Diagnosis and treatment of skeletal degeneration conditions

FIELD OF THE INVENTION

[0003] This invention relates to methods and compositions for the diagnosis and treatment of conditions that affect skeletal growth. More specifically, the invention relates to isolated molecules that can be used to promote chondrogenesis. These molecules, therefore, are useful in the treatment of various disorders that affect the skeleton, including cartilage degeneration conditions.

BACKGROUND OF THE INVENTION

[0004] Articular cartilage, the thin, fragile tissue layer covering the ends of bones, allows healthy joints to move freely and without pain. Many arthritic diseases and many degrees of trauma can, however, cause destruction or deterioration of this fragile layer, leading to pain, joint stiffness, and even crippling. A common belief has been that this fragile surface, once lost, could never be restored. Attempts made in the past to regenerate or otherwise repair articular cartilage have been unsuccessful, thereby directing medical science to the development of substitutes (such as implants), abandoning the potential for regeneration.

[0005] There exists a continued need for the development of alternative methods of cartilage regeneration and for alleviating the pain associated with cartilage degeneration conditions.

SUMMARY OF THE INVENTION

[0006] This invention provides methods and compositions for the diagnosis and treatment of congenital and/or acquired conditions affecting skeletal (cartilaginous/bone) growth. More specifically, we have identified a number of genes that are modulated in mesenchymal cells when the cells are cultured in a system that simulates physiological skeletal growth conditions. It has been discovered that such gene modulation leads to the acquirement of a chondroblastic phenotype by the mesenchymal cells (i.e., to cartilage/bone formation). In view of these discoveries, it is believed that the molecules of the present invention can be used to promote cartilage/bone formation, and in particular, to treat congenital and/or acquired conditions that affect the skeleton, such as cartilaginous tissue degeneration conditions that include all forms of arthritis such as osteoarthritis, rheumatoid arthritis, osteochondrosis, and the like. Additionally, methods for using these molecules in the diagnosis of any of the foregoing skeletal degeneration conditions, are also provided.

[0007] Furthermore, methods for using these molecules in vivo or in vitro for the purpose of modulating mesenchymal cell differentiation, methods for treating conditions associated with skeletal degeneration, and compositions useful in the preparation of therapeutic preparations for the treatment of the foregoing conditions, are also provided.

[0008] The present invention thus involves, in several aspects, polypeptides modulating mesenchymal cell differentiation, isolated nucleic acids encoding those polypeptides, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as therapeutics and diagnostics relating thereto.

[0009] According to one aspect of the invention, isolated nucleic acid molecules are provided. Such nucleic acid molecules include: (a) a nucleic acid molecule which hybridizes under stringent conditions to a molecule consisting of a nucleotide sequence set forth as SEQ ID NO:1-11 and which code for a polypeptide that induces differentiation of a mesenchymal cell, (b) nucleic acid molecules that differ from the nucleic acid molecules of (a) in codon sequence due to the degeneracy of the genetic code, and (c) complements of (a) or (b). In certain embodiments, the isolated nucleic acid molecule comprises the nucleotide sequence set forth as SEQ ID NO:1-11. The invention in another aspect provides an isolated nucleic acid molecule selected from the group consisting of (a) unique fragments of a nucleotide sequence set forth as SEQ ID NO:1-11, and (b) complements of (a), provided that a unique fragment of (a) includes a sequence of contiguous nucleotides which is not identical to any known sequence as of the filing date of the instant application.

[0010] In one embodiment, the sequence of contiguous nucleotides is selected from the group consisting of (1) at least two contiguous nucleotides nonidentical to the sequence group, (2) at least three contiguous nucleotides nonidentical to the sequence group, (3) at least four contiguous nucleotides nonidentical to the sequence group, (4) at least five contiguous nucleotides nonidentical to the sequence group, (5) at least six contiguous nucleotides nonidentical to the sequence group, and (6) at least seven contiguous nucleotides nonidentical to the sequence group.

[0011] In another embodiment, the fragment has a size selected from the group consisting of at least: 8 nucleotides, 10 nucleotides, 12 nucleotides, 14 nucleotides, 16 nucleotides, 18 nucleotides, 20, nucleotides, 22 nucleotides, 24 nucleotides, 26 nucleotides, 28 nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides, 75 nucleotides, 100 nucleotides, 200 nucleotides, 1000 nucleotides and every integer length therebetween.

[0012] According to another aspect, the invention provides expression vectors, and host cells transformed or transfected with such expression vectors, comprising the nucleic acid molecules described above.

[0013] According to another aspect of the invention, an isolated polypeptide is provided. The isolated polypeptide is encoded by the foregoing nucleic acid molecules of the invention. In some embodiments, the isolated polypeptide is encoded by the nucleic acid of SEQ ID NO:11, giving rise to a polypeptide having the sequence of SEQ ID NO:12 that induces mesenchymal cell differentiation. In other embodiments, the isolated polypeptide may be a fragment or variant of the foregoing of sufficient length to represent a sequence unique within the human genome, and identifying with a polypeptide that induces mesenchymal cell differentiation, provided that the fragment includes a sequence of contiguous amino acids which is not identical to any sequence known as of the filing date of the instant application. In another embodiment, immunogenic fragments of the polypeptide molecules described above are provided. The immunogenic fragments may or may not induce mesenchymal cell differentiation.

[0014] According to another aspect of the invention, isolated binding polypeptides are provided which selectively bind a polypeptide encoded by the foregoing nucleic acid molecules of the invention. Preferably the isolated binding polypeptides selectively bind a polypeptide which comprises the sequence of SEQ ID NO:12, or fragments thereof. In preferred embodiments, the isolated binding polypeptides include antibodies and fragments of antibodies (e.g., Fab, F(ab)2, Fd and antibody fragments which include a CDR3 region which binds selectively to the polypeptide of SEQ ID NO:12). In certain embodiments, the antibodies are human. In some embodiments, the antibodies are monoclonal antibodies. In one embodiment, the antibodies are polyclonal antisera. In further embodiments, the antibodies are humanized. In yet further embodiments, the antibodies are chimeric. According to a further aspect of the invention, a method for determining the level of SEQ ID NO:1-11 expression in a subject, is provided. The method involves measuring expression of SEQ ID NO:1-11 in a test sample from a subject to determine the level of SEQ ID NO:1-11 expression in the subject. In certain embodiments, the measured SEQ ID NO:1-11 expression in the test sample is compared to SEQ ID NO:1-11 expression in a control containing a known level of SEQ ID NO:1-11 expression. Expression is defined as SEQ ID NO:1-11 mRNA expression, expression of a polypeptide encoded by SEQ ID NO:1-11, or mesenchymal cell differentiation induction activity as defined elsewhere herein. Various methods can be used to measure expression. Preferred embodiments of the invention include PCR and Northern blotting for measuring mRNA expression, monoclonal antibodies or polyclonal antisera against polypeptides encoded by SEQ ID NO:1-11 as reagents to measure polypeptide expression, as well as methods for measuring mesenchymal cell differentiation induction activity.

[0015] In certain embodiments, test samples such as biopsy samples, and biological fluids such as blood, are used as test samples. SEQ ID NO:1-11 expression in a test sample of a subject is compared to SEQ ID NO:1-11 expression in control.

[0016] According to another aspect of the invention, a method for identifying an agent useful in modulating mesenchymal cell differentiation induction activity of a molecule, is provided. The method involves: (a) contacting a molecule having mesenchymal cell differentiation induction activity with a candidate agent, (b) measuring mesenchymal cell differentiation induction activity of the molecule, and (c) comparing the measured mesenchymal cell differentiation induction activity of the molecule to a control to determine whether the candidate agent modulates mesenchymal cell differentiation induction activity of the molecule, wherein the molecule is a nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, or an expression product thereof. In certain embodiments, the control is mesenchymal cell differentiation induction activity of the molecule measured in the absence of the candidate agent.

[0017] According to still another aspect of the invention, a method of diagnosing a condition characterized by aberrant expression of a nucleic acid molecule or an expression product thereof, is provided. The method involves: (a) contacting a biological sample from a subject with an agent, wherein said agent specifically binds to said nucleic acid molecule, an expression product thereof, or a fragment of an expression product thereof, and (b) measuring the amount of bound agent and determining therefrom if the expression of said nucleic acid molecule or of an expression product thereof is aberrant, aberrant expression being diagnostic of the condition, wherein the nucleic acid molecule is at least one nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66. In certain embodiments, the nucleic acid molecule may be at least two, at least three, at least four, or even at least five nucleic acid molecules, each selected from the group consisting of SEQ ID NO:1-11, and 13-66. In some embodiments, the condition is a cartilaginous tissue degeneration condition that includes all forms of arthritis such as osteoarthritis, rheumatoid arthritis, osteochondrosis, and the like. In important embodiments, the condition is osteoarthritis.

[0018] According to still another aspect of the invention, a method for determining regression, progression or onset of a cartilaginous tissue degeneration condition in a subject characterized by aberrant expression of a nucleic acid molecule or an expression product thereof, is provided. The method involves monitoring a sample from a patient, for a parameter selected from the group consisting of (i) a nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, (ii) a polypeptide encoded by the nucleic acid, (iii) a peptide derived from the polypeptide, and (iv) an antibody which selectively binds the polypeptide or peptide, as a determination of regression, progression or onset of said cartilaginous tissue degeneration condition in the subject. In some embodiments, the sample is a biological fluid or a tissue as described in any of the foregoing embodiments. In certain embodiments, the step of monitoring comprises contacting the sample with a detectable agent selected from the group consisting of (a) an isolated nucleic acid molecule which selectively hybridizes under stringent conditions to the nucleic acid molecule of (i), (b) an antibody which selectively binds the polypeptide of (ii), or the peptide of (iii), and (c) a polypeptide or peptide which binds the antibody of (iv). The antibody, polypeptide, peptide, or nucleic acid can be labeled with a radioactive label or an enzyme. In further embodiments, the method further comprises assaying the sample for the peptide. In still further embodiments, monitoring the sample occurs over a period of time.

[0019] According to another aspect of the invention, a kit is provided. The kit comprises a package containing an agent that selectively binds to any of the foregoing novel isolated nucleic acids, or expression products thereof, and a control for comparing to a measured value of binding of said agent to said novel isolated nucleic acids, or expression products thereof. In some embodiments, the control is a predetermined value for comparing to the measured value. In certain embodiments, the control comprises an epitope of the expression product of any of the foregoing novel isolated nucleic acids. In one embodiment, the kit further comprises a second agent that selectively binds any of the foregoing novel isolated nucleic acids, or expression products thereof, and a control for comparing to a measured value of binding of said second agent to any of the foregoing novel isolated nucleic acids, or expression products thereof.

[0020] According to a further aspect of the invention, a method for treating a cartilaginous tissue degeneration condition in a subject is provided. The method involves administering to a subject in need of such treatment an agent that modulates expression of a molecule selected from the group consisting of SEQ ID NO:1-67, in an amount effective to treat the cartilaginous tissue degeneration condition. In certain embodiments, the method further comprises co-administering an agent known to inhibit cartilaginous/bone tissue degeneration, such as an osteogenic protein (including Bone Morphogenetic Proteins—BMPs), Insulin-like Growth Factor (IGF), Transforming Growth Factor-β (TGF-β), and proteoglycans.

[0021] According to one aspect of the invention, a method for treating a subject to reduce the risk of a cartilaginous tissue degeneration condition developing in the subject is provided. The method involves administering to a subject who is known to express decreased levels of a molecule selected from the group consisting of SEQ ID NO:1-67, an agent for reducing the risk of cartilaginous tissue degeneration condition in an amount effective to lower the risk of the subject developing a future cartilaginous tissue degeneration condition, wherein the agent is known to inhibit cartilaginous/bone tissue degeneration, such as an osteogenic protein (including Bone Morphogenetic Proteins—BMPs), Insulin-like Growth Factor (IGF), Transforming Growth Factor-β (TGF-β), and proteoglycans, or an agent that modulates expression of a molecule selected from the group consisting of consisting of SEQ ID NO:1-67. According to one aspect of the invention, a method for identifying a candidate agent useful in the treatment of a cartilaginous tissue degeneration condition, is provided. The method involves determining expression of a set of nucleic acid molecules in a cell of mesenchymal origin, cartilaginous tissue, skin and/or bone marrow tissue, under conditions which, in the absence of a candidate agent, permit a first amount of expression of the set of nucleic acid molecules, wherein the set of nucleic acid molecules comprises at least one nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, contacting the cell of mesenchymal origin, cartilaginous tissue, skin and/or bone marrow tissue with the candidate agent, and detecting a test amount of expression of the set of nucleic acid molecules, wherein an increase in the test amount of expression in the presence of the candidate agent relative to the first amount of expression indicates that the candidate agent is useful in the treatment of the cartilaginous tissue degeneration condition. In certain embodiments, the cartilaginous tissue degeneration condition includes all forms of arthritis such as osteoarthritis, rheumatoid arthritis, osteochondrosis, and the like. In important embodiments, the condition is osteoarthritis. In some embodiments, the set of nucleic acid molecules comprises at least two nucleic acid molecules, each selected from the group consisting of SEQ ID NO:1-11, and 13-66.

[0022] According to another aspect of the invention, a pharmaceutical composition is provided. The composition includes an agent comprising an isolated nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, or an expression product thereof, in a pharmaceutically effective amount to treat a cartilaginous tissue degeneration condition, and a pharmaceutically acceptable carrier. In some embodiments, the agent is an expression product of the isolated nucleic acid molecule selected from the group of SEQ ID NO:1-11, and 13-66. In certain embodiments, the cartilaginous tissue degeneration condition includes all forms of arthritis such as osteoarthritis, rheumatoid arthritis, osteochondrosis, and the like.

[0023] According to a further aspect of the invention, methods for preparing medicaments useful in the treatment of a cartilaginous tissue degeneration condition are provided.

[0024] According to still another aspect of the invention, a solid-phase nucleic acid molecule array, is provided. The array consists essentially of a set of nucleic acid molecules, expression products thereof, or fragments thereof, each nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, fixed to a solid substrate. In some embodiments, the solid-phase array further comprises at least one control nucleic acid molecule. In certain embodiments, the set of nucleic acid molecules comprises at least one, at least two, at least three, at least four, or even at least five nucleic acid molecules, each selected from the group consisting of SEQ ID NO:1-11, and 13-66.

[0025] According to still another aspect of the invention, a device is provided. The device comprises a material surface coated with an amount of an agent of the invention (i.e. an agent having mesenchymal cell differentiation induction activity). The amount of the agent is effective to induce mesenchymal cell differentiation in the cells of mesenchymal origin present in the tissue to which the implantable device is to be implanted. In certain embodiments, the material surface is part of an implant. The material comprising the implant may be synthetic material or organic tissue material. Important agents, cell-types, and so on, are as described elsewhere herein.

[0026] According to a further aspect of the invention, methods for preparing medicaments useful in the treatment of a cartilaginous tissue degeneration condition, are provided.

[0027] These and other objects of the invention will be described in further detail in connection with the detailed description of the invention.

Brief Description of the Sequences

[0028] SEQ ID NO:1 is the partial nucleotide sequence of the human DF-1 cDNA (RDA2).

[0029] SEQ ID NO:2 is the partial nucleotide sequence of the human DF-2 cDNA (RDA10).

[0030] SEQ ID NO:3 is the partial nucleotide sequence of the human DF-3 cDNA (RDA11).

[0031] SEQ ID NO:4 is the partial nucleotide sequence of the human DF-4 cDNA (RDA30).

[0032] SEQ ID NO:5 is the partial nucleotide sequence of the human DF-5 cDNA (RDA31).

[0033] SEQ ID NO:6 is the partial nucleotide sequence of the human DF-6 cDNA (RDA35A).

[0034] SEQ ID NO:7 is the partial nucleotide sequence of the human DF-7 cDNA (RDA38).

[0035] SEQ ID NO:8 is the partial nucleotide sequence of the human DF-8 cDNA (RDA52).

[0036] SEQ ID NO:9 is the partial nucleotide sequence of the human DF-9 cDNA (RDA86B).

[0037] SEQ ID NO:10 is the partial nucleotide sequence of the human DF-10 cDNA (RDA90D).

[0038] SEQ ID NO:11 is the partial nucleotide sequence of the human DF-11 cDNA (RDA 15).

[0039] SEQ ID NO:12 is the predicted amino acid sequence of the translation product of human DF-11 cDNA (SEQ ID NO:11).

[0040] SEQ ID NOs:13-66 are the nucleotide sequences of known genes induced in mesenchymal cells according to the present invention.

[0041] SEQ ID NO:67 is the amino acid sequence of AminoPhospholipid-transporting ATPase (ATP10C), its expression induced in mesenchymal cells according to the present invention.

[0042] SEQ ID NOs:68-79 are various oligonucleotide sequences used in the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

[0043]
FIG. 1 depicts a kit embodying features of the present invention.

[0044]
FIG. 2 shows a schematic of an experimental design for representational difference analysis.

[0045]
FIG. 3 shows bar graphs depicting gene expression levels of genes known to be expressed in cartilage [type XI collagen (COL11A1), α-11 integrin, and FGF2], as well as of aggrecan (an abundant cartilage extracellular matrix gene), normalized to G3PDH.

DETAILED DESCRIPTION OF THE INVENTION

[0046] The invention involves the discovery of a number of genes that are upregulated in mesenchymal cells when the mesenchymal cells are cultured in a system that simulates physiological skeletal (bone and/or cartilaginous) growth conditions. It has been discovered that such upregulation leads, unexpectedly, to the acquirement of a chondroblastic phenotype by the mesenchymal cells (i.e., to cartilage/bone formation). In view of these discoveries, it is believed that the molecules of the present invention can be used to promote cartilage/bone formation, and in particular, to treat conditions that affect the skeleton, such as cartilaginous tissue degeneration conditions that include all forms of arthritis such as osteoarthritis, rheumatoid arthritis, osteochondrosis, and the like. Additionally, methods for using these molecules in the diagnosis of any of the foregoing skeletal degeneration conditions, are also provided.

[0047] Furthermore, methods for using these molecules in vivo or in vitro for the purpose of modulating mesenchymal cell differentiation, methods for treating conditions associated with skeletal degeneration, and compositions useful in the preparation of therapeutic preparations for the treatment of the foregoing conditions, are also provided.

