AU2006200418A1 - Gridlock nucleic acid molecules, polypeptides, and diagnostic and therapeutic methods - Google Patents

Description

AUSTRALIA

Patents Act 1990 COMPLETE SPECIFICATION STANDARD PATENT Applicant: THE GENERAL HOSPITAL CORPORATION Invention Title: GRIDLOCK NUCLEIC ACID MOLECULES, POLYPEPTIDES, AND DIAGNOSTIC AND THERAPEUTIC METHODS The following statement is a full description of this invention, including the best method of performing it known to

US:

GRIDLOCK NUCLEIC ACID MOLECULES, POLYPEPTIDES, AND M

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DIAGNOSTIC AND THERAPEUTIC METHODS 00 5 Statement as to Federally Sponsored Research

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SThis research has been sponsored, in part, by grant numbers SHL07208, RO1-RR0888, RO1-DK55383, and RO-HL49579 from the 0 National Institutes of Health. The government may have certain rights in the invention.

Field of the Invention This invention relates to cardiovascular diseases.

Background of the Invention The vascular system contains vessels that are morphologically and functionally distinct. For example, arteries carry oxygenated blood at high pressure from the heart, while veins serve as capacitance vessels for blood return. While some of the differences within the vascular system occur after the onset of function, a complete vascular loop, formed by the trunk artery and vein, is required to accommodate the output of the first heart beat. The major trunk vessels, the aorta and the axial vein, of vertebrate embryos are formed by the coalescence of scattered mesodermal angioblasts into simple endothelial tubes by a process termed "vasculogenesis," which is distinguished from "angiogenesis," the formation of vessels by sprouting Sand remodeling (Fishman, "Assembly of blood vessels in the embryos," Lippincott-Raven Publishers, Philadelphia, 1996; Folkman et al., Cell 87:1153-1155, 1996; Risau, Nature 386:671-674, 1997; Yancopolos et al., Cell 93:661-664, 1998).

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N The aorta, the main trunk of the systemic arterial network, is subject Sto several congenital and acquired disorders, that may lead to severe complications in infancy and adulthood. Coarctation of the aorta is one of the most common human congenital cardiovascular diseases. In 00 5 coarctation, a discrete, localized vascular malformation partially obstructs the descending aorta, the major artery to the body, and most frequently Soccurs distal to the origins of vessels supplying the head and arms. Its O effects often become more physiologically severe at birth, when closure of the ductus can exacerbate the restriction to aortic blood flow. As a consequence of coarctation, affected individuals suffer from high blood pressure in the upper extremities and i: ad, and from low pressure in the trunk and legs. Survival often depends on the development of collateral blood vessels, which facilitate blood circulation in a manner so as to bypass the lesion.

Another serious cardiovascular disease that affects large numbers of individuals is atherosclerosis. This condition is characterized by the deposition of lipids in the intima of large and medium-sized arteries. Such deposits are associated with fibrosis and calcification.

The gridlock mutation (grl" 4 is a recessive mutation that was identified in the zebrafish system and that causes a focal vascular malformation resembling coarctation of the aorta in humans. In grl

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mutant embryos, fluorescent dextran injected into the heart, to outline patent vessels, is blocked at the origin of the dorsal aorta at the region where the two anterior dorsal aortae merge to form the single aorta of the trunk. The fluorescent beads circulated normally in the head (Weinstein et al., Nature Medicine 1:1143-1147, 1995). Thus, the grl mutant embryos lack circulation to the trunk.

S imm qrv nf the Invention The invention provides a novel gene, gridlock, and its encoded C, protein, gridlock plays a role in vascular development and modeling, and a mutation in gridlock has been associated with an aortic arch disease, 00 5 coarctation. Thus, gridlock nucleic acid molecules and polypeptides can be used in methods of diagnosing, treating, and preventing gridlock-related Sdiseases and conditions, such as aortic arch diseases.

IN In one aspect, the invention provides a substantially pure gridlock Spolypeptide. In preferred embodiments of this aspect, the gridlock polypeptide includes the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4, or includes an amino acid sequence that is substantially identical to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4. In other preferred embodiments of this aspect, the polypeptide is derived from a mammal, a human.

In another aspect, the invention provides a substantially pure nucleic acid molecule, e.g.,.DNA, including a sequence encoding a gridlock polypeptide. In a preferred embodiment of this aspect, the nucleic acid molecule encodes a human gridlock polypeptide. In other preferred embodiments of this aspect, the nucleic acid molecule encodes a polypeptide including the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4, or encodes a polypeptide including an amino sequence that is substantially identical to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4. In other preferred embodiments of this aspect, the nucleic acid molecule includes a nucleotide sequence that is substantially identical to the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3.

SIn a related aspect, the invention provides a nucleic acid molecule having at least 55% nucleic acid sequence identity to a sequence encoding a gridlock polypeptide or a fragment thereof, where the fragment includes at U least six amino acids and the nucleic acid molecule hybridizes under high c stringency conditions to at least a portion of a gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related protein family member. In a 00 5 preferred embodiment of this aspect, the nucleic acid molecule has 100% complementarity to a nucleic acid molecule encoding a gridlock polypeptide or a fragment thereof including at least six amino acids, and the IDnucleic acid molecule hybridizes under high stringency conditions to at least a portion of a gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairyrelated protein family member.

In a related aspect, the invention provides a nucleic acid molecule including a sequence that is antisense to a gridlock coding strand or a fragment thereof. In a preferred embodiment of this aspect, the antisense sequence is specific for a mutated gridlock coding region.

In another related aspect, the invention provides a vector, a gene therapy vector including a gridlock nucleic acid molecule, and a cell including this vector.

In other aspects, the invention provides a non-human transgenic animal, a zebrafish, including a gridlock nucleic acid molecule, and a non-human animal having a knockout mutation in one or both alleles encoding a gridlock polypeptide. The invention also provides a cell firom a non-human animal having a knockout mutation in one or both alleles encoding a gridlock polypeptide.

In other aspects, the invention provides a probe for analyzing the gridlock nucleic acid molecules of an animal, the probe having at least nucleic acid sequence identity to a sequence encoding a gridlock polypeptide or a fragment thereof. The fragment includes at least six amino -4- Sacids and the probe hybridizes under high stringency conditions to at least a portion of a gridlock nucleic acid molecule, and does not hybridize under Cc high stringency conditions to a nucleic acid molecule encoding a hairyrelated protein family member. In a preferred embodiment, the probe has 00 5 100% complementarity to a nucleic acid molecule encoding a gridlock polypeptide or a fragment thereof including at least six amino acids, and the Sprobe hybridizes under high stringency conditions to at least a portion of a IDgridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related protein family member.

In another aspect, the invention provides an antibody that specifically binds to a gridlock polypeptide, a polypeptide including the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4.

In another aspect, the invention provides a method of detecting the presence of a gridlock polypeptide in a sample. The method involves contacting the sample with an antibody that specifically binds to a gridlock polypeptide and assaying for binding of the antibody to the polypeptide.

In another aspect, the invention provides a method of detecting the presence of a mutant gridlock polypeptide in a sample. The method involves contacting the sample with an antibody that specifically binds to a mutant gridlock polypeptide and assaying for binding of the antibody to the mutant polypeptide.

In another aspect, the invention provides a method of diagno:sing an increased likelihood of developing a gridlock-related disease or condition in a test subject. The method involves analyzing nucleic acid molecules of the test subject to determine whether the test subject contains a mutation in a gridlock gene. The presence of the mutation is an indication that the test subject has an increased likelihood of developing a gridlock-related disease.

SIn preferred embodiments of this aspect, the test subject is a mammal, e.g, a human. In other preferred embodiments of this aspect, the method includes the step of using nucleic acid molecule primers specific for the gridlock C€ gene for nucleic acid molecule amplification by the polymerase chain reaction, or includes the step of sequencing gridlock nucleic acid molecules 00 from the test subject. In another preferred embodiment of this aspect, the analyzing is carried out by restriction fragment length polymorphism (RFLP) analysis. In another preferred embodiment of this aspect, the disease or condition is coarctation of the aorta, interrupted aortic arch disease, or atherosclerosis.

In another aspect, the invention provides a kit for the analysis of a gridlock nucleic acid molecule. The kit includes a nucleic acid molecule probe for analyzing the gridlock nucleic acid molecules of a test subject.

In another aspect, the invention provides a kit for the analysis of a gridlock nucleic acid molecule. The kit includes antibodies for analyzing the gridlock protein of a test subject.

In another aspect, the invention provides a method for preventing or ameliorating the effect of a gridlock deficiency by administering to a subject having a gridlock deficiency an expression vector including a nucleic acid molecule encoding a functional gridlock polypeptide. The nucleic acid molecule is operably linked to a promoter and the gridlock polypeptide is sufficient to prevent or ameliorate the effect of the gridlock deficiency.

In a related aspect, the invention provides a method for preventing or ameliorating the effect of a gridlock deficiency by administering a functional gridlock polypeptide to a subject having a gridlock deficiency.

The gridlock polypeptide is sufficient to prevent or ameliorate the e:fect of the gridlock deficiency.

In a further aspect, the invention provides a method for preventing or ameliorating the effect of a gridlock excess by administering an antisense gridlock molecule to a subject having a gridlock excess. The antisense gridlock molecule is sufficient to prevent or ameliorate the effect of the 00 5 gridlock excess.

In a related aspect, the invention provides a method for preventing or 0 Sameliorating the effect of a gridlock excess by administering a gridlock ND antibody to a subject having a gridlock excess. The gridlock antibody is Ssufficient to prevent or ameliorate the effect of the gridlock excess.

In another aspect, the invention provides a method for identifying a compound that modulates the expression or activity of a gridlock nucleic acid molecule or polypeptide. The method involves contacting the gridlock nucleic acid molecule or polypeptide with the compound, and determining the effect of the compound on the gridlock expression or activity.

By "polypeptide" or "polypeptide fragment" is meant a chain of two or more amino acids, regardless of any post-translational modification glycosylation or phosphorylation), constituting all or part of a naturally or non-naturally occurring polypeptide. By "post-translational modification" is meant any change to a polypeptide or polypeptide fragment during or after synthesis. Post-translational modifications can be produced naturally (such as during synthesis within a cell) or generated artificially (such as by recombinant or chemical means). A "protein" can be made up of one or more polypeptides.

By "gridlock," "gridlock protein," or "gridlock polypeptide" is meant a polypeptide that has at least 45%, preferably at least 60%, more preferably at least 75%, and most preferably at least 90% amino acid sequence identity to the sequence of the human or the zebrafish gridlock polypeptides shown in Figure 2 (SEQ ID NO:2 and SEQ ID NO:4, respectively). A polypeptide -7c having at least 85% amino acid identity to the bHLH or at least 55% amino acid identity to the Orange domains of the human or the zebrafish gridlock Spolypeptides shown in Figure 2 (SEQ ID NO:2 and SEQ ID NO:4, respectively) can be considered a gridlock polypeptide. Most preferably, such a polypeptide has at least 95% amino acid identity in the bHLH domain or at least 90% amino acid identity in the Orange domain to the O human or the zebrafish gridlock polypeptides shown in Figure 2 (SEQ ID SNO:2 and SEQ ID NO:4, respectively). Polypeptide products from splice Svariants of gridlock gene sequences and gridlock genes containing c, 10 mutations the grl"' 4 5 mutation) are also included in this definition.

Preferably, a gridlock polypeptide contains a "YRPW" motif. A gridlock polypeptide as defined herein plays a role in vascular development and modeling. It can be used as an early marker of vasculogenesis or angioblast cell fate determination, as well as an artery-specific, for example, an aortaspecific, marker later in development or in adults.

By a "gridlock nucleic acid molecule" is meant a nucleic acid molecule, such as a genomic DNA, cDNA, or RNA mRNA) molecule, that encodes gridlock, a gridlock protein, a gridlock polypeptide, or a portion thereof, as defined above.

