Methods for inducing differentiation of undifferentiated mammalian cells into osteoblasts

Abstract
The present invention relates to in vivo and in vitro methods, agents and compound screening assays for inducing differentiation of undifferentiated mammalian cells into osteoblasts, including bone formation enhancing pharmaceutical compositions, and the use thereof in treating and/or preventing a disease involving a systemic or local decrease in mean bone density in a subject.
Description
FIELD OF THE INVENTION

The present invention relates to agents, and methods for identifying compounds, which agents and compounds induce the differentiation of undifferentiated cells and/or osteoblast progenitor cells into osteoblasts. In addition, the invention relates to compositions and methods for the use thereof in limiting undesired bone loss in a vertebrate at risk of such bone loss, in treating conditions that are characterized by undesired bone loss or by the need for bone growth, in treating fractures, and in treating cartilage disorders.


Bone remodeling relies on an equilibrium between an anabolic (osteogenic) and a catabolic (bone resorption) process. Bone is a dynamic tissue that is continuously being destroyed (resorbed) and rebuilt, by an intricate interplay between two distinct cell lineages: bone-forming cells, known as osteoblasts and bone-resorbing cells, known as osteoclasts.


A number of diseases are the direct result of a disturbance in the fine-tuned balance between bone resorption and bone formation. These diseases for the most part are skeletal diseases and inflict a large number of patients. Exemplary diseases include hypocalcaemia of malignancy, Paget's disease, inflammatory bone diseases such as rheumatoid arthritis and periodontal disease, focal osteogenesis occurring during skeletal metastases, Crouzon's syndrome, rickets, opsismodysplasia, pycnodysostosis/Toulouse-Lautrec disease, and osteogenesis imperfecta. Of great significance are the chronic conditions of rheumatoid- and osteo-arthritis and osteoporosis, including age-related osteoporosis and osteoporosis associated with post-menopausal hormone status. Other conditions characterized by the need for bone growth include primary and secondary hyperparathyroidism, disuse osteoporosis, diabetes-related osteoporosis, and glucocorticoid-related osteoporosis. The single most prevalent bone disease is osteoporosis, which affects 1 in 5 women over 50 and 1 in 20 men over 50.


Other conditions that are characterized by the need to enhance bone formation include bone fractures, where it would be desirable to stimulate bone growth and to hasten and complete bone repair. Bone fractures are still treated exclusively using casts, braces, anchoring devices and other strictly mechanical means. Other bone deficit conditions include bone segmental defects, periodontal disease, metastatic bone disease, osteolytic bone disease and conditions where connective tissue repair would be beneficial, such as healing or regeneration of cartilage defects or injury. To treat all of these conditions, bone remodeling processes are required; however, in many instances, patients are encountered with poorly healing fractures or bone defects. Consequently, surgical intervention is often required to accelerate the recovery. Such surgery may implant a prosthesis with or without bone grafting procedures. In many cases where the bone is too porous or where previous implants failed to be incorporated into the bone, current medical practices can offer little or no help. There are currently no satisfactory pharmaceutical approaches to managing any of these conditions. While further bone deterioration associated with post-menopausal osteoporosis has been decreased or prevented with estrogens or bisphosphonates, current therapies do not build new bone to replace bone that has already deteriorated.


The activities of bone cells are regulated by a large number of cytokines and growth factors, many of which have now been identified and cloned. Mundy has described the current knowledge related to these factors (Mundy 1996: Mundy 1993). Although there is a great deal of information available on the factors which influence the breakdown and resorption of bone, information on factors which stimulate the formation of new bone is more limited.


The cascade of transcription factors and growth factors involved in the differentiation or progression from progenitor cell to functional osteoclast is well established. In contrast, little is known about the factors involved in the progression of progenitor cells into osteoblasts. The mesenchymal progenitor or stem cells (MPCs) represent the starting point for the differentiation of both osteoclasts and osteoblasts. During embryonic development in vivo, bone formation occurs through two distinct pathways: intramembranous and/or endochondral ossification (see FIG. 1; taken from Nakashima and de Crombrugghe, (2003)). During intramembranous ossification, flat bones such as those of the skull or clavicles, are formed directly from condensations of mesenchymal cells. During endochondral ossification, long bones, such as limb bones, are formed from a cartilage intermediate formed during mesenchymal condensation, which intermediate is invaded during further development by endothelial cells, osteoclasts and mesenchymal cells that further differentiate into osteoblasts and osteocytes. As osteoblasts differentiate from precursors to mature bone-forming cells, they express and secrete a number of enzymes and structural proteins of the bone matrix, including Type-1 collagen, osteocalcin, osteopontin and alkaline phosphatase (Stein et al 1990; Harris et al 1994). During the late stage of differentiation into osteoblasts, bone alkaline phosphatase activity (BAP) is up-regulated. Like alkaline phosphatase, osteocalcin and osteopontin, the BMPs are expressed by cultured osteoblasts as they proliferate and differentiate.


A limited number of compounds have been identified that are able to induce osteoblast differentiation in vitro, e.g., dexamethasone or by recombinant human secreted proteins, e.g., BMP-2 or BMP-7 (Service, 2000). BMPs are potent stimulators of bone formation in vitro and in vivo, however there are disadvantages to their use as therapeutic agents to enhance bone healing. Receptors for the bone morphogenetic proteins have been identified in many tissues, and the BMPs themselves are expressed in a large variety of tissues in specific temporal and spatial patterns. This suggests that BMPs may have effects on many tissues other than bone, potentially limiting their usefulness as therapeutic agents when administered systemically.


It is therefore important to identify agents that can induce osteoblast differentiation starting from pluripotent bone marrow mesenchymal progenitor cells or even from totipotent stem cells. Therefore, research has expanded into the identification of human secreted proteins and human receptor or mediator TARGETs that are involved in the specific modulation of differentiation of osteoblasts or of other cell types involved in bone homeostasis.


Reported Developments

A number of treatments have been developed and made available to patients suffering from osteoporosis and related skeletal diseases. These therapeutic approaches primarily are directed to increasing net bone formation and include: hormone replacement therapy (HRT); selective estrogen receptor modulators (SERMs); bisphosphonates; and calcitonin. While these treatments slow down bone resorption, they don't abolish fracturing because the lost bone is not sufficiently replenished. Fracturing will be prevented only if bone formation is sufficiently increased. Therefore, there is great interest in identifying osteogenic pathways that enhance bone anabolism as a basis for therapeutic intervention.


Parathyroid hormone (PTH) 1-34 is the only bone anabolic therapy on the osteoporosis therapeutic market. While PTH displays bone anabolic effects when administered intermittently, it needs to be injected daily, and may have tumorgenic side effects, based on the observation that tumors form in animals treated with at PTH in high doses.


Bone morphogenetic proteins (BMPs) are another class of bone anabolic therapeutics, but have only been approved for niche markets. Receptors for the bone morphogenetic proteins have been identified in many tissues other than bone, and BMPs themselves are expressed in a large variety of tissues in specific temporal and spatial patterns. This suggests that BMPs may have effects on many tissues other than bone, potentially limiting their usefulness as therapeutic agents when administered systemically.


There is a clear need to identify additional targets that stimulate osteogenic differentiation and that can be used for the development of novel bone anabolic therapies.


The present invention relates to the relationship between the function of selected proteins identified by the present inventors (hereinafter referred to as “TARGETS”) and osteoblast differentiation in vertebrate cells.


SUMMARY OF THE INVENTION

The present invention relates to a method for identifying compounds that induce differentiation of undifferentiated vertebrate cells into osteoblasts, comprising contacting the compound with a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133 under conditions that allow said polypeptide to bind to the compound, and measuring a compound-polypeptide property related to the differentiation of said cells into osteoblasts.


The present invention also relates to expression inhibitory agents, pharmaceutical compositions comprising the same, methods for the in vitro production of bone tissue, and host cells expressing said agents.


Aspects of the present method include the in vitro assay of compounds using polypeptide of a TARGET, and cellular assays wherein TARGET inhibition is followed by observing indicators of efficacy, including bone alkaline phosphatase secretion levels.


Another aspect of the invention is a method of treatment or prevention of a condition involving loss of bone density, in a subject suffering or susceptible thereto, by administering a pharmaceutical composition comprising an effective bone formation enhancing amount of a TARGET inhibitor.


A further aspect of the present invention is a pharmaceutical composition for use in said method wherein said inhibitor comprises a polynucleotide selected from the group of an antisense polynucleotide, a ribozyme, and a small interfering RNA (siRNA), wherein said inhibitor comprises a nucleic acid sequence complementary to, or engineered from, a naturally occurring polynucleotide sequence encoding a polypeptide, comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133, or a fragment thereof.


Another further aspect of the present invention is a pharmaceutical composition comprising a therapeutically effective bone formation-enhancing amount of a TARGET inhibitor or its pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof in admixture with a pharmaceutically acceptable carrier. The present polynucleotides and TARGET inhibitor compounds are also useful for the manufacturing of a medicament for the treatment of conditions involving bone density loss.




BRIEF DESCRIPTION OF THE FIGURES


FIG. 1. Intramembranous and endochondral ossification.



FIG. 2. Principle of the osteoblast differentiation assay.



FIG. 3. Lay-out of the 96 well knock-down control plate.



FIG. 4. Lay-out of the 384 well control plate.



FIG. 5. Performance of the knock-down control plate in the AP assay



FIG. 6. Dot plot representation of raw data for one SilenceSelect screening plate



FIG. 7. Profiling of target expression in MPCs (A) and knock-down of gene expression by Ad-siRNA (B)



FIG. 8. Profiling of target expression in primary human OBs



FIG. 9. Analyzing the upregulation of BAP-mRNA versus PLAP- or IAP-mRNA



FIG. 10. Results mineralization assay



FIG. 11. Pipetting scheme used for screening the Ad-shRNAs at 3 MOIs.




DETAILED DESCRIPTION OF THE INVENTION

The following terms are used herein in accordance with the following definitions:


The term “agent” means any molecule, including polypeptides, polynucleotides and small molecules.


The term “agonist” refers to a ligand that stimulates the receptor the ligand binds to in the broadest sense.


The term “assay” means any process used to measure a specific property of a compound. A “screening assay” means a process used to characterize or select compounds based upon their activity from a collection of compounds.


The term “binding affinity” is a property that describes how strongly two or more compounds associate with each other in a non-covalent relationship. Binding affinities can be characterized qualitatively, (such as “strong”, “weak”, “high”, or “low”) or quantitatively (such as measuring the KD).


The term “carrier” means a non-toxic material used in the formulation of pharmaceutical compositions to provide a medium, bulk and/or useable form to a pharmaceutical composition. A carrier may comprise one or more of such materials such as an excipient, stabilizer, or an aqueous pH buffered solution. Examples of physiologically acceptable carriers include aqueous or solid buffer ingredients including phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™.


The term “complex” means the entity created when two or more compounds bind to each other.


The term “compound” is used herein in the context of a “test compound” or a “drug candidate compound” described in connection with the assays of the present invention. As such, these compounds comprise organic or inorganic compounds, derived synthetically or from natural sources. The compounds include inorganic or organic compounds such as polynucleotides, lipids or hormone analogs that are characterized by relatively low molecular weights. Other biopolymeric organic test compounds include peptides comprising from about 2 to about 40 amino acids and larger polypeptides comprising from about 40 to about 500 amino acids, such as antibodies or antibody conjugates.


The term “condition” or “disease” means the overt presentation of symptoms (i.e., illness) or the manifestation of abnormal clinical indicators (e.g., biochemical indicators). Alternatively, the term “disease” refers to a genetic or environmental risk of or propensity for developing such symptoms or abnormal clinical indicators.


The term “contact” or “contacting” means bringing at least two moieties together, whether in an in vitro system or an in vivo system.


The term “effective amount” or “therapeutically effective amount” means that amount of a compound or agent that will elicit the biological or medical response of a subject that is being sought by a medical doctor or other clinician. In particular, with regard to inducing undifferentiated vertebrate cells into osteoblasts, the term “effective amount” is intended to mean an effective differentiation-promoting amount of an compound or agent that will bring about a biologically meaningful increase in the levels of osteogenic markers, representative for the process of differentiation into osteoblasts.


The term “endogenous” shall mean a material that a mammal naturally produces. Endogenous in reference to the term “protease”, “kinase”, or G-Protein Coupled Receptor (“GPCR”) shall mean that which is naturally produced by a mammal (for example, and not limitation, a human). In contrast, the term non-endogenous in this context shall mean that which is not naturally produced by a mammal (for example, and not limitation, a human). Both terms can be utilized to describe both “in vivo” and “in vitro” systems. For example, and not a limitation, in a screening approach, the endogenous or non-endogenous TARGET may be in reference to an in vitro screening system. As a further example and not limitation, where the genome of a mammal has been manipulated to include a non-endogenous TARGET, screening of a candidate compound by means of an in vivo system is viable.


The term “expressible nucleic acid” means a nucleic acid coding for a proteinaceous molecule, an RNA molecule, or a DNA molecule.


The term “expression” comprises both endogenous expression and overexpression by transduction.


The term “expression inhibitory agent” means a polynucleotide designed to interfere selectively with the transcription, translation and/or expression of a specific polypeptide or protein normally expressed within a cell. More particularly, “expression inhibitory agent” comprises a DNA or RNA molecule that contains a nucleotide sequence identical to or complementary to at least about 17 sequential nucleotides within the polyribonucleotide sequence coding for a specific polypeptide or protein. Exemplary expression inhibitory molecules include ribozymes, double stranded siRNA molecules, self-complementary single-stranded siRNA molecules, genetic antisense constructs, and synthetic RNA antisense molecules with modified stabilized backbones.


The term “expressible nucleic acid” means a nucleic acid coding for a proteinaceous molecule, an RNA molecule, or a DNA molecule.


The term “GPCR” means a G-protein coupled receptor. Preferred GPCRs comprise those receptors identified by applicants as promoting osteogenic differentiation. Most preferred GPCRs are those identified in Tables 1 and 2, including the naturally occurring transcript variants thereof.


The term “hybridization” means any process by which a strand of nucleic acid binds with a complementary strand through base pairing. The term “hybridization complex” refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary bases. A hybridization complex may be formed in solution (e.g., C0t or R0t analysis) or formed between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed). The term “stringent conditions” refers to conditions that permit hybridization between polynucleotides and the claimed polynucleotides. Stringent conditions can be defined by salt concentration, the concentration of organic solvent, e.g., formamide, temperature, and other conditions well known in the art. In particular, reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature can increase stringency.


The term “inhibit” or “inhibiting”, in relationship to the term “response” means that a response is decreased or prevented in the presence of a compound as opposed to in the absence of the compound.


The term “inhibition” refers to the reduction, down regulation of a process or the elimination of a stimulus for a process that results in the absence or minimization of the expression of a protein or polypeptide.


The term “induction” refers to the inducing, up-regulation, or stimulation of a process that results in the expression of a protein or polypeptide.


The term “ligand” means an endogenous, naturally occurring molecule specific for an endogenous, naturally occurring receptor.


The term “osteoblast differentiation” means the process of differentiation of undifferentiated cells (progenitor cells or precursor cells) into osteoblasts and/or preosteoblasts. The term “osteogenesis” is used as a synonym in this context. “Abnormal osteoblast differentiation” means a situation where either too much or too little osteoblast differentiation is occurring.


The term “pharmaceutically acceptable prodrugs” as used herein means the prodrugs of the compounds useful in the present invention, which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of patients with undue toxicity, irritation, allergic response commensurate with a reasonable benefit/risk ratio, and effective for their intended use of the compounds of the invention. The term “prodrug” means a compound that is transformed in vivo to yield an effective compound useful in the present invention or a pharmaceutically acceptable salt, hydrate or solvate thereof. The transformation may occur by various mechanisms, such as through hydrolysis in blood. The compounds bearing metabolically cleavable groups have the advantage that they may exhibit improved bioavailability as a result of enhanced solubility and/or rate of absorption conferred upon the parent compound by virtue of the presence of the metabolically cleavable group, thus, such compounds act as pro-drugs. A thorough discussion is provided in Design of Prodrugs, H. Bundgaard, ed., Elsevier (1985); Methods in Enzymology; K. Widder et al, Ed., Academic Press, 42, 309-396 (1985); A Textbook of Drug Design and Development, Krogsgaard-Larsen and H. Bandaged, ed., Chapter 5; “Design and Applications of Prodrugs” 113-191 (1991); Advanced Drug Delivery Reviews, H. Bundgard, 8, 1-38, (1992); J. Pharm. Sci., 77,285 (1988); Chem. Pharm. Bull., N. Nakeya et al, 32, 692 (1984); Pro-drugs as Novel Delivery Systems, T. Higuchi and V. Stella, 14 A.C.S. Symposium Series, and Bioreversible Carriers in Drug Design, E. B. Roche, ed., American Pharmaceutical Association and Pergamon Press, 1987, which are incorporated herein by reference. An example of the prodrugs is an ester prodrug. “Ester prodrug” means a compound that is convertible in vivo by metabolic means (e.g., by hydrolysis) to an inhibitor compound according to the present invention. For example an ester prodrug of a compound containing a carboxy group may be convertible by hydrolysis in vivo to the corresponding carboxy group.


The term “pharmaceutically acceptable salts” refers to the non-toxic, inorganic and organic acid addition salts, and base addition salts, of compounds of the present invention. These salts can be prepared in situ during the final isolation and purification of compounds useful in the present invention.


The term “polynucleotide” refers to nucleic acids, such as double stranded, or single stranded DNA and (messenger) RNA, and all types of oligonucleotides. It also includes nucleic acids with modified backbones such as peptide nucleic acid (PNA), polysiloxane, and 2′-O-(2-methoxy)ethylphosphorothioate. “Derivatives of a polynucleotide” means DNA-molecules, RNA-molecules, and oligonucleotides that comprise a stretch or nucleic acid residues of the polynucleotide, e.g. polynucleotides that may have nucleic acid mutations as compared to the nucleic acid sequence of a naturally occurring form of the polynucleotide. A derivative may further comprise nucleic acids with modified backbones such as PNA, polysiloxane, and 2′-O-(2-methoxy)ethyl-phosphorothioate, non-naturally occurring nucleic acid residues, or one or more nucleic acid substituents, such as methyl-, thio-, sulphate, benzoyl-, phenyl-, amino-, propyl-, chloro-, and methanocarbanucleosides, or a reporter molecule to facilitate its detection. “Fragment of a polynucleotide” means oligonucleotides that comprise a stretch of contiguous nucleic acid residues that exhibit substantially a similar, but not necessarily identical, activity as the complete sequence.


The term “polypeptide” relates to proteins, proteinaceous molecules, fractions of proteins, peptides, oligopeptides, and enzymes (such as kinases, proteases, GCPRs). “Derivatives of a polypeptide” relate to those peptides, oligopeptides, polypeptides, proteins and enzymes that comprise a stretch of contiguous amino acid residues of the polypeptide and that retain the biological activity of the protein, e.g. polypeptides that have amino acid mutations compared to the amino acid sequence of a naturally-occurring form of the polypeptide. A derivative may further comprise additional naturally occurring, altered, glycosylated, acylated or non-naturally occurring amino acid residues compared to the amino acid sequence of a naturally occurring form of the polypeptide. It may also contain one or more non-amino acid substituents compared to the amino acid sequence of a naturally occurring form of the polypeptide, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence. “Fragment of a polypeptide” relates to peptides, oligopeptides, polypeptides, proteins and enzymes that comprise a stretch of contiguous amino acid residues, and exhibit substantially similar, but not necessarily identical, functional activity as the complete sequence.


The term “solvate” means a physical association of a compound useful in this invention with one or more solvent molecules. This physical association includes hydrogen bonding. In certain instances the solvate will be capable of isolation, for example when one or more solvent molecules are incorporated in the crystal lattice of the crystalline solid. “Solvate” encompasses both solution-phase and isolable solvates. Representative solvates include hydrates, ethanolates and methanolates.


The term “subject” includes humans and other mammals.


The term “treating” means an intervention performed with the intention of preventing the development or altering the pathology of, and thereby alleviating a disorder, disease or condition, including one or more symptoms of such disorder or condition. Accordingly, “treating” refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treating include those already with the disorder as well as those in which the disorder is to be prevented. The related term “treatment,” as used herein, refers to the act of treating a disorder, symptom, disease or condition, as the term “treating” is defined above.


The term “undifferentiated mammalian cells” are pluripotent cells which are in an early stage of specialization, i.e. cells which do not yet have their final function and can be induced to form almost any given cell type. In particular, these are cells which have not yet differentiated to the specific bone cells osteoblasts or osteoclasts. Such pluripotent cells are especially blood cells and cells present in bone marrow, as well as cells derived from adipose tissue. In addition, cells which can be differentiated into mesenchymal precursor cells are contemplated in the present invention, such as, for example, totipotent stem cells such as embryonic stem cells.


The term “vectors” also relates to plasmids as well as to viral vectors, such as recombinant viruses, or the nucleic acid encoding the recombinant virus.


The term “vertebrate cells” means cells derived from animals having vertera structure, including fish, avian, reptilian, amphibian, marsupial, and mammalian species. Preferred cells are derived from mammalian species, and most preferred cells are human cells. Mammalian cells include feline, canine, bovine, equine, caprine, ovine, porcine murine, such as mice and rats, and rabbits.


