs are found in the Golgi apparatus and microsomal bodies of cells which naturally express them, a fraction of cells including these organelles may be isolated and the proteins may be extracted from this fraction by, for example, detergent solubilization. Alternatively the 3-OST proteins, fusion proteins, or fragments thereof, may be purified from cells transformed or transfected with expression vectors. For example, insect cells such as Drosophila Schneider cells and baculovirus expression systems may be employed with vectors such as pPLUEBAC and pMELBAC (Stratagene. La Jolla, Calif.); yeast expression systems with vectors such as pYESHIS Xpress vectors (Invitrogen, San Diego, Calif.); eukaryotic expression systems with vectors such as pcDNA3 (Invitrogen, San Diego, Calif.), which causes constitutive expression, or LacSwitch (Stratagene, La Jolla, Calif.) which is inducible; or prokaryotic expression systems with vectors such as pKK233-3 (Clontech, Palo Alto, Calif.). In the event that the protein or fragment localizes within microsomes derived from the Golgi apparatus, endoplasmic reticulum. or other membrane containing structures of such cells, the protein may be purified from the appropriate cell fraction. Alternatively, if the protein does not localize within these structures, or aggregates in inclusion bodies within the recombinant cells (e.g., prokaryotic cells), the protein may be purified from whole lysed cells or from solubilized inclusion bodies by standard means.
Purification can be achieved using standard protein purification procedures including, but not limited to, affinity chromatography, gel-filtration chromatography, ion-exchange chromatography, high-performance liquid chromatography (RP-HPLC, ion-exchange HPLC, size-exclusion HPLC), high-performance chromatofocusing chromatography, hydrophobic interaction chromatography, immunoprecipitation, or immunoaffinity purification. Gel electrophoresis (e.g., PAGE, SDS-PAGE) can also be used to isolate a protein or peptide based on its molecular weight, charge properties and hydrophobicity.
A 3-OST protein, or a fragment thereof, may also be conveniently purified by creating a fusion protein including the desired 3-OST sequence fused to another peptide such as an antigenic determinant (e.g., from Protein A, see below) or poly-His tag (e.g., QIAexpress vectors, QIAGEN Corp., Chatsworth, Calif.), or a larger protein (e.g., GST using the pGEX-27 vector (Amrad, USA) or green fluorescent protein using the Green Lantern vector (GlBCO/BRL. Gaithersburg, Md.). The fusion protein may be expressed and recovered from prokaryotic or eukaryotic cells and purified by any standard method based upon the fusion vector sequence. For example, the fusion protein may be purified by immunoaffinity or immunoprecipitation with an antibody to the non-3-OST portion of the fusion or, in the case of a poly-His tag, by affinity binding to a nickel column. The desired 3-OST protein or fragment can then be further purified from the fusion protein by enzymatic cleavage of the fusion protein. Methods for preparing and using such fusion constructs for the purification of proteins are well known in the art and numerous kits are now commercially available for this purpose.
Currently preferred methods for small scale purification of 3-OST-1 proteins from the media of LTA cells grown in culture may be found in Liu et al. (26), and methods for purification of 3-OSTs produced recombinantly in COS-7 cells, CHO cells, murine primary cardiac microvascular endothelial cells (CME), murine mast cell line C57.1, and human primary endothelial cells of umbilical vein (HUVEC) may be found in the examples below. These methods may also be adapted for use with other cell and expression systems to obtain substantially pure 3-OST proteins.
In another aspect, the present invention provides for methods for producing the above-described proteins. Thus, in one set of embodiments, the isolated nucleic acids of the invention may be used to transform host cells or create transgenic animals. The proteins of the invention may then be substantially purified by well known methods including, but notlimited to, those described in the examples below. Alternatively, the isolated nucleic acids of the invention may be used in cell-free in vitro translation systems. Such systems are also well known in the art and include, but are not limited to, that described in the examples below.
Antibodies
The present invention also provides antibodies and methods of making antibodies, which will selectively bind to and, thereby, isolate or identify wild type and/or variant forms of the 3-OST proteins. The antibodies of the invention have utility as laboratory reagents for, inter alia, immunoaffinity purification of the 3-OSTs, immunoaffinity purification of 3-OST conjugates or complexes (e.g., 3-OST-AT, 3-OST-HS), Western blotting to identify cells or tissues expressing the 3-OSTs, and immunocytochemistry or immunofluorescence techniques to establish the cellular or extracellular location of the protein.
The antibodies of the invention may be generated using the entire 3-OST proteins of the invention or using any 3-OST epitope which is characteristic of that protein and which substantially distinguishes it from other host proteins. Such epitopes may be identified by comparing sequences of amino acid residues from a 3-OST sequence to computer databases of protein sequences from the relevant host. Preferably, the epitopes are chosen so as to be highly immunogenic and specific.
In a preferred embodiment, the immunogen/epitope is a protein sequence of at least 6-12, preferably 10-16, more preferably 16-22 consecutive amino acid residues of the disclosed OST genes. In particular, an analysis of the amino acid sequences of the 3-OST proteins suggests that there are regions which will have particular utility in generating antibodies. Thus, in preferred embodiments, the inventions provides antigenic 3-OST polypeptides.
3-OST immunogen preparations may be produced from crude extracts (e.g., microsomal fractions of cells expressing the proteins), from proteins or peptides substantially purified from cells which naturally or recombinantly express them or, for small immunogens, by chemical peptide synthesis. The 3-OST immunogens may also be in the form of a fusion protein in which the non-3-OST region is chosen for its adjuvant properties and/or the ability to either and/or facilitate purification. As used herein, a 3-OST immunogen shall be defined as a preparation including a peptide comprising at least 4-8, and preferably at least 9-15 consecutive amino acid residues of the 3-OST proteins or nucleic acids encoding such a peptide coupled with transcriptional elements, as disclosed or otherwise enabled herein. Therefore, any 3-OST derived polypeptide or protein sequences which are employed to generate antibodies to the 3-OSTs should be regarded as 3-OST immunogens.
The antibodies of the invention may be polyclonal or monoclonal, or may be antibody fragments, including Fab fragments, F(ab′)2, and single chain antibody fragments. In addition, after identifying useful antibodies by the method of the invention, recombinant antibodies may be generated, including any of the antibody fragments listed above, as well as humanized antibodies based upon non-human antibodies to the 3-OST proteins. In light of the present disclosures of 3-OST proteins, as well as the characterization of other 3-OSTs enabled herein, one of ordinary skill in the art may produce the above-described antibodies by any of a variety of standard means well known in the art. For an overview of antibody techniques, see Antibody Engineering, 2nd Ed., Borrebaek. ed. Oxford University Press, Oxford (1995).
As a general matter, monoclonal anti-3-OST antibodies may be produced by first injecting a mouse, rabbit, goat or other suitable animal with a 3-OST immunogen in a suitable carrier or diluent. As above, carrier proteins or adjuvants may be utilized and booster injections (e.g., bi- or tri-weekly over 8-10 weeks) are recommended. After allowing for development of a humoral response, the animals are sacrificed and their spleens are removed and resuspended in, for example, phosphate buffered saline (PBS). The spleen cells serve as a source of lymphocytes, some of which are producing antibody of the appropriate specificity. These cells are then fused with an immortalized cell line (e.g., myeloma), and the products of the fusion are plated into a number of tissue culture wells in the presence of a selective agent such as HAT. The wells are serially screened and replated, each time selecting cells making useful antibody. Typically, several screening and replating procedures are carried out until over 90% of the wells contain single clones which are positive for antibody production. Monoclonal antibodies produced by such clones may be purified by standard methods such as affinity chromatography using Protein A Sepharose, by ion-exchange chromatography, or by variations and combinations of these techniques.
The antibodies of the invention may be labeled or conjugated with other compounds or materials for diagnostic and/or therapeutic uses. For example, they may be coupled to radionuclides, fluorescent compounds, or enzymes for imaging or therapy, or to liposomes for the targeting of compounds contained in the liposomes to a specific tissue location.
Assays for Drugs which Affect 3-OST Expression
In another series of embodiments, the present invention provides assays for identifying small molecules or other compounds which are capable of inducing or inhibiting the expression of the 3-OST genes and proteins. The assays may be performed in vitro using non-transformed cells, established cell lines, or the transformed cells of the invention, or in vivo using normal non-human animals or the transgenic animal models of the invention.
In particular, the assays may detect the presence of increased or decreased expression of nucleic acids under the transcriptional control of 3-OST promoter and regulatory sequences on the basis of increased or decreased mRNA expression (using, e.g., the nucleic acid probes disclosed and enabled herein), increased or decreased levels of protein products encoded for such nucleic acids (using, e.g., the anti-3-OST antibodies disclosed and enabled herein), or increased or decreased levels of activity of such a protein (e.g., β-galactosidase or luciferase).