The term "identity" is used herein to describe the relationship of the sequence of a particular nucleic acid molecule or polypeptide to the sequence of a reference molecule of the same type. For example, if a polypeptide or nucleic acid molecule has the same amino acid or nucleotide residue at a given position, compared to a reference molecule to which it is aligned, there is said to be "identity" at that position. The level of sequence identity of a nucleic acid molecule or a polypeptide to a reference molecule is typically measured using sequence analysis software with the default parameters specified therein, such as the introduction of gaps to achieve an -8optimal alignment Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, S1710 University Avenue, Madison, WI 53705, BLAST, or PILEUP/PRETTYBOX programs). These software programs match 00 5 identical or similar sequences by assigning degrees of identity to various substitutions, deletions, or other modifications. Conservative substitutions 0 typically include substitutions within the following groups: glycine, alanine, O valine, isoleucine, and leucine; aspartic acid, glutamic acid, asparagine, and Sglutamine; serine and threonine; lysine and arginine; and phenylalanine and tyrosine.

A nucleic acid molecule or polypeptide is said to be "substantially identical" to a reference molecule if it exhibits, over its entire length, at least 51%, preferably at least 55%, 60%, or 65%, and most preferably 90%, or 95% identity to the sequence of the reference molecule. For polypeptides, the length of comparison sequences is at least 16 amino acids, preferably at least 20 amino acids, more preferably at least 25 amino acids, and most preferably at least 35 amino acids. For nucleic acid molecules, the length of comparison sequences is at least 50 nucleotides, preferably at least nucleotides, more preferably at least 75 nucleotides, and most preferably at least 110 nucleotides.

A gridlock nucleic acid molecule or gridlock polypeptide is "analyzed" or subject to "analysis" if a test procedure is carried out on it that allows the determination of its biological activity or whether it is wild type or mutated. For example, one can analyze the gridlock genes of an animal a human or a zebrafish) by amplifying genomic DNA of the animal using the polymerase chain reaction, and then determining whether the amplified DNA contains a mutation, by nucleotide sequence or restriction fragment analysis.

c By "probe" or "primer" is meant a single-stranded DNA or RNA c molecule of defined sequence that can base pair to a second DNA or RNA _molecule that contains a complementary sequence ("target"). The stability of the resulting hybrid depends upon the extent of the base pairing that occurs. This stability is affected by parameters such as the degree of 00 complementarity between the probe and target molecule, and the degree of Sstringency of the hybridization conditions. The degree of hybridization stringency is affected by parameters such as the temperature, salt Sconcentration, and concentration of organic molecules, such as formamide, 10 and is determined by methods that are well known to those skilled in the art.

Probes or primers specific for gridlock nucleic acid molecules, preferably, have greater than 45% sequence identity, more preferably at least 55-75% sequence identity, still more preferably at least 75-85% sequence identity, yet more preferably at least 85-99% sequence identity, and most preferably 100% sequence identity to the sequences designated as SEQ ID NO:1 or SEQ ID NO:3. Probes can be detectably-labeled, either radioactively or non-radioactively, by methods that are well-known to those skilled in the art. Probes can be used for methods involving nucleic acid hybridization, such as nucleic acid sequencing, nucleic acid amplification by the polymerase chain reaction, single stranded conformational polymorphism (SSCP) analysis, restriction fragment polymorphism (RFLP) analysis, Southern hybridization, northern hybridization, in situ hybridization, electrophoretic mobility shift assay (EMSA), and other methods that are well known to those skilled in the art.

A molecule, an oligonucleotide probe or primer, a gene or fragment thereof, a cDNA molecule, a polypeptide, or an antibody, can be said to be "detectably-labeled" if it is marked in such a way that its presence can be directly identified in a sample. Methods for detectably-labeling Smolecules are well known in the art and include, without limitation, radioactive labeling with an isotope, such as "P or and nonradioactive labeling with a fluorescent label, such as fluorescein).

By a "substantially pure polypeptide" is meant a polypeptide (or a 00 5 fragment thereof) that has been separated from proteins and organic Smolecules that naturally accompany it. Typically, a polypeptide is O substantially pure when it is at least 60%, by weight, free from the proteins IN and naturally-occurring organic molecules with which it is naturally Oassociated. Preferably, the polypeptide is a gridlock polypeptide that is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, pure. A substantially pure gridlock polypeptide can be obtained, for example, by extraction from a natural source isolated aorta or vascular tissue), by expression of a recombinant nucleic acid molecule encoding a gridlock polypeptide, or by chemical synthesis. Purity can be measured by any appropriate method, by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

A polypeptide is substantially free of naturally associated components when it is separated from those proteins and organic molecules that accompany it in its natural state. Thus, a protein that is chemically synthesized or produced in a cellular system different from the cell in which it is naturally produced is substantially free from its naturally associated components. Accordingly, substantially pure polypeptides not only include those derived from eukaryotic organisms, but also those synthesized in E.

coli or other prokaryotes.

An antibody is said to "specifically bind" to a polypeptide if it recognizes and binds to the polypeptide a gridlock polypeptide), but does not substantially recognize and bind to other molecules non- 11 Ncl gridlock related polypeptides) in a sample, a biological sample, that naturally includes the polypeptide.

By "high stringency conditions" is meant conditions that allow hybridization comparable with the hybridization that occurs using a DNA probe of at least 500 nucleotides in length, in a buffer containing 0.5 M NaHPO 4 pH 7.2, 7% SDS, 1 mM EDTA, and 1% BSA (fraction at a 8 temperature of 65 C, or a buffer containing 48% formamide, 4.8X SSC, 0.2 M Tris-Cl, pH 7.6, 1X Denhardt's solution, 10% dextran sulfate, and 0.1% SDS, at a temperature of 42°C. (These are typical conditions for high stringency northern or Southern hybridizations.) High stringency hybridization is also relied upon for the success of numerous techniques routinely performed by molecular biologists, such as high stringency PCR, DNA sequencing, single strand conformational polymorphism analysis, and in situ hybridization. In contrast to northern and Southern hybridizations, these techniques are usually performed with relatively short probes usually 16 nucleotides or longer for PCR or sequencing and 40 nucleotides or longer for in situ hybridization). The high stringency conditions used in these techniques are well known to those skilled in the art of molecular biology, and examples of them can be found, for example, in Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, New York, NY, 1998, which is hereby incorporated by reference.

By a "transgene" is meant a DNA molecule that is inserted by artifice into a cell the nuclear genome of a cell), and is incorporated into the genome of an organism that develops from the cell. Such a transgene can be partly or entirely heterologous foreign) to the transgenic organism, or can be a gene that is homologous to an endogenous gene of the organism. An organism or animal a mammal, such as a -12- Smouse, rat, or goat) can be said to be "transgenic" if it developed from a cell that had a transgene inserted into it by artifice.

By a "knockout mutation" is meant an artificially-induced alteration in a nucleic acid molecule (created by recombinant DNA technology or 00 5 deliberate exposure to a mutagen) that reduces the biological activity of the polypeptide normally encoded therefrom by at least 80% relative to the Ounmutated gene. The mutation can be, without limitation, an insertion, O deletion, frameshift mutation, or a missense mutation. A "knockout Sanimal" is preferably a mammal, and more preferably a mouse, containing a knockout mutation, as defined above.

By "transformation" is meant any method for introducing foreign molecules nucleic acid molecules) into a cell. Lipofection, DEAEdextran-mediated transfection, microinjection, protoplast fusion, calcium phosphate precipitation, retroviral delivery, electroporation, and biolistic transformation are just a few of the many transformation methods that are well known to those skilled in the art that can be used in the invention. For example, biolistic transformation is a method for introducing foreign molecules into a cell using velocity-driven microprojectiles such as tungsten or gold particles. Such methods can include helium-driven, air-driven, and gunpowder-driven techniques. Biolistic transformation can be applied to the transformation or transfection of a wide variety of cell types, intracellular organelles, and intact tissues including, without limitation, mitochondria, chloroplasts, bacteria, yeast, fungi, algae, animal tissue, and cultured cells.

By a "transformed cell," "transfected cell," or "transduced cell," is Smeant a cell (or a descendent of a cell) into which a DNA molecule encoding a polypeptide hasbeen introduced, by means of recombinant DNA techniques.

-13r c By a "promoter" is meant a minimal nucleic acid sequence element sufficient to direct transcription. If desired, constructs of the invention can include promoter elements that are sufficient to render promoter-dependent gene expression controllable in a cell type-specific, tissue-specific, or temporal-specific manner, or inducible by external signals or agents. Such elements can be located in the or intron regions of a gene.

O By an "operably linked sequence" is meant that a gene and one or more regulatory sequences are connected in such a way as to permit gene expression when the appropriate molecules transcriptional activator C 10 proteins) are bound to the regulatory sequences.

By an "antisense molecule," as used herein in reference to nucleic acid molecules, is meant a nucleic acid molecule having a sequence that is complementary to at least 75 nucleotides, and preferably at least 100, 150, or 200 nucleotides, of the coding strand of a gene, such as a gridlock gene.

An antisense nucleic acid molecule can be, for example, capable of preferentially lowering the production of a mutant gridlock polypeptide encoded by a mutant gridlock gene.

By "missense mutation" is meant a substitution of one purine or pyrimidine base A, T, G, or C) by another within a nucleic acid molecule, such that the resulting new codon encodes an amino acid that is distinct from the amino acid originally encoded by the wild type codon.

By "frameshift mutation" is meant an insertion or deletion of at least one nucleotide within a polynucleotide coding sequence. A frameshift mutation alters the codon reading frame at or downstream from the mutation site. Such a mutation results in either the substitution of an encoded wild type amino acid sequence by a novel amino acid sequence, or a premature termination of an encoded polypeptide, due to the creation of a stop codon, or both.

-14- SBy "sample" is meant a tissue biopsy, amniotic fluid, cell, blood, serum, urine, stool, or other specimen obtained from a patient or test subject. The sample can be analyzed to detect a mutation in a gridlock Sgene, or expression levels of a gridlock gene, by methods that are known in the art. For example, methods such as sequencing, single-strand 00 conformational polymorphism (SSCP) analysis, or restriction fragment length polymorphism (RFLP) analysis of PCR products derived from a Spatient sample can be used to detect a mutation in a gridlock gene; ELISA can be used to measure levels ofgridlock polypeptide; and PCR can be used to measure the level ofa gridlock nucleic acid molecule.

By "gridlock-related disease" or "gridlock-related condition" is meant a disease or condition that results from inappropriately high or low expression of a gridlock gene, or a mutation in a gridlock gene that alters the biological activity of a gridlock nucleic acid molecule or polypeptide.

gridlock-related diseases and conditions can arise in any vascular tissue in which gridlock is expressed during prenatal or post-natal life. gridlockrelated diseases and conditions can include congenital cardiovascular diseases congenital dysmorphogenesis) and cardiovascular disease acquired in adulthood, such as atherosclerosis. By "congenital cardiovascular disease" is meant a disease associated with the abnormal formation of the heart or blood vessels. A patient suffering from a congenital cardiovascular disease, for example, an aortic arch disease, such as interrupted aortic arch disease or coarctation of the aorta, may display constriction of the aorta.

The invention provides several advantages. For example, it provides methods and reagents that can be used in the diagnosis and treatment of diseases caused by vascular malformation or dysfunction. These disorders include congenital cardiovascular diseases, such as interrupted arch Sdiseases, aortic arch diseases, coarctation of the aorta, and N cardiovascular diseases that occur in adulthood, such as atherosclerosis, hypertension, and coronary artery disease. These disorders can be treated, C using the methods described herein, in a variety of ways including, for example, small molecule therapy, gene therapy, antisense oligonucleotide 00 therapy, and protein replacement therapy. Additionally, the nucleic acid molecules and polypeptides of the invention have diagnostic/disease 0 management applications, for example, use as prognostic markers or IN predisposition indicators of cardiovascular diseases.

Other features and advantages of the invention will be apparent from the detailed description of the invention, the drawings, and the claims.

Brief Description of the Drawings Figure 1 is a diagram showing the local genetic, physical, and radiation hybrid map of the zebrafish gridlock region.