Applicants' Invention Based on TARGET Relationship to Osteoblast Differentiation


As noted above, the present invention is based on the present inventors' discovery that TARGETS are factors in the up-regulation and/or induction of osteoblast differentiation. The term “TARGET” or “TARGETS” means the proteins identified in accordance with the present bone alkaline phosphatase assay to be involved in the induction osteoblast differentiation. The TARGETS are identified in Table 1 by gene name, gene symbol, genbank DNA/RNA accession number, genbank polypeptide accession number, and their associated SEQ ID NOS. Table 1 also provides knock-down target sequences and their associated SEQ ID NOS of the present invention. Table 1A provides additional KD TARGET Sequences for the TARGETS identified in Table 1.


The preferred TARGETS are identified in Table 2 by gene name, gene symbol, genbank DNA/RNA accession number, genbank polypeptide accession number, and their associated SEQ ID NOS. Table 2 also provides knock-down target sequences and their associated SEQ ID NOS of the present invention. Table 2A identifies exemplary protein domain fragments of the preferred polypeptide TARGETS identified in Table 2.

TABLE 1DNA/KDRNAPPTARGETSEQTARGETTARGETGenbankSEQGenbankSEQTARGETSequenceIDGeneGeneDNA/RNAIDPolypeptideIDId(5′ → 3′)NO.NameSymbolAccessionNO.AccessionNO.H24-049GTACCTGC1arginineAVPR1BNM_000707367NP_000698409AGGTGCTCvasopressinAGCreceptor 1BH24-225ATGGGCTT2arginineAVPR1BNM_000707367NP_000698409CAACAGCCvasopressinACCreceptor 1BH24-001CAACTTGT3G protein-GPR38NM_001507607NP_001498867ACCTGGGCcoupledAGCreceptor 38H24-002GGTGAAGG4serine/threonineSTK11, LKB1NM_000455608NP_000446868AGGTGCTGkinase 11GAC(Peutz-Jegherssyndrome)H24-003GAATCTCT5hypotheticalHSM801665,AL136697609AL136697's1123TCCGCAAGproteinMGC8407proteinATCMGC8407NM_024046610NP_076951869H24-004CATGCTGT6MAP kinase-MKNK2,SK236348SK236's protein390TTGAGAGCinteractingMNK2NM_017572349NP_060042391ATCserine/threonineNM_199054350NP_951009392kinase 2H24-005TTTTGTGCT7calcitoninCALCRLNM_005795611NP_005786870GATTCCATreceptor-likeGGCH24-006GACGGTGT8casein kinaseCSNK1G1,NM_00101166356NP_001011664398TAATGATA1, gamma 1CK1g1(SK647)GCCNM_022048357NP_071331399H24-007CTTCGGGCA9myosin lightHSA247087,SK536 368SK536's protein410CTCCTGAGchain kinasecaMLCK,NM_182493369NP_872299411TTCMLCK(AJ247087)H24-008GCACAGTT10Rho-ROCK2NM_004850600NP_004841601TGAGAAGCassociated,AGCcoiled-coilcontainingprotein kinase 2H24-009ACGCAAAG11tRNAIPTNM_017646612NP_060116871TGGCCAGGisopentenyl-AGCtransferase 1H24-010CGATGTGC12protein kinasePRKCN,NM_005813613NP_005804872CTTCAAGAC, nuPKD3SK489614SK489's protein1124TTCH24-011GTGCACGG13membraneMPP6NM_016447615NP_057531873ATTCAGAGprotein,AGCpalmitoylated 6H24-012;CTTCTACA14G protein-TYMSTRNM_006564616NP_006555874H24-161CGTCCATGcoupledCTCreceptorH24-013CAACCTGC15opsin 3OPN3NM_014322617NP_055137875TGGTGCTC(encephalopsin,GTCpanopsin)H24-014CTCTCTTA16granzyme KGZMKNM_002104362NP_002095404GATCTGGA(serineACCprotease,granzyme 3;tryptase II)H24-015AGCAGGAA17ubiquitin-AF073344,NM_006537618NP_006528876GGCGGACAspecificUSP3TACprotease 3 -ubiquitinspecificprotease 3H24-016CTCCAGCT18L-fucoseFUKNM_145059619NP_659496877GAGTGAGCkinaseAGCH24-017TAAACCAG19hypotheticalMGC26954NM_145025620NP_659462878CAGAGGAGproteinCTCMGC26954H24-018TCAGGTAG20coagulationF13A1NM_000129621NP_000120879TTGGTTCTfactor XIII, A1GACpolypeptideH24-019CTGCGCCG21proteasomePSMB3NM_002795622NP_002786880AACAAAATG(prosome,TACmacropain)subunit, betatype, 3H24-020TGTGGCGA22ClpXCLPXNM_006660623NP_006651881CTTGTGCAcaseinolyticCACprotease Xhomolog (E.coli)H24-021TCTCTCAG23hypotheticalC13orf6,NM_032859353NP_116248395TGTAGAATproteinFLJ14906GCCFLJ14906H24-022CCAGGAGG24HP43.8KDHP43.8KDNM_032557624NP_115946882TGAAACCAproteinCACH24-023TCAGGCGA25ubiquitinUSP9XNM_004652625NP_004643883CTACTTTAspecificNM_021906626NP_068706884CTCprotease 9, Xchromosome(fat facets-likeDrosophila)H24-024GTGTACTG26matrixMMP23A,NM_004659340NP—004650382GTACAAGGmetallopro-MMP23BNM_006983341NP_008914383ACCteinase 23A-matrixmetallopro-teinase 23BH24-025GAGCAGGT27HP43.8KDHP43.8KDNM_032557627NP_115946885TTCCAAAGproteinGACH24-026TCTCTCAT28APEXAPEXNM_001641628NP_001632886CAATACTGnucleaseNM_080648629NP_542379887GTC(multifunctionalNM_080649630NP_542380888DNA repairenzyme)H24-027TGCAGAGC29a disintegrin-ADAMTS19NM_133638631NP_598377889AGACAAGTlike andGGCmetalloprotease(reprolysintype) withthrombospondintype 1 motif,19H24-028TCATGTTG30a disintegrinADAM22NM_004194632NP_004185890ACCAAGCAandNM_016351633NP_057435891AGCmetalloprotein-NM_021721634NP_068367892ase domain 22NM_021722635NP_068368893NM_021723636NP_068369894H24-029CTATGCCA31LOC254378LOC254378XM_174812637XP_174812895TCACCTTCTGCH24-030TGTGCCGA32similar to aLOC137491XM_070459638XP_070459896AGGATGTAdisintegrin andAGCmetalloproteasedomain 25(testase 2)H24-031CCGGGACA33similar to bileLOC138529XM_070951639XP_070951897TAACTAAAsalt-dependentTCClipaseoncofetalisoformH24-032AGCAGGCT34complementC9NM_001737640NP_001728898ATGGGATCcomponent 9AACH24-033CCACAAGG35xylulokinaseXYLBNM_005108641NP_005099899TTGCAGCAhomolog (H.TTCinfluenzae)H24-035GGGCTCAG36chaperone,CABC1,NM_020247642NP_064632900CCAGGAGAABC1 activityADCK3SK609643SK609's proteinTTCof bc1 complexlike (S. pombe)H24-036CAGGTAGA37fyn-relatedFRKNM_002031644NP_002022901CATGGCGGkinaseCACH24-037CTCTCCAG38G protein-GPR113NM_153835645NP_722577902GACACTGAcoupledCTCreceptor 113(GPR113)H24-038GCACGATT39unc-51-likeULK1NM_003565646NP_003556903TGGAGGTCkinase 1 (C.GCCelegans)H24-039CGCTCTGG40neurotrophicNTRK1NM_002529647NP_002520904AGTCTCTCtyrosineTCCkinase,receptor, type 1H24-040CCCCAACT41glycogenGSK3ANM_019884648NP_063937905ACACGGAGsynthaseTTCkinase 3 alphaH24-041GGACTCTC42phosphoinos-PIK3C2BNM_002646376NP_002637418AGTTCAGCitide-3-kinase,ATCclass 2, betapolypeptideH24-042CTTTGCGA43protein kinase,PRKRNM_002759649NP_002750906TACATGAGinterferon-CCCinducibledoublestranded RNAdependentH24-043CTTCCTGA44FUSEDSTK36, FusedAF200815650AF200815's1125AGACCAGGserine/threonineproteinTTCkinaseNM_015690651NP_056505907H24-044GAATGCTG45mixed lineageHSA311797,AJ311797652AJ311797's1126GCAACAAGkinase 4alpha-HSA311798,proteinACCmixed lineageMLK4,SK691653SK691's protein1127kinase 4betaKIAA1804NM_032435654NP_115811908H24-045GAAGATGT46casein kinaseCSNK1E,NM_001894655NP_001885909CAACGCCC1, epsilonCK1eNM_152221656NP_689407910ATCH24-046TTCTACGC47calcium-CASRNM_000388657NP_000379911ACCAGAACsensingTCCreceptor(hypocalciurichypercalcemial,severe neonatalhyperparathy-roidism)H24-047TGACGGTT48gonadotropin-GNRHRNM_000406658NP_000397912GCATTTGCreleasingCAChormonereceptorH24-048CCAGACCT49adrenergic,ADRA1BNM_000679659NP_000670913CGAGCAACalpha-1B-,TCCreceptorH24-050GGAGTGCA50dopamineDRD1NM_000794660NP_000785914ATCTGGTTreceptor D1TACH24-051CAGTCAGT51dopamineDRD3NM_000796661NP_000787915GCAACAGTreceptor D3NM_033658662NP_387507916GTCNM_033659-663NP_387508917NM_033663664NP_387512918H24-052CGTGCTTG52opioidOPRD1NM_000911665NP_000902919TCATGTTCreceptor,GGCdelta 1H24-053TGACAGGT53tachykininTACR1NM_001058666NP_001049920TCCGTCTGreceptor 1GGCH24-054GTACCTGC54chemokineCCR1NM_001295342NP_001286384GGCAGTTG(C—C motif)TTCreceptor 1H24-055GACCATCA55frizzledFZD2NM_001466667NP_001457921CCATCCTGhomolog 2GCC(Drosophila)H24-056GCAGGCAG56bombesin-likeBRS3NM_001727668NP_001718922AGGACAGAreceptor 3TTCH24-057CAAAGCCA57bombesin-likeBRS3NM_001727669NP_001718923TGCCCGTAreceptor 3AGCH24-058AAGTGCCC58formyl peptideFPR1NM_002029670NP_002020924TGGCCTTCreceptor 1TTCH24-059CTACCACA59frizzledFZD5NM_003468671NP_003459925AGCAGGTGhomolog 5TCC(Drosophila)H24-060;TGCGTGCT60smoothenedSMOHNM_005631672NP_005622926H24-168TCTTTGTGhomologGGC(Drosophila)H24-061CTACGTCA61melanocortin 5MC5RNM_005913673NP_005904927TCCTGTGCreceptorCTCH24-062;TTCGGACA62retinal pigmentRRHNM_006583674NP_006574928H24-166CCCACAAAepithelium-TGCderivedrhodopsinhomologH24-064;GTTGTCCT63olfactoryOR1A2NM_012352364NP_036484406H24-164GTTCTGACreceptor,GTCfamily 1,subfamily A,member 2H24-065GCAGGCTT64paired basicPACE4NM_002570675NP_002561929TCGAGTATamino acidNM_138319676NP_612192930GGCcleavingNM_138320677NP_612193931system 4NM_138321678NP_612194932NM_138322679NP_612195933NM_138323680NP_612196934NM_138324681NP_612197935NM_138325682NP_612198936H24-066CCTCTCTG65leucine-richLGR7NM_021634683NP_067647937TCAACACArepeat-TGCcontaining Gprotein-coupledreceptor 7H24-067ATGACGCT66beta-amyloidBBPNM_032027684NP_114416938ACGCAAGAbinding proteinACCprecursorH24-068AGCGGGTG67proteasomePSMB5NM_002797685NP_002788939CTTACATT(prosome,GCCmacropain)subunit, betatype, 5H24-069GCAAGAAT68retinoic acidRARBNM_000965686NP_000956940GCACAGAGreceptor, betaNM_016152687NP_057236941AGCH24-070TTTGTGCT69similar toCTLA1NM_033423688NP_219491942GACAGCTGgranzyme BCTC(granzyme 2,cytotoxic T-lymphocyte-associatedserine esterase1) (H. sapiens)H24-071CACCTGCT70KIAA1453KIAA1453NM_025090689NP_079366943TTCTCAATproteinGCCH24-072GGTTCTCT71fetuin BFETUBNM_014375690NP_055190944GACTCGAACACH24-073AGCACCTC72sentrin/SUMO-SENP3NM_015670691NP_056485945GCTGACATspecificTCCprotease 3H24-074CCTGGGCA73DKFZP586D2DKFZP586NM_018561692NP_061031946ACACCTGC223 proteinD2223TACH24-075CTTAAGGT74carboxypeptidaseCPA6NM_020361693NP_065094947GGACCTGTA6GGCH24-076TTGCACAG75putativeSPPL2ANM_032802694NP_116191948AAAGGAGGintramembraneTGCcleavingproteaseH24-077GCCCGCAG76similar toLOC121302XM_062575695XP_062575949TCTTACACproteaseAACH24-078GCTTCTGG77transglutam-TGM6NM_198994696NP_945345950TGGAGAAGinase 6GACH24-079GTGTATGA78liver-specificLST-3NM_0010095621120NP_001009562951AGTGGTCCorganic anionACCtransporter 3H24-080GAAATCTC79similar toLOC160131XM_090078697XP_090078952ACTGCTTCcaspase 1,GACisoform alphaprecursor;interleukin 1-betaconvertase;interleukin 1-Bconvertingenzyme; IL1B-convertaseH24-081CACTTTAT80similar toLOC284964XM_209423698XP_209423953AAGCCTGCbA395L14.5GGC(novelphosphogluco-mutase likeprotein)H24-082TGGGCATC81LOC254378LOC254378XM_174812699XP_174812954CTGGCTGTAACH24-083ATAGACTG82complementC9NM_001737700NP_001728955CAGAATGAcomponent 9GCCH24-084CAGTGCCA83neuronNAV2NM_018162701NP_060632956AGAAGGAGnavigator 2NM_145117702NP_660093957CCCH24-085TGTGCTCG84highly chargedD13S106ENM_005800703NP_005791958AAGGAGGAproteinATCD13S106EH24-086ATGTATGG85butyrylcho-BCHENM_000055704NP_000046959ATTCCAGClinesteraseACCH24-087GCTCTGCT86Hin-1HSHIN1NM_017493705NP_059963960ATGTGTCANM_199324706NP_955356961GTCH24-088TGTGACTA87polycysticPKDREJNM_006071707NP_006062962AGCTGGAAkidney diseaseGAC(polycystin)and REJ(spermreceptor foregg jellyhomolog, seaurchin)-likeH24-089TGCGCACA88proteinPTPN1NM_002827708NP_002818963ATACTGGCtyrosineCACphosphatase,non-receptortype 1H24-090TTCCCGCT89glutamateGRIK4NM_014619709NP_055434964ACCAGACCreceptor,TACionotropic,kainate 4H24-091AGCATGGT90potassiumKCNK9NM_016601710NP_057685965CATTCACAchannel,TCCsubfamily K,member 9H24-092ATGCAGGT91transientTRPM6NM_017662711NP_060132966CCATATGTreceptorGACpotential cationchannel,subfamily M,member 6H24-093CCTTTCTC92ataxiaATRNM_001184712NP_001175967TGAACACGtelangiectasiaGACand Rad3relatedH24-094GTCAGGCT93p21(CDKN1A)-PAK6NM_020168374NP_064553416GAATGAGGactivatedSK429375SK429's protein417AGCkinase 6H24-095CAGGTTCT94taste receptor,TAS1R3XM_371210713XP_371210968CCTCAAACtype 1,GGCmember 3H24-096GCATAGGA95similar toLOC223021XM_167349714XP_167349969GTGGTCATtensinATCH24-097ACATCCTG96thousand andTAO1, PSKNM_016151351NP_057235393CTGTCAGAone amino acidNM_004783352NP_004774394GCCprotein kinase-prostatederivedSTE20-likekinase PSKH24-098CATGGAGT97solute carrierSLC10A1NM_003049715NP_003040970TCAGCAAGfamily 10ATC(sodium/bileacidcotransporterfamily),member 1H24-099GTTCTCCA98solute carrierSLC16A3NM_004207366NP_004198408GTGCCATTfamily 16GGC(monocarboxylicacidtransporters),member 3H24-100TTCGGCCT99organicORCTL3NM_004256716NP_004247971GGACGTCTcationicATCtransporter-like3H24-101GTGCATTG100interleukin 5IL5NM_000879717NP_000870972GTGAAAGA(colony-GACstimulatingfactor,eosinophil)H24-102TGTGCAGG101transformingTGFB2NM_003238718NP_003229973ATAATTGCgrowth factor,TGCbeta 2H24-103AGGTGTCA102tumor necrosisTNFRSF10ANM_003844719NP_003835974CTGTACAGfactor receptorTCCsuperfamily,member 10aH24-104AGTGCGCA103fibroblastFGF14NM_004115720NP_004106975TCTTCGGCgrowth factorCTC14H24-105TTTGTGGA104Ras homologRHEB2NM_005614721NP_005605976CTCCTACGenriched inATCbrain 2H24-106GCCCTGAT105NADPH-NR1NM_014434722NP_055249977GTCCATCTdependentTCCFMN and FADcontainingoxidoreductaseH24-107CATAGGGA106interleukin 1IL1F8NM_014438723NP_055253978AGGACACTfamily,TGCmember 8 (eta)H24-108CCTGGATG107interleukin 1IL1F8NM_014438724NP_055253979TGAGAGAGfamily,AGCmember 8 (eta)H24-109AACTTGTA108Ras associationRASSF2NM_014737725NP_055552980CTATGAAG(RalGDS/AF-6)NM_170774726NP_739580981GCCdomainfamily 2H24-110GTATTCTG109androgen-ARSDR1NM_016026727NP_057110982TACACCCTregulatedGGCshort-chaindehydrogenase/reductase 1H24-111TTCTCGCA110peptidylpro-PPIL1NM_016059728NP_057143983ATGGCCAAlylisomeraseTGC(cyclophilin)-like 1H24-112GAAGAACA111RAS,RASD1NM_016084365NP_057168407GCAGCCTGdexamethasone-GACinduced 1H24-113TCAGGCGG112dicarbonyl/L-DCXRNM_016286729NP_057370984ATCTTGACxyluloseAGCreductaseH24-114TTCGGCAC113casein kinaseCSNK2BNM_001320730NP_001311985TGGTTTCC2, betaCTCpolypeptideH24-115GACGAATA114protein kinase,PRKAG2NM_016203731NP_057287986TCAGCTCTAMP-GCCactivated,gamma 2 non-catalyticsubunitH24-116CCTCTCTA115ATP-bindingABCG8NM_022437732NP_071882987CGCCATCTcasette, sub-ACCfamily G(WHITE),member 8(sterolin 2)H24-117TCTCTCCA116chromosomeC20orf121NM_024331733NP_077307988CACAAACC20 openTTCreading frame121H24-118GGTCGGGA117organic cationOKB1NM_033125734NP_149116989GGAGAACAtransporterGTCOKB1H24-119GCGAATTC118solute carrierSLC26A8NM_052961735NP_443193990CACCAGCAfamily 26,TTCmember 8H24-120TGTCCAGG119UDPUGT1A1NM_000463736NP_000454991ACCTATTGglycosyltrans-AGCferase 1 family,polypeptide A1H24-121TGACCATC1203-hydroxy-3-HMGCRNM_000859737NP_000850992TGCATGATmethylglutaryl-GTCCoenzyme AreductaseH24-122GCATGGCA121hydroxypro-HPGDNM_000860738NP_000851993TAGTTGGAstaglandinTTCdehydrogenase15-(NAD)H24-123ATGCAGGA122phospholipasePLCG2NM_002661739NP_002652994CATGAACAC, gamma 2ACC(phosphatidyl-inositol-specific)H24-124ATGTGTGA123thioredoxinTXNRD1NM_182729740NP_877393995ATGTGGGTreductase 1NM_003330741NP_003321996TGCNM_182742742NP_877419997NM_182743743NP_877420998H24-125TGCAGGCT124UDP-B4GALT5NM_004776744NP_004767999ATTCTGTGGal:betaGlcNAcAGCbeta 1,4-galactosyltrans-ferase,polypeptide 5H24-126TCGGCACA125isocitrateIDH3BNM_174855745NP_7772801000ACAATCTAdehydrogenaseNM_006899746NP_0088301001GAC3 (NAD+) betaNM_174856747NP_7772811002H24-127GACAGGTG126sialyltransfer-SIAT4BNM_006927748NP_0088581003GACAGAGCase 4B (beta-ATCgalactosidasealpha-2,3-sialytrans-ferase)H24-128TGTGCGAG127HMT1 hnRNPHRMT1L3NM_019854343NP_062828385ACCTCGATmethyltrans-TTCferase-like 3(S. cervisiae)H24-129AGTTTGTG128UDP-B3GALT1NM_020981749NP_0661911004TAGGTATCGal:betaGlcNAcGCCbeta 1,3-galactosyltrans-ferase,polypeptide 1H24-130AGCATGAA1290-ENSG00000169,ENSG000001690750ENSG0000016901128AGAAACCCperoxisomalDHRS4,6666's proteinTGCshort-chainDHRS4L2NM_021004751NP_0662841005alcoholNM_198083752NP_9323491006dehydrogenaseH24-131GAAGATCA130similar toPPIA,XM_292085753XP_2920851007CCATTGCTpeptidylpro-LOC341457XM_4976211121XP_4976211008GAClylisomerase ALOC126170,XM_371409754XP_3714091009(cyclophilin A)-LOC388817,NM_203431755NP_9822551010similar to Pep-LOC402102,XM_497870756XP_4978701011tidyl-prolylLOC440892,XM_496579757XP_4965791012cis-transLOC439953,XM_495800758XP_4958001013isomerase ALOC343384,NM_203430759NP_9822541015(PPIase)OAS2,XM_291544760XP_2915441016(Rotamase)LOC390299,NM_178230761NP_8399441017(Cyclophilin A)LOC388687,XM_372452762XP_3724521018(CyclosporinLOC388686,XM_371304763XP_3713041020A-bindingLOC128192,XM_3713021122XP_3713021021protein) (SP18)LOC392352XM_060887764XP_0608871022XM_373301765XP_3733011023NM_021130766NP_0669531024767H24-132GCATGAAT131similar toPPIA,XM_4976211121XP_4976211025ATTGTGGApeptidylpro-LOC126170,XM_371409768XP_3714091026GGClylisomerase ALOC388817,NM_203431769NP_9822551027(cyclophilin A)-LOC402102,XM_497870770XP_4978701028similar to Pep-LOC391062,XM_372785771XP_3727851029tidyl-prolylPPIA,NM_203430772NP_982254-1030cis-transLOC390299,XM_372452773XP_3724521031isomerase ALOC391352,XM_372916774XP_3729161032(PPIase)LOC128192XM_060887775XP_0608871033(Rotamase)NM_021130776NP_0669531034(Cyclophilin A)(CyclosporinA-bindingprotein) (SP18)H24-133TGCAGGCA1323-oxoacid CoAOXCT2NM_022120777NP_0714031035AGCAGACGtransferase 2GTCH24-134TGACGCAG133gycosyltrans-LOC83468NM_031302778NP_1125921036ATGATGAAferaseTCCH24-135TGGCGCCA134histoneHDAC10NM_032019779NP_1144081037TGTCAGAGdeacetylase 10TGCH24-136CTTATTGT135similar toLOC170327XM_093255780XP_0932551038TCACATTGcytochrome P-GCC450H24-137TGGCACCT136similar toLOC166624XM_093980781XP_0939801039ATGAGAGGUDP-ATCglucuronosyl-transferaseH24-138TCAGGTGT137interleukin-1IRAK2NM_001570344NP_001561386CCCATTCCreceptor-SK180345SK180's protein387AGCassociatedkinase 2H24-139CTCAGAGG138IL2-inducibleITKNM_005546782NP_0055371040TGGTGGAAT-cell kinaseGACH24-140TGCAGGAG139cytochromeAF182273,AF182273783AF182273's1129GAAATTGAP450,CYP3A3,roteinTGCsubfamily IIIACYP3A4NM_000776784NP_0007671041(niphedipineNM_017460785NP_0594881042oxidase),polypeptide 3-cytochromeP450,subfamily IIIA(niphedipineoxidase),polypeptide 4H24-141GAGTCCAG140cytochromeHUMCYPIIF,J02906786J02906's protein1130CCTTCATGP450,CYP2F1NM_000774787NP_0007651043CCCsubfamily IIF,polypeptide 1H24-142GTCCAGCT141glutamateGRIN2ANM_000833339NP_000824381GAAGAAGAreceptor,TCCionotropic, N-methyl D-aspartate 2AH24-143TTCGGCAC142hypotheticalFLJ22955NM_024819359NP_079095401TGAGGTCTproteinTGCFLJ22955H24-144TTGCACAC143hypotheticalFLJ22955NM_024819866NP_0790951044TGAGCTGGproteinAGCFLJ22955H24-145CCTGCTCT144tumorTEM5NM_032777788NP_1161661045TGAGCAATendothelialAACmarker 5precursorH24-146TGTCCAGA145similar toLOC126537XM_497611789XP_4976111046CCACATGGcytochromeAGCP450,subfamily IVF,polypeptide 2;leukotriene B4omega-hydroxylase;leukotriene-B420-monooxy-genaseH24-147TTGCAGGA146G protein-GPR153NM_207370790NP_9972531047GGACAAGAcoupledTGCreceptor 153H24-148GATTGTGG147chlorideCLIC6XM_092804335XP_092804377CCAAGAAGintracellularNM_053277336NP_444507378TACchannel 6H24-149CCTCATTA148G protein-GPR150XM_094471360XP_094471402TCACCATGcoupledNM_199243361NP_954713403CTCreceptor 150H24-150CTGGTTAT149FLJ16008FLJ16008NM_001001665791NP_0010016651048TGGCGGGTproteinATCH24-151TTTGTGCT150G protein-GPR97NM_170776792NP_7407461049TCACCAAGcoupledTGCreceptor 97H24-152CTGCACAG151similar to N-LOC256135XM_172523793XP_1725231050TCAACACGformyl peptideGTCreceptorH24-153GCAGAGCC152LOC254502LOC254502XM_174355794XP_1743551051AAATATCAGCCH24-154GTTCAAGA153opsin 1 (coneOPN1MW,NM_000513795NP_0005041052AGCTGCGCpigments),OPN1LWNM_020061796NP_0644451053CACmedium-wave-sensitive (colorblindness,deutan) - opsin1 (conepigments),long-wave-sensitive (colorblindness,protan)H24-155CGTCTTCA154G protein-GPR30NM_001505797NP_0014961054TCAGCGTGcoupledCACreceptor 30H24-156GCAGTTCC155opsin 1 (coneOPN1SWNM_001708798NP_0016991055AAGCTTGCpigments),ATCshort-wave-sensitive (colorblindness,tritan)H24-157GTACCTGC156chemokineCCR3NM_178329354NP_847899396GCCACTTC(C—C motif)NM_001837355NP_001828397TTCreceptor 3H24-158GACCATCA157frizzledFZD7NM_003507799NP_0034981056CTATCCTGhomolog 7GCC(Drosophila)H24-159GTCCTTCT158G protein-GPR23NM_005296337NP_005287379ACATCAATcoupledGCCreceptor 23H24-160GAAGAAGC159G protein-GPR64NM_005756338NP_005747380AACTGGGAcoupledGCCreceptor 64H24-162GTTCCAGA160chemokineCCR9NM_006641800NP_0066321057CCTTCATG(C—C motif)NM_031200801NP_1124771058TGCreceptor 9H24-163;CTGGACCG161adrenomedullinADMRNM_007264802NP_0091951059H24-226AGCTGCTTreceptorGACH24-165GCAGAGCA162G protein-G2ANM_013345803NP_0374771060TGGGCTTAcoupledAGCreceptorH24-167;AGCAGGCG163calciumCACNB3NM_000725804NP_0007161061H24-228GAACATGTchannel,TCCvoltage-dependent,beta 3 subunitH24-169CAACCTGT164galaninGALR2NM_003857371NP_003848413TCATCCTTreceptor 2AACH24-170ATTTGGTG165chromosomeC10orf112XM_295865805XP_2958651062ACACGGCT10 openGACreading frame112H24-171CATATGGC166similar toLOC121456XM_062645806XP_0626451063TCTTCAAGsolute carrierTACfamily 9(sodium/hydrogenexchanger),isoform 7;nonselectivesodiumpotassium/pro-ton exchangerH24-172TGGCACAG167acetyl-ACAT1NM_000019807NP_0000101064TAACAGCTCoenzyme AGCCacetyltrans-ferase 1(acetoacetyl(Coenzyme Athiolase)H24-173GTTCTCTC168placentalPGFNM_002632808NP_0026231065AGCACGTTgrowth factor,CGCvascularendothelialgrowth factor-related proteinH24-174TGCAGACT169Rhesus bloodRHAGNM_000324809NP_0003151066TCAGTGCAgroup-GCCassociatedglycoproteinH24-175CTTTCTGG170solute carrierSLC39A1NM_014437810NP_0552521067AAATCCTGfamily 39 (zincCCCtransporter),member 3H24-176CAACACAG171UDP-N-acetyl-GALGTNM_001478811NP_0014691068CAGACACAalpha-D-GTCgalactosamine:N-acetylneur-aminyl)-galac-tosylglucosyl-ceramide N-acetylgalactos-aminyltransfer-ase (GalNAc-T)H24-177TGGGACCA172glycosylphos-GPLD1NM_001503812NP_0014941069GTGACTGCphatidylinositolAGCspecificphospholipaseD1H24-178AGCCAGAG173HMT1 hnRNPHRMT1L1NM_001535813NP_0015261070GAGTTTGTmethyltransfer-NM_206962814NP_9968451071GGCase-like 1 (S.cerevisiae)H24-179CTCGCAGG174GS3955GS3955NM_021643815NP_0676751072AAATTCTGproteinGACH24-180ATGCAGGT175solute carrierSLC4A10NM_022058816NP_0713411073CAGGTTGTfamily 4,TTCsodiumbicarbonatetransporter-like, member10H24-181ATCAGGCC176phosphoproteinC8FWNM_025195817NP_0794711074TTACATCCregulated byAGCmitogenicpathwaysH24-182CTGTGGGA177similar toLOC165927XM_093541818XP_0935411075GAAACAGAhypotheticalGACprotein,MNCb-4779H24-183CTCTGCGA178UDP-B3GALT6NM_080605819NP_5421721076CTACTACCGal:betaGalTGCbeta 1,3-galactosyltrans-ferasepolypeptide 6H24-184CTGATGAA179similar toLOC123326XM_063593820XP_0635931077GGCCTTCGNADH-ACCubiquinoneoxidoreductasePDSW subunit(Complex I-PDSW) (CI-PDSW)H24-185ACCGTGGA180cytochromeCYP24NM_000782370NP_000773412GGCCTATP450,CGCsubfamilyXXIV (vitaminD 24-hydroxylase)H24-186TTCCAGCT181hypotheticalFLJ11149NM_018339821NP_0608091078GATATATCproteinCACFLJ11149H24-187GCCAGACA182TTBK2SK453822SK453's protein1131CTGACAAGNM_173500823NP_7757711079H24-188TCGGCAGG183macrophageMST1NM_020998824NP_0662781080GCCAGCATstimulating 1TTC(hepatocytegrowth factor-like)H24-189GTCTTCGA184histidine-richHRGNM_000412825NP_0004031081CCCTCAGGglycoproteinAACH24-190TCAGAAGG185KIAA0943APG4BNM_013325826NP_0374571082TTGTGCAGproteinNM_178326827NP_8478961083GACH24-191CAACTTGC186amyloid betaAPPNM_201414828NP_9588171084ATGACTAC(A4) precursorNM_000484829NP_0004751085GGCproteinNM_201413830NP_9588161086(proteasenexin-II,Alzheimerdisease)H24-192TGTGCAAG187proteinPPP2CBNM_004156831NP_0041471087AGGTTCGTphosphatase 2TGC(formerly 2A),catalyticsubunit, betaisoformH24-193ACCAGTGG188dual specificityDUSP5NM_004419358NP_004410400TAAATGTCphosphatase 5AGCH24-194CTCTGTAT189mitogen-MAP3K9NM_033141346NP_149132388CCCATTCCactivatedXM_027237347XP_027237389CTCprotein kinasekinase kinase 9H24-195CTTCTTGA190mitogen-MAP3K1XM_042066832XP_0420661088AGCATCTAactivatedTGCprotein kinasekinase kinase 1H24-196CATGCTGT191leucyl/cystinylLNPEPNM_005575833NP_0055661089TGTTCCTTTaminopeptidaseACCH24-197CGAAGATG192ribonuclease LRNASELNM_021133834NP_0669561090TTGACCTG(2′,5′-GTColigoisoadenyl-ate synthetase-dependent)H24-198TGTCCTGT193protein kinase,PRKAA2NM_006252835NP_0062431091TGGATGCAAMP-CACactivated,alpha 2catalyticsubunitH24-199ATGCAGAC194tumor necrosisTNFRSF11ANM_003839836NP_0038301092CCTGGACCfactor receptorAACsuperfamily,member 11a,activator ofNFKBH24-200GTAGCACT195solute carrierSLC39A4NM_017767837NP_0602371093CTGCGACAfamily 39 (zincNM_130849838NP_5709011094TGCtransporter),member 4H24-201CTGGAATG196succinateSDHCNM_003001839NP_0029921095GGATCCGAdehydrogenaseCACcomplex,subunit C,integralmembraneprotein, 15kDH24-202GTTATTCT197nicotinamideNNMTNM_006169840NP_0061601096TCCACCATN-methyl-GGCtransferaseH24-203TGCCAGCA198ciliaryCNTFRNM_001842841NP_0018331097GTCTCTTGneurotrophicATCfactor receptorH24-204GATCTTCC199insulin-likeIGFBP5NM_000599842NP_0005901098GGCCCAAAgrowth factorCACbinding protein5H24-205AGCATGAC200UDP-glucoseUGCGL2NM_020121843NP_0645061099AGGAAACCceramideTGCglucosyltrans-ferase-like 2H24-206TCTTCTCT201similar toLOC136234XM_069782844XP_0697821100GTGAACATNADHACCdehydrogenasesubunit 1H24-207CCTTGTTG202similar toAADACNM_207365845NP_9972481101GCCAATGAArylacetamideTTCdeacetylaseH24-208CCAGGTTT203azurocidin 1AZU1NM_001700846NP_0016911102GTCAACGT(cationicGACantimicrobialprotein 37)H24-209TTCCAGCT204similar toLOC161785XM_091124847XP_0911241103CAGTGCTAmicrotubule-ATCassociatedproteins 1A/1Blight chain 3H24-210AGCAGGAA205similar toLOC219756XM_166676848XP_1666761104CATCTCTTMNK1CGCH24-211CAAGTTCT206ATPase,ATP4BNM_000705849NP_0006961105CCTGCAAGH+/K+TTCexchanging,betapolypeptideH24-212GAGCATGA207gamma-GABRR2NM_002043850NP_0020341106CCTTCGATaminobutyricGGCacid (GABA)receptor, rho 2H24-213CTGGCAGA208a disintegrin-ADAMTS1NM_006988851NP_0089191107AGCAGCAClike andAACmetalloprotease(reprolysintype) withthrombospondintype 1 motif, 1H24-214TACCTGCT209fibroblastFGF4NM_002007852NP_0019981108GGGCATCAgrowth factor 4AGC(heparinsecretorytransformingprotein 1,Kaposisarcomaoncogene)H24-215CTGGAAGT210interferon,IFNA8NM_002170853NP_0021611109CCTGTGTGalpha 8ATCH24-216GGACACCT211interleukin 19IL19NM_013371854NP_0375031110TCCCAAATNM_153758855NP_7156391111GTCH24-217GGCAGAAA212solute carrierSLC10A2NM_000452856NP_0004431112TTCCAGAGfamily 10AGC(sodium/bileacidcotransporterfamily),member 2H24-218CAACATCC213glutathioneGSRNM_000637857NP_0006281113CAACTGTGreductaseGTCH24-219TATCCTGA214potassiumKCNG1NM_002237372NP_002228414CCTTCCTGvoltage-gatedNM_172318373NP_758529415CGCchannel,subfamily G,member 1H24-220TGTTTACC215fibroblastFGF21NM_019113858NP_0619861114AGTCCGAAgrowth factorGCC21H24-221AACTGTAC216similar toLOC131961XM_067688859XP_0676881115CGCAGAGTINOSINE-5-TCCMONOPHOSPHATEDEHYDROGENASE1 (IMP DEHYDRO-GENASE 1)(IMPDH-I)(IMPD 1)H24-222AGCATGAT217topoisomeraseTOP2BNM_001068860NP_0010591116GATAGTTC(DNA) II betaCTC(180kD)H24-223CAAGTGCC218SFRS proteinSRPK1NM_003137861NP_0031281117GTATCATCkinase 1SK358862SK358's protein1132CACH24-224TATTCGTG219chromosome 9SgK071,SK521863SK521's protein1133CGGAGGAAopen readingC9orf96NM_153710864NP_7149211118GACframe 96H24-227GTACCTGC220procollagen-P4HBNM_000918865NP_0009091119TGGTGGAGproline, 2-TTCoxoglutarate 4-dioxygenase(proline 4-hydroxylase),beta polypeptide(proteindisulfideisomerase;thyroid hormonebinding proteinp55)