[0048] “Upregulated,” as used herein, refers to increased expression of a gene and/or its encoded polypeptide. Increased expression refers to increasing (i.e., to a detectable extent) replication, transcription, and/or translation of any of the nucleic acids of the, invention (SEQ ID NO:1-11, or 13-66), since upregulation of any of these processes results in concentration/amount increase of the polypeptide encoded by the gene (nucleic acid). Conversely, downregulation or decreased expression refers to decreased expression of a gene and/or its encoded polypeptide. The upregulation or downregulation of gene expression can be directly determined by detecting an increase or decrease, respectively, in the level of mRNA for the gene, or the level of protein expression of the gene-encoded polypeptide, using any suitable means known to the art, such as nucleic acid hybridization or antibody detection methods, respectively, and in comparison to controls. Upregulation or downregulation of gene expression can also be determined indirectly by detecting a change in mesenchymal cell differentiation induction activity of the gene.

[0049] The culture system used herein that simulates physiological skeletal (bone and/or cartilaginous) growth conditions, is a system that we previously developed, and is described in detail in U.S. Pat. No. 5,656,492, to Glowacki et. al., entitled “Cell Induction Device.” For the specific conditions used in the identification of the various genes of the present invention, see under Examples section.

[0050] “Mesenchymal cell differentiation induction activity” refers to the ability of a molecule to induce differentiation of a mesenchymal cell to a chondroblast. Such activity can be determined using, for example, standard tests known in the art (e.g., expression of type II collagen and/or aggrecan molecules by cells of the chondroblastic phenotype,—see also Examples section).

[0051] A “molecule,” as used herein, embraces both “nucleic acids” and “polypeptides.” The molecules of the present invention (e.g., SEQ ID NOs:1-67) are capable of inducing mesenchymal cell differentiation both in vivo and in vitro.

[0052] “Expression,” as used herein, refers to nucleic acid and/or polypeptide expression, as well as to activity of the polypeptide molecule (e.g., mesenchymal cell differentiation induction activity of the molecule).

[0053] A “cell of mesenchymal origin” as used herein refers to a cell that has been generated as a result of the differentiation of a pluripotential cell(s) of the mesenchyme (tissue giving rise to all connective tissues, including cartilage). Such pluripotential cell of the mesenchyme includes pluripotent stem cells and committed progenitor cells.

[0054] As used herein, a subject is a mammal or a non-human mammal. In all embodiments human nucleic acid and polypeptide molecules, and human subjects are preferred.

[0055] One aspect of the invention involves the cloning of cDNAs encoding polypeptides with mesenchymal cell differentiation induction activity.

[0056] The invention involves in another aspect isolated polypeptides, the cDNAs encoding these polypeptide, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as diagnostics and therapeutics relating thereto.

[0057] As used herein with respect to nucleic acids, the term “isolated” means: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation; or (iv) synthesized by, for example, chemical synthesis. An isolated nucleic acid is one which is readily manipulated by recombinant DNA techniques well known in the art. Thus, a nucleotide sequence contained in a vector in which 5′ and 3′ restriction sites are known or for which polymerase chain reaction (PCR) primer sequences have been disclosed is considered isolated but a nucleic acid sequence existing in its native state in its natural host is not. An isolated nucleic acid may be substantially purified, but need not be. For example, a nucleic acid that is isolated within a cloning or expression vector is not pure in that it may comprise only a tiny percentage of the material in the cell in which it resides. Such a nucleic acid is isolated, however, as the term is used herein because it is readily manipulated by standard techniques known to those of ordinary skill in the art.

[0058] As used herein with respect to polypeptides, the term “isolated” means separated from its native environment in sufficiently pure form so that it can be manipulated or used for any one of the purposes of the invention. Thus, isolated means sufficiently pure to be used (i) to raise and/or isolate antibodies, (ii) as a reagent in an assay, (iii) for sequencing, (iv) as a therapeutic, etc.

[0059] According to the invention, isolated nucleic acid molecules that code for polypeptides according to the present invention having mesenchymal cell differentiation induction activity include: (a) nucleic acid molecules which hybridize under stringent conditions to any nucleic acid molecule of SEQ ID NO:1-11 and which code for a polypeptide having mesenchymal cell differentiation induction activity, (b) nucleic acid molecules that differ from the nucleic acid molecules of (a) in codon sequence due to the degeneracy of the genetic code, and (c) complements of (a) or (b). “Complements,” as used herein, includes “full-length complements or 100% complements of (a) or (b).

[0060] Homologs and alleles of the novel nucleic acids of the invention (SEQ ID NOs:1-11) can be identified by conventional techniques. Thus, an aspect of the invention is those nucleic acid sequences which code for polypeptides having mesenchymal cell differentiation induction activity and which hybridize to a nucleic acid molecule consisting of the coding region of SEQ ID NOs:1-11, under stringent conditions. The term “stringent conditions,” as used herein, refers to parameters with which the art is familiar. With nucleic acids, hybridization conditions are said to be stringent typically under conditions of low ionic strength and a temperature just below the melting temperature (Tm) of the DNA hybrid complex (typically, about 3° C. below the Tm of the hybrid). Higher stringency makes for a more specific correlation between the probe sequence and the target. Stringent conditions used in the hybridization of nucleic acids are well known in the art and may be found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. An example of “stringent conditions” is hybridization at 65° C. in 6×SSC. Another example of stringent conditions is hybridization at 65° C. in hybridization buffer that consists of 3.5×SSC, 0.02% Ficoll, 0.02% polyvinyl pyrolidone, 0.02% Bovine Serum Albumin, 2.5 mM NaH2PO4[pH 7], 0.5% SDS, 2 mM EDTA. (SSC is 0.15M sodium chloride/0.15M sodium citrate, pH 7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid). After hybridization, the membrane upon which the DNA is transferred is washed at 2×SSC at room temperature and then at 0.1×SSC/0.1×SDS at temperatures up to 68° C. In a further example, an alternative to the use of an aqueous hybridization solution is the use of a formamide hybridization solution. Stringent hybridization conditions can thus be achieved using, for example, a 50% formamide solution and 42° C. There are other conditions, reagents, and so forth which can be used, and would result in a similar degree of stringency. The skilled artisan will be familiar with such conditions, and thus they are not given here. It will be understood, however, that the skilled artisan will be able to manipulate the conditions in a manner to permit the clear identification of homologs and alleles of the novel nucleic acids of the invention. The skilled artisan also is familiar with the methodology for screening cells and libraries for expression of such molecules which then are routinely isolated, followed by isolation of the pertinent nucleic acid molecule and sequencing.

[0061] In general homologs and alleles typically will share at least 40% nucleotide identity and/or at least 50% amino acid identity to any of SEQ ID NOs:1-11 and their encoded polypeptides, respectively, in some instances will share at least 50% nucleotide identity and/or at least 65% amino acid identity and in still other instances will share at least 60% nucleotide identity and/or at least 75% amino acid identity. In further instances, homologs and alleles typically will share at least 90%, 95%, or even 99% nucleotide identity and/or at least 95%, 98%, or even 99% amino acid identity to any of SEQ ID NOs:1-11 and their encoded polypeptides, respectively. The homology can be calculated using various, publicly available software tools developed by NCBI (Bethesda, Md.). Exemplary tools include the heuristic algorithm of Altschul S F, et al., (J Mol Biol, 1990, 215:403-410), also known as BLAST. Pairwise and ClustalW alignments (BLOSUM30 matrix setting) as well as Kyte-Doolittle hydropathic analysis can be obtained using public (EMBL, Heidelberg, Germany) and commercial (e.g., the MacVector sequence analysis software from Oxford Molecular Group/enetics Computer Group, Madison, Wis.). Watson-Crick complements of the foregoing nucleic acids also are embraced by the invention.

[0062] In screening for genes related to any of SEQ ID NOs:1-11, such as their homologs and alleles a Southern blot may be performed using the foregoing conditions, together with a radioactive probe. After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film or a phosphoimager plate to detect the radioactive signal.

[0063] Given the teachings herein, full-length human cDNAs, other mammalian sequences such as the mouse cDNA clone corresponding to the human DF gene can be isolated from a cDNA library, using standard colony hybridization techniques.

[0064] The invention also includes degenerate nucleic acids which include alternative codons to those present in the native materials. For example, serine residues are encoded by the codons TCA, AGT, TCC, TCG, TCT and AGC. Thus, it will be apparent to one of ordinary skill in the art that any of the serine-encoding nucleotide triplets may be employed to direct the protein synthesis apparatus, in vitro or in vivo, to incorporate a serine residue into an elongating polypeptide. Similarly, nucleotide sequence triplets which encode other amino acid residues include, but are not limited to: CCA, CCC, CCG and CCT (proline codons); CGA, CGC, CGG, CGT, AGA and AGG (arginine codons); ACA, ACC, ACG and ACT (threonine codons); AAC and AAT (asparagine codons); and ATA, ATC and ATT (isoleucine codons). Other amino acid residues may be encoded similarly by multiple nucleotide sequences. Thus, the invention embraces degenerate nucleic acids that differ from the biologically isolated nucleic acids in codon sequence due to the degeneracy of the genetic code.

[0065] The invention also provides isolated unique fragments of any of SEQ ID NOs:1-11 or complements of thereof. A unique fragment is one that is a ‘signature’ for the larger nucleic acid. For example, the unique fragment is long enough to assure that its precise sequence is not found in molecules within the human genome outside of the nucleic acids defined above (SEQ ID NOs:1-11) (and human alleles). Those of ordinary skill in the art may apply no more than routine procedures to determine if a fragment is unique within the human genome. Unique fragments, however, exclude previously published sequences as of the filing date of this application.

[0066] A fragment which is completely composed of a published sequence described in the art as of the filing date of this application, is one which does not include any of the nucleotides unique to the sequences of the invention. Thus, a unique fragment according to the invention must contain a nucleotide sequence other than the exact sequence of those in the prior art or fragments thereof The difference may be an addition, deletion or substitution with respect to the known sequence or it may be a sequence wholly separate from the known sequence.

[0067] Unique fragments can be used as probes in Southern and Northern blot assays to identify such nucleic acids, or can be used in amplification assays such as those employing PCR. As known to those skilled in the art, large probes such as 200, 250, 300 or more nucleotides are preferred for certain uses such as Southern and Northern blots, while smaller fragments will be preferred for uses such as PCR. Unique fragments also can be used to produce fusion proteins for generating antibodies or determining binding of the polypeptide fragments, or for generating immunoassay components. Likewise, unique fragments can be employed to produce nonfused fragments of the novel polypeptides of the invention, useful, for example, in the preparation of antibodies, immunoassays or therapeutic applications.

[0068] Unique fragments further can be used as antisense molecules to inhibit the expression of any of the novel nucleic acids of the invention and their encoded polypeptides, respectively. As will be recognized by those skilled in the art, the size of the unique fragment will depend upon its conservancy in the genetic code. Thus, some regions of any of SEQ ID NOs:1-11 and complements will require longer segments to be unique while others will require only short segments, typically between 12 and 32 nucleotides long (e.g. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 and 32 bases) or more, up to the entire length of the disclosed sequence. As mentioned above, this disclosure intends to embrace each and every fragment of each sequence, beginning at the first nucleotide, the second nucleotide and so on, up to 8 nucleotides short of the end, and ending anywhere from nucleotide number 8, 9, 10 and so on for each sequence, up to the very last nucleotide, (provided the sequence is unique as described above). Virtually any segment of any of the nucleic acids of SEQ ID NOs:1-11, or complements thereof, that is 20 or more nucleotides in length will be unique. Those skilled in the art are well versed in methods for selecting such sequences, typically on the basis of the ability of the unique fragment to selectively distinguish the sequence of interest from other sequences in the human genome of the fragment to those on known databases typically is all that is necessary, although in vitro confirmatory hybridization and sequencing analysis may be performed.

[0069] As mentioned above, the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a polypeptide having mesenchymal cell differentiation induction activity, to decrease such activity.

[0070] As used herein, the term “antisense oligonucleotide” or “antisense” describes an oligonucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and, thereby, inhibits the transcription of that gene and/or the translation of that mRNA. The antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene or transcript. Those skilled in the art will recognize that the exact length of the antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence of the target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with the target under physiological conditions, i.e., to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. Based upon any of SEQ ID NOs:1-11 or upon allelic or homologous genomic and/or cDNA sequences, one of skill in the art can easily choose and synthesize any of a number of appropriate antisense molecules for use in accordance with the present invention. In order to be sufficiently selective and potent for inhibition, such antisense oligonucleotides should comprise at least 10 and, more preferably, at least 15 consecutive bases which are complementary to the target, although in certain cases modified oligonucleotides as short as 7 bases in length have been used successfully as antisense oligonucleotides (Wagner et al., Nat. Med, 1995, 1(11):1116-1118; Nat. Biotech., 1996, 14:840-844). Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases. Although oligonucleotides may be chosen which are antisense to any region of the gene or mRNA transcripts, in preferred embodiments the antisense oligonucleotides correspond to N-terminal or 5′ upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3′-untranslated regions may be targeted by antisense oligonucleotides. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, e.g., Sainio et al., Cell Mol. Neurobiol. 14(5):439-457, 1994) and at which proteins are not expected to bind. Finally, although, SEQ ID No:1 discloses a cDNA sequence, one of ordinary skill in the art may easily derive the genomic DNA corresponding to this sequence. Thus, the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to any of SEQ ID NO:1-11. Similarly, antisense to allelic or homologous to the cDNAs and genomic DNAs of the invention are enabled without undue experimentation.

[0071] In one set of embodiments, the antisense oligonucleotides of the invention may be composed of “natural” deoxyribonucleotides, ribonucleotides, or any combination thereof. That is, the 5′ end of one native nucleotide and the 3′ end of another native nucleotide may be covalently linked, as in natural systems, via a phosphodiester internucleoside linkage. These oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.

[0072] In preferred embodiments, however, the antisense oligonucleotides of the invention also may include “modified” oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness.

[0073] The term “modified oligonucleotide” as used herein describes an oligonucleotide in which (1) at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage (i.e., a linkage other than a phosphodiester linkage between the 5′ end of one nucleotide and the 3′ end of another nucleotide) and/or (2) a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide. Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidates, carboxymethyl esters and peptides.

[0074] The term “modified oligonucleotide” also encompasses oligonucleotides with a covalently modified base and/or sugar. For example, modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3′ position and other than a phosphate group at the 5′ position. Thus modified oligonucleotides may include a 2′-O-alkylated ribose group. In addition, modified oligonucleotides may include sugars such as arabinose instead of ribose. The present invention, thus, contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding polypeptides having mesenchymal cell differentiation activity, together with pharmaceutically acceptable carriers. Antisense oligonucleotides may be administered as part of a pharmaceutical composition. Such a pharmaceutical composition may include the antisense oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which arc known in the art. The compositions should be sterile and contain a therapeutically effective amount of the antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. The term “physiologically acceptable” refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration. Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art.

[0075] The invention also involves expression vectors coding for proteins having mesenchymal cell differentiation activity and fragments and variants thereof and host cells containing those expression vectors. Virtually any cells, prokaryotic or eukaryotic, which can be transformed with heterologous DNA or RNA and which can be grown or maintained in culture, may be used in the practice of the invention. Examples include bacterial cells such as Escherichia coli and mammalian cells such as mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, including mast cells, fibroblasts, oocytes and lymphocytes, and they may be primary cells or cell lines. Specific examples include CHO cells and COS cells. Cell-free transcription systems also may be used in lieu of cells.

[0076] As used herein, a “vector” may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids, phagemids and virus genomes. A cloning vector is one which is able to replicate in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell. In the case of plasmids, replication of the desired sequence may occur many times as the plasmid increases in copy number within the host bacterium or just a single time per host before the host reproduces by mitosis. In the case of phage, replication may occur actively during a lytic phase or passively during a lysogenic phase. An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript. Vectors may further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector. Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., β-galactosidase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein). Preferred vectors are those capable of autonomous replication and expression of the structural gene products present in the DNA segments to which they are operably joined.

[0077] As used herein, a coding sequence and regulatory sequences are said to be “operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably joined if induction of a promoter in the 5′ regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide.

[0078] The precise nature of the regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5′ non-transcribed and 5′ non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Especially, such 5′ non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired. The vectors of the invention may optionally include 5′ leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art.

[0079] Expression vectors containing all the necessary elements for expression are commercially available and known to those skilled in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. Cells are genetically engineered by the introduction into the cells of heterologous DNA (RNA) encoding any polypeptide of the invention or fragment or variant thereof. That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.

[0080] Preferred systems for mRNA expression in mammalian cells are those such as pRc/CMV (available from Invitrogen, Carlsbad, Calif.) that contain a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences. Additionally, suitable for expression in primate or canine cell lines is the pCEP4 vector (Invitrogen, Carlsbad, Calif.), which contains an Epstein Barr virus (EBV) origin of replication, facilitating the maintenance of plasmid as a multicopy extrachromosomal element. Another expression vector is the pEF-BOS plasmid containing the promoter of polypeptide Elongation Factor 1α, which stimulates efficiently transcription in vitro. The plasmid is described by Mishizuma and Nagata (Nuc. Acids Res. 18:5322, 1990), and its use in transfection experiments is disclosed by, for example, Demoulin (Mol. Cell. Biol. 16:4710-4716, 1996). Still another preferred expression vector is an adenovirus, described by Stratford-Perricaudet, which is defective for E1 and E3 proteins (J. Clin. Invest. 90:626-630, 1992). The use of the adenovirus as an Adeno.P1A recombinant is disclosed by Warnier et al., in intradermal injection in mice for immunization against P1A (Int. J. Cancer, 67:303-310, 1996).

[0081] The invention also embraces so-called expression kits, which allow the artisan to prepare a desired expression vector or vectors. Such expression kits include at least separate portions of each of the previously discussed coding sequences. Other components may be added, as desired, as long as the previously mentioned sequences, which are required, are included.

[0082] It will also be recognized that the invention embraces the use of the above described cDNA sequence containing expression vectors, to transfect host cells and cell lines, be these prokaryotic (e.g., Escherichia coli), or eukaryotic (e.g., CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells). Especially useful are mammalian cells such as mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, and include primary cells and cell lines. Specific examples include dendritic cells, U293 cells, peripheral blood leukocytes, bone marrow stem cells and embryonic stem cells. The invention also permits the construction of gene “knock-outs” in cells and in animals, providing materials for studying certain aspects of mesenchymal cell differentiation activity.