Figure 2A is an amino acid sequence alignment of zebrafish grl and human grl (SEQ ID NO:2 and SEQ ID NO:4).

Figure 2B is an amino acid sequence alignment ofzebrafish and human grl, hHESR-1, mHESR-1, and dHESR-1 in the basic helix-loophelix, Orange, and YRPW domains.

Figure 2C is a graphical diagram of nucleic acid sequencing results, showing that the grim"' mutation results in a T to A transversion.

Figure 2D is an amino acid sequence alignment ofzebrafish and human grl, hHESR-1, mHESR-1, and dHESR-1 proteins.

Figure 3A is a histological section showing expression of grl mRNA as bilateral stripes (arrows) at the 10 somite stage (dorsal view).

-16r Figure 3B-C are histological sections showing the lateral view of the anterior trunk, posterior trunk, and tail, showing the grl transcripts at the dorsal aorta (arrows).

Figure 3D is a sagittal histological sections of the posterior trunk 00 5 showing the lumen of the dorsal aorta with the grl expression (arrow) and the grl-negative cells at axial veins (arrow).

SFigure 3E is a transverse histological section of the anterior trunk sO showing grl expression at the paired dorsal aortae (arrows) ventral to the Snotochord, but not at the bilateral cardinal veins (arrowheads).

Figure 3F-G are transverse histological sections of posterior trunk showing grl expression in the endothelial cells at the middleline dorsal aorta beneath the notochord (arrowhead), and extending into what is likely a sprout (the intersomitic artery; small arrow), but not in the vein (arrows).

Figure 3H is a transverse histological section of posterior trunk showingfli expression at both the middleline dorsal aorta (arrowhead) and the axial vein (arrows).

Figure 31 is a transverse histological section through the anterior trunk at the level of the first somite;fli is expressed at bilateral common cardinal veins (arrowheads) and the paired dorsal aortae (arrows).

Figure 3J is a longitudinal histological section of the anterior trunk showing the dorsal view of selective expression of the grl at the aortic bifurcation at the 25 somite stage (arrows).

For Figures 3A-3J, Dorsal is up at and anterior is to the left at and The in situ hybridization was carried out at the 30 somite (24 hours) stage. N, notochord; da, dorsal aorta; v, axial vein.

Figure 4A is a microangiogram showing the phenotype of wild type embryos.

-17- SFigure 4B is a microangiogram showing the phenotype of the grl mutant.

Figure 4C is a microangiogram showing the phenotype of a rescued grl mutant.

00 5 Figure 5A is a DNA sequence of the human grl gene (SEQ ID 1 NO:1) SFigure 5B is a DNA sequence of the zebrafish grl gene (SEQ ID N NO:3).

Detailed Description of the Invention The invention provides gridlock genes, which play a role in vascular development and modeling, polypeptides encoded by these genes, nucleic acid molecules related to these genes (see below), and diagnostic and therapeutic methods employing these genes, polypeptides, and nucleic acid molecules. The invention also provides methods for identifying compounds that modulate the biological activities of gridlock genes and polypeptides, and therapeutic methods employing these compounds.

The diagnostic, therapeutic, and screening methods of the invention are first described, followed by general ap-rroaches that can be used in carrying out these methods. Finally, experimental results supporting the methods of the invention are described.

Diagnostic Methods Employing gridlock Nucleic Acid Molecules, Polypeptides, and Antibodies gridlock nucleic acid molecules, polypeptides, and antibodies can be used in methods to diagnose or monitor diseases and conditions involving mutations in, or inappropriate expression of, gridlock genes. As discussed above, the gridlock mutation in zebrafish, which results in the translation of -18- San abnormally long gridlock polypeptide, is characterized by a phenotype Ct that is similar to that of coarctation in humans. Thus, detection of abnormalities in gridlock genes or their expression can be used in methods to diagnose, or to monitor treatment or development of, human interrupted 00 5 arch or aortic arch diseases, such as coarctation. gridlock may also play a role in cardiovascular diseases other than aortic arch diseases, such as atherosclerosis, and, thus, detection of abnormalities in gridlock genes or Stheir expression can be used in methods to diagnose and monitor these conditions as well.

The diagnostic methods of the invention can be used, for example, with patients that have an aortic arch disease, in an effort to determine its etiology, and, thus, to facilitate selection of an appropriate course of treatment. The diagnostic methods can also be used with patients that have not yet developed an aortic arch disease, but who may be at risk of developing such a disease, or with patients that are at an early stage of developing such a disease. Many aortic arch diseases occur during development, and, thus the diagnostic methods of the invention can be carried out on a fetus or embryo during development. Also, the diagnostic methods of the invention can be used in prenatal genetic screening, for example, to identify parents who may be carriers of a recessive gridlock mutation.

gridlock abnormalities that can be detected using the diagnostic methods of the invention include those characterized by, for example, (i) abnormal gridlock polypeptides abnormally long gridlock polypeptides), (ii) gridlock genes containing mutations that result in the production of such polypeptides, and (iii) gridlock mutations that result in production of abnormal amounts ofgridlock. Detection of such -19abnormalities, thus, can be used in methods to diagnose human aortic arch disease, such as coarctation, or atherosclerosis.

SLevels ofgridlock expression in a patient sample can be determined by using any of a number of standard techniques that are well known in the 00 5 art. For example, gridlock expression in a biological sample a blood or tissue sample, or amniotic fluid) from a patient can be monitored by standard northern blot analysis or by quantitative PCR (see, Ausubel et IDal., supra; PCR Technology: Principles and Applications for DNA SAmplification, H.A. Ehrlich, Ed., Stockton Press, NY; Yap et al. Nucl.

Acids. Res. 19:4294, 1991).

A biological sample obtained from a patient can be analyzed for one or more mutations in gridlock nucleic acid molecules using a mismatch detection approach. Generally, this approach involves PCR amplification of nucleic acid molecules from a patient sample, followed by identification of a mutation a mismatch) by detection of altered hybridization, aberrant electrophoretic gel migration, binding, or cleavage mediated by mismatch binding proteins, or by direct nucleic acid molecule sequencing. Any of these techniques can be used to facilitate detection of mutant gridlock genes, and each is well known in the art. Examples of these techniques are described, for example, by Orita et al. (Proc. Natl. Acad. Sci. U.S.A.

86:2766-2770, 1989) and Sheffield et al. (Proc. Natl. Acad. Sci. U.S.A.

86:232-236, 1989).

Mismatch detection assays also provide an opportunity to diagnose a gridlock-mediated predisposition to a disease before the onset of symptoms.

For example, a patient heterozygous for a.gridlock mutation that suppresses normal gridlock biological activity or expression may show no clinical symptoms of a gridlock-related disease, and yet possess a higher than normal probability of developing a cardiovascular disease. Given such a V diagnosis, patients can take precautions to minimize their exposure to Sadverse environmental factors and to carefully monitor their medical Scondition (for example, through frequent physical examinations). As mentioned above, this type of diagnostic approach can also be used to detect 00 5 gridlock mutations in prenatal screens.

The gridlock diagnostic assays described above can be carried out using any biological sample (for example, a blood or tissue sample, or ISO amniotic fluid) in which gridlock is normally expressed. Identification of a mutant gridlock gene can also be assayed using these sources for test samples. Alternatively, a gridlock mutation, particularly as part of a diagnosis for predisposition to a gridlock-associated disease, can be tested for using a DNA sample from any cell, for example, by mismatch detection techniques. Preferably, the DNA sample is subjected to PCR amplification prior to analysis.

In yet another diagnostic approach of the invention, an immunoassay is used to detect or monitor gridlock protein expression in a biological sample, gridlock-specific polyclonal or monoclonal antibodies (produced as described below) can be used in any standard immunoassay format ELISA, Western blot, or RIA; see, Ausubel et al., supra) to measure gridlock polypeptide levels. These levels are compared to wild-type gridlock levels. For example, a decrease in gridlock production may be indicative of a condition or a predisposition to a condition involving insufficient gridlock biological activity, such as a cardiovascular disease.

Immunohistochemical techniques can also be utilized for gridlock detection. For example, a tissue sample can be obtained from a patient, sectioned, and stained for the presence ofgridlock using an anti-gridlock antibody (see below) and any standard detection system one that includes a secondary antibody conjugated to horseradish peroxidase).

-21- "General guidance regarding such techniques can be found in, Bancroft Set al., Theory and Practice ofHistological Techniques, Churchill Livingstone, 1982, and Ausubel et al., supra.

¢€3 In a preferred example, a combined diagnostic method can be oO 5 employed that includes an evaluation ofgridlock protein production (for example, by immunological techniques or the protein truncation test 8 (Hogerrorst et al., Nature Genetics 10:208-212, 1995), and a nucleic acid ID molecule-based detection technique designed to identify more subtle gridlock mutations (for example, point mutations). As described above, a number of mismatch detection assays are available to those skilled in the art, and any preferred technique can be used. Mutations in gridlock can be detected that either result in loss of gridlock expression or loss of normal gridlock biological activity.

Therapeutic Methods Employing gridlock Nucleic Acid Molecules, Polypeptides, and Antibodies The invention includes methods of treating or preventing gridlockrelated diseases. As discussed above, a gridlock mutation may result in aortic arch disease, such as coarctation, early in development. Thus, the therapeutic methods of the invention may be, in some cases, targeted to prenatal treatment. For example, a fetus found to have a gridlock mutation can be administered a gene therapy vector including a normal gridlock gene or normal gridlock protein (see below). Such treatment may be required only for a short period of time, or may, in some form, be required throughout such a patient's lifetime. Any continued need for treatment, however, can be determined using, for example, the diagnostic methods described above. Also as discussed above, gridlock abnormalities may be associated with diseases in adults aortic arch diseases and 22- Satherosclerosis), and thus adults can be subject to the therapeutic methods of the invention as well. These methods can also be used, for example, to promote blood vessel growth, which may be desirable, for example, in wound healing.

00 5 Therapies can be designed to circumvent or overcome a gridlock gene defect, or inadequate or excessive gridlock gene expression, and thus modulate and possibly alleviate conditions involving defects in gridlock O genes or proteins. In considering various therapies, it is understood that such therapies are, preferably, targeted to the affected or potentially affected organs, for example, the aorta. Reagents that can be used to modulate gridlock biological activity can include, without limitation, full length gridlock polypeptides; gridlock DNA, mRNA, or antisense RNA; gridlock antibodies; and any compound that modulates gridlock biological activity, expression, or stability (see below).

Treatment or prevention of diseases resulting from a mutated gridlock gene can be accomplished, for example, by replacing a mutant gridlock gene with a normal gridlock gene, administering a normal gridlock gene, modulating the function of a mutant gridlock protein, delivering normal gridlock protein to the appropriate cells, or altering the levels of normal or mutant gridlock protein. It is also possible to correct a gridlock defect to modify the physiological pathway a signal transduction pathway) in which the gridlock protein participates.

To replace a mutant protein with normal protein, or to add protein to cells that do not express sufficient or normal gridlock protein, it may be necessary to obtain large amounts of pure gridlock protein from cultured cell systems in which the protein is expressed (see, below). Delivery of the protein to the affected tissue can then be accomplished using appropriate packaging or administrating systems. Alternatively, small -23molecule analogs that act as gridlock agonists or antagonists can be administered to produce a desired physiological effect (see below).

Gene therapy is another therapeutic approach for preventing or ameliorating diseases caused by gridlock gene defects. Nucleic acid 00 5 molecules encoding wild type gridlock can be delivered to cells that lack sufficient, normal gridlock biological activity cells carrying mutations 0 Sin gridlock genes). The nucleic acid molecules must be delivered to those D cells in a form in which they can be taken up by the cells and so that Ssufficient levels of protein, to provide effective gridlock function, can be produced. Alternatively, for some gridlock mutations, it may be possible slow the progression of the resulting disease or to modulate gridlock activity by introducing another copy of a homologous gene bearing a second mutation in that gene, to alter the mutation, or to use another gene to block any negative effect.