Thus, for example, one may culture cells known to express a particular 3-OST, or recombination modified to express at least a functional fragment or epitope of 3-OST protein under the transcriptional control of 3-OST promoter and add to the culture medium one or more test compounds. After allowing a sufficient period of time (e.g., 0-72 hours) for the compound to induce or inhibit the expression of the 3-OST, any change in levels of expression from an established baseline may be detected using any of the techniques well known in the art. Using the nucleic acid probes and/or antibodies disclosed and enabled herein, detection of changes in the expression of a 3-OST, and thus identification of the compound as an inducer or inhibitor of 3-OST expression, requires only routine experimentation. For example, one may assay for 3-OST activity by measuring the conversion of HSInact into HSAct by methods known in the art (70).
In other embodiments, a recombinant assay is employed in which a reporter gene is operably joined to 3-OST promoter and regulatory sequences so as to be under the transcriptional control of these sequences. The reporter gene may be any gene which encodes a transcriptional or transitional product which is readily assayed or which has a readily determinable affect or phenotype. Preferred reporter genes are those encoding enzymes with readily detectable activity, including without limitation β-galactosidase, green fluorescent protein, alkaline phosphatase, or luciferase is operably joined to the 5′ regulatory regions of a 3-OST gene. The 3-OST regulatory regions, may be readily isolated and cloned by one of ordinary skill in the art in light of the present disclosure of the coding regions of these genes. The reporter gene and regulatory regions are joined in-frame (or in each of the three possible reading frames) so that transcription and translation of the reporter gene may proceed under the control of the 3-OST regulatory elements. The recombinant construct may then be introduced into any appropriate host cell as described herein. The transformed cells may be grown in culture and, after establishing the baseline level of expression of the reporter gene, test compounds may be added to the medium. The ease of detection of the expression of the reporter gene provides for a rapid, high through-put assay for the identification of inducers and inhibitors of the 3-OST gene.
Compounds identified by this method will have potential utility in modifying the expression of the 3-OST genes in vivo. These compounds may be further tested in the animal models disclosed and enabled herein to identify those compounds having the most potent in vivo effects.
Methods for Heparan Modification
In another aspect, the present invention provides methods for 3-O-sulfating saccharide residues within a preparation of glycosaminoglycan or proteoglycan polysaccharides in which the polysaccharides include a polysaccharide sequence of GlcA→GlcNS±6S. These methods comprise contacting the GlcA→GlcNS±6S-containing polysaccharide preparation with 3-OST protein in the presence of a sulfate donor under conditions which permit the 3-OST to convert the GlcA→GlcNS±6S sequence to GlcA→GlcNS 3S±6S. In particular embodiments, the GlcA→GlcNS±6S sequence comprises a part of an HSact precursor sequence (i.e., GlcA→GlcNS±6S→IdoA 2S→GlcNS±6S or IdoA→GlcNAc 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S) or a part of an HSinact precursor sequence (i.e., IdoA→GlcNS 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S; IdoA→GlcNAc→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S; IdoA→GlcNS→GlcA→GlcNS±6S→IdoA 2S→GlcNS 6S; IdoA→GlcNAc 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS or IdoA→GlcNS 6S→GlcA→GlcNS±6S→IdoA 2S→GlcNS). Conversion of the HSact precursor pool to HSact increases the fraction with AT-binding activity and is particularly useful in the production of anticoagulant heparan sulfate products. Thus, in another embodiment, the present invention provides for means of enriching the AT-binding fraction of a heparan sulfate pool by contacting the polysaccharide preparation with 3-OST protein in the presence of a sulfate donor under conditions which permit the 3-OST HSact conversion activity. In preferred embodiments, the sulfate donor is 3′-phospho-adenosine 5′-phosphosulfate (PAPS).
Methods of Partially Sequencing Complex Polysaccharides
In another aspect, the present invention provides methods for partially sequencing complex polysaccharides such as heparan sulfates (HS) or other glycosaminoglycans (GAGs). In these methods, a pool of polysaccharides which includes sequences which may be 3-O-sulfated is contacted with a 3-OST protein in the presence of a sulfate donor.(e.g., PAPS) under conditions which permit sulfation by 3-OST. The treated polysaccharides are then subjected to degradation by enzymes which degrade polysaccharides in a sequence-specific manner (e.g., polysaccharide lyases; heparinase I, II or III) and the size profile of the resulting fragments is determined. An identical pool which has not been treated with 3-OST is similarly cleaved by the same enzymes and a size profile determined. Changes in the size profiles indicate that 3-OST activity has modified the saccharide units so as to prevent (or permit) cleavage at sites which previously were (or were not) cleaved. Thus, comparison of the profiles will indicate positions at which the target sequences for 3-OST activity are present and provide a partial polysaccharide sequence.
In another embodiment, the sequence of complex polysaccharides such as HS or GAG may be partially determined using sequence specific polysaccharide affinity fractionation. To this end, 3-OST proteins which lack enzymatic function can be identified or produced (e.g., altering or deleting a portion of the catalytic ST domain by site-directed or deletion mutagenesis). These inactive forms will bind GAGs in a sequence dependent manner. For example, the 3-OST-1 protein normally, minimally, binds a GAG sequence containing GlcA-GlcNS±6S. When the active site of this protein is neutralized, the kd of the protein for these sequences will be relatively unaffected. This reagent will allow sequence-specific saccharide affinity fractionation from complex mixtures of GAGs. The purified structures can be degraded in a step-wise fashion with exolytic, endolytic enzymes and/or nitrous acid, and the resulting degradation products can be compared to standard compounds of known structure. This method will allow the quantitation and characterization of known structures contained within unknown complex polysaccharide samples.
In another embodiment, partial sequence can be obtained using the 3-OSTs of the invention or other heparan sulfate sequence specific binding ligands as protective groups prior to treating the IIS or GAG with modifying agents that detectably alter the HS or GAG. Useful protective groups include catalytically inactive enzymes, chimeric enzymes and small molecule ligands with identified sequence binding specificities. The protecting group is contacted with the heparan or other glycosaminoglycan (GAGs), and the resultant complex is treated with one or more modifying agents. Useful modifying agents include catalytically active heparan lyases, sulfotransferases, N-deacetylases, epimerases, or chimeric proteins of the invention. In embodiments where multiple protecting groups and/or modifying reagents in are used in combination, the sample is first contacted with the protective group, then each modifying reagent may be with contacted with the protected polysaccharide, either simultaneously or in turn. The protective group will interfere with the ability of a chemically modifying agent to interact with, attach to and/or cleave specific GAG sequence motifs. The sample can then be analyzed for ligand-specific protection and/or cleavage to elucidate the sequence of the original GAG using separation and/or quantitation using methods known in the art.
In some embodiments, as a preliminary step, full length heparans and GAG oligomers can be fractionated over an immobilized affinity ligand immobilized at their reducing ends via hydrazide chemistry. The fraction of GAG captured by the immobile phase permits a quantitation of the mass or total percent of the target sequence (out of total GAG.) Thus, unique heparan or other GAG structures may be concentrated and/or specifically eluted for further analysis.
One useful method for the detection binding is the Biomolecular Interaction Assay or “BlAcore” system developed by Pharmacia Biosensor and described in the manufacturer's protocol (LKB Pharmacia, Sweden). In light of the present disclosure, one of ordinary skill in the art is now enabled to employ this system, or a substantial equivalent, to identify proteins or other compounds having sequence-specific HS or GAG binding capacity, or HS or GAGs sequences having 3-OST binding capacity. Such systems utilize surface plasmon resonance, an optical phenomenon that detects changes in refractive indices. A sample of interest is passed over an immobilized ligand (e.g., a 3-OST fusion protein or specific GAG) and binding interactions are registered as changes in the refractive index.
EXAMPLES
Cell Lines and Cell Culture
The clonal L cell line LTA (35, 41), the generation of clone 33, an LTA transfectant that over-expresses the ryudocan12CA5 cDNA (33), a rapidly growing revertant of clone 33, L-33+ (26), and RFPEC, an immortalized line derived from rat fat-pad endothelial cells (8) have previously been described. Primary mouse neonatal endothelial cells from the cardiac microvasculature of day 3-5 neonates (CME cells) (from Dr. Jay Edelberg, MIT/Beth Israel Hospital) and COS-7 cells (ATCC) were employed. Primary human umbilical cells (HUVEC) were maintain according to the supplier's (Clonetics Inc.) protocol. Unless otherwise stated, all cell lines were maintained in logarithmic growth by subculturing biweekly in Dulbecco's modified Eagle medium (Life Technologies, Inc.) containing 10% fetal bovine serum, 100 μg/ml streptomycin, and 100 units/ml penicillin at 37° C. under 5% CO2 humidified atmosphere, as previously described (42). Exponentially growing cultures were generated by inoculating 54,000 cells/cm2 and incubating for two days, whereas post-confluent cultures were produced by inoculating 250,000 cells/cm2 and allowing growth for 10 days with medium exchanges on days 4, 7, 8, and 9.