[0083] The invention also provides isolated polypeptides having mesenchymal cell differentiation activity (including whole proteins and partial proteins), encoded by the foregoing novel nucleic acids, and include the polypeptide of SEQ ID NO:12 and unique fragments thereof. Such polypeptides are useful, for example, alone or as part of fusion proteins to generate antibodies, as components of an immunoassay, etc. Polypeptides can be isolated from biological samples including tissue or cell homogenates, and can also be expressed recombinantly in a variety of prokaryotic and eukaryotic expression systems by constructing an expression vector appropriate to the expression system, introducing the expression vector into the expression system, and isolating the recombinantly expressed protein. Short polypeptides, including antigenic peptides (such as are presented by MHC molecules on the surface of a cell for immune recognition) also can be synthesized chemically using well-established methods of peptide synthesis.

[0084] A unique fragment of a polypeptide of the present invention, in general, has the features and characteristics of unique fragments as discussed above in connection with nucleic acids. As will be recognized by those skilled in the art, the size of the unique fragment will depend upon factors such as whether the fragment constitutes a portion of a conserved protein domain. Thus, some regions of any encoded polypeptide will require longer segments to be unique while others will require only short segments, typically between 5 and 12 amino acids (e.g. 5, 6, 7, 8, 9, 10, 11 and 12 amino acids long or more, including each integer up to the full length).

[0085] Unique fragments of a polypeptide preferably are those fragments which retain a distinct functional capability of the polypeptide. Functional capabilities which can be retained in a unique fragment of a polypeptide include interaction with antibodies, interaction with other polypeptides or fragments thereof, interaction with other molecules, etc. One important activity is the ability to act as a signature for identifying the polypeptide. Those skilled in the art are well versed in methods for selecting unique amino acid sequences, typically on the basis of the ability of the unique fragment to selectively distinguish the sequence of interest from non-family members. A comparison of the sequence of the fragment to those on known databases typically is all that is necessary.

[0086] The invention embraces variants of the polypeptides of the invention described above. As used herein, a “variant” of a polypeptide of the invention is a polypeptide which contains one or more modifications to the primary amino acid sequence of a polypeptide of the invention. Modifications which create a polypeptide variant are typically made to the nucleic acid which encodes the polypeptide, and can include deletions, point mutations, truncations, amino acid substitutions and addition of amino acids or non-amino acid moieties to: 1) reduce or eliminate an activity of the polypeptide; 2) enhance a property of the polypeptide, such as protein stability in an expression system or the stability of protein-ligand binding; 3) provide a novel activity or property to the polypeptide, such as addition of an antigenic epitope or addition of a detectable moiety; or 4) to provide equivalent or better binding to a polypeptide receptor or other molecule. Alternatively, modifications can be made directly to the polypeptide, such as by cleavage, addition of a linker molecule, addition of a detectable moiety, such as biotin, addition of a fatty acid, and the like. Modifications also embrace fusion proteins comprising all or part of the amino acid sequence. One of skill in the art will be familiar with methods for predicting the effect on protein conformation of a change in protein sequence, and can thus “design” a variant polypeptide according to known methods. One example of such a method is described by Dahiyat and Mayo in Science 278:82-87, 1997, whereby proteins can be designed de novo. The method can be applied to a known protein to vary only a portion of the polypeptide sequence. By applying the computational methods of Dahiyat and Mayo, specific variants of the polypeptides of the invention can be proposed and tested to determine whether the variant retains a desired conformation.

[0087] Variants can include polypeptides which are modified specifically to alter a feature of the polypeptide unrelated to its physiological activity. For example, cysteine residues can be substituted or deleted to prevent unwanted disulfide linkages. Similarly, certain amino acids can be changed to enhance expression of the polypeptide by eliminating proteolysis by proteases in an expression system (e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present).

[0088] Mutations of a nucleic acid which encodes a polypeptide of the invention preferably preserve the amino acid reading frame of the coding sequence, and preferably do not create regions in the nucleic acid which are likely to hybridize to form secondary structures, such a hairpins or loops, which can be deleterious to expression of the variant polypeptide.

[0089] Mutations can be made by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid which encodes the polypeptide. Variant polypeptides are then expressed and tested for one or more activities to determine which mutation provides a variant polypeptide with the desired properties. Further mutations can be made to variants (or to non-variant polypeptides) which are silent as to the amino acid sequence of the polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., Escherichia coli, are well known to those of ordinary skill in the art. Still other mutations can be made to the noncoding sequences of a gene or cDNA encoding the polypeptide to enhance expression of the polypeptide.

[0090] The skilled artisan will realize that conservative amino acid substitutions may be made in any of the polypeptides of the invention to provide functionally equivalent variants of the foregoing polypeptides, i.e, the variants retain the functional capabilities of the polypeptides of the invention. As used herein, a “conservative amino acid substitution” refers to an amino acid substitution which does not significantly alter the tertiary structure and/or activity of the polypeptide. Variants can be prepared according to methods for altering polypeptide sequence known to one of ordinary skill in the art, and include those that are found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. Exemplary functionally equivalent variants of the polypeptides of the invention include conservative amino acid substitutions (e.g. of SEQ ID NO:13). Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.

[0091] Thus functionally equivalent variants of polypeptides of the invention, i.e., variants of the polypeptides which retain the function of each of the natural polypeptides, are contemplated by the invention. Conservative amino-acid substitutions in the amino acid sequence of polypeptides of the invention to produce functionally equivalent variants typically are made by alteration of a nucleic acid encoding each polypeptide (e.g., SEQ ID NOs:1-11). Such substitutions can be made by a variety of methods known to one of ordinary skill in the art. For example, amino acid substitutions may be made by PCR-directed mutation, site-directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat. Acad. Sci. U.S.A. 82: 488-492, 1985), or by chemical synthesis of a gene encoding a polypeptide of the invention. The activity of functionally equivalent fragments of polypeptides of the invention can be tested by cloning the gene encoding the altered polypeptide of the invention into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the altered polypeptide, and testing for a functional capability of the polypeptides as disclosed herein (e.g., mesenchymal cell differentiation induction activity, etc.).

[0092] The invention as described herein has a number of uses, some of which are described elsewhere herein. First, the invention permits isolation of polypeptides having mesenchymal cell differentiation induction activity. A variety of methodologies well-known to the skilled practitioner can be utilized to obtain isolated polypeptides. The polypeptide may be purified from cells which naturally produce the polypeptide by chromatographic means or immunological recognition. Alternatively, an expression vector may be introduced into cells to cause production of the polypeptide. In another method, mRNA transcripts may be microinjected or otherwise introduced into cells to cause production of the encoded polypeptide. Translation of an mRNA of the invention in cell-free extracts such as the reticulocyte lysate system also may be used to produce polypeptides. Those skilled in the art also can readily follow known methods for isolating polypeptides. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography and immune-affinity chromatography.

[0093] The invention also provides, in certain embodiments, “dominant negative” polypeptides derived from polypeptides of the invention. A dominant negative polypeptide is an inactive variant of a protein, which, by interacting with the cellular machinery, displaces an active protein from its interaction with the cellular machinery or competes with the active protein, thereby reducing the effect of the active protein. For example, a dominant negative receptor which binds a ligand but does not transmit a signal in response to binding of the ligand can reduce the biological effect of expression of the ligand. Likewise, a dominant negative catalytically-inactive kinase which interacts normally with target proteins but does not phosphorylate the target proteins can reduce phosphorylation of the target proteins in response to a cellular signal. Similarly, a dominant negative transcription factor which binds to a promoter site in the control region of a gene but does not increase gene transcription can reduce the effect of a normal transcription factor by occupying promoter binding sites without increasing transcription.

[0094] The end result of the expression of a dominant negative polypeptide in a cell is a reduction in function of active proteins. One of ordinary skill in the art can assess the potential for a dominant negative variant of a protein, and use standard mutagenesis techniques to create one or more dominant negative variant polypeptides. See, e.g., U.S. Pat. No. 5,580,723 and Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. The skilled artisan then can test the population of mutagenized polypeptides for diminution in a selected activity and/or for retention of such an activity. Other similar methods for creating and testing dominant negative variants of a protein will be apparent to one of ordinary skill in the art.

[0095] The isolation of the cDNAs of the invention (SEQ ID NOs:1-11) also makes it possible for the artisan to diagnose a disorder characterized by an aberrant expression of any gene encoded by such cDNAs. These methods involve determining expression of the gene, and/or polypeptides derived therefrom. In the former situation, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes as exemplified below. In the latter situation, such determination can be carried out via any standard immunological assay using, for example, antibodies which bind to the secreted protein.

[0096] The invention also embraces isolated peptide binding agents which, for example, can be antibodies or fragments of antibodies (“binding polypeptides”), having the ability to selectively bind to polypeptides of the present invention. Antibodies include polyclonal and monoclonal antibodies, prepared according to conventional methodology.

[0097] Significantly, as is well-known in the art, only a small portion of an antibody molecule, the paratope, is involved in the binding of the antibody to its epitope (see, in general, Clark, W. R. (1986) The Experimental Foundations of Modern Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc′ and Fe regions, for example, are effectors of the complement cascade but are not involved in antigen binding. An antibody from which the pFc′ region has been enzymatically cleaved, or which has been produced without the pFc′ region, designated an F(ab′)2 fragment, retains both of the antigen binding sites of an intact antibody. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an Fab fragment, retains one of the antigen binding sites of an intact antibody molecule. Proceeding further, Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd. The Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.

[0098] Within the antigen-binding portion of an antibody, as is well-known in the art, there are complementarity determining regions (CDRs), which directly interact with the epitope of the antigen, and framework regions (FRs), which maintain the tertiary structure of the paratope (see, in general, Clark, 1986; Roitt, 1991). In both the heavy chain Fd fragment and the light chain of IgG immunoglobulins, there are four framework regions (FR1 through FR4) separated respectively by three complementarity determining regions (CDR1 through CDR3). The CDRs, and in particular the CDR3 regions, and more particularly the heavy chain CDR3, are largely responsible for antibody specificity.

[0099] It is now well-established in the art that the non-CDR regions of a mammalian antibody may be replaced with similar regions of conspecific or heterospecific antibodies while retaining the epitopic specificity of the original antibody. This is most clearly manifested in the development and use of “humanized” antibodies in which non-human CDRs are covalently joined to human FR and/or Fc/pFc′ regions to produce a functional antibody. See, e.g., U.S. Pat. Nos. 4,816,567, 5,225,539, 5,585,089, 5,693,762 and 5,859,205. Thus, for example, PCT International Publication Number WO 92/04381 teaches the production and use of humanized murine RSV antibodies in which at least a portion of the murine FR regions have been replaced by FR regions of human origin. Such antibodies, including fragments of intact antibodies with antigen-binding ability, are often referred to as “chimeric” antibodies.

[0100] Thus, as will be apparent to one of ordinary skill in the art, the present invention also provides for F(ab′)2, Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab′)2 fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in which the FR and/or CDR1 and/or CDR2 regions have been replaced by homologous human or non-human sequences. The present invention also includes so-called single chain antibodies.

[0101] Thus, the invention involves polypeptides of numerous size and type that bind specifically to polypeptides of the invention, and complexes of both polypeptides and their binding partners. These polypeptides may be derived also from sources other than antibody technology. For example, such polypeptide binding agents can be provided by degenerate peptide libraries which can be readily prepared in solution, in immobilized form, as bacterial flagella peptide display libraries or as phage display libraries. Combinatorial libraries also can be synthesized of peptides containing one or more amino acids. Libraries further can be synthesized of peptides and non-peptide synthetic moieties.

[0102] Phage display can be particularly effective in identifying binding peptides useful according to the invention. Briefly, one prepares a phage library (using e.g. m13, fd, or lambda phage), displaying inserts from 4 to about 80 amino acid residues using conventional procedures. The inserts may represent, for example, a completely degenerate or biased array. One then can select phage-bearing inserts which bind to the polypeptide or a complex of the polypeptide and a binding partner. This process can be repeated through several cycles of reselection of phage that bind to the polypeptide or complex. Repeated rounds lead to enrichment of phage bearing particular sequences. DNA sequence analysis can be conducted to identify the sequences of the expressed polypeptides. The minimal linear portion of the sequence that binds to the polypeptide or complex can be determined. One can repeat the procedure using a biased library containing inserts containing part or all of the minimal linear portion plus one or more additional degenerate residues upstream or downstream thereof. Yeast two-hybrid screening methods also may be used to identify polypeptides that bind to the polypeptides of the invention. Thus, the polypeptides of the invention, or a fragment thereof, or complexes of a polypeptide and a binding partner can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners of the polypeptides of the invention. Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of the polypeptide and for other purposes that will be apparent to those of ordinary skill in the art.

[0103] An polypeptide of the invention, or a fragment thereof, also can be used to isolate their native binding partners. Isolation of binding partners may be performed according to well-known methods. For example, isolated polypeptides can be attached to a substrate, and then a solution suspected of containing a binding partner of the polypeptide may be applied to the substrate. If the binding partner for a polypeptide of the invention is present in the solution, then it will bind to the substrate-bound polypeptide. The binding partner then may be isolated. Other proteins which are binding partners for a polypeptide of the invention, may be isolated by similar methods without undue experimentation.

[0104] The invention also provides methods to measure the level of gene expression in a subject. This can be performed by first obtaining a test sample from the subject. The test sample can be tissue or biological fluid. Tissues include brain, heart, serum, breast, colon, bladder, uterus, prostate, stomach, testis, ovary, pancreas, pituitary gland, adrenal gland, thyroid gland, salivary gland, mammary gland, kidney, liver, intestine, spleen, thymus, blood vessels, bone marrow, trachea, and lung. In certain embodiments, test samples originate from heart and blood vessel tissues, and biological fluids include blood, saliva and urine. Both invasive and non-invasive techniques can be used to obtain such samples and are well documented in the art. At the molecular level both PCR and Northern blotting can be used to determine the level of SEQ ID NOs:1-11 mRNA using products of this invention described herein, and protocols well known in the art that are found in references which compile such methods. At the protein level, polypeptide expression can be determined using either polyclonal or monoclonal anti-polypeptide sera in combination with standard immunological assays. The preferred methods will compare the measured level of expression of the test sample to a control. A control can include a known amount of a nucleic acid probe, an epitope (such as an expression product of any of SEQ ID NOs:1-11), or a similar test sample of a subject with a control or ‘normal’ level of expression.

[0105] Polypeptides of the invention preferably are produced recombinantly, although such polypeptides may be isolated from biological extracts. Recombinantly produced polypeptides include chimeric proteins comprising a fusion of a protein with another polypeptide, e.g., a polypeptide capable of providing or enhancing protein-protein binding, sequence specific nucleic acid binding (such as GAL4), enhancing stability of the polypeptide of the invention under assay conditions, or providing a detectable moiety, such as green fluorescent protein. A polypeptide fused to a polypeptide of the invention or fragment may also provide means of readily detecting the fusion protein, e.g., by immunological recognition or by fluorescent labeling.

[0106] The invention also is useful in the generation of transgenic non-human animals. As used herein, “transgenic non-human animals” includes non-human animals having one or more exogenous nucleic acid molecules incorporated in germ line cells and/or somatic cells. Thus the transgenic animals include “knockout” animals having a homozygous or heterozygous gene disruption by homologous recombination, animals having episomal or chromosomally incorporated expression vectors, etc. Knockout animals can be prepared by homologous recombination using embryonic stem cells as is well known in the art. The recombination may be facilitated using, for example, the cre/lox system or other recombinase systems known to one of ordinary skill in the art. In certain embodiments, the recombinase system itself is expressed conditionally, for example, in certain tissues or cell types, at certain embryonic or post-embryonic developmental stages, is induced by the addition of a compound which increases or decreases expression, and the like. In general, the conditional expression vectors used in such systems use a variety of promoters which confer the desired gene expression pattern (e.g., temporal or spatial). Conditional promoters also can be operably linked to nucleic acid molecules of the invention to increase expression of its encoded gene and/or polypeptide in a regulated or conditional manner. Trans-acting negative regulators of each gene's activity or expression also can be operably linked to a conditional promoter as described above. Such trans-acting regulators include antisense nucleic acids molecules, nucleic acid molecules which encode dominant negative molecules, ribozyme molecules specific for each nucleic acid of the invention, and the like. The transgenic non-human animals are useful in experiments directed toward testing biochemical or physiological effects of diagnostics or therapeutics for conditions characterized by increased or decreased gene expression. Other uses will be apparent to one of ordinary skill in the art.

[0107] The invention also contemplates gene therapy. The procedure for performing ex vivo gene therapy is outlined in U.S. Pat. No. 5,399,346 and in exhibits submitted in the file history of that patent, all of which are publicly available documents. In general, it involves introduction in vitro of a functional copy of a gene into a cell(s) of a subject which contains a defective copy of the gene, and returning the genetically engineered cell(s) to the subject. The functional copy of the gene is under operable control of regulatory elements which permit expression of the gene in the genetically engineered cell(s). Numerous transfection and transduction techniques as well as appropriate expression vectors are well known to those of ordinary skill in the art, some of which are described in PCT application WO95/00654. In vivo gene therapy using vectors such as adenovirus, retroviruses, herpes virus, and targeted liposomes also is contemplated according to the invention.

[0108] The invention further provides efficient methods of identifying agents or lead compounds for agents active at the level of a polypeptide of the invention, or of a fragment thereof, dependent cellular function. In particular, such functions include interaction with other polypeptides or fragments. Generally, the screening methods involve assaying for compounds which interfere with polypeptide activity (such as mesenchymal cell differentiation induction activity), although compounds which enhance mesenchymal cell differentiation induction activity of a polypeptide of the invention also can be assayed using the screening methods. Such methods are adaptable to automated, high throughput screening of compounds. Target indications include cellular processes modulated by a polypeptide of the invention such as mesenchymal cell differentiation induction activity.