Transducing retroviral, adenoviral, and adeno-associated viral vectors can be used for somatic cell gene therapy, especially because of their high efficiency of infection and stable integration and expression (see, Cayouette et al., Human Gene Therapy 8:423-430, 1997; Kido et al., Current Eye Research 15:833-844, 1996; Bloomer et al., Journal of Virology 71:6641-6649, 1997; Naldini et al., Science 272:263-267, 1996; and Miyoshi et al., Proc. Natl. Acad. Sci., U.S.A. 94:10319-1032, 1997).

For example, the full length gridlock gene, or a portion thereof, can be cloned into a retroviral vector and expression can be driven from its endogenous promoter, from the retroviral long terminal repeat, or from a promoter specific for a target cell type of interest (such as aortic or other vascular cells). Other viral vectors that can be used include, for example, vaccinia virus, bovine papilloma virus, or a herpes virus, such as Epstein- Barr Virus (also see, for example, the vectors of Miller, Human Gene -24- Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis et al., BioTechniques 6:608-614, 1988; Tolstoshev et al., Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337:1277-1278, 1991; Coretta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 00 5 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407- 416, 1991; Miller et al., Biotechnology 7:980-990, 1989; Le Gal La Salle et al., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995).

D Retroviral vectors are particularly well developed and have been used in Sclinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Patent No. 5,399,346).

Gene transfer can also be achieved using non-viral means involving transfection in vitro. Such methods include use of calcium phosphate, DEAE dextran, electroporation, and protoplast fusion. Liposomes can also be potentially beneficial for delivery of DNA into a cell. Transplantation of normal genes into the affected tissues of a patient can also be accomplished by transferring a normal gridlock gene into a cultivatable cell type ex vivo, after which the cell (or its descendants) are injected into a targeted tissue.

Non-viral approaches can also be employed for the introduction of therapeutic DNA into cells predicted to be subject to diseases involving gridlock. For example, a gridlock nucleic acid molecule or an antisense nucleic acid molecule can be introduced into a cell by lipofection (Feigner et al., Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger et al., Methods in Enzymology 101:512, 1983), asialoorosomucoid-polylysine conjugation (Wu et al., Journal of Biological Chemistry 263:14621, 1988; Wu et al., Journal of Biological Chemistry 264:16985, 1989), or, less preferably, micro-injection under surgical conditions (Wolff et al., Science 247:1465, 1990).

t gridlock cDNA expression for use in gene therapy methods can be directed from any suitable promoter the human cytomegalovirus c (CMV), simian virus 40 (SV40), or metallothionein promoters), and regulated by any appropriate mammalian regulatory element. For example, 00 5 if desired, enhancers known to preferentially direct gene expression in Sspecific cell types can be used to direct gridlock expression. The enhancers Sused can include, without limitation, those that are characterized as tissue- Sor cell-specific enhancers. Alternatively, if a gridlock genomic clone is O used as a therapeutic construct (such clones can be identified by hybridization with gridlock cDNA, described above), regulation can be mediated by the cognate regulatory sequences, or, if desired, by regulatory sequences derived from a heterologous source, including any of the promoters or regulatory elements described above.

Antisense-based strategies can be employed to explore gridlock gene function and as a basis for therapeutic drug design. These strategies are based on the principle that sequence-specific suppression of gene expression (via transcription or translation) can be achieved by intracellular hybridization between genomic DNA or mRNA and a complementary antisense species. The formation of a hybrid RNA duplex interferes with transcription of the target gridlock-encoding genomic DNA molecule, or processing, transport, translation, or stability of the target gridlock mRNA molecule.

Antisense strategies can be delivered by a variety of approaches. For example, antisense oligonucleotides or antisense RNA can be directly administered by intravenous injection) to a subject in a form that allows uptake into cells. Alternatively, viral or plasmid vectors that encode antisense RNA (or antisense RNA fragments) can be introduced into a cell in vivo or ex vivo. Antisense effects can be induced by control (sense) -26tUsequences; however, the extent ofphenotypic changes are highly variable.

Phenotypic effects induced by antisense effects are based on changes in Scriteria such as protein levels, protein activity measurement, and target mRNA levels.

00 5 For example, gridlock gene therapy can also be accomplished by direct administration of antisense gridlock mRNA to a cell that is expected to be adversely affected by the expression of wild-type or mutant gridlock.

IDThe antisense gridlock mRNA can be produced and isolated by any Sstandard technique, but is most readily produced by in vitro transcription using an antisense gridlock cDNA under the control of a high efficiency promoter the T7 promoter). Administration of antisense gridlock mRNA to cells can be carried out by any of the methods for direct nucleic acid molecule administration described above.

An alternative strategy for inhibiting gridlock function using gene therapy involves intracellular expression of an anti-gridlock antibody or a portion of an anti-gridlock antibody. For example, the gene (or gene fragment) encoding a monoclonal antibody that specifically binds to gridlock and inhibits its biological activity can be placed under the transcriptional control of a tissue-specific gene regulatory sequence.

The invention also includes the gridlock gene promoter and fragments thereof that direct gene expression in endothelial cells of arteries, such as the aorta. Such promoters can be used in the methods described above, to direct expression ofgridlock, antisense gridlock RNA, or antigridlock antibodies or portions thereof, or can be used to express nongridlock related molecules in arterial aortic) endothelial cells.

Another therapeutic approach within the invention involves administration of recombinant gridlock polypeptide, either directly to the site of a potential or actual disease-affected tissue (for example, by -27- Sinjection) or systemically (for example, by any conventional recombinant protein administration technique). The dosage ofgridlock depends on a Cc number of factors, including the size and health of the individual patient, but, generally, between 0.1 mg and 100 mg, inclusive, are administered per day to an adult in any pharmaceutically acceptable formulation.

In a patient diagnosed as heterozygous for a gridlock mutation, or as N susceptible to gridlock mutations or aberrant gridlock expression (even if \those mutations or expression patterns do not yet result in alterations in (gridlock expression or biological activity), any of the above-described therapies can be administered before the occurrence of the disease phenotype. In particular, compounds shown to modulate gridlock expression or gridlock biological activity can be administered to patients diagnosed with potential or actual diseases by any standard dosage and route of administration (see above). Alternatively, gene therapy using an antisense gridlock mRNA expression construct can be undertaken to reverse or prevent the gene defect prior to the development of the disease.

The methods of the present invention can be used to diagnose or treat the disorders described herein in any mammal, for example, humans, domestic pets, or livestock. Where a non-human mammal is treated or diagnosed, the gridlock polypeptide, nucleic acid molecule, or antibody employed is preferably specific for that species.

gridlock nucleic acid molecules and polypeptides can also be used in tissue engineering, for example, in the manufacture of artificial or partially artificial blood vessels. Coronary bypass surgery is, typically, carried out using vein grafts, which, as a consequence of the surgery, assume an arterial role. It is therefore desirable to impart arterial characteristics upon such vein grafts. As mentioned above, gridlock is an arterial marker and plays a role in arterial development and modeling. Thus, a vein graft can be treated -28- Swith a gridlock nucleic acid molecule or polypeptide, as described above, to impart such characteristics on a vein graft. gridlock nucleic acid molecules C and polypeptides can also be used in the construction of artificial blood vessels. For example, artificial matrices can be coated with smooth muscle OO 5 cells on the outside and lined with endothelial cells. gridlock nucleic acid molecules or polypeptides can be used in association with any of these components to enhance the arterial nature of the artificial blood vessel.

Identification of Molecules that Modulate gridlock Biological Activity or WhY s Biological Activity is Modulated by gridlock Isolation of the gridlock cDNA (as described herein) also facilitates the identification of molecules that increase or decrease gridlock biological activity. Similarly, molecules whose activity is modulated by gridlock biological activity can be identified. According to one approach, candidate molecules are added at varying concentrations to the culture medium of cells expressing gridlock mRNA. gridlock biological activity is then measured using standard techniques. The measurement of biological activity can include the measurement of gridlock protein and nucleic acid molecule levels, gridlock phosphorylation, or the effect of gridlock on vascular development.

If desired, the effect of candidate modulators on expression can, in the alternative, be measured at the level of gridlock protein production using the same general approach and standard immunological detection techniques, such as western blotting or immunoprecipitation with a gridlock-specific antibody (see below).

Candidate modulators can be purified (or substantially purified) molecules or can be one component of a mixture of compounds an extract or supernatant obtained from cells; Ausubel et al., supra). In a -29- Smixed compound assay, gridlock expression is tested against progressively .smaller subsets of the candidate compound pool produced by standard purification techniques, HPLC or FPLC) until a single compound or minimal compound mixture is demonstrated to modulate gridlock 00 5 expression.

Alternatively, or in addition, candidate compounds can be screened for those that modulate gridlock activity. In this approach, the level of Saortic development and blood circulation in the presence of a candidate compound is compared to the level of aortic development and blood circulation in its absence, under equivalent conditions. Again, such a screen can begin with a pool of candidate compounds, from which one or more useful modulator compounds is isolated in a step-wise fashion.

Aortic development and blood circulation can be examined using, for example, the zebrafish system. The zebrafish, Danio rerio, is a convenient organism to use in genetic analysis of vascular development (see below). In addition to its short generation time and fecundity, it has an accessible and transparent embryo, allowing direct observation of blood vessel function from the earliest stages.

gridlock may also play a role in angiogenesis, which, as mentioned above, is the formation of blood vessels by sprouting and remodeling.

Thus, compounds identified as modulating or mimicking gridlock or fragments thereof gridlock fragments that include a YPPW motif), using the methods described above, can be used in methods for promoting to promote wound healing) or inhibiting to prevent tumor growth) angiogenesis.

The screening assays described above can be carried out in a variety of ways that are well known to those skilled in this art. These include using C) ~gridlock variants such as the gridlock"145 mutant or by using fragments of gridlock.

00 5 A test compound that can be screened in the methods described above can be a chemical, be it naturally-occurring or artificially-derived.

SSuch compounds can include, for example, polypeptides, synthesized IND organic molecules, naturally occurring organic molecules, nucleic acid O molecules, and components thereof. Candidate gridlock modulators include peptide as well as non-peptide molecules peptide or non-peptide molecules found, in a cell extract, mammalian serum, or growth medium in which mammalian cells have been cultured).

In general, novel drugs for prevention or treatment ofgridlockrelated diseases are identified from large libraries of both natural products, synthetic (or semi-synthetic) extracts, and chemical libraries using methods that are well known in the art. Those skilled in the field of drug discovery and development will understand that the precise source of test extracts or compounds is not critical to the screening methods of the invention.

Accordingly, virtually any number of chemical extracts or compounds can be screened using these methods. Examples of such extracts or compounds include, but are not limited to, plant-, fungal-, prokaryotic-, or animral-based extracts, fermentation broths, and synthetic compounds, as well as modifications of existing compounds.

Numerous methods are also available for generating random or directed synthesis semi-synthesis or total synthesis) of any number of chemical compounds, including, but not limited to, saccharide-, lipid-, peptide-, and nucleic acid molecule-based compounds. Synthetic compound libraries are commercially available from Brandon Associates -31 S(Merrimack, NH) and Aldrich Chemical (Milwaukee, WI). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant, and Sanimal extracts are commercially available from a number of sources, including Biotics (Sussex, UK), Xenova (Slough, UK), Harbor Branch 00 5 Oceanographic Institute (Ft. Pierce, FL), and PharmaMar, U.S.A.

(Cambridge, MA). In addition, natural and synthetically produced libraries Sare produced, if desired, according to methods known in the art, by IDstandard extraction and fractionation methods. Furthermore, if desired, any Slibrary or compound can be readily modified using standard chemical, physical, or biochemical methods.

In addition, those skilled in the art of drug discovery and development readily understand that methods for dereplication taxonomic dereplication, biological dereplication, and chemical dereplication, or any combination thereof) or the elimination of replicates or repeats of materials already known for their therapeutic activities for aortic arch or other cardiovascular atherosclerosis) disorders can be employed whenever possible.