Peptide Purification and Sequencing
The purification of mouse 3-OST-1 from L-33+ has been previously described (26) and the final step 4 product was concentrated by reverse phase chromatography on a HP 1090 M system (Hewlett Packard) equipped with a C4 reverse phase HPLC column (250×2.1 mm, 300 Å pore size. 5 μm particle size) (Vydac, number 214TP52) equilibrated in 1.6% acetonitrile (v/v), 0.1% TFA (v/v). After application of sample, the reverse phase matrix was washed with 60% acetonitrile, 0.1% TFA, and bound species were eluted with 78.4% acetonitrile, 0.1% TFA. Samples of 1.5 or 3 μg, from two independent purifications, were digested with 0.15 or 0.3 μg, respectively. of endopeptidase Lys-C (Waco) in a reaction volume of 100 μl containing 1% RTX100 (Calbiochem), 10% acetonitrile and 100 mM Tris-HCl pH 8.0, at 37° C. for  ̃16 h (43). Digestion products were chromatographed on an HP 1090 M system (Hewlett Packard) equipped with the above described C4 reverse phase HPLC column equilibrated in 98% Buffer A (0.1% TFA (v/v))/2% Buffer B (80% acetonitrile (v/v)/0.85% TFA (v/v)). After application of digestion products, the reverse phase matrix was washed with 98% Buffer A/2% Buffer B, and bound species were eluted with linear gradients of Buffer B increasing to 37.5% over 60 min, to 75% over 30 min, and to 98% over 15 min (44). The eluate was monitored for absorbance at 210 and 280 nm, peptide peaks were individually collected and analyzed with a model 477A/120A Protein Sequenator (Applied Biosystems). In addition,the NH2-terminal sequence of 1 μg of concentrated 3-OST-1 sample was directly determined.
Isolation of Mouse 3-OST-1 Clones
Isolation of Cytoplasmic and Poly(A)+ RNA. Cytoplasmic RNA (17.5 mg) was isolated from post-confluent cultures of LTA cells (12 flasks of 175 cm2,  ̃1.6×109 cells) by a modification of the procedure of Favaloro (45). Monolayers were twice washed with PBS, cells were recovered by trypsinization and centrifugation (1000×g for 2 min), and cell pellets were washed by resuspension in PBS followed by centrifugation (1300×g for 4 min). Cells were lysed by vortexing for 30 sec in 12 ml of ice cold 50 mM Tris, pH 7.4, 140 mM NaCl, 5 mM EDTA, 1% Triton X-100, 5 mM vanadium ribonucleoside complexes (Life Sciences Technologies), samples were incubated on ice for 10 min and then vortexed for 1 min. Nuclei were pelleted by centrifugation at 6000×g for 10 min, the supernatant was mixed with an equal volume of 200 mM Tris, pH 7.4, 300 mM NaCl, 2% SDS, 25 mM EDTA, containing 200 μg/ml of proteinase K (Boehringer Mannheim), and the mixture was incubated at 65° C. for 2 hr. Samples were extracted twice against an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1), the aqueous phase was combined with 0.7 volumes of isopropanol, cytoplasmic RNA was pelleted by centrifugation at 3500×g for 10 min, and was resuspended in 3.6 ml of 10 mM Tris, pH 7.4, 1 mM EDTA. Poly(A)+ RNA (59 μg) was isolated from 16 mg of cytoplasmic RNA by two sequential purifications against 100 mg of oligo(dT) cellulose (Life Sciences Technologies, #15939-010) according to the manufacturer's specifications except that binding and wash buffers contained 0.1% SDS and LiCl was substituted for NaCl. The final eluate (1.5 ml) was extracted against 1.5 ml of phenol/chloroform/isoamyl alcohol (25:24:1), the aqueous phase was then adjusted to 100 mM LiCl and 260 mM NaCl, an equal volume of isopropanol was added, the mixture was centrifuged at 15,000×g for 30 min and the poly(A)+ RNA pellet was recovered in 40 μl of diethyl pyrocarbonate treated water.
PCR Cloning and Generation of a Mouse 3-OST-1 Probe. Degenerate PCR primers 1S, 2S, 2A, and 3A (described in Shworak et al. (1997) J. Biol. Chem. 272, in press) were obtained from Bio Synthesis. First strand cDNA was generated in a 50 μl volume from 5 μg of LTA poly(A)+ RNA primed with oligo(dT) using an RT-PCR kit (Stratagene, La Jolla, Calif.) according to the manufacturer's specifications. Touchdown PCR (46, 47) reactions (50 μl) contained 1 μl of first strand cDNA. 25 pmol of each primer, 0.25 μl of AmpliTaq Gold (Perkin Elmer). 200 μM of each dNTP and 1× GeneAmp PCR buffer. Two distinct sets of touchdown PCR conditions were required to obtain optimal yields of product. For amplification with primers 1S and 2A, reactions were heated to 95° C. for 9 min, subjected to 20 cycles of 94° C. for 30 see, and 68° C. for 1 min with a 0.5° C. reduction per cycle, followed by 20 cycles of 94° C. for 30 sec, 58° C. for 30 sec with a 0.5° C. reduction per cycle, and 75° C. for 30 sec, then 15 cycles of 94° C. for 30 sec, 55° C. for 10 sec, and ramping to 75° C. over 50 sec. Alternatively, for amplification with primers 1S and 3A or primers 2S and 3A, reactions were heated to 95° C. for 4 min, subjected to 47 cycles of 95° C. for 30 sec, and 69.5° C. for 2 min with 0.2° C. and 1 sec reductions per cycle, followed by 25 cycles of 95° C. for 30 see, 60° C. for 15 sec, and ramping to 75° C. over 1 min. Amplification products were purified as the retentate from centrifugal ultrafiltration against a 30,000 molecular weight cutoff membrane (Millipore, # SK1P343JO), then 200 ng of DNA was end polished with Pfu DNA polymerase and subcloned into pCR-Script Amp SK(+) (Stratagene, La Jolla, Calif., #211188) according to the manufacturer's specifications. A resulting plasmid, pNWS 182, contained the 1S/3A amplification product of 779 bp which was released by digestion with EcoRI and SacII, and isolated by low melting point agarose gel electrophoresis. A 32P-labeled primer extension probe was then generated with a random primer labeling kit (Stratagene, La Jolla, Calif., # 300385) by replacing the random primers with 5 μM of primer 3A.
Construction and Screening of an L Cell cDNA Library. Using the manufacturer's recommended conditions, an oligo(dT)-primed λ Zap Express cDNA library (Stratagene, La Jolla, Calif., # 200451) was generated from 5 μg of LTA poly(A)+ RNA which had been pretreated with methylmercury hydroxide. About 1.5×106 primary recombinants were plaque amplified by infection into E. coli XL1-Blue MRF′. From the amplified library, 1.3×106 plaques were transferred to Colony/Plaque Screen (Du Pont-New England Nuclear) and screened with the above described 32P-labeled probe specific for 3-OST-1. Hybridizations were performed at 42° C. in 1.7×SSC, 8.3% dextran sulfate, 42% formamide, 0.8% SDS and filters were washed twice with 2×SSC, 1% SDS for 30 min at 65° C. Positive clones were plaque purified and then in viva) excised into pBK-CMV based phagemids by infection with ExAssist helper phage followed by transduction of filamentous phage particles into E. coil XLOLR.
Isolation of Human 3-OST-1 cDNA Clones
The National Center for Biotechnology Information data bank of I.M.A.G.E. Consortium (LLNL) expressed sequence tag cDNA clones (48) was probed with the deduced mouse 3-OST-1 amino acid sequence to reveal three partial length species. I.M.A.G.E. Consortium CloneID 220372 (accession numbers H86812 and H86876) was from the retinal library of Soares (N2b4HR), whereas clones 301725 (accession numbers N90867 and W16558) and 301726 (accession numbers N90856 and W16555) were from the fetal lung library of Soares (NbHL19W) and were obtained from the TIGR/ATCC Special Collection (ATCC). The EcoRI/NolI insert of clone 220372 was 32P labeled by random priming and used to screen 5×105 plaques from a λ TriplEx Brain cDNA library (Clontech, Palo Alto, Calif.), as described above. Positive plaques were purified, TriplEx based plasmids were in vivo excised according to the manufacturer's protocol, and were sequenced as described below.
Characterization of Mouse and Human 3-OST-1 cDNA Clones
The 5′ and 3′ regions of all partial and full length clones were enzymatically sequenced from flanking primer sites of the respective cloning vectors. For full length clones the remaining sequence of both strands was obtained with internally priming oligonucleotides. Automated fluorescence sequencing was performed with Perkin Elmer Applied Biosystems Models 373A and 477 DNA sequencers. Each reaction typically yielded 400 to 600 bases of high quality sequence. cDNA sequence files were aligned and compiled with the program Sequencher 3.0 (Gene Codes Corp.). All additional manipulations were performed with the University of Wisconsin Genetics Computer Group sequence analysis software package. Sequence comparison searches were performed on the databases of GenBank, EMBL, DDBJ, PDB, SwissProt, PIR, and dbEST.
Expression of 3-OST-1 cDNAs
Construction of Expression Plasmids. The plasmid pCMV-3-OST contains the mouse 3-OST-1 cDNA, an EcoRI/YhoI fragment from pNWS228, inserted between the CMV promoter and the bovine growth hormone polyadenylation signal of EcoRI/XhoI digested and phosphatase treated pcDNA3 (Invitrogen). The plasmid pCMV-ProA3-OST is of similar structure, except the first 26 amino acid of 3-OST-1 are replaced with 291 amino acids encoding a fusion protein of the transin leader sequence followed by Protein A and a factor Xa cleavage site. pCMV-ProA-3-OST was generated by ligating a BamHI/SmaI fragment containing the Protein A region from pRK5F10PROTA (49), and an XmaI (end-filled with T4 polymerase)/XhoI fragment containing most of the mouse 3-OST-1 cDNA from pNWS228, into BamHI/XhoI digested and phosphatase treated pcDNA3 (Invitrogen.). The in vitro transcription plasmid, pNWS237, contains a T3 promoter site 5′ of the human 3-OST-1 cDNA and was constructed by inserting complementary oligonucleotides (Bio Synthesis) into the EcoRI site of the TriplEx based plasmid, pJL30.