TABLE 1A









SEQ

TARGET
Genbank



KD TARGET Sequence
ID

Gene
DNA/RNA


(5′ → 3′)
NO.
TARGET Gene Name
Symbol
Accession







CGTTGGCAGAATCATTTAC
247
G protein-coupled receptor 38
GPR38
NM_001507






TTCGCGGATGATGTACTTC
248
G protein-coupled receptor 38
GPR38
NM_001507





CTCTCAGTACTTTAACATC
249
G protein-coupled receptor 38
GPR38
NM_001507





CATAACAAAGGCATCGCCC
250
MAP kinase-interacting serine/threonine
MKNK2,
NM_199054




kinase 2
MNK2
NM_017572






SK236





TTAATGATAGCCATCCAGC
251
casein kinase 1, gamma 1
CSNK1G1,
NM_022048





CK1g1
SK647





ATTCCAGGCCATTTATGGC
252
granzyme K (serine protease, granzyme
GZMK
NM_002104




3; tryptase II)





TGTTAGACTACGTGATGAC
253
hypothetical protein FLJ14906
FLJ14906
NM_032859





CAACCTCACCTACAGGATC
254
matrix metalloproteinase 23A - matrix
MMP23A,
NM_006983




metalloproteinase 23B
MMP23B
NM_004659





TCTACCCGATCAACCACAC
255
matrix metalloproteinase 23A - matrix
MMP23A,
NM_006983




metalloproteinase 23B
MMP23B
NM_004659





CCCTTGGAGGAACTATGCC
256
LOC254378
LOC254378
XM_174812





CAACTCAGACAACTGCATC
257
LOC254378
LOC254378
XM_174812





TCATTGTAAGGCTGTGGCC
258
similar to bile salt-dependent lipase
LOC138529
XM_070951




oncofetal isoform





GGACCAATGGGAGATAGAC
259
fyn-related kinase
FRK
NM_002031





AGCTTATCCAGCTTTATGC
260
fyn-related kinase
FRK
NM_002031





GTGCATTAACAAGAAGAAC
261
unc-51-like kinase 1 (C. elegans)
ULK1
NM_003565





ACCTGCAGCCTTCACTTTC
262
chemokine (C—C motif) receptor 1
CCR1
NM_001295





TCCCTTCTGGATCGACTAC
263
chemokine (C—C motif) receptor 1
CCR1
NM_001295





CAATTATGAGTCCACGGTC
264
olfactory receptor, family 1, subfamily
OR1A2
NM_012352




A, member 2

NM_014565





AACGATGGGCATGTATTTC
265
olfactory receptor, family 1, subfamily
OR1A2
NM_012352




A, member 2





TGTCTCCTATGTTCAGGTC
266
olfactory receptor, family 1, subfamily
OR1A2
NM_012352




A, member 2





GTATGGACAGAACTGGCTC
267
sentrin/SUMO-specific protease 3
SENP3
NM_015670





GATGAACATGTATGGAGAC
268
sentrin/SUMO-specific protease 3
SENP3
NM_015670





ATTCCTTCAAACGTATGGC
269
sentrin/SUMO-specific protease 3
SENP3
NM_015670





GCTCCTGGAGAACATGTAC
270
taste receptor, type 1, member 3
TAS1R3
XM_371210





ACCAACCTCAGAGGTTCTC
271
thousand and one amino acid protein
TAO1
NM_016151




kinase - prostate derived STE20-like

NM_004783




kinase PSK





AAGCGGACCTACAAACTTC
272
thousand and one amino acid protein
TAO1
NM_016151




kinase - prostate derived STE20-like

NM_004783




kinase PSK





CGTCTACATGTACGTGTTC
273
solute carrier family 16 (monocar-
SLC16A3
NM_004207




boxylic acid transporters), member 3





GTGTGTACATCAACTGTTC
274
androgen-regulated short-chain
ARSDR1
NM_016026




dehydrogenase/reductase 1





GGCACAGTCCAATCTGAAC
275
androgen-regulated short-chain
ARSDR1
NM_016026




dehydrogenase/reductase 1





CGCAAGTTCTACTCCATCC
276
RAS, dexamethasone-induced 1
RASD1
NM_016084





GGTGTTCAGTCTGGACAAC
277
RAS, dexamethasone-induced 1
RASD1
NM_016084





GTGTTCAGTCTGGACAACC
278
RAS, dexamethasone-induced 1
RASD1
NM_016084





ACTTGAACTCTCTCCACAC
279
chromosome 20 open reading frame 121
C20orf121
NM_024331





GTCTTCAATAACTTGAAGC
280
chromosome 20 open reading frame 121
C20orf121
NM_024331





CCACAACAAGCACGTGTTC
281
HMT1 hnRNP methyltransferase-like 3
HRMT1L3
NM_019854




(S. cerevisiae)