[0109] A wide variety of assays for candidate (pharmacological) agents are provided, including, labeled in vitro protein-ligand binding assays, electrophoretic mobility shift assays, immunoassays, cell-based assays such as two- or three-hybrid screens, expression assays, etc. The transfected nucleic acids can encode, for example, combinatorial peptide libraries or cDNA libraries. Convenient reagents for such assays, e.g., GAL4 fusion proteins, are known in the art. An exemplary cell-based assay involves transfecting a cell with a nucleic acid encoding a polypeptide of the invention fused to a GAL4 DNA binding domain and a nucleic acid encoding a reporter gene operably linked to a gene expression regulatory region, such as one or more GAL4 binding sites. Activation of reporter gene transcription occurs when a polypeptide of the invention and a reporter fusion polypeptide bind such as to enable transcription of the reporter gene. Agents which modulate mediated cell function of a polypeptide of the invention are then detected through a change in the expression of reporter gene. Methods for determining changes in the expression of a reporter gene are known in the art.

[0110] Polypeptide fragments used in the methods, when not produced by a transfected nucleic acid are added to an assay mixture as an isolated polypeptide. Polypeptides of the invention preferably are produced recombinantly, although such polypeptides may be isolated from biological extracts. Recombinantly produced polypeptides include chimeric proteins comprising a fusion of a polypeptide of the invention with another polypeptide, e.g., a polypeptide capable of providing or enhancing protein-protein binding, sequence specific nucleic acid binding (such as GAL4), enhancing stability of the polypeptide of the invention under assay conditions, or providing a detectable moiety, such as green fluorescent protein or Flag epitope.

[0111] The assay mixture is comprised of a natural intracellular binding target of a polypeptide of the invention capable of interacting with a polypeptide of the invention. While natural binding targets of a polypeptide of the invention may be used, it is frequently preferred to use portions (e.g., peptides or nucleic acid fragments) or analogs (i.e., agents which mimic the binding properties of the natural binding target for purposes of the assay) of the binding target a polypeptide of the invention so long as the portion or analog provides binding affinity and avidity to a fragment of the polypeptide of the invention measurable in the assay.

[0112] The assay mixture also comprises a candidate agent. Typically, a plurality of assay mixtures are run in parallel with different agent concentrations to obtain a different response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration of agent or at a concentration of agent below the limits of assay detection. Candidate agents encompass numerous chemical classes, although typically they are organic compounds. Preferably, the candidate agents are small organic compounds, i.e., those having a molecular weight of more than 50 yet less than about 2500, preferably less than about 1000 and, more preferably, less than about 500. Candidate agents comprise functional chemical groups necessary for structural interactions with polypeptides and/or nucleic acids, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups and more preferably at least three of the functional chemical groups. The candidate agents can comprise cyclic carbon or heterocyclic structure and/or aromatic or polyaromatic structures substituted with one or more of the above-identified functional groups. Candidate agents also can be biomolecules such as peptides, saccharides, fatty acids, sterols, isoprenoids, purines, pyrimidines, derivatives or structural analogs of the above, or combinations thereof and the like. Where the agent is a nucleic acid, the agent typically is a DNA or RNA molecule, although modified nucleic acids as defined herein are also contemplated.

[0113] Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides, synthetic organic combinatorial libraries, phage display libraries of random peptides, and the like. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural and synthetically produced libraries and compounds can be modified through conventional chemical, physical, and biochemical means. Further, known (pharmacological) agents may be subjected to directed or random chemical modifications such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs of the agents.

[0114] A variety of other reagents also can be included in the mixture. These include reagents such as salts, buffers, neutral proteins (e.g., albumin), detergents, etc. which may be used to facilitate optimal protein-protein and/or protein-nucleic acid binding. Such a reagent may also reduce non-specific or background interactions of the reaction components. Other reagents that improve the efficiency of the assay such as protease, inhibitors, nuclease inhibitors, antimicrobial agents, and the like may also be used.

[0115] The mixture of the foregoing assay materials is incubated under conditions whereby, but for the presence of the candidate agent, the polypeptide of the invention specifically binds a cellular binding target, a portion thereof or analog thereof. The order of addition of components, incubation temperature, time of incubation, and other parameters of the assay may be readily determined. Such experimentation merely involves optimization of the assay parameters, not the fundamental composition of the assay. Incubation temperatures typically are between 4° C. and 40° C. Incubation times preferably are minimized to facilitate rapid, high throughput screening, and typically are between 0.1 and 10 hours.

[0116] After incubation, the presence or absence of specific binding between the polypeptide of the invention and one or more binding targets is detected by any convenient method available to the user. For cell free binding type assays, a separation step is often used to separate bound from unbound components. The separation step may be accomplished in a variety of ways. Conveniently, at least one of the components is immobilized on a solid substrate, from which the unbound components may be easily separated. The solid substrate can be made of a wide variety of materials and in a wide variety of shapes, e.g., microtiter plate, microbead, dipstick, resin particle, etc. The substrate preferably is chosen to maximum signal to noise ratios, primarily to minimize background binding, as well as for ease of separation and cost.

[0117] Separation may be effected for example, by removing a bead or dipstick from a reservoir, emptying or diluting a reservoir such as a microtiter plate well, rinsing a bead, particle, chromatograpic column or filter with a wash solution or solvent. The separation step preferably includes multiple rinses or washes. For example, when the solid substrate is a microtiter plate, the wells may be washed several times with a washing solution, which typically includes those components of the incubation mixture that do not participate in specific bindings such as salts, buffer, detergent, non-specific protein, etc. Where the solid substrate is a magnetic bead, the beads may be washed one or more times with a washing solution and isolated using a magnet.

[0118] Detection may be effected in any convenient way for cell-based assays such as two- or three-hybrid screens. The transcript resulting from a reporter gene transcription assay of a polypeptide of the invention interacting with a target molecule typically encodes a directly or indirectly detectable product, e.g., β-galactosidase activity, luciferase activity, and the like. For cell free binding assays, one of the components usually comprises, or is coupled to, a detectable label. A wide variety of labels can be used, such as those that provide direct detection (e.g., radioactivity, luminescence, optical or electron density, etc), or indirect detection (e.g., epitope tag such as the FLAG epitope, enzyme tag such as horseseradish peroxidase, etc.). The label may be bound to a binding partner of a polypeptide of the invention, or incorporated into the structure of the binding partner.

[0119] A variety of methods may be used to detect the label, depending on the nature of the label and other assay components. For example, the label may be detected while bound to the solid substrate or subsequent to separation from the solid substrate. Labels may be directly detected through optical or electron density, radioactive emissions, nonradiative energy transfers, etc. or indirectly detected with antibody conjugates, streptavidin-biotin conjugates, etc. Methods for detecting the labels are well known in the art.

[0120] The invention provides specific binding agents to any of the polypeptides of the invention, methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development. For example, pharmacological agents specific for any of the polypeptides of the invention are useful in a variety of diagnostic and therapeutic applications, especially where disease or disease prognosis is associated with altered polypeptide binding characteristics. Novel binding agents specific for any of the polypeptides of the invention include specific antibodies, cell surface receptors, and other natural intracellular and extracellular binding agents identified with assays such as two hybrid screens, and non-natural intracellular and extracellular binding agents identified in screens of chemical libraries and the like.

[0121] In general, the specificity of binding of any of the polypeptides of the invention to a specific molecule is determined by binding equilibrium constants. Targets which are capable of selectively binding any of the polypeptides of the invention preferably have binding equilibrium constants of at least about 107 M−1, more preferably at least about 108 M−1, and most preferably at least about 109 M−1. A wide variety of cell based and cell free assays may be used to demonstrate specific binding. Cell based assays include one, two and three hybrid screens, assays in which polypeptide mediated transcription is inhibited or increased, etc. Cell free assays include protein binding assays, immunoassays, etc. Other assays useful for screening agents which bind any of the polypeptides of the invention include fluorescence resonance energy transfer (FRET), and electrophoretic mobility shift analysis (EMSA).

[0122] According to another aspect of the invention, a method for identifying an agent useful in modulating mesenchymal cell differentiation induction activity of a molecule of the invention, is provided. The method involves (a) contacting a molecule having mesenchymal cell differentiation induction activity with a candidate agent, (b) measuring mesenchymal cell differentiation induction activity of the molecule, and (c) comparing the measured mesenchymal cell differentiation induction activity of the molecule to a control to determine whether the candidate agent modulates mesenchymal cell differentiation induction activity of the molecule, wherein the molecule is any nucleic acid molecule of SEQ ID NO:1-11, and 13-66, or an expression product thereof. “Contacting” refers to both direct and indirect contacting of a molecule having mesenchymal cell differentiation induction activity with the candidate agent. “Indirect” contacting means that the candidate agent exerts its effects on the mesenchymal cell differentiation induction activity of the molecule via a third agent (e.g., a messenger molecule, a receptor, etc.). In certain embodiments, the control is mesenchymal cell differentiation induction activity of the molecule measured in the absence of the candidate agent. Assaying methods and candidate agents are as described above in the foregoing embodiments.

[0123] According to still another aspect of the invention, a method of diagnosing a disorder characterized by aberrant expression of a nucleic acid molecule, an expression product thereof, or a fragment of an expression product thereof, is provided. The method involves contacting a biological sample isolated from a subject with an agent that specifically binds to the nucleic acid molecule, an expression product thereof, or a fragment of an expression product thereof, and determining the interaction between the agent and the nucleic acid molecule or the expression product as a determination of the disorder, wherein the nucleic acid molecule is any nucleic acid molecule of SEQ ID NO:1-11, and 13-66. In some embodiments, the disorder is a cartilaginous tissue degeneration condition is selected from the group consisting of osteoarthritis, rheumatoid arthritis, osteochondrosis. In one embodiment, the disorder is osteoarthritis.

[0124] In the case where the molecule is a nucleic acid molecule, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes as exemplified herein. In the case where the molecule is an expression product of the nucleic acid molecule, or a fragment of an expression product of the nucleic acid molecule, such determination can be carried out via any standard immunological assay using, for example, antibodies which bind to any of the polypeptide expression products.

[0125] “Aberrant expression” refers to decreased expression (underexpression) or increased expression (overexpression) of any of the foregoing molecules (SEQ ID NOs: 1-67), nucleic acids and/or polypeptides) in comparison with a control (i.e., expression of the same molecule in a healthy or “normal” subject). A “healthy subject”, as used herein, refers to a subject who is not at risk for developing a future skeletal degeneration condition. Healthy subjects also do not otherwise exhibit symptoms of disease. In other words, such subjects, if examined by a medical professional, would be characterized as healthy and free of symptoms of a skeletal degeneration condition or at risk of developing skeletal degeneration condition.

[0126] When the disorder is a skeletal degeneration condition selected from the group consisting of selected from the group consisting of osteoarthritis, rheumatoid arthritis, osteochondrosis, decreased expression of any of the foregoing molecules in comparison with a control (e.g., a healthy individual) is indicative of the presence of the disorder, or indicative of the risk for developing such disorder in the future.

[0127] The invention also provides novel kits which could be used to measure the levels of the nucleic acids of the invention, or expression products of the invention.

[0128] In one embodiment, a kit comprises a package containing an agent that selectively binds to any of the foregoing novel, isolated nucleic acids (SEQ ID NOs: 1-11), or expression products thereof, and a control for comparing to a measured value of binding of said agent any of the foregoing novel, isolated nucleic acids or expression products thereof. In some embodiments, the control is a predetermined value for comparing to the measured value. In certain embodiments, the control comprises an epitope of the expression product of any of the foregoing novel, isolated nucleic acids. In one embodiment, the kit further comprises a second agent that selectively binds to any of the foregoing novel molecules (SEQ ID NOs:1-11), and/or an expression products thereof, and a control for comparing to a measured value of binding of said second agent to said isolated nucleic acid molecule or expression product thereof.

[0129] In the case of nucleic acid detection, pairs of primers for amplifying a nucleic acid molecule of the invention can be included. The preferred kits would include controls such as known amounts of nucleic acid probes, epitopes (such as expression products of any of the foregoing novel nucleic acid molecules SEQ ID NOs:1-11, e.g., SEQ ID NO:12) or anti-epitope antibodies, as well as instructions or other printed material. In certain embodiments the printed material can characterize risk of developing a skeletal degeneration condition based upon the outcome of the assay. The reagents may be packaged in containers and/or coated on wells in predetermined amounts, and the kits may include standard materials such as labeled immunological reagents (such as labeled anti-IgG antibodies) and the like. One kit is a packaged polystyrene microtiter plate coated with a polypeptide of the invention and a container containing labeled anti-human IgG antibodies. A well of the plate is contacted with, for example, a biological fluid, washed and then contacted with the anti-IgG antibody. The label is then detected. A kit embodying features of the present invention, generally designated by the numeral 11, is illustrated in FIG. 1. Kit 11 is comprised of the following major elements: packaging 15, an agent of the invention 17, a control agent 19 and instructions 21. Packaging 15 is a box-like structure for holding a vial (or number of vials) containing an agent of the invention 17, a vial (or number of vials) containing a control agent 19, and instructions 21. Individuals skilled in the art can readily modify packaging 15 to suit individual needs.

[0130] The invention also embraces methods for treating a cartilaginous tissue degeneration condition. The method involves administering to a subject in need of such treatment an agent that modulates expression of a molecule selected from the group consisting of any of SEQ ID NOs:1-67 (or expression products thereof in the case of nucleic acids), in an amount effective to treat the cartilaginous tissue degeneration condition.

[0131] “Agents that modulate expression” of a nucleic acid or a polypeptide, as used herein, are known in the art, and refer to sense and antisense nucleic acids, dominant negative nucleic acids, antibodies to the polypeptides, and the like. Any agents that modulate exression of a molecule (and as described herein, modulate its activity), are useful according to the invention.

[0132] As used herein, “downregulating expression” refers to inhibiting (i.e., reducing to a detectable extent) replication, transcription, and/or translation of a nucleic acid molecule of the invention, or an expression product thereof, since inhibition of any of these processes results in a decrease in the concentration/amount of the polypeptide encoded by the gene. The term also refers to inhibition of post-translational modifications on the polypeptide (e.g., in its phosphorylation), since inhibition of such modifications may also prevent proper expression (i.e., expression as in a wild type cell) of the encoded polypeptide. The term also refers to an increase in, or facilitation of, polypeptide degradation (e.g., via increased ubiquitinization). Polypeptide turnover can be determined using methods well known in the art and described elsewhere herein. The inhibition of gene expression can be directly determined by detecting a decrease in the level of mRNA for the gene, or the level of protein expression of the gene, using any suitable means known to the art, such as nucleic acid hybridization or antibody detection methods, respectively. Inhibition of gene expression can also be determined indirectly by detecting a change in mesenchymal cell differentiation induction activity of the molecule as a whole.

[0133] In certain embodiments, the molecule is a nucleic acid. In some embodiments the nucleic acid is operatively coupled to a gene expression sequence which directs the expression of the nucleic acid molecule within a eukaryotic cell such as a mesenchymal cell (e.g., a dermal fibroblast). The “gene expression sequence” is any regulatory nucleotide sequence, such as a promoter sequence or promoter-enhancer combination, which facilitates the efficient transcription and translation of the nucleic acid to which it is operably linked. The gene expression sequence may, for example, be a mammalian or viral promoter, such as a constitutive or inducible promoter. Constitutive mammalian promoters include, but are not limited to, the promoters for the following genes: hypoxanthine phosphoribosyl transferase (HPTR), adenosine deaminase, pyruvate kinase, α-actin promoter and other constitutive promoters. Exemplary viral promoters which function constitutively in eukaryotic cells include, for example, promoters from the simian virus, papilloma virus, adenovirus, human immunodeficiency virus (HIV), Rous sarcoma virus, cytomegalovirus, the long terminal repeats (LTR) of moloney leukemia virus and other retroviruses, and the thymidine kinase promoter of herpes simplex virus. Other constitutive promoters are known to those of ordinary skill in the art. The promoters useful as gene expression sequences of the invention also include inducible promoters. Inducible promoters are activated in the presence of an inducing agent. For example, the metallothionein promoter is activated to increase transcription and translation in the presence of certain metal ions. Other inducible promoters are known to those of ordinary skill in the art.

[0134] In general, the gene expression sequence shall include, as necessary, 5′ non-transcribing and 5′ non-translating sequences involved with the initiation of transcription and translation, respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Especially, such 5′ non-transcribing sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined nucleic acid. The gene expression sequences optionally includes enhancer sequences or upstream activator sequences as desired.

[0135] Preferably, any of the nucleic acid molecules of the invention (e.g., SEQ ID NO:1-11, and 13-66) is linked to a gene expression sequence which permits expression of the nucleic acid molecule in a cell such as a mesenchymal cell (e.g., dermal fibroblast). A sequence which permits expression of the nucleic acid molecule in a cell such as a mesenchymal cell (e.g., a dermal fibroblast), is one which is selectively active in such a cell type, thereby causing expression of the nucleic acid molecule in these cells (e.g., a collagen gene promoter). Those of ordinary skill in the art will be able to easily identify alternative promoters that are capable of expressing a nucleic acid molecule in any of the preferred cells of the invention.

[0136] The nucleic acid sequence and the gene expression sequence are said to be “operably linked” when they are covalently linked in such a way as to place the transcription and/or translation of the nucleic acid coding sequence under the influence or control of the gene expression sequence. If it is desired that the nucleic acid sequence be translated into a functional protein, two DNA sequences are said to be operably linked if induction of a promoter in the 5′ gene expression sequence results in the transcription of the nucleic acid sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the nucleic acid sequence, and/or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a gene expression sequence would be operably linked to a nucleic acid sequence if the gene expression sequence were capable of effecting transcription of that nucleic acid sequence such that the resulting transcript might be translated into the desired protein or polypeptide.

[0137] The molecules of the invention can be delivered to the preferred cell types of the invention alone or in association with a vector. In its broadest sense, a “vector” is any vehicle capable of facilitating: (1) delivery of a molecule to a target cell and/or (2) uptake of the molecule by a target cell. Preferably, the vectors transport the molecule into the target cell with reduced degradation relative to the extent of degradation that would result in the absence of the vector. Optionally, a “targeting ligand” can be attached to the vector to selectively deliver the vector to a cell which expresses on its surface the cognate receptor for the targeting ligand. In this manner, the vector (containing a nucleic acid or a protein) can be selectively delivered to a mesenchymal cell in, e.g., a joint. Methodologies for targeting include conjugates, such as those described in U.S. Pat. No. 5,391,723 to Priest. Another example of a well-known targeting vehicle is a liposome. Liposomes are commercially available from Gibco BRL. Numerous methods are published for making targeted liposomes. Preferably, the molecules of the invention are targeted for delivery to mesenchymal cells.