When a crude extract is found to regulate vascular development, further fractionation of the positive lead extract can be carried out to isolate chemical constituents responsible for the observed effect. Thus, the goal of the extraction, fractionation, and purification process is the careful characterization and identification of a chemical entity within the crude extract having a desired activity. The same assays described herein for the detection of activities in mixtures of compounds can be used to purify the active component and to test derivatives thereof. Methods of fractionation and purification of such heterogenous extracts are known in the art. If desired, compounds shown to be useful agents for treatment are chemically -32- Smodified according to methods known in the art. Compounds identified as being of therapeutic value can be subsequently analyzed using a mammalian c vascular development model.

00 Administration of riidlock Polypeptides, gridlock Genes, and Modulators of gridlock Synthesis or Function A gridlock protein, gene, or modulator can be administered 'within a N pharmaceutically-acceptable diluent, carrier, or excipient, in unit dosage form. Also, conventional pharmaceutical practice can be employed to provide suitable formulations or compositions in which to administer neutralizing gridlock antibodies or gridlock-inhibiting compounds antisense gridlock or a gridlock dominant negative mutant) to patients suffering from a gridlock-related disease, such as an aortic arch disease or atherosclerosis. In addition, as noted above, gridlock may play a role in angiogenesis. Thus, gridlock polypeptides, genes, and modulators can be administered to stimulate or inhibit angiogenesis. For example, such a molecule may be administered to inhibit vein formation. Administration can begin before or after the patient is symptomatic.

Any appropriate route of administration can be employed, for example, administration can be parenteral, intravenous, intra-arterial, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracisternal, intraperitoneal, intranasal, aerosol, by suppositories, or oral. However, as noted above, preferably, the administration is local to the afflicted tissue, such as aortic or other cardiovascular tissue. Therapeutic formulations can be in the form of liquid solutions or suspensions; for oral administration, formulations can be in the form of tablets or capsules; and for intranasal formulations, in the form of powders, nasal drops, or aerosols.

-33- SMethods that are well known in the art for making formulations are found, for example, in Remington's Pharmaceutical Sciences, 18 th edition), ed. A. Gennaro, 1990, Mack Publishing Company, Easton, PA.

Formulations for parenteral administration can, for example, contain 00 5 excipients; sterile water; or saline; polyalkylene glycols, such as polyethylene glycol; oils of vegetable origin; or hydrogenated napthalenes.

SBiocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, Sor polyoxyethylene-polyoxypropylene copolymers can be used to control Sthe release of the compounds. Other potentially useful parenteral delivery systems for gridlock modulatory compounds include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation can contain excipients, for example, lactose, or can be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate, and deoxycholate, or can be oily solutions for administration in the form of nasal drops, or as a gel.

Synthesis of gridlock Proteins, Polypeptides. and Polypeptide Fragments Those skilled in the art of molecular biology will understand that a wide variety of expression systems can be used to produce the recombinant gridlock proteins. As discussed further below, the precise host cell used is not critical to the invention. The gridlock proteins can be produced in a prokaryotic host E. coli) or in a eukaryotic host S. cerevisiae, insect cells such as Sf9 cells, or mammalian cells such as COS-1, NIH 3T3, or HeLa cells). These cells are commercially available from, for example, the American Type Culture Collection, Rockville, MD (see also Ausubel et al., supra). The method of transformation and the choice of expression vehicle expression vector) will depend on the host system selected.

Transformation and transfection methods are described, in Ausubel et -34tUal., supra, and expression vehicles can be chosen from those provided, e.g.

in Pouwels et al., supra. Specific examples of expression systems that can be used in the invention are described further, as follows.

The characteristics of cloned gridlock genes can be analyzed by oo00 5 introducing such genes into various cell types or using in vitro extracellular systems. The function ofgridlock proteins produced in such cells or systems can then be examined under different physiological conditions.

IND Alternatively, cell lines can be produced that over-express the gridlock gene product, allowing purification ofgridlock for biochemical characterization, large-scale production, antibody production, and patient therapy.

For protein expression, eukaryotic or prokaryotic expression systems can be generated in which gridlock gene sequences are introduced into a plasmid or other vector, which is then used to transform living cells;.

Constructs in which full length gridlock cDNAs, containing the entire open reading frame, inserted in the correct orientation into an expression plasmid can be used for protein expression. Alternatively, portions ofgridlock gene sequences, including wild type or mutant gridlock sequences, can be inserted. Prokaryotic and eukaryotic expression systems allow various important functional domains of gridlock proteins to be recovered, if desired, as fusion proteins, and then used for binding, structural, and functional studies, and also for the generation of antibodies.

Typical expression vectors contain promoters that direct synthesis of large amounts ofmRNA corresponding to a nucleic acid molecule that has been inserted into the vector. They can also include a eukaryotic or prokaryotic origin of replication, allowing for autonomous replication within a host cell, sequences that confer resistance to an otherwise toxic drug, thus allowing vector-containing cells to be selected in the presence of the drug, and sequences that increase the efficiency with which the t synthesized mRNA is translated. Stable long-term vectors can be maintained as freely replicating entities by using regulatory elements of, for Sexample, viruses the OriP sequences from the Epstein Barr Virus genome). Cell lines can also be produced that have the vector integrated 00 5 into genomic DNA of the cells, and, in this manner, the gene product can be produced in the cells on a continuous basis.

SExpression of foreign molecules in bacteria, such as Escherichia \D coli, requires the insertion of a foreign nucleic acid molecule, a O gridlock nucleic acid molecule, into a bacterial expression vector. Such plasmid vectors include several elements required for the propagation of the plasmid in bacteria, and for expression of foreign DNA contained within the plasmid. Propagation of only plasmid-bearing bacteria is achieved by introducing, into the plasmid, a selectable marker-encoding gene that allows plasmid-bearing bacteria to grow in the presence of an otherwise toxic drug.

The plasmid also contains a transcriptional promoter capable of directing synthesis of large amounts of mRNA from the foreign DNA. Such promoters can be, but are not necessarily, inducible promoters that initiate transcription upon induction by culture under appropriate conditions in the presence of a drug that activates the promoter). The plasmid also, preferably, contains a polylinker to simplify insertion of the gene in the correct orientation within the vector.

Once an appropriate expression vector containing a gridlock gene, or a fragment, fusion, or mutant thereof, is constructed, it can be introduced into an appropriate host cell using a transformation technique, such as, for example, calcium phosphate transfection, DEAE-dextran transfection, electroporation, microinjection, protoplast fusion, or liposome-mediated transfection. Host cells that can be transfected with the vectors of this invention can include, but are not limited to, E. coli or other bacteria, yeast, -36-

C

N fungi, insect cells (using, for example, baculoviral vectors for expression), c or cells derived from mice, humans, or other animals. Mammalian cells can also be used to express gridlock proteins using a virus expression system a vaccinia virus expression system) described, for example, in 00 5 Ausubel et al., supra.

In vitro expression of gridlock proteins, fusions, polypeptide fragments, or mutants encoded by cloned DNA can also be carried out using Sthe T7 late-promoter expression system. This system depends on the regulated expression ofT7 RNA polymerase, an enzyme encoded in the DNA of bacteriophage T7. The T7 RNA polymerase initiates transcription at a specific 23-bp promoter sequence called the T7 late promoter. Copies of the T7 late promoter are located at several sites on the T7 genome, but none is present in E. coli chromosomal DNA. As a result, in T7-infected E.

coli, T7 RNA polymerase catalyzes transcription of viral genes, but not E.

coli genes. In this expression system, recombinant E. coli cells are first engineered to carry the gene encoding T7 RNA polymerase next to the lac promoter. In the presence ofIPTG, these cells transcribe the T7 polymerase gene at a high rate and synthesize abundant amounts of T7 RNA polymerase. These cells are then transformed with plasmid vectors that carry a copy of the T7 late promoter protein. When IPTG is added to the culture medium containing these transformed E. coli cells, large amounts of T7 RNA polymerase are produced. The polymerase then binds to the T7 late promoter on the plasmid expression vectors, catalyzing transcription of the inserted cDNA at a high rate. Since each E. coli cell contains many copies of the expression vector, large amounts of mRNA corresponding to the cloned cDNA can be produced in this system and the resulting protein can be radioactively labeled.

-37- SPlasmid vectors containing late promoters and the corresponding RNA polymerases from related bacteriophages, such as T3, T5, and SP6, C can also be used for in vitro production of proteins from cloned DNA. E.

coli can also be used for expression using an M13 phage, such as mGPI-2.

0 0 5 Furthermore, vectors that contain phage lambda regulatory sequences, or vectors that direct the expression of fusion proteins, for example, a maltosebinding protein fusion protein or a glutathione-S-transferase fusion protein, N also can be used for expression in E. coli.

SEukaryotic expression systems are useful for obtaining appropriate post-translational modification of expressed proteins. Transient transfection of a eukaryotic expression plasmid containing a gridlock gene, into a eukaryotic host cell allows the transient production of gridlock by the transfected host cell. gridlock proteins can also be produced by a stablytransfected eukaryotic(e.g., mammalian) cell line. A number of vectors suitable for stable transfection of mammalian cells are available to the public (see, Pouwels et al., Cloning Vectors: A Laboratory Manual, 1985, Supp. 1987), as are methods for constructing lines including such cells (see, Ausubel et al., supra).

In one example, cDNA encoding a gridlock protein, fusion, mutant, or polypeptide fragment is cloned into an expression vector that includes the dihydrofolate reductase (DHFR) gene. Integration of the plasmid and, therefore, integration of the gridlock-encoding gene, into the host cell chromosome is selected for by inclusion of 0.01-300 u±M methotrexate in the cell culture medium (Ausubel et al., supra). This dominant selection can be accomplished in most cell types. Recombinant protein expression can be increased by DHFR-mediated amplification of the transfected gene.

Methods for selecting cell lines bearing gene amplifications are described in Ausubel et al., supra. These methods generally involve extended culture in -38medium containing gradually increasing levels ofmethotrexate. The most commonly used DHFR-containing expression vectors are pCVSEII-DHFR and pAdD26SV(A) (described, for example, in Ausubel et al., supra). The host cells described above or, preferably, a DHFR-deficient CHO cell line 00 5 CHO DHFR cells, ATCC Accession No. CRL 9096) are among those Sthat are most preferred for DHFR selection of a stably-transfected cell line

O

Sor DHFR-mediated gene amplification.

\0 Another preferred eukaryotic expression system is the baculovirus Ssystem using, for example, the vector pBacPAK9, which is available from Clontech (Palo Alto, CA). If desired, this system can be used in conjunction with other protein expression techniques, for example, the myc tag approach described by Evan et al. (Molecular and Cellular Biology 5:3610-3616, 1985).

Once a recombinant protein is expressed, it can be isolated from the expressing cells by cell lysis followed by protein purification techniques, such as affinity chromatography. In this example, an anti-gridlock antibody, which can be produced by the methods described herein, can be attached to a column and used to isolate the recombinant gridlock proteins.

Lysis and fractionation of gridlock protein-harboring cells prior to affinity chromatography can be performed by standard methods (see Ausubel et al., supra). Once isolated, the recombinant protein can, if desired, be purified further by by high performance liquid chromatography (HPLC; see Fisher, Laboratory Techniques In Biochemistry and Molecular Biology, Work and Burdon, Eds., Elsevier, 1980).

Polypeptides of the invention, particularly short gridlock fragments and longer fragments of the N-terminus and C-terminus of the gridlock protein, can also be produced by chemical synthesis by the methods described in Solid Phase Peptide Synthesis, 2 nd ed., 1984, The Pierce -39- Chemical Co., Rockford, IL). These general techniques ofpolypeptide expression and purification can also be used to produce and isolate useful c gridlock polypeptide fragments or analogs, as described herein.