Transient Expression of the Mouse 3-OST-1 cDNA in COS-7 Cells. For each expression construct, three 175 cm2 flasks were seeded with 3.6×106 COS-7 cells, 6 h later the medium was exchanged with DMEM containing 10% Nu-Serum (Life Technologies, Inc.) with 100 μg/ml streptomycin and 100 units/ml penicillin, and cells were grown for an additional day. Monolayers were washed with PBS then incubated at 37° C. for 2.5 h with 10 ml/flask of freshly prepared DMEM containing 235 μg/ml DEAE-dextran (M.W. 500,000, Pharmacia), 9.5 mM Tris-HCl, pH 7.4, 0.9 mM chloroquine-diphosphate (Sigma), and 3 μg/ml of the appropriate pcDNA3 based expression plasmid. Monolayers were then exposed to freshly prepared 10% DMSO in PBS for 1.5 min, washed twice with nonsupplemented DMEM, fed 30 ml/flask of DMEM containing 10% fetal bovine serum, 100 μg/ml streptomycin, and 100 units/ml penicillin, and cells were grown for an additional day. Monolayers were washed with PBS, then cells were grown in 40 ml/flask Serum-Free Medium (DMEM containing 25 mM HEPES, pH 8.0, 1% Nutridoma SP (Boehringer Mannheim) (v/v.), an additional 2 mM glutamine, 10 ng/ml biotin (Pierce), 100 μg/ml streptomycin, 100 units/ml penicillin, and 1× of a previously described Trace Metal Mix (26)) for 24 h. COS-cell conditioned Serum-Free Medium was harvested, debris was removed by centrifugation at 1,000×g for 10 min followed by filtration through a 0.45 μm membrane, then samples were either immediately processed or were snap frozen with liquid nitrogen and stored at −80° C. Occasionally, conditioned medium from a second incubation of 8-24 h was also collected.
Purification of Wild-type and Protein A Tagged Mouse Recombinant 3-OST-1. Wild-type mouse recombinantly expressed 3-OST-1 enzyme (r3-OST-1) was purified, at 4° C., from 240 ml. of freshly generated Serum-Free Medium conditioned by COS-7 cells transfected with pCMV-3-OST. The medium was adjusted to pH 8.0, mixed with an equal volume 2% glycerol, then loaded (25 ml/h) onto a heparin-AF Toyopearl-650M column (0.8×5.7 cm) (TosoHaas, Montgomeryville, Pa.) equilibrated in 50 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1% glycerol (v/v) (Buffer C). The column was washed with 20 ml of Buffer C at a flow rate of 0.8 ml/min, then with 20 ml of 150 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1% glycerol (v/v) at a flow rate of 0.5 ml/min, and protein was eluted at a flow rate of 0.25 ml/min with a 20 ml linear NaCl gradient extending from 150 mM to 750 mM NaCl in Buffer C. The fractions exhibiting HSact conversion activity (approximately 4 ml) were pooled, brought to a final concentration of 0.6% CHAPS (w/v) (Sigma) and dialyzed for 16 h against 41 of 25 mM MOPS (3-[N-morpholino] propanesulfonic acid) (Sigma), pH 7.0, 1% glycerol (v/v), 0.6% CHAPS (w/v) (MCG buffer) containing 50 mM NaCl. The dialysate was applied to a 3′,5′-ADP-agarose column (0.8×1.2 cm, 3.7 mmol of 3′,5′-ADP/ml of gel) (Sigma ) and eluted as previously described (26). The fractions containing HSact conversion activity were pooled (approximately 4 ml), aliquoted, frozen in liquid nitrogen and stored at −80° C.
Protein A tagged mouse r3-OST-1 was purified, at 4° C., from 155 ml of previously frozen Serum-Free Medium conditioned by COS-7 cells transfected with pCMV-ProA3-OST. IgG agarose beads (310 μl of a 50/50 slurry; Sigma) were gently stirred with the conditioned medium for 3 h, recovered by centrifugation at 2,000×g for 10 min, and washed twice with 1 ml of MCG containing 250 mM NaCl to remove nonspecifically bound protein. Protein A fusion-protein was eluted from the beads with two sequential 30 min incubations in 100 μl of 50 mM sodium acetate, pH 4.5, 150 mM NaCl, 0.6% CHAPS and 1% glycerol. The pooled eluates were combined with an equal volume of 500 mM MOPS, pH 7.0, 0.6% CHAPS, and 1% glycerol, then aliquoted, frozen in liquid nitrogen and stored at −80° C.
Retroviral Transduction of CHO and MNE Cells with 3-OST-1
Plasmid retrovirus vector construction. A retroviral transduction system was used to transduce CHO cells and mouse neonatal endothelial (MNE) cells. This system may serve as a model for in vivo transduction for use in gene therapy.
The retrovirus backbone plasmid pMSCV-PGK-EGFP is a derivative of pMSCVpac a (Dr. Robert Hawley University of Toronto.) The puromycin acetyl transferase gene cassette in pMSCVpac was removed and replaced with an Enhanced GFP (Dr. David Baltimore MIT). The pMSCV-PGK-GFP vector was assembled by digestion of the plasmid with HindIII and Clal, followed by treatment with Klenow fragment. The EGFP cistron 720 bp fragment was derived from the digestion of pMSCV-EGFPpac with EcoRI, and blunting with the Klenow fragment. The EGFP blunt-ended fragment was then ligated into the blunt-ended pMSCV vector. The resulting plasmids were tested for proper orientation by restriction analysis. The reporter virus, pMSCVPLAP, is designed to express the wild type human placental alkaline phosphatase (PLAP) transcribed from the 5′ LTR. pMSCV-SEAP-PGK-EGFP was made by cloning the secreted alkaline phoshphatase (SEAP) BgIII and HpaI 1.723 kb fragment from pSEAP2-basic plasmid (Clontech, Palo Alto, Calif.) into the BgIII and HpaI cut pMSCV-PGKEGFP vector. pCMV3-OST was digested with BgIII and XhoI to release the wild type mouse 3-OST-1 cDNA. The 1.623 kb 3-OST-1 cDNA fragment was cloned into the BgIII and XhoI sites in pMSCV-PGK-EGFP. The occurrence of the insert of interest present in the correct orientation was ascertained by restriction analysis. All plasmid DNA prepared for transfection was made with the Invitrogen SNAP-MIDI kits according to the manufacturer's directions.
Cells and cell culture. Dulbecco's modified Eagle medium (DMEM), F-12 Ham's medium and penicillin/streptomycin, 0.25% trypsin, 10 mM EDTA, were obtained from Life Technologies, Inc., GlBCO-BRL (Gaithersburg, Md.). The PHOENIX ecotropic retroviral packaging cell line (ATCC #SD 3444) was grown, in DMEM, 10% heat-treated fetal bovine serum (FBS) (JRH Biosciences. Lenexa, Kans.), 100 units/ml penicillin, 100 μg/ml. PHOENIX cells were subcultured three times weekly at a split ratio of approximately 1:8 in a 37° C. humidified, 5.0% CO2 incubator. CHOK1 ATCC CCL 61 cells (CHO) were grown in F-12 medium supplemented with 10% fetal bovine serum, and 100 units/ml penicillin, 100 μg/ml in a 37° C. humidified, 5.0% CO2 incubator. CHO cells were subcultured three times weekly at a split ratio of approximately 1:4 in a 37° C. humidified, 5.0% CO2 incubator. 1×106 CHO cells were transfected with 10 μg of pcB7-ECOTROPIC (generous gift of Dr. Harvey Lodish) by the standard calcium phosphate precipitation technique. Plasmid pcB7-ECOTROPIC expresses the MCAT1 gene (ecotropic retrovirus receptor cDNA) and hygromycin resistance gene transcribed from separate constitutive promoters. The transfected cells were selected for hygromycin resistance in 200 μg/ml hygromycin (Life Technologies). The stable, hygromycin-resistant clones were assayed for their ability to-take up and express reporter virus (MSCVPLAP). Fixation and staining for cell-bound alkaline phosphatase was performed by standard techniques. CHO clone 4B was chosen because it transduced most efficiently at the highest dilution tested (i.e., 1:10,000), and was expanded for further analysis. Transduction of CHO4B with ecotropic retroviruses is equal to that achievable with NIH3T3 cells. Low passage number (passage 2-5), primary mouse neonatal cardiac endothelial cells (MNE) were prepared by standard techniques. MNE cells were cultured in a 1:1 vol./vol. admixture of EGM:EGM-2 (CLONETICS) in a 37° C., humidified, 5.0% CO2 incubator. MNE cells were subcultured once weekly at a split ratio of approximately 1:3 in a 37° C., humidified, 5.0% CO2 incubator.
Northern blot analysis. Total RNA was prepared from confluent T-80 flasks of each of the transduced and untransduced cells using the QIAGEN RNAeasy kit with QIASHREDDER. 10 μg of total cellular RNA was denatured and resolved by electrophoresis in a 1.5% agarose gel, and then blotted onto GENE-Screen+ (DuPont NEN) with 2×SSPE. The membrane was then UV cross-linked using a STRATAlinker. 32P-radiolabeled cDNA probes were prepared from the fragments of DNA used for cloning the mouse 3-OST-1 and SEAP as described above. Radiolabeled probes were prepared using 25 ng of each template and the Amersham Megaprime kit, and α 32P dCTP from DuPont NEN according to the manufacturer's directions. Hybridizations were performed in sealable plastic bags at 68° C. with 1×106 cpm of probe/ml in 10 ml of QUICKHYB (Stratagene, La Jolla, Calif.), following the manufacturer's instructions. Post-hybridization washes were: once for 15 minutes in 1×SSPE, 1.0% SDS at 45° C.; and then twice for 15 minutes each in 0.2×SSPE, 0.5% SDS 650C. After washing, the blots were briefly air dried, placed in sealable plastic bags then exposed to Kodak XAR-MS film with intensifying screens at −80° C. for from overnight to five days. Quantitation of hybridizing signal intensity was performed using a Betascope 603 blot analyzer. Transcripts derived from the 5′ LTR of these engineered proviruses are large (ca. 7 kb). Since they are large, have multiple sites of transcriptional initiation provirus (5′ LTR and pgk promoters), and the 3-OST-1 construct has more than one poly(A) addition signal, bona-fide hybridizable mRNA will appear as different sizes in northern blot analysis. The total amount of hybridizing material detected, per sample lane, with any one probe was used to calculate and compare mRNA expression levels.
Virion production. Virions were produced by programming ecotropic PHOENIX packaging cells with recombinant provirus plasmids using the calcium phosphate transfection technique. 10 μg/well of each recombinant retroviral construct plasmid was transfected via calcium precipitation with an overnight incubation period. Following the precipitation step, the cells were re-fed with 2 ml/well of fresh DMEM and incubated overnight. Each 2 ml of viral supernatant was collected and flash-frozen in liquid nitrogen and stored at −80° C., or used directly after a low-speed centrifugation.