[0138] In general, the vectors useful in the invention include, but are not limited to, plasmids, phagemids, viruses, other vehicles derived from viral or bacterial sources that have been manipulated by the insertion or incorporation of the nucleic acid sequences of the invention, and additional nucleic acid fragments (e.g., enhancers, promoters) which can be attached to the nucleic acid sequences of the invention. Viral vectors are a preferred type of vector and include, but are not limited to, nucleic acid sequences from the following viruses: adenovirus; adeno-associated virus; retrovirus, such as moloney murine leukemia virus; harvey murine sarcoma virus; murine mammary tumor virus; rouse sarcoma virus; SV40-type viruses; polyoma viruses; Epstein-Barr viruses; papilloma viruses; herpes virus; vaccinia virus; polio virus; and RNA virus such as a retrovirus. One can readily employ other vectors not named but known in the art.

[0139] A particularly preferred virus for certain applications is the adeno-associated virus, a double-stranded DNA virus. The adeno-associated virus is capable of infecting a wide range of cell types and species and can be engineered to be replication-deficient. It further has advantages, such as heat and lipid solvent stability, high transduction frequencies in cells of diverse lineages, including hematopoictic cells, and lack of superinfection inhibition thus allowing multiple series of transductions. Reportedly, the adeno-associated virus can integrate into human cellular DNA in a site-specific manner, thereby minimizing the possibility of insertional mutagenesis and variability of inserted gene expression. In addition, wild-type adeno-associated virus infections have been followed in tissue culture for greater than 100 passages in the absence of selective pressure, implying that the adeno-associated virus genomic integration is a relatively stable event. The adeno-associated virus can also function in an extrachromosomal fashion.

[0140] In general, other preferred viral vectors are based on non-cytopathic eukaryotic viruses in which non-essential genes have been replaced with the gene of interest. Non-cytopathic viruses include retroviruses, the life cycle of which involves reverse transcription of genomic viral RNA into DNA with subsequent proviral integration into host cellular DNA. Adenoviruses and retroviruses have been approved for human gene therapy trials. In general, the retroviruses are replication-deficient (i.e., capable of directing synthesis of the desired proteins, but incapable of manufacturing an infectious particle). Such genetically altered retroviral expression vectors have general utility for the high-efficiency transduction of genes in vivo. Standard protocols for producing replication-deficient retroviruses (including the steps of incorporation of exogenous genetic material into a plasmid, transfection of a packaging cell lined with plasmid, production of recombinant retroviruses by the packaging cell line, collection of viral particles from tissue culture media, and infection of the target cells with viral particles) are provided in Kriegler, M., “Gene Transfer and Expression, A Laboratory Manual,” W. H. Freeman C.O., New York (1990) and Murry, E. J. Ed. “Methods in Molecular Biology,” vol. 7, Humana Press, Inc., Cliffton, N.J. (1991).

[0141] Another preferred retroviral vector is the vector derived from the moloney murine leukemia virus, as described in Nabel, E. G., et al., Science, 1990, 249:1285-1288. These vectors reportedly were effective for the delivery of genes to all three layers of the arterial wall, including the media. Other preferred vectors are disclosed in Flugelman, et al., Circulation, 1992, 85:1110-1117. Additional vectors that are useful for delivering molecules of the invention are described in U.S. Pat. No. 5,674,722 by Mulligan, et. al.

[0142] In addition to the foregoing vectors, other delivery methods may be used to deliver a molecule of the invention to a cell such as a mesenchymal cell, and facilitate uptake thereby.

[0143] A preferred such delivery method of the invention is a colloidal dispersion system. Colloidal dispersion systems include lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system of the invention is a liposome. Liposomes are artificial membrane vessels which are useful as a delivery vector in vivo or in vitro. It has been shown that large unilamellar vessels (LUV), which range in size from 0.2-4.0 μm can encapsulate large macromolecules. RNA, DNA, and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, et al., Trends Biochem. Sci., 1981, 6:77). In order for a liposome to be an efficient gene transfer vector, one or more of the following characteristics should be present: (1) encapsulation of the gene of interest at high efficiency with retention of biological activity; (2) preferential and substantial binding to a target cell in comparison to non-target cells; (3) delivery of the aqueous contents of the vesicle to the target cell cytoplasm at high efficiency; and (4) accurate and effective expression of genetic information.

[0144] Liposomes may be targeted to a particular tissue, such as the myocardium or the vascular cell wall, by coupling the liposome to a specific ligand such as a monoclonal antibody, sugar, glycolipid, or protein. Ligands which may be useful for targeting a liposome to the vascular wall include, but are not limited to the viral coat protein of the Hemagglutinating virus of Japan. Additionally, the vector may be coupled to a nuclear targeting peptide, which will direct the nucleic acid to the nucleus of the host cell.

[0145] Liposomes are commercially available from Gibco BRL, for example, as LIPOFECTIN™ and LIPOFECTACE™, which are formed of cationic lipids such as N-[1-(2,3 dioleyloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA) and dimethyl dioctadecylammonium bromide (DDAB). Methods for making liposomes are well known in the art and have been described in many publications. Liposomes also have been reviewed by Gregoriadis, G. in Trends in Biotechnology, V. 3, p. 235-241 (1985). Novel liposomes for the intracellular delivery of macromolecules, including nucleic acids, are also described in PCT International application no. PCT/US96/07572 (Publication No. WO 96/40060, entitled “Intracellular Delivery of Macromolecules”).

[0146] In one particular embodiment, the preferred vehicle is a biocompatible micro particle or implant that is suitable for implantation into the mammalian recipient. Exemplary bioerodible implants that are useful in accordance with this method are described in PCT International application no. PCT/US/03307 (Publication No. WO 95/24929, entitled “Polymeric Gene Delivery System”, claiming priority to U.S. patent application Ser. No. 213,668, filed Mar. 15, 1994). PCT/US/0307 describes a biocompatible, preferably biodegradable polymeric matrix for containing an exogenous gene under the control of an appropriate promoter. The polymeric matrix is used to achieve sustained release of the exogenous gene in the patient. In accordance with the instant invention, the nucleic acids described herein are encapsulated or dispersed within the biocompatible, preferably biodegradable polymeric matrix disclosed in PCT/US/03307. The polymeric matrix preferably is in the form of a micro particle such as a micro sphere (wherein a nucleic acid is dispersed throughout a solid polymeric matrix) or a microcapsule (wherein a nucleic acid is stored in the core of a polymeric shell). Other forms of the polymeric matrix for containing the nucleic acids of the invention include films, coatings, gels, implants, and stents. The size and composition of the polymeric matrix device is selected to result in favorable release kinetics in the tissue into which the matrix device is implanted. The size of the polymeric matrix devise further is selected according to the method of delivery which is to be used, typically injection into a tissue or administration of a suspension by aerosol into the nasal and/or pulmonary areas. The polymeric matrix composition can be selected to have both favorable degradation rates and also to be formed of a material which is bioadhesive, to further increase the effectiveness of transfer when the devise is administered to a vascular surface. The matrix composition also can be selected not to degrade, but rather, to release by diffusion over an extended period of time.

[0147] Both non-biodegradable and biodegradable polymeric matrices can be used to deliver the nucleic acids of the invention to the subject. Biodegradable matrices are preferred. Such polymers may be natural or synthetic polymers. Synthetic polymers are preferred. The polymer is selected based on the period of time over which release is desired, generally in the order of a few hours to a year or longer. Typically, release over a period ranging from between a few hours and three to twelve months is most desirable. The polymer optionally is in the form of a hydrogel that can absorb up to about 90% of its weight in water and further, optionally is cross-linked with multi-valent ions or other polymers.

[0148] In general, the nucleic acids of the invention are delivered using the bioerodible implant by way of diffusion, or more preferably, by degradation of the polymeric matrix. Exemplary synthetic polymers which can be used to form the biodegradable delivery system include: polyamides, polycarbonates, polyalkylenes, polyalkylene glycols, polyalkylene oxides, polyalkylene terepthalates, polyvinyl alcohols, polyvinyl ethers, polyvinyl esters, poly-vinyl halides, polyvinylpyrrolidone, polyglycolides, polysiloxanes, polyurethanes and co-polymers thereof, alkyl cellulose, hydroxyalkyl celluloses, cellulose ethers, cellulose esters, nitro celluloses, polymers of acrylic and methacrylic esters, methyl cellulose, ethyl cellulose, hydroxypropyl cellulose, hydroxy-propyl methyl cellulose, hydroxybutyl methyl cellulose, cellulose acetate, cellulose propionate, cellulose acetate butyrate, cellulose acetate phthalate, carboxylethyl cellulose, cellulose triacetate, cellulose sulphate sodium salt, poly(methyl methacrylate), poly(ethyl methacrylate), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), poly(octadecyl acrylate), polyethylene, polypropylene, poly(ethylene glycol), poly(ethylene oxide), poly(ethylene terephthalate), poly(vinyl alcohols), polyvinyl acetate, poly vinyl chloride, polystyrene and polyvinylpyrrolidone.

[0149] Examples of non-biodegradable polymers include ethylene vinyl acetate, poly(meth) acrylic acid, polyamides, copolymers and mixtures thereof.

[0150] Examples of biodegradable polymers include synthetic polymers such as polymers of lactic acid and glycolic acid, polyanhydrides, poly(ortho)esters, polyurethanes, poly(butic acid), poly(valeric acid), and poly(lactide-cocaprolactone), and natural polymers such as alginate and other polysaccharides including dextran and cellulose, collagen, chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), albumin and other hydrophilic proteins, zein and other prolamines and hydrophobic proteins, copolymers and mixtures thereof. In general, these materials degrade either by enzymatic hydrolysis or exposure to water in vivo, by surface or bulk erosion.

[0151] Bioadhesive polymers of particular interest include bioerodible hydrogels described by H. S. Sawhney, C. P. Pathak and J. A. Hubell in Macromolecules, 1993, 26, 581-587, the teachings of which are incorporated herein, polyhyaluronic acids, casein, gelatin, glutin, polyanhydrides, polyacrylic acid, alginate, chitosan, poly(methyl methacrylates), poly(ethyl methacrylates), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), and poly(octadecyl acrylate). Thus, the invention provides a composition of the above-described molecules of the invention for use as a medicament, methods for preparing the medicament and methods for the sustained release of the medicament in vivo.

[0152] Compaction agents also can be used in combination with a vector of the invention. A “compaction agent”, as used herein, refers to an agent, such as a histone, that neutralizes the negative charges on the nucleic acid and thereby permits compaction of the nucleic acid into a fine granule. Compaction of the nucleic acid facilitates the uptake of the nucleic acid by the target cell. The compaction agents can be used alone, i.e., to deliver an isolated nucleic acid of the invention in a form that is more efficiently taken up by the cell or, more preferably, in combination with one or more of the above-described vectors.

[0153] Other exemplary compositions that can be used to facilitate uptake by a target cell of the nucleic acids of the invention include calcium phosphate and other chemical mediators of intracellular transport, microinjection compositions, electroporation and homologous recombination compositions (e.g., for integrating a nucleic acid into a preselected location within the target cell chromosome).

[0154] According to another aspect of the invention, a device is provided. The device comprises a material surface coated with an amount of an agent of the invention (i.e. an agent having mesenchymal cell differentiation induction activity). The amount of the agent is effective to induce mesenchymal cell differentiation in the cells of mesenchymal origin present in the tissue to which the implantable device is to be implanted. In certain embodiments, the material surface is part of an implant. The material comprising the implant may be synthetic material or organic tissue material. Important agents, cell-types, and so on, are as described elsewhere herein.

[0155] “Material surfaces” as used herein, include, but are not limited to, dental and orthopedic prosthetic implants, and organic implantable tissue such as allogeneic and/or xenogeneic tissue, organ and/or vasculature.

[0156] Implantable prosthetic devices have been used in the surgical repair or replacement of internal tissue for many years. Orthopedic implants include a wide variety of devices, each suited to fulfill particular medical needs. Examples of such devices are hip joint replacement devices, knee joint replacement devices, shoulder joint replacement devices, and pins, braces and plates used to set fractured bones. Some contemporary orthopedic and dental implants, use high performance metals such as cobalt-chrome and titanium alloy to achieve high strength. These materials are readily fabricated into the complex shapes typical of these devices using mature metal working techniques including casting and machining.

[0157] In important embodiments, in addition to an agent of the invention, the material surface may also be coated with an osteogenic protein, a cell-growth potentiating agent, an anti-infective agent, and/or an antiinflammatory agent.

[0158] Osteogenic proteins are described elsewhere herein.

[0159] A cell-growth potentiating agent as used herein is an agent which stimulates growth of a cell and includes growth factors such as PDGF, EGF, FGF, TGF, NGF, CNTF, and GDNF.

[0160] An anti-infectious agent as used herein is an agent which reduces the activity of or kills a microorganism and includes: Aztreonam; Chlorhexidine Gluconate; Imidurea; Lycetamine; Nibroxane; Pirazmonam Sodium; Propionic Acid; Pyrithione Sodium; Sanguinarium Chloride; Tigemonam Dicholine; Acedapsone; Acetosulfone Sodium; Alamecin; Alexidine; Amdinocillin; Amdinocillin Pivoxil; Amicycline; Amifloxacin; Amifloxacin Mesylate; Amikacin; Amikacin Sulfate; Aminosalicylic acid; Aminosalicylate sodium; Amoxicillin; Amphomycin; Ampicillin; Ampicillin Sodium; Apalcillin Sodium; Apramycin; Aspartocin; Astromicin Sulfate; Avilamycin; Avoparcin; Azithromycin; Azlocillin; Azlocillin Sodium; Bacampicillin Hydrochloride; Bacitracin; Bacitracin Methylene Disalicylate; Bacitracin Zinc; Bambermycins; Benzoylpas Calcium; Berythromycin; Betamicin Sulfate; Biapenem; Biniramycin; Biphenamine Hydrochloride; Bispyrithione Magsulfex; Butikacin; Butirosin Sulfate; Capreomycin Sulfate; Carbadox; Carbenicillin Disodium; Carbenicillin Indanyl Sodium; Carbenicillin Phenyl Sodium; Carbenicillin Potassium; Carumonam Sodium; Cefaclor; Cefadroxil; Cefamandole; Cefamandole Nafate; Cefamandole Sodium; Cefaparole; Cefatrizine; Cefazaflur Sodium; Cefazolin; Cefazolin Sodium; Cefbuperazone; Cefdinir; Cefepime; Cefepime Hydrochloride; Cefetecol; Cefixime; Cefmenoxime Hydrochloride; Cefmetazole; Cefmetazole Sodium; Cefonicid Monosodium; Cefonicid Sodium; Cefoperazone Sodium; Ceforanide; Cefotaxime Sodium; Cefotetan; Cefotetan Disodium; Cefotiam Hydrochloride; Cefoxitin; Cefoxitin Sodium; Cefpimizole; Cefpimizole Sodium; Cefpiramide; Cefpiramide Sodium; Cefpirome Sulfate; Cefpodoxime Proxetil; Cefprozil; Cefroxadine; Cefsulodin Sodium; Ceftazidime; Ceftibuten; Ceftizoxime Sodium; Ceftriaxone Sodium; Cefuroxime; Cefuroxime Axetil; Cefuroxime Pivoxetil; Cefuroxime Sodium; Cephacetrile Sodium; Cephalexin; Cephalexin Hydrochloride; Cephaloglycin; Cephaloridine; Cephalothin Sodium; Cephapirin Sodium; Cephradine; Cetocycline Hydrochloride; Cetophenicol; Chloramphenicol; Chloramphenicol Palmitate; Chloramphenicol Pantothenate Complex; Chloramphenicol Sodium Succinate; Chlorhexidine Phosphanilate; Chloroxylenol; Chlortetracycline Bisulfate; Chlortetracycline Hydrochloride; Cinoxacin; Ciprofloxacin; Ciprofloxacin Hydrochloride; Cirolemycin; Clarithromycin; Clinafloxacin Hydrochloride; Clindamycin; Clindamycin Hydrochloride; Clindamycin Palmitate Hydrochloride; Clindamycin Phosphate; Clofazimine; Cloxacillin Benzathine; Cloxacillin Sodium; Cloxyquin; Colistimethate Sodium; Colistin Sulfate; Coumermycin; Coumermycin Sodium; Cyclacillin; Cycloserine; Dalfopristin; Dapsone; Daptomycin; Demeclocycline; Demeclocycline Hydrochloride; Demecycline; Denofungin; Diaveridine; Dicloxacillin; Dicloxacillin Sodium; Dihydrostreptomycin Sulfate; Dipyrithione; Dirithromycin; Doxycycline; Doxycycline Calcium; Doxycycline Fosfatex; Doxycycline Hyclate; Droxacin Sodium; Enoxacin; Epicillin; Epitetracycline Hydrochloride; Erythromycin; Erythromycin Acistrate; Erythromycin Estolate; Erythromycin Ethylsuccinate; Erythromycin Gluceptate; Erythromycin Lactobionate; Erythromycin Propionate; Erythromycin Stearate; Ethambutol Hydrochloride; Ethionamide; Fleroxacin; Floxacillin; Fludalanine; Flumequine; Fosfomycin; Fosfomycin Tromethamine; Fumoxicillin; Furazolium Chloride; Furazolium Tartrate; Fusidate Sodium; Fusidic Acid; Gentamicin Sulfate; Gloximonam; Gramicidin; Haloprogin; Hetacillin; Hetacillin Potassium; Hexedine; Ibafloxacin; Imipenem; Isoconazole; Isepamicin; Isoniazid; Josamycin; Kanamycin Sulfate; Kitasamycin; Levofuraltadone; Levopropylcillin Potassium; Lexithromycin; Lincomycin; Lincomycin Hydrochloride; Lomefloxacin; Lomefloxacin Hydrochloride; Lomefloxacin Mesylate; Loracarbef; Mafenide; Meclocycline; Meclocycline Sulfosalicylate; Megalomicin Potassium Phosphate; Mequidox; Meropenem; Methacycline; Methacycline Hydrochloride; Methenamine; Methenamine Hippurate; Methenamine Mandelate; Methicillin Sodium; Metioprim; Metronidazole Hydrochloride; Metronidazole Phosphate; Mezlocillin; Mezlocillin Sodium; Minocycline; Minocycline Hydrochloride; Mirincamycin Hydrochloride; Monensin; Monensin Sodium; Nafcillin Sodium; Nalidixate Sodium; Nalidixic Acid; Natamycin; Nebramycin; Neomycin Palmitate; Neomycin Sulfate; Neomycin Undecylenate; Netilmicin Sulfate; Neutramycin; Nifuradene; Nifuraldezone; Nifuratel; Nifuratrone; Nifurdazil; Nifurimide; Nifurpirinol; Nifurquinazol; Nifurthiazole; Nitrocycline; Nitrofurantoin; Nitromide; Norfloxacin; Novobiocin Sodium; Ofloxacin; Ormetoprim; Oxacillin Sodium; Oximonam; Oximonam Sodium; Oxolinic Acid; Oxytetracycline; Oxytetracycline Calcium; Oxytetracycline Hydrochloride; Paldimycin; Parachlorophenol; Paulomycin; Pefloxacin; Pefloxacin Mesylate; Penamecillin; Penicillin G Benzathine; Penicillin G Potassium; Penicillin G Procaine; Penicillin G Sodium; Penicillin V; Penicillin V Benzathine; Penicillin V Hydrabamine; Penicillin V Potassium; Pentizidone Sodium; Phenyl Aminosalicylate; Piperacillin Sodium; Pirbenicillin Sodium; Piridicillin Sodium; Pirlimycin Hydrochloride; Pivampicillin Hydrochloride; Pivampicillin Pamoate; Pivampicillin Probenate; Polymyxin B Sulfate; Porfiromycin; Propikacin; Pyrazinamide; Pyrithione Zinc; Quindecamine Acetate; Quinupristin; Racephenicol; Ramoplanin; Ranimycin; Relomycin; Repromicin; Rifabutin; Rifametane; Rifamexil; Rifamide; Rifampin; Rifapentine; Rifaximin; Rolitetracycline; Rolitetracycline Nitrate; Rosaramicin; Rosaramicin Butyrate; Rosaramicin Propionate; Rosaramicin Sodium Phosphate; Rosaramicin Stearate; Rosoxacin; Roxarsone; Roxithromycin; Sancycline; Sanfetrinem Sodium; Sarmoxicillin; Sarpicillin; Scopafungin; Sisomicin; Sisomicin Sulfate; Sparfloxacin; Spectinomycin Hydrochloride; Spiramycin; Stallimycin Hydrochloride; Steffimycin; Streptomycin Sulfate; Streptonicozid; Sulfabenz; Sulfabenzamide; Sulfacetamide; Sulfacetamide Sodium; Sulfacytine; Sulfadiazine; Sulfadiazine Sodium; Sulfadoxine; Sulfalene; Sulfamerazine; Sulfameter; Sulfamethazine; Sulfamethizole; Sulfamethoxazole; Sulfamonomethoxine; Sulfamoxole; Sulfanilate Zinc; Sulfanitran; Sulfasalazine; Sulfasomizole; Sulfathiazole; Sulfazamet; Sulfisoxazole; Sulfisoxazole Acetyl; Sulfisoxazole Diolamine; Sulfomyxin; Sulopenem; Sultamicillin; Suncillin Sodium; Talampicillin Hydrochloride; Teicoplanin; Temafloxacin Hydrochloride; Temocillin; Tetracycline; Tetracycline Hydrochloride; Tetracycline Phosphate Complex; Tetroxoprim; Thiamphenicol; Thiphencillin Potassium; Ticarcillin Cresyl Sodium; Ticarcillin Disodium; Ticarcillin Monosodium; Ticlatone; Tiodonium Chloride; Tobramycin; Tobramycin Sulfate; Tosufloxacin; Trimethoprim; Trimethoprim Sulfate; Trisulfapyrimidines; Troleandomycin; Trospectomycin Sulfate; Tyrothricin; Vancomycin; Vancomycin Hydrochloride; Virginiamycin; Zorbamycin; Difloxacin Hydrochloride; Lauryl Isoquinolinium Bromide; Moxalactam Disodium; Ornidazole; Pentisomicin; and Sarafloxacin Hydrochloride.