As discussed above, eukaryotic cells expressing gridlock proteins 00 can be used to identify and test the effectiveness of pharmacological agents O on gridlock-associated diseases. Such cells can also be used to produce N gridlock polypeptides for use in the methods described above. Eukaryotic

\D

Scell expression of gridlock proteins facilitates further studies of the gridlock C1 gene and gene products, including determination of proper expression and post-translational modifications required for biological activity, and identifying regulatory elements located in the and intron regions of gridlock genes and determining their roles in tissue regulation of gridlock protein expression. It also permits the production of large amounts of normal and mutant proteins for isolation and purification, and the use of cells expressing gridlock proteins as a functional assay system for antibodies generated against the protein. Expression of gridlock proteins, fusions, mutants, and polypeptide fragments in eukaryotic cells also enables the study of the function of the normal complete protein, specific portions of the protein, or of naturally occurring polymorphisms and artificiallyproduced mutated proteins. The gridlock DNA sequences can be altered using procedures known in the art, such as restriction endonuclease digestion, DNA polymerase fill-in, exonuclease deletion, terminal deoxynucleotide transferase extension, ligation of synthetic or cloned DNA sequences, and site-directed sequence alteration using specific oligonucleotides and PCR.

F gridlock Fragments Polypeptide fragments that include various portions of gridlock c proteins are useful in identifying the domains of gridlock important for its biological activities, such as protein-protein interactions and transcription.

00 5 Methods for generating such fragments are well known in the art (see, for example, Ausubel et al., supra), using the nucleotide sequences provided Sherein. For example, a gridlock protein fragment can be generated by PCR t amplifying a desired gridlock nucleic acid molecule fragment using oligonucleotide primers designed based upon the gridlock nucleic acid sequences. Preferably, the oligonucleotide primers include unique restriction enzyme sites that facilitate insertion of the amplified fragment into the cloning site of an expression vector a mammalian expression vecoor, see above). This vector can then be introduced into a cell a mammalian cell; see above) by artifice, using any of the various techniques known in the art such as those described herein, resulting in the production of a gridlock polypeptide fragment in the cell containing the expression vector.

gridlock polypeptide fragments chimeric fusion proteins) can also be used to raise antibodies specific for various regions of gridlock using, for example, the methods described below. Preferred gridlock fragments include, without limitation, fragments corresponding to the Cterminal domain containing the YRPW motif, fragments lying outside the conserved regions, and fragments thereof.

gridlock Antibodies To prepare polyclonal antibodies, gridlock proteins, fragments of gridlock proteins, or fusion proteins containing defined portions of gridlock proteins can be synthesized in, bacteria by expression of corresponding -41- SDNA sequences contained in a suitable cloning vehicle. Fusion proteins are commonly used as a source of antigen for producing antibodies. Two Swidely used expression systems for E. coli are lacZ fusions using the pUR series of vectors and trpE fusions using the pATH vectors. The proteins can 00 5 be purified, and then coupled to a carrier protein, mixed with Freund's Sadjuvant (to enhance stimulation of the antigenic response in an inoculated O animal), and injected into rabbits or other laboratory animals. Alternatively, O protein can be isolated from gridlock-expressing cultured cells. Following O booster injections at bi-weekly intervals, the rabbits or other laboratory animals are then bled and the sera isolated. The sera can be used directly or can be purified prior to use by various methods, including affinity chromatography employing reagents such as Protein A-Sepharose, antigen- Sepharose, and anti-mouse-Ig-Sepharose. The sera can then be used to probe protein extracts from gridlock-expressing tissue fractionated by polyacrylamide gel electrophoresis to identify gridlock proteins.

Alternatively, synthetic peptides can be made that correspond to antigenic portions of the protein and used to inoculate the animals.

To generate peptide or full-length protein for use in making, for example, gridlock-specific antibodies, a gridlock coding sequence can be expressed as a C-terminal or N-terminal fusion with glutathione Stransferase (GST; Smith et al., Gene 67:31-40, 1988). The fusion protein can be purified on glutathione-Sepharose beads, eluted with glutathione, cleaved with a protease, such as thrombin or Factor-Xa (at the engineered cleavage site), and purified to the degree required to successfully immunize rabbits. Primary immunizations can be carried out with Freund's complete adjuvant and subsequent immunizations performed with Freund's incomplete adjuvant. Antibody titers can be monitored by Western blot and immunoprecipitation analyses using the protease-cleaved gridlock fragment -42of the GST-gridlock fusion protein. Immune sera can be affinity purified using CNBr-Sepharose-coupled gridlock protein. Antiserum specificity can be determined using a panel of unrelated GST fusion proteins.

Alternatively, monoclonal gridlock antibodies can be produced by 00 5 using, as an antigen, gridlock protein isolated from gridlock-expressing Scultured cells or gridlock protein isolated from tissues. The cell extracts, or

O

Srecombinant protein extracts containing gridlock protein, can, for example, IND be injected with Freund's adjuvant into mice. Several days after being Sinjected, the mouse spleens can be removed, the tissues disaggregated, and the spleen cells suspended in phosphate buffered saline (PBS). The spleen cells serve as a source of lymphocytes, some of which would be producing antibody of the appropriate specificity. These can then be fused with permanently growing myeloma partner cells, and the products of the fusion plated into a number of tissue culture wells in the presence of selective agents, such as hypoxanthine, aminopterine, and thymidine (HAT). The wells can then be screened by ELISA to identify those containing cells making antibody capable of binding to a gridlock protein, polypeptide fragment, or mutant thereof. These cells can then be re-plated and, after a period of growth, the wells containing these cells can be screened again to identify antibody-producing cells. Several cloning procedures can be carried out until over 90% of the wells contain single clones that are positive for specific antibody production. From this procedure, a stable line of clones that produce the antibody can be established. The monoclonal antibody can then be purified by affinity chromatography using Protein A Sepharose and ion-exchange chromatography, as well as variations and combinations of these techniques. Once produced, monoclonal antibodies are also tested for specific gridlock protein recognition by Western blot or immunoprecipitation analysis (see, Kohler et al., Nature 256:495, -43- 1975; Kohler et al., European Journal of mmunology 6:511, 1976; Kohler et al., European Journal of Immunology 6:292, 1976; Hammerling et al., In

T

Monoclonal Antibodies and T Cell Hybridomas, Elsevier, New York, NY, 1981; Ausubel et al., supra).

00 5 As an alternate or adjunct immunogen to GST fusion proteins, peptides corresponding to relatively unique hydrophilic regions of gridlock can be generated and coupled to keyhole limpet hemocyanin (KLH) through I an introduced C-terminal lysine. Antiserum to each of these peptides can be Ssimilarly affinity-purified on peptides conjugated to BSA, and specificity tested by ELISA and Western blotting using peptide conjugates, and by Western blotting and immunoprecipitation using gridlock, for example, expressed as a GST fusion protein.

Antibodies of the invention can be produced using gridlock amino acid sequences that do not reside within highly conserved regions, and that appear likely to be antigenic, as analyzed by criteria such as those provided by the Peptide Structure Program (Genetics Computer Group Sequence Analysis Package, Program Manual for the GCG Package, Version 7, 1991) using the algorithm of Jameson et al., CABIOS 4:181, 1988. These fragments can be generated by standard techniques, by the PCR, and cloned into the pGEX expression vector. GST fusion proteins can be expressed in E. coli and purified using a glutathione-agarose affinity matrix (Ausubel et al., supra). To generate rabbit polyclonal antibodies, and to minimize the potential for obtaining antisera that is non-specific, or exhibits low-affinity binding to a gridlock, two or three fusions are generated for each protein, and each fusion is injected into at least two rabbits. Antisera are raised by injections in series, preferably including at least three booster injections.

-44- In addition to intact monoclonal and polyclonal anti-gridlock antibodies, the invention features various genetically engineered antibodies, Shumanized antibodies, and antibody fragments, including F(ab')2, Fab', Fab, Fv, and sFv fragments. Truncated versions of monoclonal antibodies, for 00 5 example, can be produced by recombinant methods in which plasmids are Sgenerated that express the desired monoclonal antibody fragment(s) in a Ssuitable host. Antibodies can be humanized by methods known in the art, IN monoclonal antibodies with a desired binding specificity can be Scommercially humanized (Scotgene, Scotland; Oxford Molecular, Palo Alto, CA). Fully human antibodies, such as those expressed in transgenic animals, are also included in the invention (Green et al., Nature Genetics 7:13-21, 1994).

Ladner Patent Nos. 4,946,778 and 4,704,692) describes methods for preparing single polypeptide chain antibodies. Ward et al., Nature 341:544-546, 1989, describes the preparation of heavy chain variable domains, which they term "single domain antibodies," and which have high antigen-binding affinities. McCafferty et al., Nature 348:552- 554, 1990, show that complete antibody V domains can be displayed on the surface of fd bacteriophage, that the phage bind specifically to antigen, and that rare phage (one in a million) can be isolated after affinity chromatography. Boss et al., U.S. Patent No. 4,816,397, describes various methods for producing immunoglobulins, and immunologically functional fragments thereof, that include at least the variable domains of the heavy and light chains in a single host cell. Cabilly et al., U.S. Patent No.

4,816,567, describes methods for preparing chimeric antibodies.

SI Jse of gridlock Antibodies Antibodies to gridlock proteins can be used, as noted above, to detect Sgridlock proteins or to inhibit the biological activities of gridlock proteins.

For example, a nucleic acid molecule encoding an antibody or portion of an 00 5 antibody can be expressed within a cell to inhibit gridlock function. In Saddition, the antibodies can be coupled to compounds, such as radionuclides Sand liposomes for diagnostic or therapeutic uses. Antibodies that I0 specifically recognize extracellular domains of gridlock are useful for Stargeting such attached moieties to cells displaying such gridlock polypeptide domains at their surfaces. Antibodies that inhibit the activity of a gridlock polypeptide described herein can also be useful in preventing or slowing the development of a disease caused by inappropriate expression of a wild type or mutant gridlock gene.

Detection Of Pridlock Gene Expression As noted, the antibodies described above can be used to monitor gridlock protein expression. In situ hybridization of RNA can be used to detect the expression of gridlock genes. RNA in situ hybridization techniques rely upon the hybridization of a specifically labeled nucleic acid probe to the cellular RNA in individual cells or tissues. Therefore, RNA in situ hybridization is a powerful approach for studying tissue- and temporalspecific gene expression. In this method, oligonucleotides, cloned DNA fragments, or antisense RNA transcripts of cloned DNA fragments corresponding to unique portions of gridlock genes are used to detect specific mRNA species, in the tissues of animals, such as mice, at various developmental stages. Other gene expression detection techniques are known to those of skill in the art and can be employed for detection of gridlock gene expression.

-46- SIdentification of Additional gridlock Genes Standard techniques, such as the polymerase chain reaction (PCR) c and DNA hybridization, can be used to clone gridlock homologues in other species and gridlock-related genes in humans. gridlock-related genes and 00 5 homologues can be readily identified using low-stringency DNA hybridization or low-stringency PCR with human gridlock probes or primers. Degenerate primers encoding human gridlock or human gridlock- S related amino acid sequences can be used to clone additional gridlock- Srelated genes and homologues by RT-PCR.

Construction of Transgenic Animals and Knockout Animals Characterization of gridlock genes provides information that allows gridlock knockout animal models to be developed by homologous recombination. Preferably, a gridlock knockout animal is a mammal, most preferably a mouse. Similarly, animal models of gridlock overproduction can be generated by integrating one or more gridlock sequences into the genome of an animal, according to standard transgenic techniques.

Moreover, the effect of gridlock gene mutations dominant gene mutations) can be studied using transgenic mice carrying mutated gridlock transgenes or by introducing such mutations into the endogenous gridlock gene, using standard homologous recombination techniques.

A replacement-type targeting vector, which can be used to create a knockout model, can be constructed using an isogenic genomic clone, for example, from a mouse strain such as 129/Sv (Stratagene Inc., LaJolla, CA).