Transduction Drotocol. Target cells were trypsinized, counted with a Coulter cell counter and then plated at 150,000 cells (NIH 3T3/CHO4B) or 50,000 cells (MNE) per well of a cluster-6 well plate. 24 hours later, target cells (<70% confluent) were incubated overnight with viral supernatants containing as adjuvants either 5 μg/ml polybrene for NIH3T3/CHO4B or 25 μg/ml DEAE-dextran (Pharmacia) for MNE. After 12 hours of virus exposure, the growth media was replaced. CHO cells destined for FACS sorting were exposed to recombinant retrovirus two times at a multiplicity of infection (MOI) of 0.3. MNE cells were transduced one time for 12 hours at an MOI of 0.74 for recombinant 3-OST-1 virus and 0.72 for recombinant SEAP virus. Transduced cells were allowed to incubate in fresh growth medium for 48 hours prior to FACS to allow for maximum proviral expression. Recombinant virus titers ranged from 1×105-2×106 infectious particles per ml as measured with either NIH3T3 or CHO4B cells using. FACS analysis scoring for EGFP positive cells. Virus titers were reduced approximately eight to ten-fold on primary MNE cells relative to NIH3T3.
Cell-Free Synthesis of Mouse and Human r3-OST-1.
Synihetic capped mouse and human 3-OST-1 mRNAs were generated from NolI linearized pNWS228 and HinDIII linearized pNWS237, respectively, using T3 polymerase and m7G(5′)ppp(5′)G, as previously described (50). Unlabeled in vitro translation reactions (25 μl) contained 0.25 μg of synthetic mRNA, 1.8 μl canine pancreatic microsomal membranes (Promega), 0.5 μl each of Amino Acid Mixture Minus Leucine and Amino Acid Mixture Minus Methionine, and were performed with nuclease-treated reticulocyte lysate (Promega), according to the manufacturer's specifications.
Measurement of HSact Conversion Activity. The HSact conversion activity, a 3-OST-1 catalyzed reaction which requires unlabeled PAPS to convert 35S-HSinact into 35 S-HSact, of crude and purified r3-OST-1 samples was determined by comparison against a standard curve generated with 1 to 32 units of previously purified native 3-OST-1, as previously described (26). The 35S-HSinact substrate was purified from metabolically labeled cell surface HS of exponentially growing clone 33 cells, as previously described (35).
Identification of Enzymatic Reaction Products
35S-labeling of HS by r3-OST-1. 35S-labeled HS was generated by incubating the various forms of r3-OST-1 with [35S]PAPS and unlabeled HSinact, which were prepared as previously described (26, 35). Wild-type and Protein A tagged r3-OST-1 (2500 units of HSact conversion activity) purified from COS cell conditioned medium, were incubated in a 500 μl reaction mixture, as previously described (26), for 2 h at 37° C. and 35S-labeled polysaccharides were purified by DEAE-Sepharose chromatography as previously described (26). For cell-free synthesized r3-OST-1, 35S-labeling of HS was performed in a reticulocyte lysate based reaction mixture (35) except that 100 μl reactions contained 100 to 300 units of in vitro translated r3-OST, 180 nM unlabeled HSinact, 5 μM PAPS (60×106 cpm) and samples were incubated at 37° C. for 2 h. The reaction was quenched by the addition of 300 μl of 267 mM NaCl, 13.3 μg/ml glycogen and extraction against 600 μl of phenol/chloroform/isoamyl alcohol (25:24:1). 35S-labeled GAGs were ethanol precipitated (35) and then isolated by DEAE chromatography as previously described (26).
Identification of the Site of Sulfation on HSact and HSinact. The DEAE eluates containing 35S-labeled polysaccharide were vacuum concentrated to 1/5 volume, then desalted at a flow rate of 0.9 ml/min on TSK G3000 PWXL (0.78×30 cm) and TSK G2500 PWXL (0.78×30 cm) (TosoHaas) columns connected in series equilibrated in 0.1 M ammonium bicarbonate. The desalted product was then affinity fractionated using AT/ConA gel to obtain HSact and HSinact as described previously (26). Analysis of labeled products by treatment with GAG lyases and low pH nitrous acid were performed as previously described (42). In addition, the HSact and HSinact samples were each subjected to hydrazinolysis, high pH nitrous acid (pH 5.5), low pH nitrous acid (pH 1.5), and sodium borohydride reduction with the resultant disaccharides characterized on reverse phase ion pairing HPLC (RPIP-HPLC) as previously reported (33, 34). The identification of [35]GlcA→AMN-3-O—SO3 and [35S]GlcA→AMN-3,6-O—(SO3)2 Was confirmed by co-chromatography on RPIC-HPLC with the appropriate 3H-labeled disaccharide standards, as described in prior publications (33,34).
Northern Blot Analysis
Total RNA from RFPEC and primary mouse CME cells was isolated by the method of Chomczynski and Sacchi (51I), whereas poly(A)+ RNA was isolated from HUVEC cells as described above for LTA cells. Total RNA from the mast cell line CI.MC/C57.1 (C57.1) (52) was from Dr. Stephen J. Galli (Beth Israel Hospital). Samples were resolved on 1.2% formaldehyde-agarose gels and subjected to Northern blot analysis as previously described (50). Mouse and human samples were hybridized with mouse or human probes, respectively, and washed as described for library screening, above, except hybridizations were performed at 60° C.
Peptide Sequencing and PCR Generation of a Mouse 3-O-Sulfotransferase-1 (3-OST-1)
1) Probe
The information necessary for the molecular cloning of mouse heparan sulfate D-glucosaminyl 3-O-sulfotransferase-1 (3-OST-1) was obtained by sequencing the amino terminus and Lys-C generated peptides of the enzyme that we had previously purified from large quantities of serum-free tissue culture medium conditioned by an L cell line (26). These studies established the structures of 14 partially overlapping peptides which encompass 185 amino acid residues. Degenerate PCR primers were synthesized based on the sequence of the amino terminus (primer 1S) and two endopeptidase derived fragments (primers 2S, 2A, and 3A). When PCR was performed on an LTA first strand cDNA template, products of about 210 (primers 1S/2A) and 780 (primers 1S/3A) and 610 (primers 2S/3A) bp were obtained, which suggests that all of the primer sites are contained within a single cDNA. To confirm this supposition, the two largest fragments were cloned into pCR-Script Amp SK(+) and inserts were sequenced, which revealed that the 1S/3A product is 779 bp and contains the 611 bp 2S/3A product. The 779 bp insert encodes 12 of the sequenced peptide fragments and so was 32P-labeled, as described above, and used as a probe for cDNA library screening.
Isolation and Characterization of Mouse 3-OST-1 cDNAs
An amplified λ Zap Express LTA cDNA library of 1.5×106 primary recombinants was constructed and 1.3×106 plaques were screened with the above described probe, which revealed 40 positives that were plaque purified and in vivo excised into plasmids. The cDNA inserts of each plasmid were characterized to eliminate duplicated recombinants due to library amplification. Size was determined by liberating cDNA inserts with digestion at flanking EcoRI and XhoI restriction sites followed by agarose gel electrophoresis; furthermore, the sequence at both ends of each insert was obtained from flanking vector primer sites. This analysis revealed 25 unique primary recombinants which predominantly contained inserts of approximately 1.7, 2.3, or 3.3 kb. These different species were considered to reflect natural size variants of the mouse message since northern blots of LTA poly(A)+ RNA hybridized with 3-OST-1 probe revealed the same three size categories of message. The complete sequencing of 9 distinct primary recombinants, at least 2 from each size category, in conjunction with the partial sequencing of the remaining 16 clones showed that the size variants result from differences in the length of 5′ untranslated region due to the insertion of 0-1629 bp at a single common internal point, the splice variant site. Most importantly, all clones shared identical protein coding regions and, therefore. the characterization and analysis of only the shortest species, the Class 1 cDNA, which lacks additional sequence at the splice variant site, is described below.
Sequence data was obtained from 2 essentially full length Class 1 cDNAs, and 5 partial length cDNAs to create a composite cDNA structure of 1685 bp (SEQ ID NO: 1), excluding the 3′ poly(A) tract. The 5′ untranslated region is 322 bp with the splice variant site occurring between nucleotides 216 and 217. This region contains 6 ATG sites which do not conform to consensus initiation sites (53) and are followed by near in-frame termination codons. An open reading frame of 933 bp begins at position 323 with the first consensus initiation ATG (a purine occurs at −3) (53). The length of the 3′ untranslated region from all of the cDNA clones analyzed ranged from 301-430 bp. Within this terminal 129 bp, 5 distinct polyadenylation sites were observed and 13-18 bp upstream from each site is a variant of the consensus polyadenylation signal. Poly(A) tails were most frequently observed at the first site (position 1556,  ̃50% of clones).
Isolation and Characterization of Human 3-OST-1 cDNAs
Three clones containing partial length human 3-OST-1 cDNAs were identified by EST database searching (48) and were obtained from the TIGR/ATCC Special Collection, as described above. Sequencing of the insert ends revealed the clones to be essentially equivalent, as each contained the same 947 bp region of the human 3-OST-1 cDNA. The insert of I.M.A.G.E. Consortium CloneID 220372 was 32P-labeled and used to screen 5×105 plaques from a λ TriplEx Brain cDNA library. Three positives were identified and isolated as TriplEx plasmids, and the largest cDNA 1.3 kb was sequenced completely.
The nucleic acid sequence of mouse and human 3-OST-1 cDNAs are  ̃85% identical. The largest isolated human clone contains 118 bp of 5′ untranslated region with 2 nonconsensus ATG sites. The sequences of human and mouse cDNAs ranking the splice variant site on the 5′ limit are distinct (positions 211-216 of SEQ ID NO: 1 and positions 5-10 of SEQ ID NO: 3), but on the 3′ limit are identical (positions 217-222 of SEQ ID NO: 1 and positions 11-16 of SEQ ID NO: 3), which raises the possibility that human 3-OST-1 mRNA may also exhibit 5′ splice variants. The first consensus ATG (with a purine occurring at −3 and a G at +4) (53) initiates an open reading frame of 921 bp. For all 4 human cDNA clones examined, only a single polyadenylation site was observed resulting in a 3′ untranslated region of 266 bp, which is 26 bp less than the most frequently observed 3′ limit for the mouse cDNAs.