[0161] Anti-inflammatory agents are well known in the art and include: Alclofenac; Alclometasone Dipropionate; Algestone Acetonide; Alpha Amylase; Amcinafal; Amcinafide; Amfenac Sodium; Amiprilose Hydrochloride; Anakinra; Anirolac; Anitrazafen; Apazone; Balsalazide Disodium; Bendazac; Benoxaprofen; Benzydamine Hydrochloride; Bromelains; Broperamole; Budesonide; Carprofen; Cicloprofen; Cintazone; Cliprofen; Clobetasol Propionate; Clobetasone Butyrate; Clopirac; Cloticasone Propionate; Cormethasone Acetate; Cortodoxone; Deflazacort; Desonide; Desoximetasone; Dexamethasone Dipropionate; Diclofenac Potassium; Diclofenac Sodium; Diflorasone Diacetate; Diflumidone Sodium; Diflunisal; Difluprednate; Diftalone; Dimethyl Sulfoxide; Drocinonide; Endrysone; Enlimomab; Enolicam Sodium; Epirizole; Etodolac; Etofenamate; Felbinac; Fenamole; Fenbufen; Fenclofenac; Fenclorac; Fendosal; Fenpipalone; Fentiazac; Flazalone; Fluazacort; Flufenamic Acid; Flumizole; Flunisolide Acetate; Flunixin; Flunixin Meglumine; Fluocortin Butyl; Fluorometholone Acetate; Fluquazone; Flurbiprofen; Fluretofen; Fluticasone Propionate; Furaprofen; Furobufen; Halcinonide; Halobetasol Propionate; Halopredone Acetate; Ibufenac; Ibuprofen; Ibuprofen Aluminum; Ibuprofen Piconol; Ilonidap; Indomethacin; Indomethacin Sodium; Indoprofen; Indoxole; Intrazole; Isoflupredone Acetate; Isoxepac; Isoxicam; Ketoprofen; Lofemizole Hydrochloride; Lornoxicam; Loteprednol Etabonate; Meclofenamate Sodium; Meclofenamic Acid; Meclorisone Dibutyrate; Mefenamic Acid; Mesalamine; Meseclazone; Methylprednisolone Suleptanate; Morniflumate; Nabumetone; Naproxen; Naproxen Sodium; Naproxol; Nimazone; Olsalazine Sodium; Orgotein; Orpanoxin; Oxaprozin; Oxyphenbutazone; Paranyline Hydrochloride; Pentosan Polysulfate Sodium; Phenbutazone Sodium Glycerate; Pirfenidone; Piroxicam; Piroxicam Cinnamate; Piroxicam Olamine; Pirprofen; Prednazate; Prifelone; Prodolic Acid; Proquazone; Proxazole; Proxazole Citrate; Rimexolone; Romazarit; Salcolex; Salnacedin; Salsalate; Sanguinarium Chloride; Seclazone; Sermetacin; Sudoxicam; Sulindac; Suprofen; Talmetacin; Talniflumate; Talosalate; Tebufelone; Tenidap; Tenidap Sodium; Tenoxicam; Tesicam; Tesimide; Tetrydamine; Tiopinac; Tixocortol Pivalate; Tolmetin; Tolmetin Sodium; Triclonide; Triflumidate; Zidometacin; Zomepirac Sodium.

[0162] The invention also provides methods for the diagnosis and therapy of congenital and/or acquired conditions that affect the skeleton. Such disorders include cartilaginous tissue degeneration conditions (e.g., all forms of arthritis including, but not limited to, osteoarthritis, rheumatoid arthritis, gout arthritis, adjuvant arthritis, arthritis deformans, infectious arthritis, and osteochondrosis).

[0163] The methods of the invention are useful in both the acute and the prophylactic treatment of any of the foregoing conditions. As used herein, an acute treatment refers to the treatment of subjects having a particular condition. Prophylactic treatment refers to the treatment of subjects at risk of having the condition, but not presently having or experiencing the symptoms of the condition.

[0164] In its broadest sense, the terms “treatment” or “to treat” refer to both acute and prophylactic treatments. If the subject in need of treatment is experiencing a condition (or has or is having a particular condition), then treating the condition refers to ameliorating, reducing or eliminating the condition or one or more symptoms arising from the condition. In some preferred embodiments, treating the condition refers to ameliorating, reducing or eliminating a specific symptom or a specific subset of symptoms associated with the condition. If the subject in need of treatment is one who is at risk of having a condition, then treating the subject refers to reducing the risk of the subject having the condition.

[0165] The mode of administration and dosage of a therapeutic agent of the invention will vary with the particular stage of the condition being treated, the age and physical condition of the subject being treated, the duration of the treatment, the nature of the concurrent therapy (if any), the specific route of administration, and the like factors within the knowledge and expertise of the health practitioner.

[0166] As described herein, the agents of the invention are administered in effective amounts to treat any of the foregoing skeletal degeneration conditions. In general, an effective amount is any amount that can cause a beneficial change in a desired tissue of a subject. Preferably, an effective amount is that amount sufficient to cause a favorable phenotypic change in a particular condition such as a lessening, alleviation or elimination of a symptom or of a condition as a whole.

[0167] In general, an effective amount is that amount of a pharmaceutical preparation that alone, or together with further doses, produces the desired response. This may involve only slowing the progression of the condition temporarily, although more preferably, it involves halting the progression of the condition permanently or delaying the onset of or preventing the condition from occurring. This can be monitored by routine methods. Generally, doses of active compounds would be from about 0.01 mg/kg per day to 1000 mg/kg per day. It is expected that doses ranging from 50-500 mg/kg will be suitable, preferably orally and in one or several administrations per day.

[0168] Such amounts will depend, of course, on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. Lower doses will result from certain forms of administration, such as intravenous administration. In the event that a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits. Multiple doses per day are contemplated to achieve appropriate systemic levels of compounds. It is preferred generally that a maximum dose be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.

[0169] The agents of the invention may be combined, optionally, with a pharmaceutically-acceptable carrier to form a pharmaceutical preparation. The term “pharmaceutically-acceptable carrier” as used herein means one or more compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human. The term “carrier” denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The components of the pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy. In some aspects, the pharmaceutical preparations comprise an agent of the invention in an amount effective to treat a disorder.

[0170] The pharmaceutical preparations may contain suitable buffering agents, including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; or phosphoric acid in a salt. The pharmaceutical compositions also may contain, optionally, suitable preservatives, such as: benzalkonium chloride; chlorobutanol; parabens or thimerosal.

[0171] A variety of administration routes are available. The particular mode selected will depend, of course, upon the particular drug selected, the severity of the condition being treated and the dosage required for therapeutic efficacy. The methods of the invention, generally speaking, may be practiced using any mode of administration that is medically acceptable, meaning any mode that produces effective levels of the active compounds without causing clinically unacceptable adverse effects. Such modes of administration include oral, rectal, topical, nasal, intradermal, transdermal, or parenteral routes. The term “parenteral” includes subcutaneous, intravenous, intramuscular, or infusion. Intravenous or intramuscular routes are not particularly suitable for long-term therapy and prophylaxis. As an example, pharmaceutical compositions may be formulated in a variety of different ways and for a variety of administration modes including tablets, capsules, powders, suppositories, injections and nasal sprays. A preferred mode of administration is a local, site-specific administration to the tissue location in need of repair.

[0172] The pharmaceutical preparations may conveniently be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy. All methods include the step of bringing the active agent into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.

[0173] Compositions suitable for oral administration may be presented as discrete units, such as capsules, tablets, lozenges, each containing a predetermined amount of the active compound. Other compositions include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion.

[0174] Compositions suitable for parenteral administration conveniently comprise a sterile aqueous preparation of an agent of the invention, which is preferably isotonic with the blood of the recipient. This aqueous preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil may be employed including synthetic mono-or di-glycerides. In addition, fatty acids such as oleic acid may be used in the preparation of injectables. Formulations suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa.

[0175] The term “permit entry” of a molecule into a cell according to the invention has the following meanings depending upon the nature of the molecule. For an isolated nucleic acid it is meant to describe entry of the nucleic acid through the cell membrane and into the cell nucleus, where upon the “nucleic acid transgene” can utilize the cell machinery to produce functional polypeptides encoded by the nucleic acid. By “nucleic acid transgene” it is meant to describe all of the nucleic acids of the invention with or without the associated vectors. For a polypeptide, it is meant to describe entry of the polypeptide through the cell membrane and into the cell cytoplasm, and if necessary, utilization of the cell cytoplasmic machinery to functionally modify the polypeptide (e.g., to an active form).

[0176] Various techniques may be employed for introducing nucleic acids of the invention into cells, depending on whether the nucleic acids are introduced in vitro or in vivo in a host. Such techniques include transfection of nucleic acid-CaPO4 precipitates, transfection of nucleic acids associated with DEAE, transfection with a retrovirus including the nucleic acid of interest, liposome mediated transfection, and the like. For certain uses, it is preferred to target the nucleic acid to particular cells. In such instances, a vehicle used for delivering a nucleic acid of the invention into a cell (e.g., a retrovirus, or other virus; a liposome) can have a targeting molecule attached thereto. For example, a molecule such as an antibody specific for a surface membrane protein on the target cell or a ligand for a receptor on the target cell can be bound to or incorporated within the nucleic acid delivery vehicle. For example, where liposomes are employed to deliver the nucleic acids of the invention, proteins which bind to a surface membrane protein associated with endocytosis may be incorporated into the liposome formulation for targeting and/or to facilitate uptake. Such proteins include capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half life, and the like. Polymeric delivery systems also have been used successfully to deliver nucleic acids into cells, as is known by those skilled in the art. Such systems even permit oral delivery of nucleic acids.

[0177] Other delivery systems can include time-release, delayed release or sustained release delivery systems. Such systems can avoid repeated administrations of an agent of the present invention, increasing convenience to the subject and the physician. Many types of release delivery systems are available and known to those of ordinary skill in the art. They include polymer base systems such as poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters, polyhydroxybutyric acid, and polyanhydrides. Microcapsules of the foregoing polymers containing drugs are described in, for example, U.S. Pat. No. 5,075,109. Delivery systems also include non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides; hydrogel release systems; sylastic systems; peptide based systems; wax coatings; compressed tablets using conventional binders and excipients; partially fused implants; and the like. Specific examples include, but are not limited to: (a) erosional systems in which an agent of the invention is contained in a form within a matrix such as those described in U.S. Pat. Nos. 4,452,775, 4,675,189, and 5,736,152, and (b) diffusional systems in which an active component permeates at a controlled rate from a polymer such as described in U.S. Pat. Nos. 3,854,480, 5,133,974 and 5,407,686. In addition, pump-based hardware delivery systems can be used, some of which are adapted for implantation.

[0178] Use of a long-term sustained release implant may be desirable. Long-term release, as used herein, means that the implant is constructed and arranged to deliver therapeutic levels of the active ingredient for at least 30 days, and preferably 60 days. Long-term sustained release implants are well-known to those of ordinary skill in the art and include some of the release systems described above. Specific examples include, but are not limited to, long-term sustained release implants described in U.S. Pat. No. 4,748,024, and Canadian Patent No. 1330939.

[0179] The invention also involves the administration, and in some embodiments co-administration, of agents other than the molecules of the invention (e.g., osteogenic proteins such as Bone Morphogenetic Protein [BMP] nucleic acids and polypeptides, and/or fragments thereof) that when administered in effective amounts can act cooperatively, additively or synergistically with a molecule of the invention to: (i) modulate mesenchymal cell differentiation induction activity, and (ii) treat any of the conditions in which mesenchymal cell differentiation induction activity of a molecule of the invention is involved. Agents other than the molecules of the invention include osteogenic factors.

[0180] True osteogenic factors capable of inducing the above-described cascade of events that result in cartilage/bone formation are well known in the art. Certain of these proteins, occur in nature as disulfide-bonded dimeric proteins, and are referred to in the art as “osteogenic” proteins, “osteoinductive” proteins, and “bone morphogenetic” proteins. Whether naturally-occurring or synthetically prepared, these osteogenic proteins, when implanted in a mammal typically in association with a substrate that allows the attachment, proliferation and differentiation of migratory cells, are capable of inducing recruitment of accessible cells (such as chondroblasts) and stimulating their proliferation, inducing differentiation into chondrocytes and osteoblasts, and further inducing differentiation of intermediate cartilage, vascularization, bone formation, remodeling, and finally marrow differentiation. Those proteins are referred to as members of the Vgr-1/OP1 protein subfamily of the TGF-β super gene family of structurally related proteins. Members include the proteins described in the art as OP1 (BMP-7), OP2 (BMP-8), BMP2, BMP3, BMP4, BMP5, BMP6, 60A, DPP, Vgr-1 and Vg1. See., e.g., U.S. Pat. No. 5,011,691; U.S. Pat. No. 5,266,683, Ozkaynak et al. (1990) EMBO J. 9: 2085-2093, Wharton et al. (1991) PNAS 88: 9214-9218), (Ozkaynak (1992) J. Biol. Chem. 267: 25220-25227 and U.S. Pat. No. 5,266,683); (Celeste et al. (1991) PNAS 87: 9843-9847); (Lyons et al. (1989) PNAS 86: 4554-4558). These disclosures describe the amino acid and DNA sequences, as well as the chemical and physical characteristics of these proteins. See also (Wozney et al. (1988) Science 242: 1528-1534); BMP 9 (WO93/00432, published Jan. 7, 1993); DPP (Padgett et al. (1987) Nature 325: 81-84; and Vg-1 (Weeks (1987) Cell 51: 861-867).

[0181] “Co-administcring,” as used herein, refers to administering simultaneously two or more compounds of the invention (e.g., a nucleic acid and/or polypeptide with mesenchymal cell differentiation induction activity, and an agent known to be beneficial in the treatment of a skeletal degeneration condition—e.g., an osteogenic protein—), as an admixture in a single composition, or sequentially, close enough in time so that the compounds may exert an additive or even synergistic effect, i.e., on regenerating cartilage/bone.