ATCAATCGAAAGATTCTTC
282
interleukin-1 receptor-associated
IRAK2
NM_001570




kinase 2

SK180





CGACGTTGACAATTCCAGC
283
interleukin-1 receptor-associated
IRAK2
NM_001570




kinase 2

SK180





GCAGAGTTGCAGATTTGTC
284
interleukin-1 receptor-associated
IRAK2
NM_001570




kinase 2

SK180





TCAGCATTCCTACGATAAC
285
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





CCGGCAGAAGGATAACCTC
286
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





CCAGAACTGTGAAGTTTAC
287
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





GCATGGCAAGAAAGTTAAC
288
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





AGCATGTTATGCCTTATGC
289
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





TCATTGTTTCTGCCATAGC
290
glutamate receptor, ionotropic, N-
GRIN2A
NM_000833




methyl D-aspartate 2A





GATCTTTAACCAGCCTGAC
291
hypothetical protein FLJ22955
FLJ22955
NM_024819





GCACACCGTGGTAGTATAC
292
hypothetical protein FLJ22955
FLJ22955
NM_024819





GTCCTTCCACATCAAGAAC
293
tumor endothelial marker 5 precursor
TEM5
NM_032777





TGCAACCTCTTACCCAAGC
294
chloride intracellular channel 6
CLIC6
NM_053277





CTCAATCCCTTCGTCTACC
295
G protein-coupled receptor 150
GPR150
NM_199243





CGTGGTCTACGCGTTCTAC
296
LOC167417
XM_094471
XM_094471





CATTATCACCATGCTCGGC
297
G protein-coupled receptor 150
GPR150
NM_199243





TCTCTCTTCCTATCAATCC
298
chemokine (C—C motif) receptor 3
CCR3
NM_178329






NM_001837





CCAAACGTGTCTGGAAGAC
299
G protein-coupled receptor 23
GPR23
NM_005296





GTACCTGTAGCCATCTAAC
300
G protein-coupled receptor 64
GPR64
NM_005756





GCTAGTGAATAATGATTGC
301
G protein-coupled receptor 64
GPR64
NM_005756





ACACGACTATAAGTCTAAC
302
G protein-coupled receptor 64
GPR64
NM_005756





ACATTGCAATGGACAACAC
303
KIAA0943 protein
APG4B
NM_013325






NM_178326





GGAATATCCTGAGTGTTGC
304
dual specificity phosphatase 5
DUSP5
NM_004419





TGCCAGAGGGATGAACTAC
305
mitogen-activated protein kinase kinase
MAP3K9
NM_033141




kinase 9





ATGGAAGACTGCTGGAATC
306
mitogen-activated protein kinase kinase
MAP3K9
NM_033141




kinase 9





GAGCGCTTCAAACGAGATC
307
mitogen-activated protein kinase kinase
MAP3K9
NM_033141




kinase 9





ACCTGTCCCTAGATTCTTC
308
KIAA0943 protein
APG4B
NM_013325





ACGCATCTTGGCAAAGAGC
309
casein kinase 1, gamma 1
CSNK1G1-
NM_022048





CK1g1
SK647





ATTCCAGGGTTTATGTGTC
310
peptidylprolyl isomerase A
PPIA,
XM_372328





LOC390006,
XM_371409





LOC388817,
NM_203431





LOC442744,
XM_499491





LOC342541,
XM_292596





LOC344178,
XM_292963





LOC388687,
XM_371304





LOC391352,
XM_372916





LOC256374,
XM_170597





LOC388686,
XM_371302





LOC122335,
NM_021130





LOC390827,
XM_063084





LOC390956,
XM_497571





LOC442362,
XM_372741





LOC343384,
NM_203430





COAS2,
XM_498254





LOC44006,
XM_291544





LOC392352
NM_178230






XM_495896






XM_373301






XM_060887






XM_377444





CAACAGTGCATCTCTTATC
311
liver-specific organic anion trans-
LST-3
NM_001009562




porter 3

(XM_292093)





CAGCATCTACCTCCTGAAC
312
chemokine (C—C motif) receptor 1
CCR1
NM_001295





CAGCGCTCTCAATCCCTTC
313
G protein-coupled receptor 150
GPR150
NM_199243





CATCGACTATATAGCAGGC
314
carboxyl ester lipase (bile salt-
CEL
NM_001807




stimulated lipase)





CCAAGAGTCTATTCAAAGC
315
olfactory receptor, family 1, subfamily
OR1A2
NM_012352




A, member 2





CCACTAATGTCAACAATGC
316
G protein-coupled receptor 23
GPR23
NM_005296





CCACTCGTCAGATGTTTGC
317
LOC254378
LOC254378
XM_174812





CCCTGTCATTGATGGAGAC
318
carboxyl ester lipase (bile salt-
CEL
NM_001807




stimulated lipase)





CCGAGCCATATACTTGACC
319
chromosome 20 open reading frame 121
C20orf121
NM_024331





CCTAGAGCTGATTGAGTTC
320
MAP kinase-interacting serine/threonine
MKNK2-
NM_199054




kinase 2
MNK2
NM_017572






SK236





CCTCGACACCAAGTCTTGC
321
RAS, dexamethasone-induced 1
RASD1
NM_016084





CGCTCTTTAACATGAATGC
322
thousand and one amino acid protein
TAO1
NM_016151




kinase - prostate derived STE20-like

NM_004783




kinase PSK





CGTGGACATGGAGTACGAC
323
taste receptor, type 1, member 3
TAS1R3
XM_371210





CTCGTAATGAGACTATAGC
324
androgen-regulated short-chain
ARSDR1
NM_016026




dehydrogenase/reductase 1





CTGCAAATCTTCAGGTTTC
325
G protein-coupled receptor 64
GPR64
NM_005756





GAAGCACGATTTGGAGGTC
326
unc-51-like kinase 1 (C. elegans)
ULK1
NM_003565





GATGATGAAGGAGACGTTC
327
hypothetical protein FLJ22955
FLJ22955
NM_024819





GATTTGGTTATAAGGGTTC
328
peptidylprolyl isomerase A
LOC126170
XM_497621





LOC388817
XM_371409





PPIA
NM_203431





KBTBD9
XM_496546





LOC256374
XM_170597





LOC131055
XM_067176





LOC390956
NM_021130





LOC391062
XM_372741





LOC343384
XM_372785





LOC401859
NM_203430






XM_291544






XM_377444





GCTACTGCCCTATATGATC
329
solute carrier family 39 (zinc
SLC39A4
NM_017767




transporter), member 4

NM_130849





TCCGGTTCTATTTGATCGC
330
tumor endothelial marker 5 precursor
TEM5
NM_032777





TCGCCCTTCCTATTCCTTC
331
mitogen-activated protein kinase kinase
MAP3K9
NM_033141




kinase 9





TGTACGTGTTCATCCTGGC
332
solute carrier family 16 (monocar-
SLC16A3
NM_004207




boxylic acid transporters), member 3





TGTGACATTATGCCTTTGC
333
olfactory receptor, family 1, subfamily
OR1A2
NM_102352




A, member 2
























TABLE 2









KD










TARGET
TARGET

Genbank
DNA/RNA
Genbank
Polypeptide


TARGET
SEQ ID
Gene

DNA/RNA
SEQ ID
Polypeptide
SEQ ID


Id
NO.
Symbol
Class
Accession
NO.
Accession
NO.























H24-148
147
CLIC6
Ion Channel
XM_092804
335
XP_092804
377







NM_053277
336
NP_444507
378





H24-159
158
GPR23
GPCR
NM_005296
337
NP_005287
379





H24-160
159
GPR64
GPCR
NM_005756
338
NP_005747
380





H24-142
141
GRIN2A
Receptor
NM_000833
339
NP_000824
381





H24-024
26
MMP23A
Protease
NM_004659
340
NP_004650
382




MMP23B

NM_006983
341
NP_008914
383





H24-054
54
CCR1
GPCR
NM_001295
342
NP_001286
384





H24-128
127
HRMT1L3
Enzyme
NM_019854
343
NP_062828
385





H24-138
137
IRAK2
Kinase
NM_001570
344
NP_001561
386






SK180
345
SK180's protein
387





H24-194
189
MAP3K9
Kinase
NM_033141
346
NP_149132
388






XM_027237
347
XP_027237
389





H24-004
6
MKNK2
Kinase
SK236
348
SK236's protein
390






NM_017572
349
NP_060042
391






NM_199054
350
NP_951009
392





H24-097
96
TAOK2,
Kinase
NM_016151
351
NP_057235
393




PSK,

NM_004783
352
NP_004774
394




TAO1





H24-021
23
C13orf6,
Protease
NM_032859
353
NP_116248
395




FLJ14906





H24-157
156
CCR3
GPCR
NM_178329
354
NP_847899
396






NM_001837
355
NP_001828
397





H24-006
8
CSNK1G1
Kinase
NM_001011664
356
NP_001011664
398






(SK647)






NM_022048
357
NP_071331
399





H24-193
188
DUSP5
Phosphatase
NM_004419
358
NP_004410
400





H24-143
142
FLJ22955
Kinase
NM_024819
359
NP_079095
401





H24-149
148
GPR150
GPCR
XM_094471
360
XP_094471
402






NM_199243
361
NP_954713
403





H24-014
16
GZMK
Protease
NM_002104
362
NP_002095
404





H24-064;
63
OR1A1
GPCR
NM_014565
363
NP_055380
405


H24-164





H24-064;
63
OR1A2
GPCR
NM_012352
364
NP_036484
406


H24-164





H24-112
111
RASD1
Enzyme
NM_016084
365
NP_057168
407





H24-099
98
SLC16A3
Transporter
NM_004207
366
NP_004198
408





H24-049
1
AVPR1B
GPCR
NM_000707
367
NP_000698
409





H24-007
9
caMLCK
Kinase
SK536
368
SK536's protein
410






NM_182493
369
NP_872299
411






(AJ247087)





H24-185
180
CYP24A1
Cytochrome
NM_000782
370
NP_000773
412





P450





H24-169
164
GALR2
GPCR
NM_003857
371
NP_003848
413





H24-219
214
KCNG1
Ion Channel
NM_002237
372
NP_002228
414






NM_172318
373
NP_758529
415





H24-094
93
PAK6
Kinase
NM_020168
374
NP_064553
416






SK429
375
SK429's protein
417





H24-041
42
PIK3C2B
Kinase
NM_002646
376
NP_002637
418





H24-008
10
ROCK2
Kinase
NM_004850
600
NP_004841
601



















TABLE 2A











Seq ID





protein


Accession
Name
Protein Segment
segment







NP_444507
CLIC6
O—ClC: intracellular
419




chloride channel protein


NP_005287
GPR23
Extracellular domain
420




Transmembrane domain
421




Intracellular domain
422




Transmembrane domain
423




Extracellular domain
424




Transmembrane domain
425




Intracellular domain
426




Transmembrane domain
427




Extracellular domain
428




Transmembrane domain
429




Intracellular domain
430




Transmembrane domain
431




Extracellular domain
432




Transmembrane domain
433




Intracellular domain
434


NP_005747
GPR64
Extracellular domain
435




Transmembrane domain
436




Intracellular domain
437




Transmembrane domain
438




Extracellular domain
439




Transmembrane domain
440




Intracellular domain
441




Transmembrane domain
442




Extracellular domain
443




Transmembrane domain
444




Intracellular domain
445




Transmembrane domain
446




Extracellular domain
447




Transmembrane domain
448




Intracellular domain
449


NP_000824
GRIN2A
Lig_chan
450


NP_004650
MMP23A
ZnMc
451




Peptidase_M10
452




ShKToxin domain
453




Immunoglobulin
454


NP_008914
MMP23B
ZnMc
455




Peptidase_M10
456




ShKToxin domain
457




Immunoglobulin
458


NP_001286
CCR1
Extracellular domain
459




Transmembrane domain
460




Intracellular domain
461




Transmembrane domain
462




Extracellular domain
463




Transmembrane domain
464




Intracellular domain
465




Transmembrane domain
466




Extracellular domain
467




Transmembrane domain
468




Intracellular domain
469




Transmembrane domain
470




Extracellular domain
471




Transmembrane domain
472




Intracellular domain
473


NP_062828
HRMT1L3
Predicted RNA methylase
474


NP_001561
IRAK2
Death domain
475


SK180's protein

protein kinase
476


NP_149132
MAP3K9
SH3_1
477


XP_027237

protein kinase
478


SK236's protein
MKNK2
protein kinase
479


NP_060042
MKNK2
protein kinase
480


NP_951009


NP_057235
TAOK2 =
protein kinase
481


NP_004774
PSK = TAO1


NP_116248
C13orf6 =
Alpha/beta hydrolase
482



FLJ14906
fold-1


NP_847899
CCR3
Rhodopsin-like GPCR
483


NP_001828

superfamily




Extracellular domain
484




Transmembrane domain
485




Intracellular domain
486




Transmembrane domain
487




Extracellular domain
488




Transmembrane domain
489




Intracellular domain
490




Transmembrane domain
491




Extracellular domain
492




Transmembrane domain
493




Intracellular domain
494




Transmembrane domain
495




Extracellular domain
496




Transmembrane domain
497




Intracellular domain
498


NP_001011664
CSNK1G1
protein kinase
499


NP_071331


NP_004410
DUSP5
Rhodanese-like
500




Dual specificity protein
501




phosphatase


NP_079095
FLJ22955
Dephospho-CoA kinase
502


XP_094471
GPR150
Intracellular domain
503




Transmembrane domain
504




Extracellular domain
505




Transmembrane domain
506




Intracellular domain
507




Transmembrane domain
508




Extracellular domain
509




Transmembrane domain
510




Intracellular domain
511


NP_954713
GPR150
Extracellular domain
512




Transmembrane domain
513




Intracellular domain
514




Transmembrane domain
515




Extracellular domain
516




Transmembrane domain
517




Intracellular domain
518




Transmembrane domain
519




Extracellular domain
520




Transmembrane domain
521




Intracellular domain
522


NP_002095
GZMK
Peptidase S1 and S6,
523




chymotrypsin/Hap


NP_055380
OR1A1
Extracellular domain
524




Transmembrane domain
525




Intracellular domain
526




Transmembrane domain
527




Extracellular domain
528




Transmembrane domain
529




Intracellular domain
530




Transmembrane domain
531




Extracellular domain
532




Transmembrane domain
533




Intracellular domain
534




Transmembrane domain
535




Extracellular domain
536




Transmembrane domain
537




Intracellular domain
538


NP_036484
OR1A2
Extracellular domain
539




Transmembrane domain
540




Intracellular domain
541




Transmembrane domain
542




Extracellular domain
543




Transmembrane domain
544




Intracellular domain
545




Transmembrane domain
546




Extracellular domain
547




Transmembrane domain
548




Intracellular domain
549




Transmembrane domain
550




Extracellular domain
551




Transmembrane domain
552




Intracellular domain
553


NP_057168
RASD1
Ras small GTPase,
554




Ras type


NP_004198
SLC16A3
Major facilitator
555




superfamily MFS_1


NP_000698
AVPR1B
Extracellular domain
556




Transmembrane domain
557




Intracellular domain
558




Transmembrane domain
559




Extracellular domain
560




Transmembrane domain
561




Intracellular domain
562




Transmembrane domain
563




Extracellular domain
564




Transmembrane domain
565




Intracellular domain
566




Transmembrane domain
567




Extracellular domain
568




Transmembrane domain
569




Intracellular domain
570


SK536's protein
caMLCK
Protein kinase
571


NP_872299
caMLCK
Serine/threonine
572




protein kinase


NP_000773
CYP24A1
Cytochrome P450
573


NP_003848
GALR2
Extracellular domain
574




Transmembrane domain
575




Intracellular domain
576




Transmembrane domain
577




Extracellular domain
578




Transmembrane domain
579




Intracellular domain
580




Transmembrane domain
581




Extracellular domain
582




Transmembrane domain
583




Intracellular domain
584




Transmembrane domain
585




Extracellular domain
586




Transmembrane domain
587




Intracellular domain
588


NP_002228
KCNG1
K+ channel
589




tetramerisation




Ion transport
590


NP_758529
KCNG1
K+ channel
591




tetramerisation


NP_064553
PAK6
PAK-box/P21-Rho-binding
592


SK429's protein




Serine/threonine
593




protein kinase


NP_002637
PIK3C2B
Phosphoinositide
594




3-kinase, ras-binding




Phosphoinositide
595




3-kinase, C2




Phosphoinositide
596




3-kinase accessory




region PIK




Phosphatidylinositol
597




3-and 4-kinase, catalytic




Phox-like
598




C2
599


NP_004841
ROCK2
Serine/threonine
602




protein kinase




Protein kinase, C-terminal
603




PKN/rhophilin/rhotekin
604




rho-binding repeat




Pleckstrin-like
605




Protein kinase C,
606




phorbol ester/dia-




cylglycerol binding









Table 3 lists the preferred loop sequence for a shRNA.

TABLE 3NameSequenceSEQ ID NO:Loop regionGTTTGCTATAAC334


The present invention relates to a method for assaying for compounds that induce osteoblast differentiation, comprising contacting the compound with a polypeptide comprising an amino acid sequence of the polypeptides of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133 (“TARGETS”) under conditions that allow said polypeptide to bind to the compound, and detecting the formation of a complex between the polypeptide and the compound. One preferred means of measuring the complex formation is to determine the binding affinity of said compound to said polypeptide.


More particularly, the invention relates to a method for identifying an agent that induces differentiation of undifferentiated mammalian cells into osteoblasts, the method comprising further:

    • (a) contacting a population of undifferentiated vertebrate cells with one or more of said compound that exhibits binding affinity for said TARGETS, and
    • (b) measuring a compound-polypeptide property related to the differentiation of said cells into osteoblasts.


The compound-polypeptide property referred to above is related to the differentiation of cells into osteoblasts, and is a measurable phenomenon chosen by the person of ordinary skill in the art. The measurable property may e.g. be the binding affinity for a peptide domain of the polypeptide TARGET or the level of any one of a number of biochemical marker levels of osteoblast differentiation. Osteoblast differentiation can e.g. be measured by measuring the level of enzymes that are induced during the differentiation process, such as alkaline phosphatase, type-1 collagen, osteocalcin and osteopontin. The alkaline phosphatase activity can be measured by adding methylumbelliferyl heptaphosphate (MUP) solution (Sigma) to the cells. The fluorescence generated upon cleavage of the MUP substrate by the AP activity is measured on a fluorescence plate reader (Fluostar, BMG).


In a preferred embodiment of the invention, the polypeptide TARGET comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133 (Tables 1, 2, and 2A). In another preferred embodiment of the invention, the polypeptide TARGET comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606 (Tables 2 and 2A).


A preferred class of the polypeptides used as TARGETS are G-Protein Coupled Receptors (GPCR), wherein the expression and/or activity of said GPCR may be measured by determining the level of any one of the second messengers cyclic AMP, Ca2+ or both. Preferably, the level of the second messenger is determined with a reporter gene under the control of a promoter that is responsive to the second messenger. More preferably, the promoter is a cyclic AMP-responsive promoter, an NF-KB responsive promoter, or a NF-AT responsive promoter. In another preferred embodiment, the reporter gene is selected from the group consisting of: alkaline phosphatase, GFP, eGFP, dGFP, luciferase and b-galactosidase.


Other preferred classes of polypeptides used as TARGETS include kinases and phosphatases. Kinases are enzymes that transfer phosphate groups from high-energy donor molecules, such as ATP, to specific target molecules (substrates); the process is termed phosphorylation. Phosphatases remove phosphate groups from substrates. The activity of kinases or phosphatases may be measured by determining the level of phosphorylation or dephosphorylation of a substrate of said polypeptide. It is well known in the art how to measure this activity by using the respective substrate and to perform assays in which the substrate gets phosphorylated or dephosphorylated upon activation of the kinase or phosphatase. This means that the activity of the kinase or phosphatase can easily be scored through the phosphorylation status of its substrate.


Another preferred class of polypeptides used as TARGETS are proteases. Proteases are enzymes that break peptide bonds between amino acids of proteins; the process is called proteolytic cleavage. Protease activity can be measured through the level of cleavage of the respective substrate, which is a preferred method according to the invention to determine the activity level of the protease. Classically, substrates are used in which a fluorescent group is linked to a quencher through a peptide sequence that is a substrate that can be cleaved by the target protease. Cleavage of the linker separates the fluorescent group and quencher, giving rise to an increase in fluorescence.


Another preferred class of polypeptides used as TARGETS are ion channels. Ion channels are membrane protein complexes and their function is to facilitate the diffusion of ions across biological membranes. Membranes, or phospholipid bilayers, build a hydrophobic, low dielectric barrier to hydrophilic and charged molecules. Ion channels provide a high conducting, hydrophilic pathway across the hydrophobic interior of the membrane. The activity of an ion channel can be measured using classical patch clamping. High-throughput fluorescence-based or tracer-based assays are also widely available to measure ion channel activity. These fluorescent-based assays screen compounds on the basis of their ability to either open or close an ion channel thereby changing the concentration of specific fluorescent dyes across a membrane. In the case of the tracer based assay, the changes in concentration of the tracer within and outside the cell are measured by radioactivity measurement or gas absorption spectrometry.


Depending on the choice of the skilled artisan, the present assay method may be designed to function as a series of measurements, each of which is designed to determine whether the drug candidate compound is indeed acting on the polypeptide to thereby induce the differentiation of undifferentiated cells into osteoblasts. For example, an assay designed to determine the binding affinity of a compound to the polypeptide, or fragment thereof, may be necessary, but not sufficient, to ascertain whether the test compound would be useful for increasing mean bone density when administered to a subject. Nonetheless, such binding information would be useful in identifying a set of test compounds for use in an assay that would measure a different property, further down the biochemical pathway, such as bone mineralization, assayed by measuring the amount of deposited calcium. Such second assay may be designed to confirm that the test compound, having binding affinity for the polypeptide, actually induces the differentiation of undifferentiated cells into osteoblasts. Suitable controls should always be in place to insure against false positive readings.