Predicted Protein Structures of Mouse and Human 3-OST-1
The mouse and human cDNAs encode novel 311 and 307 amino acid proteins of 35,876 and 35,750 daltons, respectively, that exhibit 93% similarity. The deduced mouse primary structure contains regions corresponding to all 13 sequenced peptides and the amino terminus. For both types of 3-OST-1, the encoded protein is predicted to be an intraluminal resident. Kyte-Doolittle hydropathy analysis reveals only a single major hydrophobic region which begins at the amino terminus and lacks sufficient length for a membrane spanning domain. Moreover, the hydrophobic region differs from a membrane anchor in that it contains two glutamine residues and is not flanked by cationic residues. Thus, the above stretch of 18 residues constitutes a hydrophobic leader signal, and this region is followed by a signal peptidase cleavage site between amino acids 20 and 21, as determined by the method of von Heijne (54). The possibility of signal peptidase cleavage is supported by the amino-terminal analysis of mouse 3-OST-1, which began with His21. Given that heparan biosynthesis is considered to occur in the trans-Golgi, the above data suggest that the 3-OST-1 is an intraluminal enzyme. Just past the signal peptidase cleavage site, the mouse 3-OST-1 contains an extra 4 residues (ASp24-Pro25-Gly26-Pro27) not found in the human form. Both 3-OST-1 proteins exhibit 5 potential N-glycosylation sites which account for the apparent discrepancy between the molecular weights of the predicted amino terminus trimmed enzyme (34 kDa) and the previously purified enzyme (a broad band of 46 kDa was observed on SDS-PAGE) (26). Only two cysteine residues are present, and these closely spaced residues are likely to form a disulfide bond which generates a peptide loop of 10 amino acids. Interestingly, the carboxy 140 residue region is extremely basic (25% H, K, R; 12% E, D); however, this region does not exhibit previously recognized heparin binding motifs.
Recombinant Expression of Mouse and Human 3-OST-1 Enzyme (r3-OST-1)
Three distinct expression approaches were employed to confirm that the isolated cDNAs encode 3-OST-1 enzyme. The resulting recombinantly expressed 3-OST-1 enzyme was designated as r3-OST-1, to distinguish this form from the previously purified native 3-OST-1 enzyme. First, the vector pCMV-3-OST (a pcDNA3 derivative in which the CMV promoter transcribes the mouse 3-OST-1 cDNA) was transiently expressed in COS-7 cells and the resulting level of HSact conversion activity accumulated in Serum-Free Medium over 32 h was measured, as described above. HSact conversion activity is a 3-OST-1 catalyzed reaction which requires unlabeled PAPS to convert 35S-HSinact into 35S-HSact. Before or after pcDNA3 transfection, typically COS-7 conditioned Serum-Free Medium contained a low but detectable amount of HSact conversion activity, whereas transfection by pCMV-3-OST elevated levels  ̃2,000-fold.
Second, to exclude the remote possibility that the expression of the mouse 3-OST-1 cDNA indirectly induces, rather than directly encodes, HSact conversion activity, a Protein A/3-OST-1 fusion protein was analyzed. COS-7 cells were transiently transfected with pCMV-ProA3-OST, a pCMV-3-OST derivative in which the amino-terminal 26 residues of the mouse 3-OST-1 are replaced with a Protein A tag, and Protein A tagged mouse r3-OST-1 was extracted with IgG agarose beads from 155 ml of conditioned Serum-Free Medium, as described above. The affinity purification recovered undetectable and less than 0.5% of initial HSact conversion activity from control pcDNA3 and pCMV-3-OST transfection samples, respectively, whereas  ̃7,000 units (10% recovery) were extracted from pCMV-ProA3-OST transfection samples. Thus, the mouse 3-OST-1 cDNA directly encodes HSact conversion activity.
Third, the activities of cell-free synthesized mouse and human r3-OST-1 were examined. Synthetic capped mouse and human 3-OST-1 mRNAs were generated by in vitro transcription and then in vitro translated with reticulocyte lysate in the presence and absence of canine pancreatic microsomal membranes, as described above. HSact conversion activity was undetectable in the control in vitro translation reactions which lacked mRNA template, with or without microsomal membranes. A low level HSact conversion activity resulted from the addition of synthetic 3-OST-1 mRNA templates to translation reactions lacking microsomal membranes (mouse, 0.86±0.028 units/μl, n=3; human, 2.1±0.063 units/μl, n=3); however,  ̃15-fold greater levels occurred when microsomal membranes were included in translation reactions (mouse, 14.3±0.27 units/μl, n=3; human, 32.4±2.1 units/μl, n=3). The apparent activation of nascent r3-OST-1 by co-translational processing within microsomes may result from signal peptidase cleavage, N-linked glycosylation, and/or a facilitation of correct protein folding. The slightly greater production from the human 3-OST-1 cDNA may reflect the more favorable context of the human initiation codon, or the reduced length of the human 5′ untranslated region. Independent of the above considerations, the above data confirm that isolated mouse and human cDNAs encode HSact conversion activity.
Next, the biochemical specificity of the HSact conversion activity generated from each expression approach was examined by incubating crude or purified enzyme with [35S]PAPS and unlabeled HSinact, recovering radiolabeled GAG by DEAE chromatography and characterizing the resultant products. The HSact conversion activity of the wild-type mouse r3-OST-1 produced by transfecting COS-7 cells with pCMV-3-OST (1.35×106 units in 240 ml of conditioned Serum-Free Medium) was first purified away from potential contaminating sulfotransferase activities by heparin-AF Toyopearl chromatography followed by 3′,5′-ADP-agarose chromatography, which yielded  ̃1 μg of protein containing 340,000 units ( ̃20,000-fold purification with 25% overall recovery); whereas, the IgG agarose-purified Protein A tagged r3-OST-1 and in vitro translation reactions of mouse and human 3-OST-1 mRNA templates were directly analyzed, as described above. About 0.5-1×106 cpm of product was generated with purified wild-type r3-OST-1, purified Protein A tagged r3-OST-1, and nonpurified in vitro translation reactions containing mouse and human r3-OST-1, respectively. Portions of each labeled product were incubated with purified heparitinase (0.5 units/ml) or chondroitinase ABC (0.5 units/ml) and HPLC-GPC analysis indicated that in all cases label was exclusively incorporated into HS. Portions of the labeled HS samples were also N-desulfated with nitrous acid at pH 1.5, and analyzed by P-2 polyacrylamide gel filtration to determine the amounts of liberated free [35S]sulfate, as described above: The results demonstrated no increased generation of free [35S]sulfate. Finally, portions of the labeled samples were AT affinity fractionated, which revealed that in each case  ̃40% of the 35S-label was incorporated in HSact and approximately  ̃60% of the 35S-label was incorporated in HSinact. The labeled HSact and HSinact generated by the wild-type purified r3-OST-1 were chemically cleaved to disaccharides with nitrous acid treatment, appropriate 3H-labeled disaccharides standards were added, and the 35S- and 3H-labeled species were coresolved by RPIP-HPLC as outlined above. The results show that the 35S-label coelutes with [3H]GlcA→AMN-3-O—SO3 and [3H]GlcA→AMN-3,6-O—(SO3)2, respectively. This approach also revealed that Protein A tagged r3-OST-1, and in viiro translation derived mouse and human r3-OST-1 generated 35S-HS which only contained 35S-labeled disaccharides that coeluted with [3H]GlcA→AMN-3-O—SO3 and [3H]GlcA→AMN-3,6-O—(SO3)2, respectively. It was previously shown that 35S-labeled GlcA→AMN-3,6-O—(SO3)2 generated by purified 3-OST-1 enzyme contains 35S solely in the 3-O-position (26). Thus, the expressed HSact conversion activities exclusively catalyze the transfer of sulfate to the 3-O-position of glucosamine units in HSact and HSinact.
Northern Analysis of Rodent and Human 3-OST-1 Expression
Northern blot analysis reveals the presence of 3-OST-1 message in different kinds of endothelial cells as well as a mast cell line. Both cell types have previously been shown to form HSact and anticoagulant heparin, respectively (6, 8, 55). Three size categories of rodent 3-OST-1 mRNA (about 1.7, 2.3, 3.3 kb) and a single size species of the human message (about 1.7 kb) were evident. As described above, the mouse forms arise from differential splicing within the 5′ untranslated region. Similar size categories are also expressed by rat (RFPEC) endothelial cells, suggesting a similar mechanism of origin. The abundance of each category varies with each cell line, which suggests that a mechanism exists to regulate such differential splicing. The immortalized mouse mast cell line, C57.1, expresses high levels of the same three size categories, which suggests that expression of a single 3-OST-1 gene is required for the synthesis of both HSact and anticoagulant heparin.
The 3-OST-1 Sequence Defines a Heparan Sulfotransferase Family
Extensive computer-aided data bank searching revealed the 3-OST-1 protein to be a previously unidentified protein; furthermore, the carboxy-terminal 250 residues exhibit a low homology ( ̃30% similarity) to many previously identified sulfotransferases (which are typically  ̃300 residues in length) including chondroitin-, aryl-/phenol-, N-hydroxyarylamine-, alcohol-lhydroxysteroid-, flavonol-, and nodulation factor sulfotransferases. We also observed a slightly greater homology ( ̃40% similarity) to a functionally unidentified open reading frame of 247 amino acids from Aeromonas salmonicida (GenBank accession number L37077). More importantly, the 3-OST-1 protein exhibits 50% similarity with all previously identified forms of the heparan biosynthetic enzyme N-deacetylase/N-sulfotransferase (NST). In particular, extensive homology exists across the entire 250-270 carboxy-terminal residues of these enzymes. Thus, it appears that a common sulfotransferase structure is shared by two distinct types of heparan biosynthetic enzyme. Given that NST is a bifunctional enzyme, the above observation suggests that NST enzymes possess sulfotransferase activity within a  ̃270 residue carboxy-terminal domain, whereas dcacetylase activity would be contained within the remaining  ̃560 luminal residues. Interestingly, the region of consensus Lys302-Arg323, which encompasses the presumptive cysteine bridged peptide loop (described above), exhibits complete conservation for 12 of the 22 residues (including both cysteines) among all 3-OST-1 and NST species.