The targeting vector can be introduced into a suitably-derived line of embryonic stem (ES) cells by electroporation to generate ES cell lines that carry a profoundly truncated form of a gridlock gene. To generate chimeric founder mice, the targeted cell lines are injected into a mouse blastula-stage -47- Sembryo. Heterozygous offspring can be interbred to homozygosity.

gridlock knockout mice provide a tool for studying the role of gridlock in Sembryonic development and in disease. Moreover, such mice provide the means, in vivo, for testing therapeutic compounds for amelioration of 00 5 diseases or conditions involving a gridlock-dependent or gridlock-affected pathway.

Experimental Results SThe grl gene was isolated using positional cloning strategies. grl encodes a novel basic helix-loop-helix (bHLH) protein, with a carboxylterminal motif characteristic of the hairy-related family of bHLH proteins.

These bHLH proteins have been shown to be important for cell fate determination in other cell types. In the Drosophila nervous system, for example, members of the hairy family act as transcriptional repressors that help to pattern and establish "equivalence groups" of neuronal progenitor cells. It is likely that grl plays a similar role in angioblasts, functioning as an artery-specific marker. It is also possible that grl functions at the VEGF/FLK pathway, which appears to be critical for vasculogenesis (Fouquet et al., Developmental Biology 183:37-48, 1997; Liao et al., Development 124:381-389, 1997).

The grl r 4 5 mutant was found to have a mutation in the stop codon following the carboxyl-terminal motif characteristic of the hairy-related family of bHLH proteins. This mutation can be complemented by the injection of a wild type grl mRNA, but not by a grl mRNA lacking the carboxyl-terminal motif.

grl was expressed in the lateral plate mesoderm at the early stage of the embryos, anticipating vessel formation, and thereafter was selectively expressed in the aorta. The grl mutation clearly marks cells of the nascent -48aorta, even prior to formation of a lumen or onset of blood flow, and is not expressed by the vein, suggesting that angioblasts can be distinctive even prior to assembly. This mutation perturbs assembly of the aorta, but does

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not affect the axial veins or the vessels of the head. Thus, grl establishes an 00 5 aorta-specific endothelial cell fate.

As indicated above, the aorta is a region affected by several congenital disorders, some of which perturb a region analogous, on an IND embryological basis, to the anterior aortic bifurcation, the region most affected by the grl mutation. Some of these disorders, such as coarctation, show a high sibling recurrence, suggesting a genetic basis.

Positional Cloning of the grl Gene To clone the grl mutation, its position was first established on a zebrafish genetic map, using single strand length polymorphism (SSLP) markers and random amplified polymorphic DNA (RAPD) molecules, and then a physical map of the region was generated using yeast artificial chromosomes (YACs) and bacterial artificial chromosomes (BACs) (Figure 1; G, H, I, J, K, and L correspond to YAC, BAC, and PAC ends). Some of the polymorphic landing markers were used to integrate the local radiation hybrid (RH) map, genetic map, and physical map at the mutation region, indicating that these markers are correlated at their corresponding positions (Figure The number ofrecombinants between the markers and the gridlock locus are shown below the chromosome line. Some of the genetic markers were used for genotyping on the RH panel, and the distance (cM) between these markers is indicated below the RH line.

The gridlock mn145 allele was mapped to linkage group 20 between genetic markers z536 and z9794, with 1,200 mutants providing 2,400 informative meioses. Marker z536 was used for chromosomal walking, and -49- Swas isolated to link to the gridlock locus by bulk segregation analysis. Five and twelve recombinants, among the 1,200 mutants, were identified using markers z536 and z9794, respectively. Recombinant analysis defined a 0.71 cM interval containing the mutation.

00 5 A YAC map of about 2 megabases spanning the region Scontaining the gridlock mutation, was then constructed. The YAC contig 0was constructed from YAC5, YAC 21, YAC133, YAC187, and YAC140, I and the YAC ends were rescued by self-circularization (Zhong et al., SGenomics 48:136-138, 1998) and sequenced. The YAC sizes, from 300 Kb to 1.2 Mb, were determined by pulsed field gel electrophoresis.

Recombinant fine mapping analysis was performed using single stranded conformation polymorphisms (SSCP) from the rescued YAC end sequences. Polymorphisms were detected by SSCP analysis from the T3 ends of both YAC187 and YAC133, and identified one recombinant after the mutation, and three recombinants before the mutation, respectively.

These experiments physically located gri m 4 S between the T3 ends of YAC 133 and YAC 187, in a 500 Kb interval.

To refine this 500 Kb interval further, a BAC/PAC contig from three BACs and three PACs, using the T3 end of YAC133 as a starting point, was assembled. SSCP analyses, from the end sequences of PAC14, BAC 1, and PAC11 identified 1 recombinant before the mutation, two 0 recombinants at the locus, and 2 recombinants after the mutation, corresponding to the recombination points zP14, zBl la, zBl lb, and zPl 1. Thus, fine mapping, using recombination frequency among 2,400 meioses, permitted the refinement of the 500 Kb interval to 120 Kb enclosed on overlapping BAC14 and PAC14 (Figure Recombinant fine mapping analysis was Sperformed using single stranded conformation polymorphisms (SSCP) from the sequence of rescued BAC and PAC ends. The BAC/PAC ends were .rescued by inverse PCR or directly sequenced.

To identify the grl gene, five-fold shotgun sequencing from genomic 00 5 libraries, constructed from BAC 14 and PAC14 containing the grl mutation, was performed. Ten-fold shotgun libraries of BAC14 and PAC14 were made from sheared DNA using Sonic Dismembrator (8 x followed by \0 Mung Bean Nuclease treatment, two sizing selections on an agarose gel, and blunt-end ligation. High throughput minipreps were performed using Qiagene Robot 9600, and shotgun sequencing, estimated to provide fivefold coverage, was carried out using an ABI 377 sequencer. Large contigs were assembled using 2,000 shotgun sequences. The flanking sequence of the vector was clipped off using CrossMatch. The sequences of both BAC 14 and PAC14 were analyzed by the phred/phrap/consed program, establishing 11 sequence contigs. The sequence contigs were assembled using Phrap, and edited by Consed. Computational algorithms (combinatory Genescan and Blast Search) identified exons, introns, and exon-intron boundaries that formed four putative genes at the grl region (termed genes A to D).

The BAC and PAC were then used as probes to screen embryonic cDNA libraries. cDNAs were isolated from whole mount in situ hybridization and histology analyses. A 24 hour-cDNA library was screened with a3 2 P-labeled BAC14 or PAC 14, which was pre-annealed overnight in a genomic repeat-repressing cocktail (5 X SSC, 2.5 tg/tl genomic DNA, 0.5 pg/.l CA and GT oligo, 0.5 gg/tl of mermaid and epd repeats) in hybridization buffer (6 X SSC, 0.5% SDS, 100 gg/pl calf thymus DNA). The filters were washed in 2 X SSC/0.1% SDS, 0.2 X SSC/0.1%SDS. Subsequent fine mapping with single nucleotide -51 Spolymorphism (SNPs) showed gene B to be outside of the grl region. The other three genes were sequenced from wild type and mutant embryos, and c their expression patterns examined. Gene C appeared to be a zebrafish ortholog of human Pex7, and Gene D appeared to be novel. No consistent 00 5 mutations were found in the coding regions of C and D in mutant embryos, and the expression pattern of C and D was not related to the aorta or Ssurrounding tissues.

Gene A was expressed at the merging regions of bilateral dorsal aortae. As the grl mutant was defective in the merging process from bilateral dorsal aortae to single midline dorsal aorta, gene A seemed a promising candidate. Genomic sequence analysis defined six coding exons and intron-exon boundaries of gene A. To search for a mutation, all exons and intron-exon boundaries of gene A in grl" 1 4 mutants and homologous wild type siblings were sequenced. A single T to A transversion mutation, also found from sequencing gri mutant cDNA isolated by RT-PCR, was identified.

Gene A, thus, mapped to the critical interval (Figure 1) and had a mutation present in mutant embryos, but absent in wild type siblings.

Furthermore, as shown below, Gene A was expressed selectively in the aorta at the merging regions of bilateral dorsal aortae, consistent with the grl phenotype, and its microinjected synthetic wild type RNA rescued the grl mutant. Therefore, gene A is the grl gene.

The Protein Encoded by grl Translation of the grl genomic DNA and cDNA sequences predicted that the zebrafish grl encoded a novel protein of 301 amino acids (Figure 2A; SEQ ID NO:2). The human ortholog of grl, referred to as hgrl (Figure 2A; SEQ ID NO:4) was also identified by EST database searching, and was -52- Sassembled from human ESTs AI727779 and AA 116067. Alignment of the predicted human and zebrafish amino acid sequences of the grls indicated C€ 78% overall identity, with more extensive identity in the bHLH (100%) and Orange domains. Outside these domains, the grl proteins are 0 0 5 identical. The grl proteins have a YRPW protein interaction domain motif at the carboxyl terminal.

SThe grl genes show sequence similarity to the hairy/enhancer of Ssplit-related (hesr) bHLH genes (Fisher et al., Molecular and Cellular Biology, 2670-2677, 1996; Kokubo et al., Biochemical Biophysical Research Communications 260:459-465, 1999). hesr genes (Figures 2B and 2D) are a subgroup of the hairy-related bHLH genes. Like other hairy genes, they are predicted to have an N-terminal bHLH domain, an Orange domain, and a protein-protein interaction motif near the carboxyl terminus.

Figure 2B shows a sequence comparison of the grl genes with the hesr genes in the bHLH domain, Orange domain, and C-terminal motif. In particular, there are six amino acids that are distinct between grl and hesr proteins in the Orange domain. The sequence alignment was performed using Pileup of GCG package (Version 10) and displayed by interface of MacBoxshade 2.15. The grl genes are related to the mouse Hey2/HRT-2 gene, which is also a member of the hesr gene family of bHLH genes (Leimeister et al., Mechanisms of Development 85:173-177, 1999).

The carboxyl-terminal motif is critical for action of the hairy proteins, but is divergent in hesr proteins. The hesr proteins are distinguished from other members of the hairy-related family by a glycinefor-proline substitution in the basic domain, and a change from the carboxyl-terminal WRPW motif to YRPW, the latter being embedded within a 13 amino acid hesr motif. grl shows the highest similarity to the hesr, hes, and hairy proteins in the bHLH domain some similarity in -53- Sthe Orange domain and also has a YRPW motif, a protein-protein interaction domain, at its carboxyl terminal. grl proteins show only about Cr 21% identity with hesr proteins outside the conserved regions. The low extent of overall similarity between these proteins indicates that 0 0 5 they belong to distinct gene families.

The genomic sequence of grl mutant embryos revealed a consistent ST-to-A transversion mutation, when compared with wild type, that changed San invariant stop codon to glycine and added an extra 44 amino acids to the wild type protein (Figure 2C). The mutation was found in the genomic region of all eight grl mutant embryos examined and also found in RT-PCR of cDNA from a pool of 10 mutant embryos. The position of the mutation at the carboxyl terminus, adjacent to the YRPW domain, suggested a role in protein-protein interaction, although protein stability can be affected as well.

Expression of gri mRNA To examine patterns ofgrl expression during zebrafish embryogenesis, whole mount in situ RNA hybridization was carried out at various time points. The grl transcript was first detected at the 10 somite stage, prior to vessel formation, in the anterior and posterior regions of the lateral plate mesoderm, and appeared as bilateral stripes (Figure 3A, dorsal view).

Whole amount RNA in situ hybridization was carried out as described (Jowett et al., Trends Genet. 10:73-74, 1994). A 1891-bp fragment of cDNA that contains both ORF and 3'UTR was subcloned for in vitro transcription. For histological analysis, specimens were fixed in 4% paraformaldehyde, dehydrated, and embedded in plastic Nomarski photomicroscopy was performed with an Axiophot using Ektachrome 160T -54film (Zeiss). Wild M5 and M10 dissecting microscopes, equipped with Nikon cameras, were used for low-power photomicroscopy. Embryos were staged according to Kimmel et al. (Dev. Dyn. 203:253-310, 1995).