The order of taking these measurements is not believed to be critical to the practice of the present invention, which may be practiced in any order. For example, one may first perform a screening assay of a set of compounds for which no information is known respecting the compounds' binding affinity for the polypeptide. Alternatively, one may screen a set of compounds identified as having binding affinity for a polypeptide domain, or a class of compounds identified as being an inhibitor of the polypeptide. However, for the present assay to be meaningful to the ultimate use of the drug candidate compounds, a measurement of bone alkaline phosphatase levels or bone mineralization is necessary. Validation studies including controls, and measurements of binding affinity to the polypeptides of the invention are nonetheless useful in identifying a compound useful in any therapeutic or diagnostic application.


The binding affinity of the compound with the polypeptide TARGET can be measured by methods known in the art, such as using surface plasmon resonance biosensors (Biacore), by saturation binding analysis with a labeled compound (e.g. Scatchard and Lindmo analysis), by differential UV spectrophotometer, fluorescence polarization assay, Fluorometric Imaging Plate Reader (FLIPR®) system, Fluorescence resonance energy transfer, and Bioluminescence resonance energy transfer. The binding affinity of compounds can also be expressed in dissociation constant (Kd) or as IC50 or EC50. The IC50 represents the concentration of a compound that is required for 50% inhibition of binding of another ligand to the polypeptide. The EC50 represents the concentration required for obtaining 50% of the maximum effect in any assay that measures TARGET function. The dissociation constant, Kd, is a measure of how well a ligand binds to the polypeptide, it is equivalent to the ligand concentration required to saturate exactly half of the binding-sites on the polypeptide. Compounds with a high affinity binding have low Kd, IC50 and EC50 values, i.e. in the range of 100 nM to 1 pM; a moderate to low affinity binding relates to a high Kd, IC50 and EC50 values, i.e. in the micromolar range.


The present assay method may also be practiced in a cellular assay, A host cell expressing TARGET can be a cell with endogenous expression or a cell over-expressing the TARGET e.g. by transduction. When the endogenous expression of the polypeptide is not sufficient to determine a baseline that can easily be measured, one may use host cells that over-express TARGET. Over-expression has the advantage that the level of the TARGET substrate end products is higher than the activity level by endogenous expression. Accordingly, measuring such levels using presently available techniques is easier. In such cellular assay, the biological activity of TARGET may be measured by following the production of bone alkaline phosphatase (BAP) or bone mineralization.


The present invention further relates to a method for identifying a compound that induces differentiation of undifferentiated mammalian cells into osteoblasts, comprising:

    • (a) contacting a compound with a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133;
    • (b) determining the binding affinity of the compound to the polypeptide;
    • (c) contacting a population of mammalian cells expressing said polypeptide with the compound that exhibits a binding affinity of at least 10 micromolar; and
    • (d) identifying the compound that induces the differentiation of said undifferentiated cells.


For high-throughput purposes, libraries of compounds may be used such as antibody fragment libraries, peptide phage display libraries, peptide libraries (e.g. LOPAP™, Sigma Aldrich), lipid libraries (BioMol), synthetic compound libraries (e.g. LOPAC™, Sigma Aldrich) or natural compound libraries (Specs, TimTec).


Preferred drug candidate compounds are low molecular weight compounds. Low molecular weight compounds, i.e. with a molecular weight of 500 Dalton or less, are likely to have good absorption and permeation in biological systems and are consequently more likely to be successful drug candidates than compounds with a molecular weight above 500 Dalton (Lipinski et al. (1997)). Peptides comprise another preferred class of drug candidate compounds. Peptides may be excellent drug candidates and there are multiple examples of commercially valuable peptides such as fertility hormones and platelet aggregation inhibitors. Natural compounds are another preferred class of drug candidate compound. Such compounds are found in and extracted from natural sources, and which may thereafter be synthesized. The lipids are another preferred class of drug candidate compound.


Another preferred class of drug candidate compounds is an antibody. The present invention also provides antibodies directed against a TARGET. These antibodies may be endogenously produced to bind to the TARGET within the cell, or added to the tissue to bind to TARGET polypeptide present outside the cell. These antibodies may be monoclonal antibodies or polyclonal antibodies. The present invention includes chimeric, single chain, and humanized antibodies, as well as FAb fragments and the products of a FAb expression library, and Fv fragments and the products of an Fv expression library.


In certain embodiments, polyclonal antibodies may be used in the practice of the invention. The skilled artisan knows methods of preparing polyclonal antibodies. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. Antibodies may also be generated against the intact TARGET protein or polypeptide, or against a fragment, derivatives including conjugates, or other epitope of the TARGET protein or polypeptide, such as the TARGET embedded in a cellular membrane, or a library of antibody variable regions, such as a phage display library.


It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants that may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). One skilled in the art without undue experimentation may select the immunization protocol.


In some embodiments, the antibodies may be monoclonal antibodies. Monoclonal antibodies may be prepared using methods known in the art. The monoclonal antibodies of the present invention may be “humanized” to prevent the host from mounting an immune response to the antibodies. A “humanized antibody” is one in which the complementarity determining regions (CDRs) and/or other portions of the light and/or heavy variable domain framework are derived from a non-human immunoglobulin, but the remaining portions of the molecule are derived from one or more human immunoglobulins. Humanized antibodies also include antibodies characterized by a humanized heavy chain associated with a donor or acceptor unmodified light chain or a chimeric light chain, or vice versa. The humanization of antibodies may be accomplished by methods known in the art (see, e.g. Mark and Padlan, (1994) “Chapter 4. Humanization of Monoclonal Antibodies”, The Handbook of Experimental Pharmacology Vol. 113, Springer-Verlag, New York). Transgenic animals may be used to express humanized antibodies.


Human antibodies can also be produced using various techniques known in the art, including phage display libraries (Hoogenboom and Winter, (1991) J. Mol. Biol. 227:381-8; Marks et al. (1991). J. Mol. Biol. 222:581-97). The techniques of Cole, et al. and Boerner, et al. are also available for the preparation of human monoclonal antibodies (Cole, et al. (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77; Boerner, et al (1991). J. Immunol., 147(1):86-95).


Techniques known in the art for the production of single chain antibodies can be adapted to produce single chain antibodies to the TARGET polypeptides and proteins of the present invention. The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain cross-linking. Alternatively; the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent cross-linking.


Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens and preferably for a cell-surface protein or receptor or receptor subunit. In the present case, one of the binding specificities is for one domain of the TARGET; the other one is for another domain of the same or different TARGET.


Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, (1983) Nature 305:537-9). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. Affinity chromatography steps usually accomplish the purification of the correct molecule. Similar procedures are disclosed in Trauneeker, et al. (1991) EMBO J. 10:3655-9.


According to another preferred embodiment, the assay method uses a drug candidate compound identified as having a binding affinity for a TARGET, and/or has already been identified as having down-regulating activity such as antagonist activity vis-à-vis one or more TARGET.


The present invention further relates to a method for inducing differentiation of undifferentiated mammalian cells into osteoblasts comprising contacting said cells with an expression inhibitory agent comprising a polynucleotide sequence that complements at least about 17 nucleotides of the polyribonucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 335-376, 600, 607-866, 1120-1122.


Another aspect of the present invention relates to a method for inducing the differentiation of undifferentiated mammalian cells into osteoblasts, comprising by contacting said cell with an expression-inhibiting agent that inhibits the translation in the cell of a polyribonucleotide encoding a TARGET polypeptide. A particular embodiment relates to a composition comprising a polynucleotide including at least one antisense strand that functions to pair the agent with the TARGET mRNA, and thereby down-regulate or block the expression of TARGET polypeptide. The inhibitory agent preferably comprises antisense polynucleotide, a ribozyme, and a small interfering RNA (siRNA), wherein said agent comprises a nucleic acid sequence complementary to, or engineered from, a naturally-occurring polynucleotide sequence encoding a portion of a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133. In a preferred embodiment the expression-inhibiting agent is complementary to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 335-376, 600, 607-866, 1120-1122. In another preferred embodiment the expression-inhibiting agent is complementary to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-220, 247-333.


An embodiment of the present invention relates to a method wherein the expression-inhibiting agent is selected from the group consisting of antisense RNA, antisense oligodeoxynucleotide (ODN), a ribozyme that cleaves the polyribonucleotide coding for SEQ ID NO: 377-418, 601, 867-1119, 1123-1133, a small interfering RNA (siRNA, preferably shRNA,) that is sufficiently complementary to a portion of the polyribonucleotide coding for SEQ ID NO: 377-418, 601, 867-1119, 1123-1133, such that the siRNA, preferably shRNA, interferes with the translation of the TARGET polyribonucleotide to the TARGET polypeptide. Preferably the expression-inhibiting agent is an antisense RNA, ribozyme, antisense oligodeoxynucleotide, or siRNA, preferably shRNA, complementary to a nucleotide sequence selected from the group consisting of SEQ ID NO: 335-376, 600, 607-866, 1120-1122.


A special embodiment of the present invention relates to a method wherein the expression-inhibiting agent is a nucleic acid expressing the antisense RNA, antisense oligodeoxynucleotide (ODN), a ribozyme that cleaves the polyribonucleotide coding for SEQ ID NO: 377-418, 601, a small interfering RNA (siRNA, preferably shRNA,) that is sufficiently complementary to a portion of the polyribonucleotide corresponding to SEQ ID NO: 377-418, 601, such that the siRNA, preferably shRNA, interferes with the translation of the TARGET polyribonucleotide to the TARGET polypeptide. Preferably the nucleotide sequence is complementary to a polynucleotide selected from the group consisting of SEQ ID NO: 335-376, 600. In another preferred embodiment nucleotide sequence is complementary to a polynucleotide selected from the group consisting of SEQ ID NO: 1, 6, 8, 9, 10, 16, 23, 26, 42, 54, 63, 93, 96, 98, 111, 127, 137, 141, 142, 147, 148, 156, 158, 159, 164, 180, 188, 189, 214.


The down regulation of gene expression using antisense nucleic acids can be achieved at the translational or transcriptional level. Antisense nucleic acids of the invention are preferably nucleic acid fragments capable of specifically hybridizing with all or part of a nucleic acid encoding a TARGET polypeptide or the corresponding messenger RNA. In addition, antisense nucleic acids may be designed which decrease expression of the nucleic acid sequence capable of encoding a TARGET polypeptide by inhibiting splicing of its primary transcript. Any length of antisense sequence is suitable for practice of the invention so long as it is capable of down-regulating or blocking expression of a nucleic acid coding for a TARGET. Preferably, the antisense sequence is at least about 17 nucleotides in length. The preparation and use of antisense nucleic acids, DNA encoding antisense RNAs and the use of oligo and genetic antisense is known in the art.


One embodiment of expression-inhibitory agent is a nucleic acid that is antisense to a nucleic acid comprising SEQ ID NO: 335-376, 600, 607-866, 1120-1122. For example, an antisense nucleic acid (e.g. DNA) may be introduced into cells in vitro, or administered to a subject in vivo, as gene therapy to inhibit cellular expression of nucleic acids comprising SEQ ID NO: 335-376, 600, 607-866, 1120-1122. Antisense oligonucleotides preferably comprise a sequence containing from about 17 to about 100 nucleotides and more preferably the antisense oligonucleotides comprise from about 18 to about 30 nucleotides. Antisense nucleic acids may be prepared from about 10 to about 30 contiguous nucleotides complementary to a nucleic acid sequence selected from the sequences of SEQ ID NO: 335-376, 600, 607-866, 1120-1122.


The antisense nucleic acids are preferably oligonucleotides and may consist entirely of deoxyribo-nucleotides, modified deoxyribonucleotides, or some combination of both. The antisense nucleic acids can be synthetic oligonucleotides. The oligonucleotides may be chemically modified, if desired, to improve stability and/or selectivity. Since oligonucleotides are susceptible to degradation by intracellular nucleases, the modifications can include, for example, the use of a sulfur group to replace the free oxygen of the phosphodiester bond. This modification is called a phosphorothioate linkage. Phosphorothioate antisense oligonucleotides are water soluble, polyanionic, and resistant to endogenous nucleases. In addition, when a phosphorothioate antisense oligonucleotide hybridizes to its TARGET site, the RNA-DNA duplex activates the endogenous enzyme ribonuclease (RNase) H, which cleaves the mRNA component of the hybrid molecule.


In addition, antisense oligonucleotides with phosphoramidite and polyamide (peptide) linkages can be synthesized. These molecules should be very resistant to nuclease degradation. Furthermore, chemical groups can be added to the 2′ carbon of the sugar moiety and the 5 carbon (C-5) of pyrimidines to enhance stability and facilitate the binding of the antisense oligonucleotide to its TARGET site. Modifications may include 2′-deoxy, O-pentoxy, O-propoxy, O-methoxy, fluoro, methoxyethoxy phosphorothioates, modified bases, as well as other modifications known to those of skill in the art.


Another type of expression-inhibitory agent that reduces the levels of TARGETS is the ribozyme. Ribozymes are catalytic RNA molecules (RNA enzymes) that have separate catalytic and substrate binding domains. The substrate binding sequence combines by nucleotide complementarity and, possibly, non-hydrogen bond interactions with its TARGET sequence. The catalytic portion cleaves the TARGET RNA at a specific site. The substrate domain of a ribozyme can be engineered to direct it to a specified mRNA sequence. The ribozyme recognizes and then binds a TARGET mRNA through complementary base pairing. Once it is bound to the correct TARGET site, the ribozyme acts enzymatically to cut the TARGET mRNA. Cleavage of the mRNA by a ribozyme destroys its ability to direct synthesis of the corresponding polypeptide. Once the ribozyme has cleaved its TARGET sequence, it is released and can repeatedly bind and cleave at other mRNAs.


Ribozyme forms include a hammerhead motif, a hairpin motif, a hepatitis delta virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) motif or Neurospora VS RNA motif. Ribozymes possessing a hammerhead or hairpin structure are readily prepared since these catalytic RNA molecules can be expressed within cells from eukaryotic promoters (Chen, et al. (1992) Nucleic Acids Res. 20:4581-9). A ribozyme of the present invention can be expressed in eukaryotic cells from the appropriate DNA vector. If desired, the activity of the ribozyme may be augmented by its release from the primary transcript by a second ribozyme (Ventura, et al. (1993) Nucleic Acids Res. 21:3249-55).


Ribozymes may be chemically synthesized by combining an oligodeoxyribonucleotide with a ribozyme catalytic domain (20 nucleotides) flanked by sequences that hybridize to the TARGET mRNA after transcription. The oligodeoxyribonucleotide is amplified by using the substrate binding sequences as primers. The amplification product is cloned into a eukaryotic expression vector.


Ribozymes are expressed from transcription units inserted into DNA, RNA, or viral vectors. Transcription of the ribozyme sequences are driven from a promoter for eukaryotic RNA polymerase I (pol (I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on nearby gene regulatory sequences. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Gao and Huang, (1993) Nucleic Acids Res. 21:2867-72). It has been demonstrated that ribozymes expressed from these promoters can function in mammalian cells (Kashani-Sabet, et al. (1992) Antisense Res. Dev. 2:3-15).


A particularly preferred inhibitory agent is a small interfering RNA (siRNA, preferably shRNA). siRNA, preferably shRNA, mediate the post-transcriptional process of gene silencing by double stranded RNA (dsRNA) that is homologous in sequence to the silenced RNA. siRNA according to the present invention comprises a sense strand of 17-25 nucleotides complementary or homologous to a contiguous 17-25 nucleotide sequence selected from the group of sequences described in SEQ ID NO: 335-376, 600, 607-866, 1120-1122, preferably from the group of sequences described in SEQ ID No: 335-376, 600, and an antisense strand of 17-23 nucleotides complementary to the sense strand. Exemplary sequences are described as sequences complementary to SEQ ID NO: 1-220, 247-333. The most preferred siRNA comprises sense and anti-sense strands that are 100 per cent complementary to each other and the TARGET polynucleotide sequence. Preferably the siRNA further comprises a loop region linking the sense and the antisense strand.


A self-complementing single stranded siRNA molecule polynucleotide according to the present invention comprises a sense portion and an antisense portion connected by a loop region linker. Preferably, the loop region sequence is 4-30 nucleotides long, more preferably 5-15 nucleotides long and most preferably 12 nucleotides long. In a most preferred embodiment the linker sequence is GTTTGCTATAAC (SEQ ID NO: 334). Self-complementary single stranded siRNAs form hairpin loops and are more stable than ordinary dsRNA. In addition, they are more easily produced from vectors.


Analogous to antisense RNA, the siRNA can be modified to confirm resistance to nucleolytic degradation, or to enhance activity, or to enhance cellular distribution, or to enhance cellular uptake, such modifications may consist of modified internucleoside linkages, modified nucleic acid bases, modified sugars and/or chemical linkage the siRNA to one or more moieties or conjugates. The nucleotide sequences are selected according to siRNA designing rules that give an improved reduction of the TARGET sequences compared to nucleotide sequences that do not comply with these siRNA designing rules (For a discussion of these rules and examples of the preparation of siRNA, WO2004094636, published Nov. 4, 2004, and UA20030198627, are hereby incorporated by reference).


The present invention also relates to compositions, and methods using said compositions, comprising a DNA expression vector capable of expressing a polynucleotide capable of inducing osteoblast differentiation and described hereinabove as an expression inhibition agent.


A special aspect of these compositions and methods relates to the down-regulation or blocking of the expression of a TARGET polypeptide by the induced expression of a polynucleotide encoding an intracellular binding protein that is capable of selectively interacting with the TARGET polypeptide. An intracellular binding protein includes any protein capable of selectively interacting, or binding, with the polypeptide in the cell in which it is expressed and neutralizing the function of the polypeptide. Preferably, the intracellular binding protein is a neutralizing antibody or a fragment of a neutralizing antibody having binding affinity to an epitope of the TARGET polypeptide of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133, preferably SEQ ID NO: 377-599, 601-606. More preferably, the intracellular binding protein is a single chain antibody.


A special embodiment of this composition comprises the expression-inhibiting agent selected from the group consisting of antisense RNA, antisense oligodeoxynucleotide (ODN), a ribozyme that cleaves the polyribonucleotide coding for SEQ ID NO: 377418, 601, 867-1119, 1123-1133, preferably SEQ ID NO: 377418, 601, and a small interfering RNA (siRNA) that is sufficiently homologous to a portion of the polyribonucleotide coding for SEQ ID NO: 377-418, 601, 867-1119, 1123-1133, preferably SEQ ID NO: 377-418, 601, such that the siRNA interferes with the translation of the TARGET polyribonucleotide to the TARGET polypeptide.


The polynucleotide expressing the expression-inhibiting agent is preferably included within a vector. The polynucleic acid is operably linked to signals enabling expression of the nucleic acid sequence and is introduced into a cell utilizing, preferably, recombinant vector constructs, which will express the antisense nucleic acid once the vector is introduced into the cell. A variety of viral-based systems are available, including adenoviral, retroviral, adeno-associated viral, lentiviral, herpes simplex viral or a sendaviral vector systems, and all may be used to introduce and express polynucleotide sequence for the expression-inhibiting agents in TARGET cells.


Preferably, the viral vectors used in the methods of the present invention are replication defective. Such replication defective vectors will usually pack at least one region that is necessary for the replication of the virus in the infected cell. These regions can either be eliminated (in whole or in part), or be rendered non-functional by any technique known to a person skilled in the art. These techniques include the total removal, substitution, partial deletion or addition of one or more bases to an essential (for replication) region. Such techniques may be performed in vitro (on the isolated DNA) or in situ, using the techniques of genetic manipulation or by treatment with mutagenic agents. Preferably, the replication defective virus retains the sequences of its genome, which are necessary for encapsidating, the viral particles.


In a preferred embodiment, the viral element is derived from an adenovirus. Preferably, the vehicle includes an adenoviral vector packaged into an adenoviral capsid, or a functional part, derivative, and/or analogue thereof. Adenovirus biology is also comparatively well known on the molecular level. Many tools for adenoviral vectors have been and continue to be developed, thus making an adenoviral capsid a preferred vehicle for incorporating in a library of the invention. An adenovirus is capable of infecting a wide variety of cells. However, different adenoviral serotypes have different preferences for cells. To combine and widen the TARGET cell population that an adenoviral capsid of the invention can enter in a preferred embodiment, the vehicle includes adenoviral fiber proteins from at least two adenoviruses. Preferred adenoviral fiber protein sequences are serotype 17, 45 and 51. Techniques or construction and expression of these chimeric vectors are disclosed in US Published Patent Applications 20030180258 and 20040071660, hereby incorporated by reference.