[0182] The invention also embraces solid-phase nucleic acid molecule arrays. The array consists essentially of a set of nucleic acid molecules, expression products thereof, or fragments (of either the nucleic acid or the polypeptide molecule) thereof, each nucleic acid molecule selected from the group consisting of SEQ ID NO:1-11, and 13-66, fixed to a solid substrate. In some embodiments, the solid-phase array further comprises at least one control nucleic acid molecule. In certain embodiments, the set of nucleic acid molecules comprises at least one, at least two, at least three, at least four, or even at least five nucleic acid molecules, each selected from the group consisting of SEQ ID NO:1-11, and 13-66. In preferred embodiments, the set of nucleic acid molecules comprises a maximum number of 100 different nucleic acid molecules. In important embodiments, the set of nucleic acid molecules comprises a maximum number of 10 different nucleic acid molecules. In further important embodiments, the set of nucleic acid molecules comprises at least one, at least two, at least three, at least four, or even at least five nucleic acid molecules, each selected from the group consisting of SEQ ID NOs:1-11.

[0183] According to the invention, standard hybridization techniques of microarray technology are utilized to assess patterns of nucleic acid expression and identify nucleic acid expression. Microarray technology, which is also known by other names including: DNA chip technology, gene chip technology, and solid-phase nucleic acid array technology, is well known to those of ordinary skill in the art and is based on, but not limited to, obtaining an array of identified nucleic acid probes (e.g., molecules described elsewhere herein—SEQ ID NO:1-11, and 13-66) on a fixed substrate, labeling target molecules with reporter molecules (e.g., radioactive, chemiluminescent, or fluorescent tags such as fluorescein, Cye3-dUTP, or Cye5-dUTP), hybridizing target nucleic acids to the probes, and evaluating target-probe hybridization. A probe with a nucleic acid sequence that perfectly matches the target sequence will, in general, result in detection of a stronger reporter-molecule signal than will probes with less perfect matches. Many components and techniques utilized in nucleic acid microarray technology are presented in The Chipping Forecast, Nature Genetics, Vol.21, January 1999, the entire contents of which is incorporated by reference herein.

[0184] According to the present invention, microarray substrates may include but are not limited to glass, silica, aluminosilicates, borosilicates, metal oxides such as alumina and nickel oxide, various clays, nitrocellulose, or nylon. In all embodiments a glass substrate is preferred. According to the invention, probes are selected from the group of nucleic acids including, but not limited to: DNA, genomic DNA, cDNA, and oligonucleotides; and may be natural or synthetic. Oligonucleotide probes preferably are 20 to 25-mer oligonucleotides and DNA/cDNA probes preferably are 500 to 5000 bases in length, although other lengths may be used. Appropriate probe length may be determined by one of ordinary skill in the art by following art-known procedures. In one embodiment, preferred probes are sets of two or more of the nucleic acid molecules set forth as SEQ ID NO:1-11, and 13-66. Probes may be purified to remove contaminants using standard methods known to those of ordinary skill in the art such as gel filtration or precipitation.

[0185] In one embodiment, the microarray substrate may be coated with a compound to enhance synthesis of the probe on the substrate. Such compounds include, but are not limited to, oligoethylene glycols. In another embodiment, coupling agents or groups on the substrate can be used to covalently link the first nucleotide or oligonucleotide to the substrate. These agents or groups may include, but are not limited to: amino, hydroxy, bromo, and carboxy groups. These reactive groups are preferably attached to the substrate through a hydrocarbyl radical such as an alkylene or phenylene divalent radical, one valence position occupied by the chain bonding and the remaining attached to the reactive groups. These hydrocarbyl groups may contain up to about ten carbon atoms, preferably up to about six carbon atoms. Alkylene radicals are usually preferred containing two to four carbon atoms in the principal chain. These and additional details of the process are disclosed, for example, in U.S. Pat. No. 4,458,066, which is incorporated by reference in its entirety.

[0186] In one embodiment, probes are synthesized directly on the substrate in a predetermined grid pattern using methods such as light-directed chemical synthesis, photochemical deprotection, or delivery of nucleotide precursors to the substrate and subsequent probe production.

[0187] In another embodiment, the substrate may be coated with a compound to enhance binding of the probe to the substrate. Such compounds include, but are not limited to: polylysine, amino silanes, amino-reactive silanes (Chipping Forecast, 1999) or chromium (Gwynne and Page, 2000). In this embodiment, presynthesized probes are applied to the substrate in a precise, predetermined volume and grid pattern, utilizing a computer-controlled robot to apply probe to the substrate in a contact-printing manner or in a non-contact manner such as ink jet or piezo-electric delivery. Probes may be covalently linked to the substrate with methods that include, but are not limited to, UV-irradiation. In another embodiment probes are linked to the substrate with heat.

[0188] Targets are nucleic acids selected from the group, including but not limited to: DNA, genomic DNA, cDNA, RNA, mRNA and may be natural or synthetic. In all embodiments, nucleic acid molecules from subjects suspected of developing or having a skeletal degeneration condition, are preferred. In certain embodiments of the invention, one or more control nucleic acid molecules are attached to the substrate. Preferably, control nucleic acid molecules allow determination of factors including but not limited to: nucleic acid quality and binding characteristics; reagent quality and effectiveness; hybridization success; and analysis thresholds and success. Control nucleic acids may include, but are not limited to, expression products of genes such as housekeeping genes or fragments thereof.

[0189] To select a set of skeletal degeneration condition markers, the expression data generated by, for example, microarray analysis of gene expression, is preferably analyzed to determine which genes in different categories of patients (each category of patients being a different skeletal degeneration disorder), are significantly differentially expressed. The significance of gene expression can be determined using Permax computer software, although any standard statistical package that can discriminate significant differences is expression may be used. Permax performs permutation 2-sample t-tests on large arrays of data. For high dimensional vectors of observations, the Permax software computes t-statistics for each attribute, and assesses significance using the permutation distribution of the maximum and minimum overall attributes. The main use is to determine the attributes (genes) that are the most different between two groups (e.g., control healthy subject and a subject with a particular skeletal degeneration disorder), measuring “most different” using the value of the t-statistics, and their significance levels.

[0190] Expression of nucleic acid molecules of the invention can also be determined using protein measurement methods to determine expression of SEQ ID NO:1-11, and 13-66, e.g., by determining the expression of polypeptides encoded by SEQ ID NO:1-11, and 13-66, respectively. Preferred methods of specifically and quantitatively measuring proteins include, but are not limited to: mass spectroscopy-based methods such as surface enhanced laser desorption ionization (SELDI; e.g., Ciphergen ProteinChip System), non-mass spectroscopy-based methods, and immunohistochemistry-based methods such as 2-dimensional gel electrophoresis.

[0191] SELDI methodology may, through procedures known to those of ordinary skill in the art, be used to vaporize microscopic amounts of tumor protein and to create a “fingerprint” of individual proteins, thereby allowing simultaneous measurement of the abundance of many proteins in a single sample. Preferably SELDI-based assays may be utilized to characterize skeletal degeneration conditions as well as stages of such conditions. Such assays preferably include, but are not limited to the following examples. Gene products discovered by RNA microarrays may be selectively measured by specific (antibody mediated) capture to the SELDI protein disc (e.g., selective SELDI). Gene products discovered by protein screening (e.g., with 2-D gels), may be resolved by “total protein SELDI” optimized to visualize those particular markers of interest from among SEQ ID NOs:1-67. Predictive models of classification from SELDI measurement of multiple markers from among SEQ ID NOs:1-67 may be utilized for the SELDI strategies.

[0192] The use of any of the foregoing microarray methods to determine expression of any of the foregoing nucleic acids of the invention can be done with routine methods known to those of ordinary skill in the art and the expression determined by protein measurement methods may be correlated to predetermined levels of a marker used as a prognostic method for selecting treatment strategies for patients with skeletal degeneration.

[0193] The invention will be more fully understood by reference to the following examples. These examples, however, are merely intended to illustrate the embodiments of the invention and are not to be construed to limit the scope of the invention.

EXAMPLES

[0194] Introduction

[0195] Much of what is known regarding differentiation of chondroblasts has been obtained from studies on skeletal development. In embryogenesis, mesenchymal cells condense to form cartilaginous anlagen. Several genes have been identified that regulate this process, for example, sox9 [1], gdf5 [2], and noggin [3], but the role that those genes play in post-natal chondroblastic differentiation is unclear.

[0196] We previously described a novel in vitro model of induced chondroblast differentiation [4]. We designed the collagen sponge culture system to mimic the three-dimensional (3-D) geometry and density of subcutaneous implants of demineralized bone powder (DBP) [5]. Human dermal fibroblasts (hDF) that were cultured with DBP in three-dimensional collagen sponges for 7 days developed a chondroblastic phenotype. Those cells produced metachromatic extracellular matrix that contained sulfated glycosaminoglycans [4], and they expressed RNA transcripts for the cartilage-specific genes aggrecan and type II collagen [6].

[0197] The purpose of the present study was to use this novel DBP/collagen sponge culture system to identify genes that are upregulated early in the process of chondroinduction of human dermal fibroblasts.

[0198] Representational difference analysis (RDA) is a subtractive hybridization method known in the art that uses PCR to amplify differentially expressed genes [7]. We used RDA to identify a pool of genes upregulated in hDFs cultured in DBP/collagen sponges. The analysis was performed at an early timepoint (3 days), prior to expression of the chondroblast phenotype. Upregulation of those genes was specific to cellular interactions with DBP because RDA subtracted those genes whose expression was increased due to cell attachment to the collagen matrix of control sponges. These experiments are described in detail below and in our manuscript (Yates et al., Experimental Cell Research, 2001, 265:203-211), the contents of which are expressly incorporated herein by reference.

[0199] Materials and Methods

[0200] Collagen sponges. 3-D collagen sponges were prepared from pepsin-digested bovine collagen [5]. Briefly, 250 μL of 0.5% collagen solution (Cellagen PC-5, ICN Biomedicals, Costa Mesa, Calif.) was neutralized with 1M HEPES (pH 7.4) and 1M NaHCO3, poured into a mold, frozen, lyophilized, then irradiated with ultraviolet light. DBP was prepared from rat long bones [8]. Bilaminate DBP/collagen sponges were prepared by placing a spacer of moistened paper between two layers of collagen, and were packed with 3 mg of DBP between the layers of the sponge. Control sponges consisted of a single layer of collagen.

[0201] Cells and cell seeding. Human dermal fibroblasts were obtained from discarded tissue under an approved institutional protocol (Brigham and Women's Hospital #86-01858). Cells were isolated from neonatal foreskins by outgrowth culture, and were expanded in vitro to passage #12 prior to seeding onto DBP/collagen and control collagen sponges (106 cells per sponge) [4]. The sponges were cultured for 3 to 21 days.

[0202] Histology. Sponges were fixed for 24 hours in 2% paraformaldehyde, 0.1 M cacodylate buffer (pH 7.4), were rinsed in 0.1 M cacodylate buffer, and were embedded in glycolmethacrylate (JB-4, Polysciences, Warrington, Pa.). Twenty micron-thick sections were cut and stained with 0.5% toluidine blue-O, pH 4.0 (Fisher Scientific, Pittsburgh, Pa.). The thick sections allowed visualization of metachromatic extracellular matrix above and below individual cells [4].

[0203] Demonstration of chondroinduction in vitro. Human dermal fibroblasts cultured in DBP/collagen and collagen sponges for 7 days were analyzed for metachromatic extracellular matrix by histology as above, and for synthesis of cartilage chondroitin 4-sulfate by ELISA [4].

[0204] RNA isolation. Total RNA was extracted from cultured sponges on day 3 for representational difference analysis, and on days 3, 7, 14, and 21 for Northern blot and RT-PCR. Sponges were homogenized in Trizol reagent (Life Technologies, Inc., Grand Island, N.Y.) according to the manufacturer's instructions [6]. RNA quality was evaluated by absorbance readings at 260 and 280 nm, and by ethidium bromide staining of RNA formaldehyde agarose gels.

[0205] Preparation of cDNA representations. Poly A+ mRNA was purified (Micro-Fast Track mRNA Isolation Kit, Invitrogen, Carlsbad, Calif.) from 100 μg of total RNA isolated from hDFs cultured in DBP/collagen and collagen sponges for 3 days (FIG. 2). The entire poly A+ mRNA preparation was reverse-transcribed into oligo dT-primed cDNA using Superscript II according to the manufacturer's instructions (Life Technologies, Inc.). Second strand synthesis was performed and the reactions were extracted with phenol/chloroform, were ethanol precipitated, and were resuspended in a total volume of 20 μl. cDNA synthesis was evaluated by gel electrophoresis of 2 μl of the reaction. The profiles of the two cDNAs (DBP/collagen and collagen sponges) were indistinguishable. Eight microliters of each cDNA was digested with Dpn II restriction enzyme (New England Biolabs, Inc., Beverly Mass.). RBgl12/RBgl24 primers (RBgl12, 5′-GATCTGCGGTGA-3′(SEQ ID NO: 68), RBgl 24, 5′-AGCACTCTCCAGCCTCTCACCGCA-3′(SEQ ID NO: 69)) [9] were annealed and ligated to the digested cDNAs (E. coli DNA ligase, Life Technologies, Inc.). Representations were generated by PCR amplification with RBgl24 primers. The representations were digested with Dpn II to remove RBgl24 primers then purified using the PCR Purification Kit (Qiagen, Chatsworth, Calif.). Representations were evaluated by gel electrophoresis and the profiles were similar for DBP/collagen and collagen representations.

[0206] Representational difference analysis. The specific conditions for RDA were essentially as described [9], except that mung bean nuclease treatment was omitted. All oligonucleotides were purchased from Life Technologies, Inc. Primer sequences were as follows [9]: JBgl12, 5′-GATCTGTTCATG-3′(SEQ ID NO: 70); JBgl24, ACCGACGTCGACTATCCATGAACA-3′(SEQ ID NO: 71); NBgl12, 5′-GATCTTCCCTCG-3′(SEQ ID NO: 72); NBgl24, 5′-AGGCAACTGTGCTATCCGAGGGAA-3′(SEQ ID NO: 73);. Tester DNA was generated by ligating 0.5 μg of each cDNA representation to pre-annealed JBgl12/JBgl24 primers. A molar ratio of 1:100 (tester DNA:driver DNA) was used for the initial hybridization step (67° C. for 2 days). The hybridization reaction was diluted and used in PCR reactions with JBgl24 primers to amplify tester-tester DNA hybrids. The difference products (DP) were digested with Dpn II, purified, ligated to the next set of primers and then used as the tester DNA in the subsequent round. The ratios of tester:driver DNA and primers used for PCR in successive rounds were as follows: round 2, 1:400, NBgl12/NBgl24; round 3, 1:4000, JBgl12/JBgl24; round 4, 1:40,000, NBgl12/NBgl24.

[0207] Difference analyses were performed to identify genes that were differentially expressed in hDFs cultured in DBP/collagen sponges for 3 days (FIG. 1). A pool of Upregulated genes was identified by subtracting collagen driver DNA from DBP/collagen tester DNA. A pool of Downregulated genes was identified by subtracting DBP/collagen driver DNA from collagen tester DNA. Control difference analyses were performed with yeast tRNA to ensure that RDA enriched differentially expressed DNA sequences.

[0208] Successive iterations of hybridization/amplification produced a number of difference products with gel electrophoresis profiles that were unique to each combination of tester and driver. A loss of difference products was observed in the Upregulated analysis at the highest stringency (1:40,000). Thus, difference products from the third round were analyzed.

[0209] DNA dot blots. One microliter of each difference product was dot-blotted onto positively charged nylon membranes (Roche Molecular Biochemicals, USA). Non-radioactive DNA probes were generated from the pools of Upregulated and Downregulated DP using the DIG High Prime Kit (Roche Molecular Biochemicals) and were hybridized to dot blots according to the manufacturer's instructions. Chemiluminescent detection was performed with Blocking Buffer, anti-DIG antibody and CDP-Star according to the manufacturer's instructions (Roche Molecular Biochemicals).

[0210] Subcloning and sequencing of difference products. Upregulated DP3 was subcloned with the Topo Cloning Kit (Invitrogen). A total of 2300 transformants were grown in 96-well plates. Eighty-nine individual clones were randomly selected for analysis. Plasmid minipreps were prepared using the Wizard Plus SV Miniprep kit (Promega, Madison Wis.) and analyzed by Eco RI restriction enzyme digest (Promega) and DNA sequencing (Brigham and Women's Hospital Core DNA Sequencing Facility, Boston Mass.). Matches for DNA sequences were identified by searching the GenBank database [10], and novel sequences were compared to each other with BLAST 2 Sequences [11].

[0211] Northern hybridization. Total RNA isolated from hDFs cultured in collagen and DBP/collagen sponges was subjected to electrophoresis through 1% agarose gels (10 μg per lane) and was blotted onto a positively-charged nylon membrane (Roche Molecular Biochemicals). The membrane was hybridized overnight at 42° C. with rotation to purified, [32P]-labeled DNA probes in hybridization buffer containing 50% formamide, 5×SSC, 1% SDS, 5× Denhardt's solution, and 100 μg/ml denatured herring sperm DNA. The membrane was washed (2×SSC, 0.1% SDS, 25° C. for 5 minutes, twice; 0.2×SSC, 0.1% SDS, 25° C. for 5 minutes, twice; 0.2×SSC, 0.1% SDS, 42° C. for 15 minutes, twice) prior to autoradiography. The X-ray films were scanned with an Epson 1200s Scanner with a transparency adapter and the images were analyzed with Scion Image software (Scion Corporation, Frederick, Md.). The vigilin probe was an RDA-identified fragment that contains a portion of the carboxy-terminal protein coding sequence. Vigilin gene expression levels were normalized to total RNA (18S rRNA oligonucleotide, Ambion, Inc., Austin Tex.).