Identification and Molecular Cloning of 3-OST-2, 3-OST-3A, 3-OST-3B and 3-OST-4
The 3-OST-1 protein exhibits a COOH-terminal region of  ̃260 residues which was determined to be a sulfotransferase (ST) domain based on homology to all known sulfotransferases. The National Center for Biotechnology Information data bank of expressed sequence tags (ESTs) was searched with amino acid sequences of the ST domain from the human 3-OST-1 cDNA to reveal seven human cDNAs encoding three novel related species. The forms were subsequently designated as 3-OST-2 (I.M.A.G.E. Consortium (LLNL) CloneID c-20d10), 3-OST-3 (Clone ID 284542) and 3-OST-4 (Clone IDs HIBCX69, IB727, 166466, 23279, and c-3ie01). These EST clones were obtained from the TIGRIATCC Special Collection, and the inserts were completely sequenced, revealing that all clones were of partial length.
To obtain full length clones, isoform specific probes were generated from the EST clones and used to screen λ TriplEx human cDNA libraries. 7 and 4 additional 3-OST-2 and 3-OST-4 cDNAs were isolated from a brain library, and 8 new 3-OST-3 cDNAs were recovered from a liver library. The cDNA inserts were completely sequenced, revealing the full length form for 3-OST-2 as well as 2 distinct full length forms for 3-OST-3 (3-OST-3A and 3-OST-3B). The additional 3-OST-4 clones were also of partial length.
3-OST-2, 3-OST-3A, 3-OST-3B and 3-OST-4 Protein Structures and Activities
The 3-OST-2, 3-OST-3A, and 3-OST-3B proteins are 367, 406, and 390 amino acids in length, respectively. All three proteins conform to the architecture of a type-II integral membrane protein. These proteins and the partial length 3-OST-4 share a common (85% similarity) ST domain region of  ̃260 amino acid at their COOH-terminus. To characterize the encoded HS sulfotransferase activities, the 3-OST-2, 3-OST-3A, and 3-OST-3B cDNAs were individually expressed in COS-7 cells.
The analysis of transfected cell extracts demonstrated that each enzyme transfers sulfate specifically to the 3-O position of glucosamine residues within HS; however distinct specificities occur. 3-OST-2 preferentially sulfates regions containing GlcA 2S→GlcNS to generate GlcA 2S→GlcNS 3S; whereas both 3-OST-3A, and 3-OST-3B recognize regions with IdoA 2S→GlcNS to generate IdoA 2S→GlcNS 3S.
Expression Patterns Indicate Biological Function
The biologic function of these novel enzymes was elucidated by performing northern blot analysis. 3-OST-4 is exclusively expressed in the brain, whereas 3-OST-2 mRNA predominantly occurs in the brain with minor levels also found in heart, lung, skeletal muscle and placenta. 3-OST-3 forms occur in virtually all tissues but with barely detectable levels in brain, low levels in heart, lung, skeletal muscle and kidney, and extremely abundant expression in liver and placenta. Thus 3-OST-2 and 3-OST-4 appear to be the brain counterparts of 3-OST-3. The product of 3-OST-3 (IdoA 2S→GlcNS 3S) has previously been shown to be extremely abundant in HSPGs isolated from the glomerular basement membrane (GBM) of the kidney. These HSPGs are critical to regulating the permselectivity of the GBM. This function occurs through interactions with extracellular matrix components that regulate the pore size of the matrix. Given that the liver, placenta, and kidney glomerulus are all responsible for the filtration of macromolecular components from blood and all exhibit high 3-OST-3 expression, it appears that 3-OST-3 serves a common function in each situation: to regulate macromolecular permeability. In this functional regard, the high brain expression of 3-OST-2 and 3-OST-4 correlates with the major molecular permeability barrier of the central nervous system, the blood brain barrier.
Therapeutic Utilities
The 3-OST heparan biosynthetic enzymes may be generated by recombinant expression of the isolated cDNAs to generate novel glycosaminoglycan drugs of specific structure through an in vitro biochemical synthesis approach. Specifically, 3-OST-1 may be used to generate anticoagulant pentasaccharides, which may be administered subcutaneously to treat thrombotic disorders such as deep vein thrombosis and pulmonary embolism. The 3-OST-1 enzyme may also be used to generate an orally absorbable form of pentasaccharide from an appropriate carbohydrate substrate linked to a hydrophobic group. In an analogous fashion, specific glycosaminoglycan products may be generated from 3-OST-2, 3-OST-3 and 3-OST-4, which may be used as therapeutics to alter macromolecular permeability of various vascular beds. Drugs which reduce capillary permeability may, at the very least, be used to treat (1) microproteinurea and macroproteinurea of renal diseases including diabetic nephropathy and the various forms of glomerulonephrititis; (2) neoplastic growths by limiting nutrient supply to tumors; and (3) inflammatory diseases were macromolecular constituents of the plasma are required for initiating and maintaining a localized inflammation. Conversely, drugs which enhance capillary permeability may be used (1) as an adjunctive treatment to facilitate pharmacological access to vascular beds, which exhibit highly selective drug entry, such as the blood brain barrier and the placental barrier; and (2) to enhance nutrient supply to under-perfused tissues such as the myocardium after an infarct.
Specific heparan sulfate structures regulate additional biologic processes by interacting with numerous protein effector molecules including growth and differentiation factors (e.g., FGF family members, HB-EGF, HGF/SF, interferon γ, PDGF, SDGF, and VEGFNVPF), chemokines (e.g., MIP-1β, RANTES, and GRO), receptors (e.g., TGF-β receptors), mast cell proteases, protease inhibitors (e.g., AT, heparin cofactor II, leuserpin, plasminogen activator inhibitor-1, protease nexins), degradative enzymes (e.g., elastase, acetylcholinesterase, extra cellular superoxide dismutase, thrombin, tissue plasminogen activator, lipoprotein lipase. hepatic and pancreatic triglyceride lipase, and cholesterol esterase), apolipoproteins (e.g., apoB and apoE), matrix components (e.g., fibronectin, wnt-1, interstitial collagens, laminin, pleiotropin, tenascin, thrombospondin, and vitronectin) viral coat proteins (e.g., gC and gB of HSV types I and II, gC-II of CMV, and gp120 of HIV), nuclear proteins (e.g., c-fos, c-jun, RNA and DNA polymerases, and steroid receptors), cellular adhesion molecules (e.g., L-selectin, P-selectin, PECAM-1, and N-CAM) and other molecules (e.g., HB-GAM/pleiothrophin, amphoterin, and PF4).
Using routine methods (e.g., site-directed mutagenesis) the available 3-OST cDNAs may be selectively mutated to alter substrate recognition properties so as to produce enzymes that generate novel glycosaminoglycan structures which modulate the biologic processes regulated by the above effector molecules. Thus, novel drugs may also be biochemically synthesized from recombinantly expressed mutated enzymes. Such substances may serve to (1) enhance growth or regeneration of specific cell types such as the endothelial cells of the heart after infarction, or neurons in neurodegenerative diseases; (2) suppress undesirable cell growth in conditions such as cancer (either directly by acting on the cancers cells or indirectly by preventing endothelial cells from neovascularizing the tumor), atherosclerosis (by preventing smooth muscle cell growth), and inflammatory diseases characterized by cellular proliferation; (3) prevent metastasis of tumors by modulating cell/matrix interactions; (4) reduce the destructive side effects of inflammatory reactions by inhibiting degradative enzymes or by activating inhibitory molecules (e.g. protease inhibitors) which may be directly or indirectly protective by limiting extravasation of lymphocytes; (5) modulate serum lipid levels by enhancing or reducing the cellular or tissue uptake or degradation of specific lipoprotein classes; (6) treat viral infections by preventing viral entry into cells; and (7) facilitate axon regeneration subsequent to nerve severing.
Bacterial expression of 3-OST-1. The human and mouse 3-OST-1 proteins have been expressed as active, soluble protein in E. coli, This has been achieved using the pET system from NOVEGEN (Madison, Wis.). The human and mouse 3-OST-1 cDNA's were PCR amplified with pfu DNA polymerase and purified cloned plasmids as template. The primers that were used were designed to amplify a cDNA fragment starting, in frame, after the native signal sequence and including the native translational termination codon. Additionally, the PCR primers were designed to include restriction sites that would facilitate cloning into the vectors described below in the correct transcriptional/translational reading frames. 3-OST-1 was cloned into vectors pET12a, 15B and 28a according to the manufacturer's instructions. This places the 3-OST-1 cDNA downstream of a powerful, inducible T7 transcription site and includes an efficient Shine-Dalgamo sequence at the appropriate distance from the initiator methionine of the construct.
Good yields of active protein result from IPTG induction at room temperature. The specific activity appears to be less than purified, or Baculovirus/sf9 produced material. The exact magnitude of the diminution of activity is unclear at this time; however, it may be 10-1000 fold. The presently preferred purification scheme is: (1) Induction at 22° C. (2) Sonication of bacteria, centrifugation to remove inclusion bodies and cell debris, purification of crude bacterial sonicate on heparin sepharose as described eslewhere. (3) PAP column chromatography. (4) Gel permeation chromatography. Step (4) is only needed for obtaining monomeric, pure 3-OST-1, and not for active protein preparation.
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## Claims