In a preferred embodiment, the nucleic acid derived from an adenovirus includes the nucleic acid encoding an adenoviral late protein or a functional part, derivative, and/or analogue thereof. An adenoviral late protein, for instance an adenoviral fiber protein, may be favorably used to TARGET the vehicle to a certain cell or to induce enhanced delivery of the vehicle to the cell. Preferably, the nucleic acid derived from an adenovirus encodes for essentially all adenoviral late proteins, enabling the formation of entire adenoviral capsids or functional parts, analogues, and/or derivatives thereof. Preferably, the nucleic acid derived from an adenovirus includes the nucleic acid encoding adenovirus E2A or a functional part, derivative, and/or analogue thereof. Preferably, the nucleic acid derived from an adenovirus includes the nucleic acid encoding at least one E4-region protein or a functional part, derivative, and/or analogue thereof, which facilitates, at least in part, replication of an adenoviral derived nucleic acid in a cell. The adenoviral vectors used in the examples of this application are exemplary of the vectors useful in the present method of treatment invention.


Certain embodiments of the present invention use retroviral vector systems. Retroviruses are integrating viruses that infect dividing cells, and their construction is known in the art. Retroviral vectors can be constructed from different types of retrovirus, such as, MoMuLV (“murine Moloney leukemia virus” MSV (“murine Moloney sarcoma virus”), HaSV (“Harvey sarcoma virus”); SNV (“spleen necrosis virus”); RSV (“Rous sarcoma virus”) and Friend virus. Lentiviral vector systems may also be used in the practice of the present invention.


In other embodiments of the present invention, adeno-associated viruses (“AAV”) are utilized. The AAV viruses are DNA viruses of relatively small size that integrate, in a stable and site-specific manner, into the genome of the infected cells. They are able to infect a wide spectrum of cells without inducing any effects on cellular growth, morphology or differentiation, and they do not appear to be involved in human pathologies.


In the vector construction, the polynucleotide agents of the present invention may be linked to one or more regulatory regions. Selection of the appropriate regulatory region or regions is a routine matter, within the level of ordinary skill in the art. Regulatory regions include promoters, and may include enhancers, suppressors, etc.


Promoters that may be used in the expression vectors of the present invention include both constitutive promoters and regulated (inducible) promoters. The promoters may be prokaryotic or eukaryotic depending on the host. Among the prokaryotic (including bacteriophage) promoters useful for practice of this invention are lac, lacZ, T3, T7, lambda Pr, Pl, and trp promoters. Among the eukaryotic (including viral) promoters useful for practice of this invention are ubiquitous promoters (e.g. HPRT, vimentin, actin, tubulin), intermediate filament promoters (e.g. desmin, neurofilaments, keratin, GFAP), therapeutic gene promoters (e.g. MDR type, CFTR, factor VIII), tissue-specific promoters (e.g. actin promoter in smooth muscle cells, or Flt and Flk promoters active in endothelial cells), including animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells (Swift, et al. (1984) Cell 38:639-46; Omitz, et al. (1986) Cold Spring Harbor Symp. Quant. Biol. 50:399-409; MacDonald, (1987) Hepatology 7:425-515); insulin gene control region which is active in pancreatic beta cells (Hanahan, (1985) Nature 315:115-22), immunoglobulin gene control region which is active in lymphoid cells (Grosschedl, et al. (1984) Cell 38:647-58; Adames, et al. (1985) Nature 318:533-8; Alexander, et al. (1987) Mol. Cell. Biol. 7:143-644), mouse mammary tumor virus control region which is active in testicular, breast, lymphoid and mast cells (Leder, et al. (1986) Cell 45:485-95), albumin gene control region which is active in liver (Pinkert, et al. (1987) Genes and Devel. 1:268-76), alpha-fetoprotein gene control region which is active in liver (Krumlauf, et al. (1985) Mol. Cell. Biol., 5:1639-48; Hammer, et al. (1987) Science 235:53-8), alpha 1-antitrypsin gene control region which is active in the liver (Kelsey, et al. (1987) Genes and Devel., 1: 161-71), beta-globin gene control region which is active in myeloid cells (Mogram, et al. (1985) Nature 315:338-40; Kollias, et al. (1986) Cell 46:89-94), myelin basic protein gene control region which is active in oligodendrocyte cells in the brain (Readhead, et al. (1987) Cell 48:703-12), myosin light chain-2 gene control region which is active in skeletal muscle (Sani, (1985) Nature 314.283-6), and gonadotropic releasing hormone gene control region which is active in the hypothalamus (Mason, et al. (1986) Science 234:1372-8).


Other promoters which may be used in the practice of the invention include promoters which are preferentially activated in dividing cells, promoters which respond to a stimulus (e.g. steroid hormone receptor, retinoic acid receptor), tetracycline-regulated transcriptional modulators, cytomegalovirus immediate-early, retroviral LTR, metallothionein, SV40, E1a, and MLP promoters.


Additional vector systems include the non-viral systems that facilitate introduction of polynucleotide agents into a patient. For example, a DNA vector encoding a desired sequence can be introduced in vivo by lipofection. Synthetic cationic lipids designed to limit the difficulties encountered with liposome-mediated transfection can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Felgner, et. al. (1987) Proc. Natl. Acad Sci. USA 84:7413-7); see Mackey, et al. (1988) Proc. Natl. Acad. Sci. USA 85:8027-31; Ulmer, et al. (1993) Science 259:1745-8). The use of cationic lipids may promote encapsulation of negatively charged nucleic acids, and also promote fusion with negatively charged cell membranes (Felgner and Ringold, (1989) Nature 337:387-8). Particularly useful lipid compounds and compositions for transfer of nucleic acids are described in International Patent Publications WO 95/18863 and WO 96/17823, and in U.S. Pat. No. 5,459,127. The use of lipofection to introduce exogenous genes into the specific organs in vivo has certain practical advantages and directing transfection to particular cell types would be particularly advantageous in a tissue with cellular heterogeneity, for example, pancreas, liver, kidney, and the brain. Lipids may be chemically coupled to other molecules for the purpose of targeting. Targeted peptides, e.g., hormones or neurotransmitters, and proteins for example, antibodies, or non-peptide molecules could be coupled to liposomes chemically. Other molecules are also useful for facilitating transfection of a nucleic acid in vivo, for example, a cationic oligopeptide (e.g., International Patent Publication WO 95/21931), peptides derived from DNA binding proteins (e.g., International Patent Publication WO 96/25508), or a cationic polymer (e.g., International Patent Publication WO 95/21931).


It is also possible to introduce a DNA vector in vivo as a naked DNA plasmid (see U.S. Pat. Nos. 5,693,622, 5,589,466 and 5,580,859). Naked DNA vectors for therapeutic purposes can be introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun, or use of a DNA vector transporter (see, e.g., Wilson, et al. (1992) J. Biol. Chem. 267:963-7; Wu and Wu, (1988) J. Biol. Chem. 263:14621-4; Hartmut, et al. Canadian Patent Application No. 2,012,311, filed Mar. 15, 1990; Williams, et al (1991). Proc. Natl. Acad. Sci. USA 88:2726-30). Receptor-mediated DNA delivery approaches can also be used (Curiel, et al. (1992) Hum. Gene Ther. 3:147-54; Wu and Wu, (1987) J. Biol. Chem. 262:4429-32).


The present invention also provides biologically compatible, bone formation-enhancing compositions comprising an effective amount of one or more compounds identified as TARGET inhibitors, and/or the expression-inhibiting agents as described hereinabove.


A biologically compatible composition is a composition, that may be solid, liquid, gel, or other form, in which the compound, polynucleotide, vector, and antibody of the invention is maintained in an active form, e.g., in a form able to effect a biological activity. For example, a compound of the invention would have inverse agonist or antagonist activity on the TARGET; a nucleic acid would be able to replicate, translate a message, or hybridize to a complementary mRNA of a TARGET; a vector would be able to transfect a TARGET cell and expression the antisense, antibody, ribozyme or siRNA as described hereinabove; an antibody would bind a TARGET polypeptide domain.


A preferred biologically compatible composition is an aqueous solution that is buffered using, e.g., Tris, phosphate, or HEPES buffer, containing salt ions. Usually the concentration of salt ions will be similar to physiological levels. Biologically compatible solutions may include stabilizing agents and preservatives. In a more preferred embodiment, the biocompatible composition is a pharmaceutically acceptable composition. Such compositions can be formulated for administration by topical, oral, parenteral, intranasal, subcutaneous, and intraocular, routes. Parenteral administration is meant to include intravenous injection, intramuscular injection, intraarterial injection or infusion techniques. The composition may be administered parenterally in dosage unit formulations containing standard, well-known non-toxic physiologically acceptable carriers, adjuvants and vehicles as desired.


A particularly preferred embodiment of the present composition invention is a bone formation-enhancing pharmaceutical composition comprising a therapeutically effective amount of an expression-inhibiting agent as described hereinabove, in admixture with a pharmaceutically acceptable carrier. Another preferred embodiment is a pharmaceutical composition for the treatment or prevention of a condition a systemic or local decrease in mean bone density, or a susceptibility to the condition, comprising an effective bone formation-enhancing amount of a TARGET antagonist or inverse agonist, its pharmaceutically acceptable salts, hydrates, solvates, or prodrugs thereof in admixture with a pharmaceutically acceptable carrier.


Pharmaceutical compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient. Pharmaceutical compositions for oral use can be prepared by combining active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethyl-cellulose; gums including arabic and tragacanth; and proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate. Dragee cores may be used in conjunction with suitable coatings, such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinyl-pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.


Pharmaceutical preparations that can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol. Push-fit capsules can contain active ingredients mixed with filler or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.


Preferred sterile injectable preparations can be a solution or suspension in a non-toxic parenterally acceptable solvent or diluent. Examples of pharmaceutically acceptable carriers are saline, buffered saline, isotonic saline (e.g. monosodium or disodium phosphate, sodium, potassium; calcium or magnesium chloride, or mixtures of such salts), Ringer's solution, dextrose, water, sterile water, glycerol, ethanol, and combinations thereof 1,3-butanediol and sterile fixed oils are conveniently employed as solvents or suspending media. Any bland fixed oil can be employed including synthetic mono- or di-glycerides. Fatty acids such as oleic acid also find use in the preparation of injectables.


The composition medium can also be a hydrogel, which is prepared from any biocompatible or non-cytotoxic homo- or hetero-polymer, such as a hydrophilic polyacrylic acid polymer that can act as a drug absorbing sponge. Certain of them, such as, in particular, those obtained from ethylene and/or propylene oxide are commercially available. A hydrogel can be deposited directly onto the surface of the tissue to be treated, for example during surgical intervention.


Embodiments of pharmaceutical compositions of the present invention comprise a replication defective recombinant viral vector encoding the polynucleotide inhibitory agent of the present invention and a transfection enhancer, such as poloxamer. An example of a poloxamer is Poloxamer 407, which is commercially available (BASF, Parsippany, N.J.) and is a non-toxic, biocompatible polyol. A poloxamer impregnated with recombinant viruses may be deposited directly on the surface of the tissue to be treated, for example during a surgical intervention. Poloxamer possesses essentially the same advantages as hydrogel while having a lower viscosity.


The active expression-inhibiting agents may also be entrapped in microcapsules prepared, for example, by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences (1980) 16th edition, Osol, A. Ed.


Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semi-permeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g. films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and gamma-ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT™. (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated antibodies remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37° C., resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.


As defined above, therapeutically effective dose means that amount of protein, polynucleotide, peptide, or its antibodies, agonists or antagonists, which ameliorate the symptoms or condition. Therapeutic efficacy and toxicity of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50. Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.


For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models, usually mice, rabbits, dogs, or pigs. The animal model is also used to achieve a desirable concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. The exact dosage is chosen by the individual physician in view of the patient to be treated. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Additional factors which may be taken into account include the severity of the disease state, age, weight and gender of the patient; diet, desired duration of treatment, method of administration, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long acting pharmaceutical compositions might be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation.


The pharmaceutical compositions according to this invention may be administered to a subject by a variety of methods. They may be added directly to TARGET tissues, complexed with cationic lipids, packaged within liposomes, or delivered to TARGET cells by other methods known in the art. Localized administration to the desired tissues may be done by direct injection, transdermal absorption, catheter, infusion pump or stent. The DNA, DNA/vehicle complexes, or the recombinant virus particles are locally administered to the site of treatment. Alternative routes of delivery include, but are not limited to, intravenous injection, intramuscular injection, subcutaneous injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery. Examples of ribozyme delivery and administration are provided in Sullivan et al. WO 94/02595.


Antibodies according to the invention may be delivered as a bolus only, infused over time or both administered as a bolus and infused over time. Those skilled in the art may employ different formulations for polynucleotides than for proteins. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.


As discussed hereinabove, recombinant viruses may be used to introduce DNA encoding polynucleotide agents useful in the present invention. Recombinant viruses according to the invention are generally formulated and administered in the form of doses of between about 104 and about 1014 pfu. In the case of AAVs and adenoviruses, doses of from about 106 to about 1011 pfu are preferably used. The term pfu (“plaque-forming unit”) corresponds to the infective power of a suspension of virions and is determined by infecting an appropriate cell culture and measuring the number of plaques formed. The techniques for determining the pfu titre of a viral solution are well documented in the prior art.


The present invention also provides methods of enhancing bone formation, which comprise the administration to said subject a therapeutically effective amount of an expression-inhibiting agent of the invention. A further aspect of the invention relates to a method of treating or preventing a disease involving a systemic or local decrease in mean bone density, comprising administering to said subject a bone formation enhancing pharmaceutical composition as described herein.


The invention also relates to the use of an agent as described above for the preparation of a medicament for treating or preventing a disease involving a systemic or local descrease in mean bone density.


In a preferred embodiment of the present invention the disease is selected from the group consisting of osteoporosis, hypercalcemia of malignancy, multiple myelomatosis, hyperparathyroidism, and hyperthyroidism. A special embodiment of this invention is a method wherein the disease is osteoporosis.


Still another aspect of the invention relates to a method for diagnosing a pathological condition involving a systemic or local decrease in mean bone density or a susceptibility to the condition in a subject, comprising determining the amount of polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133 in a biological sample, and comparing the amount with the amount of the polypeptide in a healthy subject, wherein an increase of the amount of polypeptide compared to the healthy subject is indicative of the presence of the pathological condition.


Preferably the pathological condition is selected from the group consisting of osteoporosis, hypercalcemia of malignancy, multiple myelomatosis, hyperparathyroidism, and hyperthyroidism. More preferably, the pathological condition is osteoporosis.


The polypeptides or the polynucleotides of the present invention employed in the methods described herein may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. To perform the methods it is feasible to immobilize either the polypeptide of the present invention or the compound to facilitate separation of complexes from uncomplexed forms of the polypeptide, as well as to accommodate automation of the assay. Interaction (e.g., binding of) of the polypeptide of the present invention with a compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtitre plates, test tubes, and microcentrifuge tubes. In one embodiment, a fusion protein can be provided which adds a domain that allows the polypeptide to be bound to a matrix. For example, the polypeptide of the present invention can be “His” tagged, and subsequently adsorbed onto Ni-NTA microtitre plates, or ProtA fusions with the polypeptides of the present invention can be adsorbed to IgG, which are then combined with the cell lysates (e.g., (35)S-labelled) and the candidate compound, and the mixture incubated under conditions favorable for complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the plates are washed to remove any unbound label, and the matrix is immobilized. The amount of radioactivity can be determined directly, or in the supernatant after dissociation of the complexes. Alternatively, the complexes can be dissociated from the matrix, separated by SDS-PAGE, and the level of the protein binding to the protein of the present invention quantitated from the gel using standard electrophoretic techniques.


Other techniques for immobilizing protein on matrices can also be used in the method of identifying compounds. For example, either the polypeptide of the present invention or the compound can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated protein molecules of the present invention can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with the polypeptides of the present invention but which do not interfere with binding of the polypeptide to the compound can be derivatized to the wells of the plate, and the polypeptide of the present invention can be trapped in the wells by antibody conjugation. As described above, preparations of a labeled candidate compound are incubated in the wells of the plate presenting the polypeptide of the present invention, and the amount of complex trapped in the well can be quantitated.


The polynucleotides of the invention, complementary to SEQ ID NO: 1-220, 247-333 increase osteoblast differentiation.


Accordingly, another embodiment of the present invention relates to a method for in vitro production of bone tissue, comprising the steps of contacting undifferentiated mammalian cells with a polynucleotide sequence comprising a sequence selected from the group consisting of sequences complementary to SEQ ID No: 335-376, 600, 607-866, 1120-1122, preferably selected from the group consisting of sequences complementary to SEQ ID NO: 1-220, 247-333 for a time sufficient to differentiate the undifferentiated cells into osteoblasts, thereby producing a continuous bone matrix.


In a preferred embodiment, the method comprises the steps of:

    • (a) applying undifferentiated mammalian cells on a substrate to form a cellular substrate,
    • (b) introducing a polynucleotide comprising a nucleotide sequence selected from the group consisting of sequences complementary to SEQ ID No: 335-376, 600, 607-866, 1120-1122, preferably selected from the group consisting of sequences complementary to SEQ ID NO: 1-220, 247-333, for a time sufficient to differentiate the undifferentiated cells into osteoblasts, thereby producing a continuous bone matrix.


The invention thus provides a method for producing a substrate with a matrix grown thereon, which matrix may be used for the provision of load-bearing implants, including joint prostheses, such as artificial hip joints, knee joints and finger joints, and maxillofacial implants, such as dental implants. It can also be used for special surgery devices, such as spacers, or bone fillers, and for use in augmentation, obliteration or reconstitution of bone defects and damaged or lost bone. Bone formation can be optimized by variation in mineralization, both by inductive and by conductive processes.


The present invention also relates to a combination of a load-bearing implant (preferably coated with a matrix as described above) with a bone filler comprising a matrix as described.


The method of the invention is also very suitable in relation to revision surgery, i.e., when previous surgical devices require replacement.


Suitable undifferentiated cells are bone marrow cells, including haematopoietic cells and in particular stromal cells. The marrow cells, and especially the stromal cells are found to be very effective in the bone producing process when taken from their original environment.


The undifferentiated cells can be directly applied on the substrate or they can advantageously be multiplied in the absence of the substrate before being applied on the substrate. In the latter mode, the cells are still largely undifferentiated after multiplication and, for the purpose of the invention, they are still referred to as undifferentiated. Subsequently, the cells are allowed to differentiate. Differentiation can be induced or enhanced by the presence of suitable inductors, such as glucocorticoids, and dexamethasone. Suitable inductors of differentiation are the expression inhibitory agents of the present invention.


The use of undifferentiated cells provides several advantages. Firstly, their lower differentiation implies a higher proliferation rate and allows the eventual functionality to be better directed and controlled. Moreover, culturing these cells not only produces the required bone matrix containing organic and inorganic components, but also results in the presence, in the culture medium and in the matrix, of several factors which are essential for growth of the tissue and for adaptation to existing living tissue. Also, the culture medium can be a source of active factors such as growth factors, to be used in connection with the implanting process. Furthermore, such undifferentiated cells are often available in large quantities and more conveniently than e.g., mature bone cells, and exhibit a lower morbidity during recovery. Moreover, the undifferentiated cells can be obtained from the patient for whom the implant is intended. The bone resulting from these cells is autologous to the patient and thus no immune response will be induced. Matrices as thick as 100 μm can be produced as a result of the use of undifferentiated cells.


The substrate on which the undifferentiated cells can be applied and cultured can be a metal, such as titanium, cobalt/chromium alloy or stainless steel, a bioactive surface such as a calcium phosphate, polymer surfaces such as polyethylene, and the like. Although less preferred, siliceous material such as glass ceramics, can also be used as a substrate. Most preferred are metals, such as titanium, and calcium phosphates, even though calcium phosphate is not an indispensable component of the substrate. The substrate may be porous or non-porous. The cells can be applied at a rate of e.g., 103-106 per cm2, in particular 104-2×105 cells per cm2.


The culture medium to be used in the method according to the invention can be a commonly known culture medium such as MEM (minimum essential medium). Advantageously, the medium can be a conditioned medium. In this context, a conditioned medium is understood to be a medium wherein similar cells have previously been incubated, causing the medium to contain factors such as polypeptides, secreted by the cells which are important for cell growth and cell differentiation.


The cells are cultured for a time sufficient to produce a matrix layer, e.g., a matrix layer having a thickness of at least 0.5 μm, in particular from 1 up to 100 μm, more in particular of 10-50 μm. The cells may be contacted with the culture medium for e.g. 2-15 weeks, in particular 4-10 weeks.


The production of the matrix, when applied on a substrate, results in a continuous or quasi-continuous coating covering the substrate for at least 50%, in particular at least 80% of its surface area.


The present invention further relates to the osteoblast cells obtainable by the above method.


Still another aspect or the invention relates to a method for diagnosing a pathological condition involving cognitive impairment or a susceptibility to the condition in a subject, comprising determining the amount of polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133 in a biological sample, and comparing the amount with the amount of the polypeptide in a healthy subject, wherein an increase of the amount of polypeptide compared to the healthy subject is indicative of the presence of the pathological condition.


The invention is further illustrated in the following figures and examples.


Experimental Section


EXAMPLE 1
Development of a High-Throughput Screening Method for the Detection of Endogenous Alkaline Phosphatase

Adenoviral Controls.


Ad-BMP2: described in WO 03/018799


Ad-eGFP: Referred to as pIPspAdApt6-EGFP in WO 02070744


Ad-hCAR: hCAR cDNA is isolated using a PCR methodology. The hCAR cDNA is PCR amplified from a HeLa cell cDNA library (Quick clone, Clontech). A single fragment of 1119 bp is obtained and digested with the HindIII and BamHI restriction enzymes. pIPspAdapt6 vector (WO99/64582) is digested with the same enzymes, gel-purified and used to ligate to the digested PCR hCAR fragment. AdC15 (Ad5/Ad35) and AdC20 (Ad5/Ad51) viruses are generated as described in WO02/24933


Ad5-luc_v13: Cloned by PCR and virus generated as described in WO 03020931


Ad5-M6PR_v1: Cloned using Sap1-sites into vector and virus generated as described in WO03/020931.