[0212] RT-PCR. Total RNA from hDFs cultured in DBP/collagen and control collagen sponges was diluted to 100 ng/ml and treated with DNase I (Roche Molecular Biochemicals, USA) to eliminate any contaminating genomic DNA. Two μg of DNase-treated RNA were used in random hexamer-primed cDNA synthesis according to the manufacturer's instructions (Superscript II, Life Technologies, Inc). PCR primers specific for difference product DNA sequences were designed using the Primer3 program [12]. Primer sequences were as follows: COL11A1, 5′-GCTGCTCAAGCTCAGAAACC-3′(SEQ ID NO: 74), 5′-CCCTGCCGTCTATTTCTTTG-3′(SEQ ID NO: 75); α-11 integrin, 5′-TAGTAGCTGGGGCAGCAAA-3′(SEQ ID NO: 76), 5′-TGGAAGCTCGGCTTCTTTAG-3′(SEQ ID NO: 77); FGF2, 5′-ACAAAAGCCTTGAGGATTGC-3′(SEQ ID NO: 78), 5′-AAAACTGCCGTTGGCATTAG-3′(SEQ ID NO: 79);. PCR primers specific for the cartilage matrix gene aggrecan [6] and the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (G3PDH) [13] were as described. The cycling conditions for each primer pair were determined in PCR reactions that used the corresponding RDA product as a template. Cycling conditions were as follows: COL11A1: 94° C. for 5 min; 94° C. for 45 sec, 55° C. for 45 sec, 72° C. for 2 min (35 cycles); 2 min at 72° C. α-11 integrin and FGF2: 94° C. for 5 min; 94° C. for 1 min, 55° C. for 2 min, 72° C. for 3 min (40 cycles); 10 min at 72° C. Aggrecan and G3PDH: 94° C. for 5 min; 94° C. for 45 sec, 60° C. for 45 sec, 72° C. for 2 min (35 cycles); 72° C. for 2 min. The primers were used in PCR reactions with cDNA from hDFs cultured in DBP/collagen sponges for 3 days, and the resulting PCR products were subcloned and sequenced to ensure that the desired gene had been amplified.

[0213] For kinetic gene expression analysis by RT-PCR, 1 μl of cDNA (the equivalent of 50 ng total RNA) was used in each PCR reaction. Eight μl of each PCR reaction was subjected to electrophoresis on 2% agarose gels. Photographs of ethidium bromide-stained gels were scanned with an Epson 1200s Scanner and the images were analyzed with Scion Image software. Gene expression levels were normalized to G3PDH.

[0214] Results

[0215] This analysis was designed to identify a pool of genes upregulated early in hDFs exposed to DBP in collagen sponges, prior to the expression of cartilage extracellular matrix. Histologic evaluation of human dermal fibroblasts cultured in control collagen sponges for 3 days revealed that cells were distributed throughout the lattice and were attached along and across collagen fibers. In the DBP/collagen sponges, many hDFs were attached to the collagen lattice at 3 days; those cells that had migrated into the packet of DBP were attached to and between the particles of DBP. After 3 days, no metachromatic extracellular matrix was observed in either the control collagen or the DBP/collagen sponges. Metachromatic matrix was visible, however, in DBP/collagen sponges after 7 days. In addition, biochemical analysis of chondroitin 4-sulfate content showed 20% more in DBP/collagen sponges (265+/−19 ng/sponge) than control collagen sponges (222+/−24 ng/sponge) after 7 days in culture (n=6, p<0.01). Three days was therefore taken to represent a time point at which early interactions were occurring between the cells and DBP and was chosen for analysis of differentially expressed genes.

[0216] Representational difference analysis (RDA) is a PCR-based method of subtractive hybridization in which differentially expressed cDNAs are amplified [Hubank and Schatz 1999]. We used RDA to identify pools of Upregulated and Downregulated genes in hDFs cultured in DBP/collagen sponges for 3 days. The uniqueness of the DNA sequences present in each pool was confirmed by dot blot. Upregulated difference products (DP) did not hybridize with the Downregulated DP, but did hybridize with self. Similarly, the Downregulated DP did not hybridize with the Upregulated DP, but hybridized with self. Control analyses should contain essentially all amplifiable sequences within the original collagen or DBP/collagen representation. As expected, difference products from the Upregulated and Downregulated analyses hybridized with difference products from the corresponding Control analysis. That the Upregulated DP also hybridized with the Downregulated Control DP and vice versa indicates that at least some of the genes identified as Upregulated were initially present in both representations (as opposed to de novo transcription).

[0217] Of 97 Upregulated clones that were randomly selected for analysis, 6 clones did not contain insert, 14 clones contained 11 novel sequences (SEQ ID NOs:1-11), and 77 clones matched DNA sequences deposited in GenBank. Sixty of the latter clones corresponded to 49 mRNAs (Table 1). The additional 17 clones corresponded to 6 GenBank sequences with unknown gene product function (Table 2).

[0218] The kinetics of vigilin expression in hDFs cultured in DBP/collagen and collagen sponges were discerned by Northern hybridization. Vigilin was selected from the Upregulated genes because its expression had been reported to decrease with time in cultured primary fibroblasts [14]. Three different-sized messages were detected. The 4.5- and 6.0-kb transcripts were of a size as previously reported mRNAs in human tissue [15]. An approximately 8.0-kb transcript was also detected, which likely represents an alternatively spliced message [14-16]. The total increase in vigilin transcript (relative to monolayer culture) was 5.6-fold. The majority of this increase (4.7-fold) was due to upregulation of the 8.0-kb transcript. The 8.0-kb vigilin transcript was also elevated 2.0-fold after 7 days in DBP/collagen sponges. In contrast, vigilin RNA levels in the control collagen sponge did not exceed 2.0-fold over monolayer culture and the levels of the individual transcripts remained relatively constant.

[0219] The above gene expression analysis shows that vigilin is transiently upregulated in hDFs cultured in DBP/collagen sponges. To compare this transient pattern to gene expression during cartilage matrix production (chondrogenesis), we analyzed sponge samples for expression of cartilage signature genes identified by RDA (Table 1). Several of the genes identified as Upregulated have been previously described in the context of chondrocytes or cartilage tissues. RT-PCR was used to characterize the kinetics of their expression in hDFs cultured in DBP/collagen and collagen sponges. After 3 days in culture, there was 3.0-fold more type XI collagen (COL11A1) mRNA in DBP/collagen sponges than control collagen sponges (FIG. 3). Expression was maximal on days 7 and 14, and declined thereafter. Similarly, on day 3, there was 2.8-fold more α-11 integrin mRNA in DBP/collagen sponges than in control collagen sponges (FIG. 3). Expression of that gene was maximal on day 14. FGF2 expression was maximal on day 14 (FIG. 3).

[0220] These kinetic analyses show two different patterns of expression for genes that were identified by RDA as Upregulated in hDFs cultured in DBP/collagen sponges. These patterns, transient or intermediate, are distinct from the expression of cartilage extracellular matrix genes. As an example of an abundant cartilage matrix gene, expression of aggrecan mRNA was analyzed. Aggrecan was not identified as Upregulated in hDFs cultured in DBP/collagen sponges for 3 days. As expected, an increase in expression of aggrecan mRNA in DBP/collagen sponges was observed after 7 days and continued to increase at later timepoints (FIG. 3).

[0221] Discussion

[0222] Treatment options for damaged articular cartilage are limited because of that tissue's poor capacity for repair. Possible approaches to this problem are to stimulate cartilage matrix production in situ or to engineer replacement tissue. Both of these approaches would benefit from a clearer understanding of the molecular mechanisms of chondroblast differentiation. Demineralized bone induces endochondral bone formation in vivo [17], is available through regional bone banks, and is used in humans for orthopedic [18], oral and maxillofacial [19], and hand problems [20]. As an endochondral process, DBP-induced cartilage becomes calcified and replaced with bone, but the cartilage phase can be prolonged by hypocalcemia and anti-angiogenic factors [21]. An in vitro analysis of early cellular effects of interaction with demineralized bone may reveal information regarding the mechanisms of induced chondrogenesis in post-natal mesenchymal cells.

[0223] Representational difference analysis was used to identify a pool of genes that were upregulated during chondroinduction of human dermal fibroblasts in a DBP/collagen sponge culture system. The upregulation of genes was specific to cellular interactions with DBP because RDA subtracted those genes whose expression was increased due to cell attachment to the collagen matrix of control sponges. Those genes represented several functional classes, including protein synthesis and trafficking, transcriptional regulation, and extracellular and cytoskeletal elements.

[0224] The expression pattern of several genes known to be expressed in, or to have an effect on cartilage tissues was characterized in hDFs cultured in DBP/collagen sponges. Vigilin [P14, 15] and type XI collagen [22] are expressed in articular cartilage. α-11 integrin expression has been observed in chondrosarcoma [23]. FGF2 has multiple actions on chondrocytes [rev. in 24]. A DBP-induced increase in expression of these genes was confirmed by Northern blot and RT-PCR. Kinetic analysis of gene expression showed two patterns of expression—transient and intermediate—for genes that were identified as Upregulated on day 3. In contrast, kinetic analysis of an abundant cartilage matrix gene, aggrecan, showed a later increase in gene expression.

[0225] Upregulation of several genes is consistent with an increase in protein synthesis and export, as would be expected in cells undergoing chondroblastic differentiation. Tryptophanyl tRNA synthetase catalyzes the attachment of tryptophan to its tRNA [25]. Exportin-t [26] and vigilin [27] have been implicated in tRNA export from the nucleus. Sec23 [28] is present in a multiprotein complex that functions in selective transport of proteins from the transitional endoplasmic reticulum to the cis golgi [29].

[0226] Two of these gene products have documented roles in transcriptional regulation. TRAX and translin are part of a nuclear complex that binds the Egr response element in a strand-specific manner [T30]. TRAX contains a nuclear localization signal that probably functions to transport TRAX and its binding partner, translin (which lacks a nuclear localization signal), to the nucleus [31]. Chromodomain helicase DNA binding protein 4 (CHD4, also known as Mi-2β) [32] is present in protein complexes that activate or repress transcription via an ATP-dependent mechanism or histone deacetylase activity, respectively [33-35]. Upregulation of TRAX and CHD4 implies that changes in chromatin structure occur to permit silencing of some genes (fibroblast-specific) and expression of others (chondroblast-specific).

[0227] Others of the Upregulated gene products are known to stabilize mRNA associations with the cytoskeleton, which is important for the establishment of cell polarity [36]. Vigilin has been shown to bind 3′ untranslated regions in the vitellogenin mRNA, which results in stabilization of the message [37]. TRAX, in association with translin and an ATPase in the transitional endoplasmic reticulum, binds cytosolic γ-actin and is thought to function in mRNA stabilization on the cytoskeleton [38]. Fibroblasts and chondrocytes are strikingly different in shape both in vivo and in vitro, the former being spindle-shaped, and the latter, round.

[0228] A number of upregulated genes encode proteins that are cytoskeletal components. β1 integrin interacts via its cytoplasmic tail with the carboxy-terminal end of ABP280 [39]. This protein, in turn, binds actin via its amino-terminus [40]. Integrin α11 [23] also associates with β1 integrin [41]. The RING-finger protein, MID 1, interacts with microtubules [42].

[0229] The increase in distinctive cytoskeletal elements upon interaction with DBP may reflect specific shape changes induced by attachment to DBP. Because a number of those proteins have been implicated in mechanotransduction, it is also possible that the shifts are related to the chondroblast phenotype. ABP280 redistributed to the surface of lamellipodia of lymphocytes after adherence to a collagen matrix [43]. In human gingival fibroblasts, calcium-dependent assembly of actin filaments and ABP280 recruitment (and its subsequent serine phosphorylation) was induced at the site of force application [44]. Moreover, activity of stretch-activated calcium channels was decreased upon cytoskeletal reorganization, suggesting a mechanism for mechanoprotection of the cell membrane [44]. Mechanical tension on the cytoskeleton (via β1-integrin binding to extracellular matrix) has also been linked to localized protein synthesis [45].

[0230] Finally, a number of extracellular matrix proteins were identified. Type XI collagen [46] forms cross-links with type II collagen fibrils in cartilage [22] and is essential for skeletal development [47]. Another fibrillar collagen, type III, is essential for successful formation of type I collagen fibrils during development [48]. Type VI collagen is expressed in a variety of tissues, including cartilage [49, 50].

[0231] Taken together, the profile of upregulated genes represents a variety of cellular functions. The significance of these changes in gene expression is that DBP appears to elicit a programmatic shift in cell physiology of the target cells related to chondroinduction.

1TABLE 1Genes upregulated in human dermal fibroblasts cultured in three-dimensionalcollagen sponges with demineralized bone powder for 3 days.Category/SubcategoryGene (GenBank Locus)Extracellular matrixCOL3A1 (NM_000090) (SEQ ID NO: 13)COL6A3 (NM_004369.1) (SEQ ID NO: 14)COL11A1 (NM_001854) (SEQ ID NO: 15)CytoskeletonActin-associated Actin-binding protein 280 (NM_001456.1) (SEQ ID NO: 16)RhoGAP1 (NM_004815) (SEQ ID NO: 17)Microtubule-associated MID1 (AF041210) (SEQ ID NO: 18)Cell adhesion β1 integrin (NM_002211) (SEQ ID NO: 19)α11 integrin (AF109681) (SEQ ID NO: 20)erythroblast macrophage protein (AF084928) (SEQ ID NO: 21)Vigilin (NM_005336) (SEQ ID NO: 22)Translin-associated factor X (HSTRAXGEN) (SEQ ID NO: 23)Protein synthesisrRNA synthesis: RNA polymerase I, largest subunit (HSU33460) (SEQ ID NO: 24tRNA aminoacylation: tryptophanyl tRNA synthase2 (NM_015836) (SEQ IDNO: 25)tRNA export: Exportin-t (AF039022) (SEQ ID NO: 26)Vigilin (SEQ ID NO: 22)Protein trafficking: Sec23 homolog A (NM006364.1) (SEQ ID NO: 27)TranscriptionTranslin-associated factor X (SEQ ID NO: 23)Chromodomain helicase DNA binding protein 4 (NM_001273.1) (SEQ ID NO: 28)Nucleosome assembly protein (HUMNAP) (SEQ ID NO: 29)ID-2H Homo sapiens (HUMID2HC) (SEQ ID NO: 30)Growth factorsFibroblast growth factor 2 (NM_002006) (SEQ ID NO: 31)Insulin-like growth factor binding protein-3 (HSIGFBP3M) (SEQ ID NO: 32)Wnt-5a Homo sapiens (HUMWNT5A) (SEQ ID NO: 33)OtherGolgin A4 (NM_002078) (SEQ ID NO: 34)Multidrug resistance-associated protein (HUMMRPX) (SEQ ID NO: 35)ATP-specific succinyl-CoA synthetase beta subunit (AF058953) (SEQ ID NO: 36)Aspartyl beta-hydroxylase (AF289489) (SEQ ID NO: 37)Ras-related GTP binding protein (AF106681) (SEQ ID NO: 38)RNF11 (AB024703) (SEQ ID NO: 39)Lysyl oxidase-like protein 2 (AF117949) (SEQ ID NO: 40)C2orf2ropp120 (AF177377) (SEQ ID NO: 41)Sec61 homolog (AF077032) (SEQ ID NO: 42)LYST-interacting protein LIP6 (AF141342) (SEQ ID NO: 43)Breast carcinoma amplified sequence 2 (NM_005872) (SEQ ID NO: 44)Hepatocellular carcinoma novel gene-3 protein (AF251079) (SEQ ID NO: 45)KIAA0908 (AB020715) (SEQ ID NO: 46)KIAA0294 (AB002292) (SEQ ID NO: 47)KIAA0184 (D80006) (SEQ ID NO: 48)cDNA DKFZp58611418 (AL049378) (SEQ ID NO: 49)cDNA FLJ10704 fis, clone NT2RP3000841 (AK001566) (SEQ ID NO: 50)cDNA FLJ10051 fis, clone HEMBA1001281 (AK000913) (SEQ ID NO: 51)cDNA FLJ12487 fis, clone NT2RM2000609 (AK022549) (SEQ ID NO: 52)cDNA FLJ23177 fis, clone LNG10649 (AK026830) (SEQ ID NO: 53)Decorin (XM_012239) (SEQ ID NO: 60)Lysyl Oxidase (XM_003695) (SEQ ID NO: 61)Lysyl hydroxylase 2 (XM_002844) (SEQ ID NO: 62)Prolyl 4-hydroxylase (XM_005728.2) (SEQ ID NO: 63)F-box only protein 32 (NM_058229) (SEQ ID NO: 64)Fibronectin receptor, alpha polypeptide (ITGA5) (NM_002205) (SEQ ID NO: 65)Ras-related GTPase (XM_003032) (SEQ ID NO: 66)Aminophospholipid-transporting ATPase (ATP10C) (AY029489) (SEQ ID NO: 67)

[0232]

2

TABLE 2

GenBank sequences upregulated by cellular interactions with

demineralized bone powder (DBP)

Sequence ID (GenBank Locus)
Corresponding Bases

BAC GS1-99H8 (AC004010)
110,957-112,715

(SEQ ID NO: 54)

BAC RP11-394J1 (AC008149)
8,825-9,566

(SEQ ID NO: 55)

clone 117O3 (HS117O3)
119,269-119,527

(SEQ ID NO: 56)

clone RP1-191N21 (HS191N21)
96,784-97,438

(SEQ ID NO: 57)

clone RP4-562A11 (AC006451)
65,010-65,577

(SEQ ID NO: 58)

clone RP11-436D10 (AL133417)
124,873-125,466

(SEQ ID NO: 59)

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DETAILED DESCRIPTION OF THE DRAWINGS

[0283]
FIG. 2. Schematic of experimental design for representational difference analysis. Human dermal fibroblasts (hDF) are seeded onto DBP/collagen and control collagen sponges. After 3 days in culture, RNA is isolated and is used to generate cDNA representations of the genes expressed at that timepoint. Ligation of short oligonucleotide primers (JBgl) to the representations creates tester DNA. No primers are added to the representations that are used as the driver DNA. Hybridizations are performed with the 4 combinations of tester and driver DNA shown. Those sequences that are present in the tester in excess are amplified by PCR with JBgl primers. Control analyses use yeast tRNA as driver so that all DNA sequences in each tester are amplified. JBgl primers are removed from the 1st round difference products (DP1). A new set of primers (NBgl) are ligated and the DNA is used as tester in the next cycle of hybridization/amplification (Round 2). Differentially expressed DNAs are enriched in subsequent rounds of hybridization and amplification.

[0284]
FIG. 3. Kinetic analyses of cartilage signature genes. Gene expression levels were analyzed by RT-PCR and normalized to G3PDH. The cartilage signature genes type XI collagen (COL11A1), α-11 integrin, and FGF2 were revealed by RDA. Aggrecan was used as an example of an abundant cartilage extracellular matrix gene.

[0285] Equivalents

[0286] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

[0287] All references disclosed herein are incorporated by reference in their entirety.

[0288] What is claimed is presented below and is followed by a Sequence Listing.

Diagnosis and treatment of skeletal degeneration conditions

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