By the 14-somite stage, the grl-expressing cells began to converge 00 -5 towards the ventral midline to form the primordium of the dorsal aorta, just Sventral to the notochord. No grl-expressing cells were observed in the Sregion of the precursors of the axial vein, below the aorta. At the LO stage, grl was expressed strongly throughout the dorsal aorta (Figure 3B- O 3C, lateral view of the anterior trunk, posterior trunk, and tail showing the grl transcripts at the dorsal aorta; Figure 3D, sagittal histological sections of the posterior trunk showing the lumen of the dorsal aorta with grl expression and grl-negative cells at the axial veins). Anteriorly, grl was expressed in the endothelial cells of the paired aortae, but not in the bilateral cardinal veins (Figure 3E; transverse histological section of the anterior trunk showing grl expression at the paired dorsal aortae below the notochord). In the trunk, grl expression was detected in the midline aorta, but not in the axial vein (Figures 3F-3G; transverse histological sections of posterior trunk showing gri expression in endothelial cells at the midline dorsal aorta and the intersomitic artery, and no grl expression in the endothelial cells at the axial veins). By contrast,fli, an early endothelial marker, was expressed in both arteries and veins (Figure 3H-3I). At the anterior trunk, grl was expressed selectively at the region of aortic bifurcation, the region most affected by the grl mutation. In addition, grl is transiently expressed in the heart, aortic arches, and lateral somites, a pattern that is similar to that described for the mouse Hey and HRT genes (Leimeister et al., Mechanisms of Development 85:173-177, 1999).

SEctopic Expression of grl Rescues the grl Mutant If the m145 mutation in the grl gene is responsible for the aortic C dysmorphogenesis of the mutant zebrafish embryos, wild type grl RNA should be able to rescue the mutant phenotype.

5 To ascertain whether wild type grl can rescue the defect of the grlm 1 4 mutation, in vitro transcribed grl RNA, encoding either wild-type grl protein (grl") or a mutant grl protein, truncated at amino acid 250 before

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the YRPW motif (grl d el) was microinjected into one- to four- cell stage wild C type and mutant embryos from grl in-crosses. Different doses of mR.NA were tested, and about 55 pg ofmRNA was used for the injections. An average of 90% of the wild type embryos, injected with 55 pg of grl" or grlde', developed normally. A high dosage ofmRNA (about 200 pg) caused developmental defects in about 60% of the wild type embryos. Sensecapped RNA was synthesized for injection using 17 RNA polymerase and the mMESSAGE mMACHINE system (Ambion) after HindIII digestion of wild type grl and a grl RNA having a C-terminal truncation. Injection was carried out using Microinjector 5242.

Microinjected embryos were scored based on the phenotype of the mutation and then genotyped. The grl"' 1 4 mutation is a fully penetrant, recessive mutation and the most robust phenotype is the absence of angiographically demonstrable circulation to the trunk at 48 hours (Figure 4A-4B). Microangiography was carried out as described (Weinstein et al., Nature Medicine 1:1143-1147, 1995). Phenotypic analysis was carried out based on the condition of circulation at the trunk and tail and some of the embryos were analyzed by angiogram 48 hours after fertilization. The injected embryos were classified as phenotypically wild-type if they had normal tail circulation and mutant if they lacked tail circulation. All -56g injected embryos were genotyped by a closely linked microsatellite marker; some of the genotyped embryos were further confirmed by sequence Cc analysis.

Figures 4A-C show phenotypic complementation of the grl mutation 0 0 5 by microangiography. Figure 4A indicates the phenotype of wild type embryos, displaying blood flow to the trunk through the dorsal aorta (arrow) Sand its return via the axial vein (arrow). Figure 4B shows the grl mutant Swith a lack of circulation in the trunk, due to the blockage at the aortic Sjunction of the paired dorsal aortae. Figure 4C shows a phenotypically wild type and genotypically mutant embryo in which circulation in the trunk was restored. The C-terminal nucleotide sequence of the grl is shown to the right in four wild type, four mutant, and four rescued embryos, respectively.

The grl mutant embryos and the rescued grl mutant embryos have a T-to-A point mutation, compared to the wild type sequence.

Table 1 Rescue of gri Mutants by RNA Injection Injected Total Phenotypically Mutant Phenotypically Wild-type RNA Embryos Genotypically Mutant Genotypically Mutant grl" 151 29 grldel 66 16 0 As shown in Table 1 and Figures 4A-C, in clutches injected with wild type grl RNA, the predicted number of embryos manifesting the grl mutant phenotype was reduced by 26%. By contrast, a grl truncated mutant gene, in which the carboxyl terminal region is deleted, including the YRPW motif, as shown in Table 1, was not capable of rescuing the ml45 mutation.

-57r" The apparently wild type, rescued embryos were confirmed to be genetically mutant by sequence analysis. The grl mutant embryos and the rescued grl mutant embryos had a T-to-A point mutation, compared with the wild type sequence.

00 5 As noted above, grl is a member of the hairy-related family of bHLH proteins, which are important for cell fate determination in other cell types.

SIn the Drosophila nervous system, for example, members of the hairy Sfamily act downstream of Notch as transcriptional repressors, and help to pattern and establish equivalence groups of neural progenitor cells. Our studies show that grl could play a similar role specifically for aortic angioblasts, showing a role ofbHLH genes in vasculogenesis.

Other Embodiments All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.

While the invention has been described in connection with specific embodiments thereof, it is to be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and can be applied to the essential features hereinbefore set forth, and follows in the scope of the appended claims.

The entire disclosure in the complete specification of our Australian Patent Application No. 14643/01 is by this cross-reference incorporated into the present specification.

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Claims (30)

1. 3. The polypeptide of claim 2, comprising the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4. (O
2. 4. The polypeptide of claim 1, wherein said polypeptide is derived from a mammal. The polypeptide of claim 4, wherein said mammal is a human.
3. 6. A substantially pure nucleic acid molecule comprising a sequence encoding a gridlock polypeptide.
4. 7. The nucleic acid molecule of claim 6, wherein said nucleic acid molecule encodes a human gridlock polypeptide.
5. 8. The nucleic acid molecule of claim 6, wherein said nucleic acid molecule encodes a polypeptide comprising an amino sequence that is substantially identical to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4.
6. 9. The nucleic acid molecule of claim 8, wherein said nucleic acid molecule encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4. -59- The nucleic acid molecule of claim 6, wherein said nucleic acid rC, molecule comprises a nucleotide sequence that is substantially identical to c the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO:3. M
7. 11. The nucleic acid molecule of claim 6, wherein said nucleic acid molecule is DNA. 00 S12. A nucleic acid molecule having at least 55% nucleic acid "1sequence identity to a sequence encoding a gridlock polypeptide or a Sfragment thereof, wherein said fragment comprises at least six amino acids and said nucleic acid molecule hybridizes under high stringency conditions to at least a portion of a gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related protein family member.
8. 13. The nucleic acid molecule of claim 12, wherein said nucleic acid molecule has 100% complementarity to a nucleic acid molecule encoding a gridlock polypeptide or a fragment thereof comprising at least six amino acids, and said nucleic acid molecule hybridizes under high stringency conditions to at least a portion ofa gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related protein family member.
9. 14. A nucleic acid molecule comprising a sequence that is antisense to a gridlock coding strand or a fragment thereof. The nucleic acid molecule of claim 14, wherein said antisense sequence is specific for a mutated gridlock coding region. I
10. 16. A vector comprising the nucleic acid molecule of claim 6.
11. 17. The vector of claim 16, wherein said vector is a gene therapy Cc vector. 00
12. 18. A cell comprising the vector of claim 16.
13. 19. A non-human transgenic animal comprising the nucleic acid molecule of claim 6. The non-human transgenic animal of claim 19, wherein said animal is a zebrafish.
14. 21. A non-human animal having a knockout mutation in one or both alleles encoding a gridlock polypeptide.
15. 22. A cell from the non-human knockout animal of claim 21.
16. 23. A probe for analyzing the gridlock nucleic acid molecules of an animal, said probe having at least 55% nucleic acid sequence identity to a sequence encoding a gridlock polypeptide or a fragment thereof, wherein said fragment comprises at least six amino acids and said probe hybridizes under high stringency conditions to at least a portion of a gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related protein family member. -61- I O 24. The probe of claim 23, wherein said probe has 100% I complementarity to a nucleic acid molecule encoding a gridlock Spolypeptide or a fragment thereof comprising at least six amino acids, and said probe hybridizes under high stringency conditions to at least a portion 5 of a gridlock nucleic acid molecule, and does not hybridize under high stringency conditions to a nucleic acid molecule encoding a hairy-related 00 protein family member. CN 25. An antibody that specifically binds to a gridlock polypeptide. O C 26. The antibody of claim 25, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4.
17. 27. A method of detecting the presence of a gridlock polypeptide in a sample, said method comprising contacting said sample with an antibody that specifically binds to a gridlock polypeptide and assaying for binding of said antibody to said polypeptide.
18. 28. A method of detecting the presence of a mutant gridlock polypeptide in a sample, said method comprising contacting said sample with an antibody that specifically binds to a mutant gridlock polypeptide and assaying for binding of said antibody to said mutant polypeptide. -62-
19. 29. A method of diagnosing an increased likelihood of developing a Sgridlock-related disease or condition in a test subject, said method c' comprising analyzing nucleic acid molecules of the test subject to determine CC whether said test subject contains a mutation in a gridlock gene, wherein the presence of said mutation is an indication that said test subject has an 0_ increased likelihood of developing a gridlock-related disease.
20. 30. The method of claim 29, further comprising the step of using Inucleic acid molecule primers specific for the gridlock gene for nucleic acid Smolecule amplification by the polymerase chain reaction.
21. 31. The method of claim 30, further comprising the step of sequencing gridlock nucleic acid molecules from said test subject.
22. 32. The method of claim 29, wherein said test subject is a mammal.
23. 33. The method of claim 32, wherein said test subject is human.
24. 34. The method of claim 29, wherein said analyzing is carried out by restriction fragment length polymorphism (RFLP) analysis. The method of claim 29, wherein said disease or condition is coarctation of the aorta, interrupted aortic arch disease, or atherosclerosis.
25. 36. A kit for the analysis ofa gridlock nucleic acid molecule, said kit comprising a nucleic acid molecule probe of claim 23 or 24 for analyzing the nucleic acid molecules of a test subject. -63-
26. 37. A kit for the analysis ofa gridlock nucleic acid molecule, said kit comprising antibodies for analyzing the gridlock protein of a test subject. _38. A method for preventing or ameliorating the effect of a gridlock deficiency, said method comprising administering to a subject having a gridlock deficiency an expression vector comprising a nucleic acid 00 molecule encoding a functional gridlock polypeptide, wherein said nucleic Sacid molecule is operably linked to a promoter and said gridlock ¢1polypeptide is sufficient to prevent or ameliorate said effect of said gridlock Sdeficiency.
27. 39. A method for preventing or ameliorating the effect of a gridlock deficiency, said method comprising administering a functional gridloclk polypeptide to a subject having a gridlock deficiency, wherein said gridtlock polypeptide is sufficient to prevent or ameliorate said effect of said gridlock deficiency.
28. 40. A method for preventing or ameliorating the effect of a gridlock excess, said method comprising administering an antisense gridlock molecule to a subject having a gridlock excess, wherein said antisense gridlock molecule is sufficient to prevent or ameliorate said effect of said gridlock excess.
29. 41. A method for preventing or ameliorating the effect ofa gridlock excess, said method comprising administering a gridlock antibody to a subject having a gridlock excess, wherein said gridlock antibody is sufficient to prevent or ameliorate said effect of said gridlock excess. -64-
30. 42. A method for identifying a compound that modulates the expression or activity of a gridlock nucleic acid molecule or polypeptide, said method comprising contacting said gridlock nucleic acid molecule or polypeptide with said compound, and determining the effect of said compound on said gridlock expression or activity. 00 Dated this 31st day of January 2006 STHE GENERAL HOSPITAL CORPORATION \By their Patent Attorneys SGRIFFITH HACK Fellows Institute of Patent and Trade Mark Attorneys of Australia