H9: Cloned using Sap1-sites into vector and virus generated as described in WO03/020931


H11: Cloned using Sap1-sites into vector and virus generated as described in WO03/020931


Principle of the Assay


Mesenchymal progenitor cells (MPCs) differentiate into osteoblasts in the presence of appropriate factors (e.g. BMP2). An assay to screen for such factors is developed by monitoring the activity of alkaline phosphatase (AP) enzyme, an early marker in the osteoblast differentiation program. MPCs are seeded in 384 well plates and simultaneously co-infected one day later with adenoviruses encoding the human coxsackie and adenovirus receptor (HCAR; Ad-hCAR) and individual siRNA adenoviruses (Ad-siRNA) from the SilenceSelect™ collection. AdC15-hCAR/ AdC20-hCAR co-infection increases the AdC01-siRNA infection efficiency. Cellular AP activity is determined 13 days after the start of the infection (13 dpi). (FIG. 2 illustrates the principle of the assay).


Development of the Assay


MPCs are isolated from the bone marrow of healthy volunteers, obtained after informed consent (Cambrex/Biowhittaker, Verviers, Belgium).


In a series of experiments, carried out in 384 well plates, several parameters are optimized: cell seeding density, multiplicities of infection (MOI) of control viruses (Ad-BMP2 or Ad-eGFP), MOI of Ad-hCAR, duration of infection, toxicity, infection efficiency (using Ad-eGFP) and the day of readout.


Using Ad-BMP2 (BMP2 overexpression) as a positive control for assay development, the following protocol results in the highest dynamic range for the assay with the lowest standard deviation on the background signal:


MPCs are seeded on day 0 at 500 cells per well of a 384 well plate and co-infected the next day using a mix of Ad-hCAR (5 μl of an Ad-hCAR solution: mix total MOI=155.7) and 1 μl of Ad-control-virus (Ad-BMP2 or Ad-eGFP; corresponds to a theoretical MOI of 5000). On day 5, the medium containing the virus is removed and replaced by fresh medium containing no virus. Up-regulation of alkaline phosphatase is read at 13 dpi (days post infection): 15 μl 4-Methylumbelliferylphosphate (MUP, Sigma) is added to each well, the plates are incubated for 15 min at 37° C. and monitored for AP activity using a fluorescence plate reader (Fluostar, BMG).


After optimisation of the assay, a small pilot screen is run (103 different Ad-siRNA viruses) with the use of robotics (96/384 channel dispensor Tecan Freedom 200 equipped with TeMO96, TeMO384 and RoMa, Tecan AG, Switzerland). The TARGETS from this screen are collected and retested in the same assay. The two Ad-siRNAs that score strongest (H9=H24-010; H10=H24-011) are used to generate a control plate (knock-down (KD) control plate) containing Ad-siRNAs. The control plate, a 96 well plate containing 3 negative (N1,N2,N3) and 3 positive (P1,P2,P3) control viruses is depicted in FIG. 3. This “knock-down” control plate contains Ad-H9 (H24-010) and Ad-H 10 (H24-011) as positive controls; Ad-eGFP (knock-in virus) as infection control; and Ad-eGFP-siRNA, Ad-M6PR-siRNA and Ad-Luc-siRNA (all 3 are knock-down viruses) as negative controls.


The control viruses are pipetted from 96 well KD control plates into 384 well plates using robotics. (The final lay-out of the 384 well plate is depicted in FIG. 4).



FIG. 5 shows the results of the automated screening procedure using the KD control plate. The mean and standard deviations of the KD negative controls (N1-N3) are used to calculate a cut-off for TARGET analysis, which is set at the mean for N1, N2, N3 (‘All negatives’) plus 3 times the standard deviation for ‘All negatives’. The positive controls (P1 and P2), scored in more than 95% of the infected wells. The negative control viruses scored in less than 5% of the wells.


EXAMPLE 2
Screening of 7980 Ad-siRNA Adenoviruses in the Osteogenesis Assay

The optimized protocol for screening the SilenceSelect library is the following: on day 0, MPC cells are seeded in black 384 well plates with clear bottom (Costar or Nunc) in 60 μl medium at a density of 500 cells per well. One day later, 1 μl Ad-siRNA virus from the SilenceSelect™ collection, stored in 384 well plates (estimated titer of 2.5×109 viral particles per ml) and 5 μl of Ad-hCAR solution (total MOI=155), dispensed in 96 well V-bottom plates, is transferred with the aid of a 96/384 channel dispenser (Tecan Freedom 200 equipped with TeMO96, TeMO384 and RbMa, Tecan AG, Switzerland) from the wells of a 96 well plate containing the Ad-hCAR solution to each of the wells of the 384 well plates containing MPCs. The KD control plate is run under the same conditions as the aliquot plates from the SilenceSelect collection. All Ad-siRNA viruses are screened in duplicate, with each singular on a different MPC plate. Plates are then incubated at 37° C. Four days post infection the medium containing the adenoviruses is replaced by fresh medium free of virus. Thirteen days post infection, the AP activity readout is performed. A typical result of a 384 well screening plate is depicted in FIG. 6, in which the relative fluorescence units (RFU) are plotted for each of the data points of the 384 well plate on the Y-axis; while the numbers on the X-axis correspond to positions in the 384 well plate.


This duplicate screen is done twice, and all four data points are used for TARGET identification (see Example 3).


EXAMPLE 3
Target Identification Using the AP Assay

The data obtained from measuring the AP activity in Examples 1 and 2 are analyzed as follows: the background is calculated by taking the mean of the data points from all the plates except the control plate. A cut-off value for TARGET identification is calculated by adding 3 times the standard deviation of all data points, excluding the control plate. Each data point is analyzed for scoring above or under the cut-off. Only Ad-siRNAs inducing endogenous AP activity levels above the cut-off are of further interest. TARGETS are prioritized according to their scoring in single or duplicate, in one or both of the screens. Data are collected for 7980 Ad-siRNA virus constructs representing 4091 independent genes. An overview of the constructs is given in Table 1.


One of the identified hits has been shown to be a bone anabolic factor before and therefore validates the assay:


H24-034: SRC


Marzia et al. (2000) showed that bone formation was increased in Src null mice compared to wild-type mice. Most relevant to this work, osteoblasts isolated from Src null mice or osteoblasts isolated from wild-type mice but transfected with Src-antisense oligonucleotides showed increased AP activity in vitro.


8 genes identified in the screen were targeted by 2 Ad-siRNAs. These genes are AVPR1B, FLJ22955, IL1F8, PPIA, USP38, C9, LOC254378 and BRS3 (see Table 1).


The siRNA sequences of the present invention comprise sequences complementary to sequences corresponding to the identified KD TARGETS (SEQ ID NO: 1-220, 247-333). For the preferred TARGETS, the corresponding polynucleotides known in public databases (referred to as SEQ ID NO: 335-376, 600, 607-866, 1120-1122), their respective names and the polypeptides translated from those polynucleotides (referred to as SEQ ID NO: 377-418, 601, 867-1119, 1123-1133), are listed in Table 1.


EXAMPLE 4
Quality Control of the Target Ad-siRNAs

The Ad-siRNA TARGETS are subjected to further analysis to establish their therapeutic application as bone anabolic factors. The Ad-siRNA is subjected to quality control analysis (this example). Other validation steps are the validation of the TARGETS at the mRNA level (Example 5), screening of the targets in osteogenesis assays such as the mineralization assay (Example 6), and development of additional Ad-siRNAs targeting the identified genes (Example 9). TARGETS that remain of interest after these validation assays are considered for drug discovery and assays are developed allowing the discovery and optimization of compounds that mimick the bone anabolic actions of the target Ad-siRNAs (Example 7). In addition, the anti-resorptive activities of the identified Ad-siRNAs are validated in osteoclast assays (Example 8).


Verifying the Identity of the siRNA Insert from the TARGET Ad-siRNAs


TARGET Ad-siRNAs are propagated using PERC6/E2A cells (see WO99/64582) seeded in a 96-well plate, followed by re-screening of these viruses at several MOI's in the primary assay (see Example 1) and by sequencing the siRNAs encoded by the TARGET Ad-siRNA viruses. This procedure is carried out as follows.


PERC6/E2A cells are seeded in 96-well plates at a density of 40,000 cells/well in 180 μl PERC6/E2A medium. Cells are then incubated overnight at 39° C. in a 10% CO2 humidified incubator. One day later, cells are infected with 1 μl of crude cell lysate from SilenceSelect™ stocks containing TARGET Ad-siRNAs. Cells are further incubated at 34° C., 10% CO2 until appearance of cytopathic effect (cpe, as revealed by the swelling and rounding up of the cells which typically occurs 7 days post infection). The supernatant is collected and the virus crude lysate is treated with proteinase K: 12 μl crude lysate is added to 4 μl Lysis buffer (1× Expand High Fidelity buffer with MgCl2 (Roche Molecular Biochemicals, Cat. No 1332465) supplemented with 1 mg/ml proteinase K (Roche Molecular Biochemicals, Cat No 745 723) and 0.45% Tween-20 (Roche Molecular Biochemicals, Cat No 1335465) in sterile PCR tubes. These are incubated at 55° C. for 2 h followed by a 15 min inactivation step at 95° C. For the PCR reaction, 1 μl lysate is added to a PCR master mix composed of 5 μl 10× Expand High Fidelity buffer with MgCl2, 0.5 μl of dNTP mix (10 mM for each dNTP), 1 μl of ‘Forward primer’ (10 mM stock, sequence: 5′ CCG TfT ACG TGG AGA CTC GCC, SEQ ID NO: 245) and 1 μl ‘Reverse Primer’ (10 mM stock, sequence: 5′ CCC CCA CCT TAT ATA TAT TCT TTC C, SEQ ID NO: 246), 0.2 μl of Expand High Fidelity DNA polymerase (3.5 U/μl, Roche Molecular Biochemicals) and 41.3 μl H2O. PCR is performed in a PE Biosystems GeneAmp PCR system 9700 as follows: the PCR mixture (50 μl in total) is incubated at 95° C. for 5 min; each cycle runs at 95° C. for 15 sec, 55° C. for 30 sec, 68° C. for 4 min, and is repeated for 35 cycles. A final incubation at 68° C. is performed for 7 min. 5 μl of the PCR mixture is mixed with 2 μl of 6× gel loading buffer, loaded on a 0.8% agarose gel containing 0.5 μg/μl ethidium bromide to resolve the amplification products. The size of the amplified fragments is estimated from a standard DNA ladder loaded on the same gel. The expected size is 500 bp.


For sequencing analysis, the siRNA constructs expressed by the TARGET adenoviruses are amplified by PCR using primers complementary to vector sequences flanking the SapI site of the pIPspAdapt6-U6 plasmid. The sequences of the PCR fragments are determined and compared with the expected sequence.


For the KD TARGET sequences identified (Table 1), sequence analysis confirmed that the siRNA present in the TARGET Ad-siRNA had the expected sequence.


Multiple MOI Rescreen


The propagated TARGET Ad-siRNAs were rescreened at several MOIs in the AP assay (Example 1). The Ad-siRNAs had to score in duplo at at least one MOI to pass this quality control step.


All TARGETS listed in Table 1 fulfilled this quality control step and thus:


a) showed the correct length of the PCR fragment


b) showed the correct sequence of the PCR fragment


c) induced AP activity in duplicate for at least 1 MOI.


EXAMPLE 5
mRNA Validation Experiments for Identified Targets

A validation of the target Ad-siRNAs is carried out on RNA isolated from infected MPCs. First, the expression of the targets is analyzed in several isolates of primary human MPCs and osteoblasts (hOBs). Second, the knock-down of the target gene expression by the Ad-siRNA is verified at the mRNA level. Third, the upregulation of endogenous bone AP mRNA versus that of placental or intestinal AP mRNA is analyzed.


MPC and Osteoblast Expression Analysis for the Identified Targets Profiling


Expression levels of target genes are determined in 4 different isolates of MPCs and 2 different isolates of hOBs. The MPCs and hOBs (obtained from Cambrex/Biowhittaker, Verviers, Belgium) are seeded at 3000 resp. 5000 cells/cm2 in T180 flasks and cultured until they reach 80% confluency. The cells are washed with ice-cold PBS and harvested by adding 1050 μl SV RNA Lysis Buffer to a T180 flask. Total RNA is prepared using the SV Total RNA isolation System (Promega, Cat #Z3100). The concentration of the total RNA is measured with the Ribogreen RNA Quantification kit (Molecular Probes, Leiden, The Netherlands, Cat No. R-11490). cDNA synthesis is performed using 40 ng total RNA per reaction using the TaqMan Universal PCR Master Mix, No AmpErase UNG, kit (Applied Biosystems, Warrington, UK,Part number 4324018). For each RT reaction a minus-RT reaction (negative control: no enzyme included in the reaction) is performed.


The real-time reverse transcriptase (rtRT)-PCR reaction is performed with gene specific primers on both cDNA and minus-RT samples, using the SYBR Green PCR Master Mix (Applied Biosystems, Warrington, UK, Part number 4309155). For the normalization of the expression levels, a RT-PCR reaction is performed on human β-actin using the Human β-actin kit (Applied Biosystems, Warrington, UK, Part number 4310881E). The following program is run on a real-time PCR apparatus (ABI PRISM 7000 Sequence Detection System): 10 min at 25° C., 30 min at 48° C., 5 min at 95° C. In FIGS. 7A and 8, relative expression levels for 10 genes are depicted for respectively MPC and hOB isolates. For the data in FIG. 7A, total RNA is extracted from 4 different MPC isolates and used to analyze expression levels of target genes identified through the target Ad-siRNAs. RtRT-PCR compatible primer sets (Table 4) are developed for 10 genes and compared to expression levels of β-actin. Data are expressed as −log(difference to β-actin) (Y-axis). For the data presented in FIG. 8, total RNA is extracted from 2 different hOB isolates.

TABLE 4SEQIDGenePrimer NameSequenceNO.CALCRLCALCRL_RevAGAGACCAAAAGACCCTGGAAGT222SRCSRC_ForACAGCGGCGGCTTCTACA223SRCSRC_RevCATCGGCGTGTTTGGAGTAGT224PSMB3PSMB3_ForATCCGGATCACCTGTTTGAAAC225PSMB3PSMB3_RevGTGGTGATTTTGTCCTTCTCGAT226HP43.8KDHP43.8KD_ForCCATACACAGAGGGAAGCATACG227HP43.8KDHP43.8KD_RevCAGTCTTGCTGTGATCTGGGAGTA228APEXAPEX_ForGCATAGGCGATGAGGAGCAT229APEXAPEX_RevGACCTCGGCCTGCATTAGG230GPR38GPR38_ForCATCGTCGCTCTGCAACTTTT231GPR38GPR38_RevCCGCTCTGTACTTCTTTGAAATGA232ROCK2ROCK2_ForCCTGGTGGAGACCTTGTAAACCT233ROCK2ROCK2_RevAGCAAGAACAACTTCAGCAGTGTAA234CXCR6CXCR6_ForGCCATGACCAGCTTTCACTACA235CXCR6CXCR6_RevGTTAAGGCAGGCCCTCAGGTA236OPN3OPN3_ForCTAACCGTGCTGGCCTATGAAC237OPN3OPN3_RevCAGGCCCAGGAAAAATTGATC238FUKFUK_ForTTCGCGATCAGCCCCTTAC239FUKFUK_RevACTCACTGGCTGAGGAGGTCAT240


Analysis of the Knock-down of the Target Gene Expression by the Ad-siRNA is Verified at the mRNA Level.


To determine whether the target Ad-siRNAs result in knock-down of expression from the corresponding gene, total RNA is harvested from Ad-siRNA infected MPCs and gene expression is analyzed using gene-specific primers.


MPCs are seeded at 25,000 cells per well of a 24 well plate. After 24 hours the cells are infected with knock-down hit viruses or negative control viruses Ad-gPPARg and Ad-GL2.2 that knock down the expression of respectively PPARy (all four known splice variants) and luciferase, both of which are not related to osteogenesis. For Ad-siRNAs, cells are co-infected with Ad-hCAR and Ad-siRNA crude lysates (MOI Ad-hCAR: 750; 40, 10, 3.3 μL virus with average titer of 2.5×10E9 virus particles/ml). At 5 dpi the medium is refreshed and at 14 dpi the cell lysates are prepared. Cells are processed for mRNA analysis as described in the previous section. mRNA levels for a specific gene are normalized for β-actin levels and compared to levels measured for the negative control Ad-siRNAs. An example of these kind of analyses is provided in FIG. 7B. Data are normalized for β-actin expression levels and compared to endogenous gene expression for MPCs infected with negative control viruses (Y-axis: percent gene expression of endogenous gene; 100%=endogenous mRNA levels present in negative control sample).


Analysis of the Upregulation of Endogenous Bone AP mRNA Versus that of Placental or Intestinal AP mRNA.


BAP is the physiologically relevant AP involved in bone formation. In order to determine whether the measured AP activities are due to upregulation of BAP expression or of another AP gene product, mRNA levels for all AP genes are analysed for infected MPCs. mRNA levels are determined as described in the previous sections. The difference is in the primer set used (see Table 5): one set detects BAP ALPL (human alkaline phosphatase liver/bone/kidney) mRNA expression. Another set detects the expression of the 3 other AP genes (ALPI (human alkaline phosphatase intestinal), ALPP (human alkaline phosphatase placental (PLAP)), and ALPPL2 (human alkaline phosphatase placental-like)). ALPI, ALPP and ALPPL2 are highly similar at the nucleotide level and can therefore be amplified using one primer pair.


The primer pairs are first validated on RNA isolated from MPCs infected with Ad-eGFP and Ad-BMP2. FIG. 7 illustrates the strong upregulation of BAP mRNA by Ad-BMP2 and the absence of upregulation of expression of any of the other AP genes. MPCs are infected in 24 well plate format using Ad-eGFP (negative control) or the osteogenic Ad-BMP2. Cells are harvested and RNA is prepared and subjected to rtRT-PCR using primer sets amplifying BAP mRNA or mRNA from the other 3 AP genes (PLAP/IAP). Ad-BMP2 strongly upregulates BAP mRNA levels but not the mRNA levels of the other 3 AP genes.


Both primer sets are then used to measure mRNA levels for all AP genes in RNA isolated from Ad-siRNA infected MPCs.

TABLE 5SEQIDNameSequenceNO:JDO-05F (PLAP)TTCCAGACCATTGGCTTGAGT241JDO-05bisRACTCCCACTGACTTTCCTGCT242(PLAP/ALPI/ALPPL2)JDO-21F (BAP)CATGCTGAGTGACACAGACAAGAAG243JDO-21R (BAP)TGGTAGTTGTTGTGAGCATAGTCCA244


EXAMPLE 6
Mineralization

The process of osteogenesis consists of several successive events. During the initial phases of osteogenesis, bone alkaline phosphatase (BAP) becomes upregulated. It is however equally important to look at specific events occurring in later stages of osteogenesis such as mineralization. During differentiation, cells deposit (hydroxy)apatite (Ca2+-phosphate precipitate) on an extracellular matrix consisting mostly of collagen type I to form mineralized bone.


Assay Setup


In the bone cell mineralizing assay (BM assay), primary human MSCs are differentiated in vitro into mineralizing osteoblasts using BMP2 (recombinant or delivered by adenoviral transduction) as an osteogenic agent. Mineralization is then visualized by staining the MSCs with Alizarin Red, a dye with a high affinity for calcium (see FIG. 8).


Screening and TARGET Identification


The following optimized protocol is used for screening Ad-siRNA and Ad-cDNA TARGETS identified in the primary assay:


100,000 MPCs are seeded in each well of a 6 well plate in 2 ml MSC medium, containing 10% FCS. The next day, after incubation at 37° C., 10% CO2 in a humidified incubator, cells are co-infected with AdCI5-hCAR (final MOI of 750) and Ad-siRNA, Ad-cDNA or control viruses at a final MOI of 1250, 2500 and 5000. Cells are incubated at 37° C., 10% CO2 in a humidified incubator for a further six days. Virus is removed and replaced by 2 ml fresh MSC medium, 10% FCS. Over the next 22 days, medium is refreshed 3 times in 2 weeks. Every other time, medium is refreshed half or completely. At 28 days after the start of the experiment, the conditioned medium is removed, cells are fixed using 10% paraformaldehyde and the monolayers stained with 1 mL of ˜1% Alizarin Red (Sigma, #A5533) in MilliQ water (pH adjusted to 4.2). Ad-eGFP, to assess infection efficiency, Ad-BMP2 as strong osteogenic inducer and Ad-H4-2 as a weak osteogenic factor are included in each experiment as negative and positive controls, respectively. Every experiment where Ad-H4-2 did not induce mineralization is entirely repeated.


The KD TARGET sequences of Ad-shRNAs that induced mineralization are presented in Table 6.