1. An isolated nucleic acid molecule comprising a nucleic acid sequence consisting of nucleotides 323 to 1255 of SEQ ID NO: 1, wherein said nucleic acid sequence encodes a polypeptide having 3-O-sulfotransferase activity.

2. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes a polypeptide comprising amino acid residues 53-311 or 21-307 of SEQ ID NO: 2, and wherein said polypeptide has 3-O-sulfortransferase activity.

3. An isolated nucleic acid molecule, wherein said nucleic acid molecule comprises the nucleotide sequence in SEQ ID NO: 1.

4. An isolated nucleic acid molecule, comprising a nucleic acid sequence that has at least 90% nucleotide sequence identity with nucleotides 323-1255 of SEQ ID NO: 1, wherein said nucleic acid sequence encodes a polypeptide having 3-O-sulfotransferase activity.

5. An isolated nucleic acid molecule, wherein said nucleic acid molecule comprises the nucleotide sequence of SEQ ID NO: 3, and wherein said nucleic acid molecule encodes a polypeptide having 3-O-sulfotransferase activity.

6. An isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 2, wherein said polypeptide has 3-O-sulfotransferase activity.

7. An isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising amino acid residues 53-311 of SEQ ID NO: 2, wherein said polypeptide has 3-O-sulfotransferase activity.

8. An isolated nucleic acid molecule, comprising a nucleic acid sequence consisting of nucleotides 119-1039 of SEQ ID NO: 3, wherein said nucleic acid sequence encodes a polypeptide having 3-O-sulfotransferase activity.

9. The isolated nucleic acid of claim 8, wherein said nucleic acid sequence encodes a polypeptide comprising amino acid residues 21-303 or 49-307 of SEQ ID NO: 4, wherein said polypeptide has 3-O-sulfotranferase activity.

10. An isolated nucleic acid molecule, comprising a nucleic acid encoding a polypeptide comprising amino acid residues 49-307 of SEQ ID NO: 4, wherein said polypeptide has 3-O-sulfotransferase activity.

11. An isolated nucleic acid molecule comprising a nucleic acid sequence that has at least 90% nudeotide sequence identity with nucleotides 119 to 1039 of SEQ ID NO: 3, wherein said nucleic acid sequence encodes a polypeptide having 3-O-sulfotransferase activity.

12. An isolated nucleic acid molecule comprising a nucleic acid sequence that encodes a polypeptide comprising the amino acid sequence set forth in of SEQ ID NO: 4, wherein said polypeptide has 3-O-sulfotransferase activity.

13. An isolated host cell comprisinga nucleic acid of claim 1, 4, 7, 8, 9 or 12.

14. The isolated host cell of claim 13, wherein said host cell is selected from the group consisting of bacterial cells, yeast cells and insect cells.

15. The isolated host cell of claim 13, wherein said cell is a mammalian cell.

16. The isolated host cell of claim 13, wherein said cell is selected from the group consisting of COS-7 cells, CHO cells, murine primary cardiac microvascular endothelial cells, murine mast cell line C57.1, human primary endothelial cells of umbilical vein, F9 embryonal carcinoma cells, rat fat pad endothelial cells, and L cells.

17. A vector comprising the isolated nucleic acid of claim 1, 4, 6, 7, 8, 9, 11 or 12.

18. An isolated host cell comprising the vector of claim 17.