TABLE 6KD TARGETSEQGenbankTARGETSequenceIDTARGETDNA/RNAId(5′→3′)NO.TARGET Gene NameGene SymbolAccessionH24-001CAACTTGTACCTG3G protein-coupledGPR38NM_001507GGCAGCreceptor 38H24-004CATGCTGTTTGAG6MAP kinase-interactingMKNK2-NM_017572-AGCATCserine/threonine kinase 2MNK2SK236H24-006GACGGTGTTAATG8casein kinase 1, gamma 1CSNK1G1-NM_022048-ATAGCCCK1g1SK647H24-007CTTCGGCACTCCT9myosin light chain kinaseHSA247087-AJ247087-GAGTTCcaMLCKSK536H24-009ACGCAAAGTGGC11tRNAIPTNM_017646CAGGAGCisopentenyltransferase 1H24-013CAACCTGCTGGTG15opsin 3 (encephalopsin,OPN3NM_014322CTCGTCpanopsin)H24-014CTCTCTTAGATCT16granzyme K (serineGZMKNM_002104GGAACCprotease, granzyme 3;tryptase II)H24-015AGCAGGAAGGCG17ubiquitin-specific pro-AF073344-AF073344-GACATACtease 3 - ubiquitinUSP3NM_006537specific protease 3H24-018TCAGGTAGTTGGT20coagulation factor XIII,F13A1NM_000129TCTGACA1 polypeptideH24-019CTGCGCCGAACA21proteasome (prosome,PSMB3NM_002795AATGTACmacropain) subunit, betatype, 3H24-020TGTGGCGACTTGT22ClpX caseinolyticCLPXNM_006660GCACACprotease X homolog (E.coli)H24-021TCTCTCAGTGTAG23hypothetical proteinFLJ14906NM_032859AATGCCFLJ14906H24-024GTGTACTGGTACA26matrix metalloproteinaseMMP23A-NM_004659-AGGACC23A - matrixMMP23BNM_006983metalloproteinase 23BH24-026TCTCTCATCAATA28APEX nucleaseAPEXNM_001641-GTGGTC(multifunctional DNANM_080648-repair enzyme)NM_080649H24-029CTATGCCATCACC31LOC254378LOC254378XM_174812TTCTGCH24-030TGTGCCGAAGGAT32similar to a disintegrinLOC137491XM_070459GTAAGCand metalloproteasedomain 25 (testase 2)H24-031CCGGGACATAACT33similar to bile salt-LOC138529XM_070951AAATCCdependent lipaseoncofetal isoformH24-032AGCAGGCTATGG34complement component 9C9NM_001737GATCAACH24-033CCACAAGGTTGCA35xylulokinase homolog (H.XYLBNM_005108GCATTCinfluenzae)H24-035GGGGCTCAGCCAG36chaperone, ABC1 activityCABC1-NM_020247-GAGATTCof bc1 complex like (S.ADCK3SK609pombe)H24-036CAGGTAGACATG37fyn-related kinaseFRKNM_002031GCGGCACH24-038GCACGATTTGGAG39unc-51-like kinase 1 (C.ULK1NM_003565GTCGCCelegans)H24-041GGACTCTCAGTTC42phosphoinositide-3-PIK3C2BNM_002646AGCATCkinase, class 2, betapolypeptideH24-049GTACCTGCAGGTG1arginine vasopressinAVPR1BNM_000707CTCAGCreceptor 1 BH24-054GTACCTGCGGCAG54chemokine (C—C motif)CCR1NM_001295TTGTTCreceptor 1H24-062TTCGGACACCCAC62retinal pigmentRRHNM_006583AAATGCepithelium-derivedrhodopsin homologH24-064GTTGTCCTGTTCT63olfactory receptor,OR1A2NM_012352GACGTCfamily 1, subfamily A,member 2H24-071CACCTGCTTTCTC70KIAA1453 proteinKIAA1453NM_025090AATGCCH24-073AGCACCTCGCTGA72sentrin/SUMO-specificSENP3NM_015670CATTCCprotease 3H24-078GCTTCTGGTGGAG77transglutaminase 3-likeTGM3LXM_066181AAGGACH24-079GTGTATGAAGTGG78similar to solute carrierLOC160662XM_090422TCCACCfamily 21 (organic aniontransporter), member 8H24-084CAGTGCCAAGAA83neuron navigator 2NAV2NM_018162GGAGCCCH24-092ATGCAGGTCCATA91transient receptor poten-TRPM6NM_017662TGTGACtial cation channel,subfamily M, member 6H24-093CCTTTCTCTGAAC92ataxia telangiectasia andATRNM_001184ACGGACRad3 relatedH24-095CAGGTTCTCCTCA94similar to TPA: G-proteinLOC126788XM_060177AACGGCcoupled receptorH24-097ACATCCTGCTGTC96thousand and one aminoTAO1 - PSKNM_004783-AGAGCCacid protein kinase-NM_016151prostate derived STE20-like kinase PSKH24-099GTTCTCCAGTGCC98solute carrier family 16SLC16A3NM_004207ATTGGC(monocarboxylic acidtransporters), member 3H24-104AGTGCGCATCTTC103fibroblast growth factorFGF14NM_004115GGCCTC14H24-106GCCCTGATGTCCA105NADPH-dependent FMNNR1NM_014434TCTTCCand FAD containingoxidoreductaseH24-107CATAGGGAAGGA106interleukin 1 family,IL1F8NM_014438CACTTGCmember 8 (eta)H24-108CCTGGATGTGAGA107interleukin 1 family,IL1F8NM_014438GAGAGCmember 8 (eta)H24-109AACTTGTACTATG108Ras associationRASSF2NM_014737AAGGCCRalGDS/AF-6) domainfamily 2H24-110GTATTCTGTACAC109adrogen-regulated short-ARSDR1NM_016026CCTGGCchaindehydrogenase/reductase1H24-111TTCTCGCAATGGC110peptidylprolyl isomerasePPIL1NM_016059CAATGC(cyclophilin)-like 1H24-112GAAGAACAGCAG111RAS, dexamethasone-RASD1NM_016084CCTGGACinduced 1H24-113TCAGGCGGATCTT112dicarbonyl/L-xyluloseDCXRNM_016286GACAGCreductaseH24-117TCTCTCCACACAA116chromosome 20 openC20orf121NM_024331ACCTTCreading frame 121H24-119GCGAATTCCACCA118solute carrier family 26,SLC26A8NM_052961GCATTCmember 8H24-120TGTCCAGGACCTA119UDP glycosyltransferase 1UGT1A1NM_000463TTGAGCfamily, polypeptide A1H24-128TGTGCGAGACCTC127HMT1 hnRNPHRMT1L3NM_019854GATTTCmethyltransferase-like 3(S. cerevisiae)H24-130AGCATGAAAGAA129peroxisomal short-chainENSG00000169066-ENSG00000169066-ACCCTGCalcohol dehydrogenasehumNRDRNM_021004H24-131GAAGATCACCATT130similar to peptidylpro-PPIA-NM_021130-GCTGAClylisomerase A (cyclo-LOC127711-XM_060625-philin A) - similar toLOC128430-XM_066074-Peptidylprolyl cis-transLOC138130-XM_070771-isomerase A (PPIase)LOC165317-XM_092514-(Rotamase) (CyclophilinLOC257232XM_172314A) (Cyclosporin A-binding protein) (SP18)H24-133TGCAGGCAAGCA1323-oxoacid CoA transfer-OXCT2NM_022120GACGGTCase 2H24-136CTTATTGTTCACA135similar to glyceraldehydeLOC170327XM_093255TTGGCC3-phosphatedehydrogenaseH24-138TCAGGTGTCCCAT137interleukin-1 receptor-IRAK2NM_001570-TCCAGCassociated kinase 2SK180H24-141GAGTCCAGCCTTC140cytochrome P450,HUMCYPIIF-J02906-ATGCCCsubfamily IIF, poly-CYP2F1NM_000774peptide 1H24-142GTCCAGCTGAAG141glutamate receptor,GRIN2ANM_000833AAGATCCionotropic, N-methyl D-aspartate 2AH24-143TTCGGCACTGAGG142hypothetical proteinFLJ22955NM_024819TCTTGCFLJ22955H24-145CCTGCTCTTGAGC144tumor endothelial markerTEM5NM_032777AATAAC5 precursorH24-146TGTCCAGACCACA145similar to cytochromeLOC126538XM_065152TGGAGCP450, subfamily IVF,polypeptide 2; leuko-triene B4 omega-hydroxyl-ase; leukotriene-B4 20-monooxygenaseH24-148GATTGTGGCCAAG147chloride intracellularCLIC6XM_092804AAGTACchannel 6H24-149CCTCATTATCACC148LOC167417LOC167417XM_094471ATGCTCH24-150CTGGTTATTGGCG149similar to 25-LOC165245XM_103864GGTATChydroxyvitamin D-1 alphahydroxylase,mitochondrial precursor(25-OHD-1 alpha-hydroxylase) (25-hydroxyvitamin D3 1-alpha-hydroxylase) (VD31A hydroxylase) (P450C1alpha) (P450VD1-alpha)H24-154GTTCAAGAAGCTG153opsin 1 (cone pigments),OPN1MW-NM_000513-CGCCACmedium-wave-sensitiveOPN1LWNM_020061(color blindness,deutan)-opsin 1 (conepigments), long-wave-sensitive (colorblindness, protan)H24-156GCAGTTCCAAGCT155opsin 1 (cone pigments),OPN1SWNM_001708TGCATCshort-wave-sensitive(color blindness, tritan)H24-157GTACCTGCGCCAC156chemokine (C—C motif)CCR3NM_001837TTCTTCreceptor 3H24-159GTCCTTCTACATC158G protein-coupledGPR23NM_005296AATGCCreceptor 23H24-160GAAGAAGCAACT159G protein-coupledGPR64NM_005756GGGAGCCreceptor 64H24-169CAACCTGTTCATC164galanin receptor 2GALR2NM_003857CTTAACH24-173GTTCTCTCAGCAC168placental growth factor,PGFNM_002632GTTCGCvascular endothelialgrowth factor-relatedproteinH24-180ATGCAGGTCAGGT175solute carrier family 4,SLC4A10NM_022058TGTTTCsodium bicarbonatetransporter-like, member10H24-185ACCGTGGAAGGC180cytochrome P450,CYP24NM_000782CTATCGCsubfamily XXIV (vitaminD 24-hydroxylase)H24-188TCGGCAGGGCCA183macrophage stimulating 1MST1NM_020998GCATTTC(hepatocyte growth factor-like)H24-190TCAGAAGGTTGTG185KIAA0943 proteinApg4BNM_013325CAGGACH24-191CAACTTGCATGAC186amyloid beta (A4)APPNM_000484TACGGCprecursor protein(protease nexin-II,Alzheimer disease)H24-193ACCAGTGGTAAAT188dual specificityDUSP5NM_004419GTCAGCphosphatase 5H24-194CTCTGTATCCCAT189mitogen-activated proteinMAP3K9XM_027237TCCCTCkinase kinase kinase 9H24-200GTAGCACTCTGCG195solute carrier family 39SLC39A4NM_017767-ACATGC(zinc transporter),NM_130849member 4H24-202GTTATTCTTCCAC197nicotinamide N-NNMTNM_006169CATGGCmethyltransferaseH24-205AGCATGACAGGA200UDP-glucose ceramideUGCGL2NM_020121AACCTGCglucosyltransferase-like 2H24-207CCTTGTTGGCCAA202similar to arylacetamideLOC166161XM_093702TGATTCdeacetylase (esterase)H24-211CAAGTTCTCCTGC206ATPase, H+/K+ATP4BNM_000705AAGTTCexchanging, betapolypeptideH24-218CAACATCCCAACT213glutathione reductaseGSRNM_000637GTGGTCH24-219TATCCTGACCTTC214potassium voltage-gatedKCNG1NM_002237CTGCGCchannel, subfamily G,member 1H24-224TATTCGTGCGGAG219chromosome 9 openSgK071SK521GAAGACreading frame 96H4-225ATGGGCTTCAACA220arginine vasopressinAVPR1BNM_000707GCCACCreceptor 1B


EXAMPLE 7
Drug Discovery Against the Identified TARGETs

Compounds are screened for binding to the polypeptides of the present invention. The affinity of the compounds to the polypeptides is determined in a displacement experiment. Such displacement experiments are well known in the art, and can be considered as a common technique among others to identify compounds that bind to polypeptides.


In brief, the polypeptides of the present invention are incubated with a labeled (radio-labeled, fluorescent- or antibody-labeled, or any other detectable label) ligand that is known to bind to the polypeptide and is further incubated with an unlabeled compound.


The displacement of the labeled ligand from the polypeptide is determined by measuring the amount of labeled ligand that is still associated with the polypeptide. The amount of the labeled ligand associated with the peptide is an indication of the affinity for the unlabeled compound.


The amount of labeled ligand associated with the polypeptide is plotted against the concentration of the unlabeled compound to calculate IC50 values. This value reflects the binding affinity of the unlabeled compound to its TARGET, i.e. the polypeptides of the present invention.


Compounds are considered strong binders, when having an IC50 in the nanomolar and even picomolar range. Compounds that have an IC50 of at least 10 micromol or even better in the nmol to pmol range are applied in either the bone alkaline phosphatase assay (BAP) and/or in assays to determine their effect on the induction of osteoblast markers and osteoblast function. Compounds with a lower IC50 are generally considered as of less interest. The polypeptides of the present invention can be prepared in a number of ways depending on whether the assay will be run on cells, cell fractions, or biochemically on purified proteins. Such preparations are well known in the art, as are the different assays.


EXAMPLE 8
Osteoclast Assays: Validate Anti-resorptive Activity of Identified TARGETs

Throughout life, the skeleton is in a constant state of remodeling. Focal areas of bone are resorbed by osteoclasts and then replaced by bone matrix newly formed by osteoblasts. The development of osteoporosis is characterized by severe bone loss due to the deregulation of the balance between osteoclast and osteoblast activity, leading to an increased osteoclast-mediated bone resorption.


Osteoclasts emanate from cells of the monocyte/macrophage lineage. In vivo, the differentiation of osteoclast precursor cells towards osteoclasts is controlled by two central factors expressed by stromal cells (MPCs): receptor activator of NFKB ligand (RANKL) and osteoprotegerin (OPG). RANKL is a membrane bound ligand expressed on the surface of MPCs which drives osteoclast differentiation. OPG is a soluble decoy receptor for RANKL which inhibits osteoclast differentiation by scavenging active RANKL. The balance between RANKL and OPG expression by MPCs determines the level of osteoclast differentiation.


As MPCs control the differentiation of osteoclasts, it is important to know the effect of the identified TARGET Ad-siRNAs on osteoclast differentiation or activity. Target Ad-siRNAs that decrease osteoclast differentiation/activity, are very valuable, as these are expected to increase bone apposition by two mechanisms: increase of differentiation/activity of osteoblasts and decrease in osteoclast activity. As illustrated by various precedents (Thirunavukkarasu et al., (2000) J Biol Chem 275 : 25163-72 ; Yamada et al., (2003) Blood 101: 2227-34) such a pleiotropic effect of osteogenic factors can be expected.


Osteoclast Differentiation Assay


The effect of osteogenic factors on osteoclastogenesis is evaluated through two types of assays.


In a first assay setup, a coculture of MPCs with primary human mononuclear cells is performed. The effect of the infection of the MPC monolayer with a knock-down virus on its capacity to support osteoclastogenesis is evaluated. The desired effect is the following: knock-down of the Ad-siRNA TARGET gene expression in the MPCs should inhibit osteoclast differentiation driven by a physiological trigger as e.g. a mixture of 10 nM 1,25(OH)2vitD3 and 50 nM M-CSF. The monocytes used can be derived from bone marrow or peripheral blood. In the present example, a differentiation experiment based on peripheral blood derived mononuclear cells (PBMCs) is described. MPCs (obtained from Cambrex/Biowhittaker, Verviers, Belgium) are seeded in 96 well plates (1000 cells per well) in α-MEM medium (GIBCO-Life Technologies) supplemented with 10% FBS and a day later, these are infected with a TARGET Ad-siRNA. At least three days later, 100 000 PBMCs per well are added as well as M-CSF (R&D systems, 50 ng/ml final concentration). Half the volume of medium is refreshed twice a week by medium +50 ng/ml M-CSF and 10 nM 1,25(OH)2vitD3. Readout is performed 14 days after addition of the PBMCs to the coculture. Spontaneous osteoclast differentiation driven by the physiologically relevant mixture of triggers can be assessed by multiple readouts. Microscopic assessment of the number of ‘TRAP positive’, multinucleated cells per well is a generally accepted measure for the level of osteoclast differentiation. ‘TRAP positive’ means that the cells possess a tartrate resistant acidic phosphatase (TRAP) activity. To assess this, the coculture is subjected to an in situ TRAP staining performed according to the Acid Phosphatase detection kit (SIGMA, 386-A). Positive cells aquire a purple color upon treatment. As an alternative readout, a marker specific for mature osteoclasts is measured e.g. TRACP5b (tartrate resistant acidic phosphatase type 5b), calcitonin receptor (CTR) or Cathepsin K (CTSK). Measurement of the amounts of osteoclast-derived tartrate resistant acidic phosphatase protein (TRACP5b) in the coculture supernatant is performed by a commercially available ELISA (BoneTRAP assay, Sba sciences, Turku, Finland). CTR or CTSK are detected by immunocytochemistry, upon application of following general protocol. Medium is removed and the coculture is fixed (4% paraformaldehyde, 0.1% TritonX-100, 4° C., 30 min), washed and blocking buffer (PBS+1% BSA+0.1% Tween20) is added for an incubation of at least 4hrs. The blocking buffer is removed and the primary antibody directed against CathepsinK (e.g. Oncogene, IM55L) or Calcitonin receptor (e.g. Serotec, AHP635), dissolved at the desired concentration in a suited buffer (e.g. 0.05M Tris.HCl pH 7.4, 1% BSA), is added to the wells. Incubation is performed overnight, 4° C. The mixture is removed, the cells washed (PBS+0.1% Tween20) and the suited, HRP conjugated secondary antibody, diluted in the same buffer as the primary antibody, is added. After an incubation of at least 4 hrs, a washing step is performed (PBS+0.1% Tween20) and luminol (a substrate for HRP yielding a luminescent signal: BM Chemiluminescence ELISA Substrate [POD] (luminol), Roche Diagnostics, Cat No 1582950) is added. After 5 min incubation, readout is performed with a luminometer (Luminoskan Ascent, Labsystem). The 2 assays described (assessment of the amount of multinuclear cells and imnmunochemistry for the detection of osteoclast-specific markers) allow to assess the differentiation of the mononuclear cells towards osteoclasts, but do not yield information about the bone resorptive activity of the osteoclasts formed.


Activity of the osteoclasts is measured in the pit formation assay. For this purpose, the co-culture and infection of cells is performed as described for assays described above with the difference that a bone-like substrate is present at the bottom of the well in which the co-culture is performed. This bone-like substrate can be a dentin slice (e.g. Kamiya Biomedical Company, Seattle (Cat No KT018)) or equivalent (Calcium carbonate coating, OAAS™, Gentaur; Biocoat™ Osteologic™, BD Biosciences) that is commercially available. The co-culture is performed for at least 14 days on the bone like substrate. Cells are then removed by treatment with sodium hypochlorite and the area resorbed by the osteoclasts (the resorption pit) can be assessed microsopically. This can be facilitated by the treatment of the surface of the dentin slice with toluidine blue.


In a second assay setup, the effect of the infection of the osteoclast precursor cells (PBMCs or BMMCs) with a TARGET virus on its ability to differentiate towards an osteoclast is measured in a monoculture assay. For this purpose, the monocytes (PBMCs or BMMCs) are seeded in a 384 well plate in aMEM medium supplemented with 10% serum and 25 ng/ml recombinant M-CSF (R&D systems). One day after seeding, the cells are infected with TARGET Ad-siRNAs. Four days after infection, recombinant RANKL is added to the wells (25 ng/ml, R&D systems). Medium is refreshed twice a week. Fourteen days after addition of RANKL, the differentiation of the monocytes towards osteoclasts is measured using one of the readouts described for the former assay setup. This assay allows the identification of factors that are indispensable for the response of osteoclast precursor cells to M-CSF or RANKL.


PBMC Isolation


PBMCs are obtained from peripheral blood (obtained from patients after informed consent) subjected to the following protocol. Blood is aseptically poured into 50 ml Falcon tubes and spun at 3000 g for 10 min at 25° C. The buffy coat is then collected and diluted 1:1 with PBS. The diluted buffy coat is poured on top of 20 ml Lymphoprep (Sigma) contained in a 50 ml Falcon tube. Upon centrifugation (35 min at 400 g at 25° C.), a white layer of mononuclear cells on top of the Lymphoprep is collected and washed twice with PBS (centrifugation at 200 g, 10 min, 25° C.) and rediluted in 7 ml PBS. This solution is pipetted onto a layer of 7 ml of hyperosmolar Percoll gradient contained in a 15 ml Falcon tube and centrifuged 35 min at 400 g at 25° C. The hyperosmolar Percoll gradient is prepared as follows: 1 volume of 1.5 M NaCl and 9 volumes of Percoll (Pharmacia, d=1,130 g/ml) are mixed. This mixture is added 1:1 to a PBS/Citrate buffer (NaH2PO4 1.49 mM, Na2HPO4 9.15 mM, NaCl 139.97 mM, Na-citrate (dihydrate) 13 mM, pH 7.2). After centrifugation, monocytes form a discrete ring on top of the gradient. Monocytes are collected and washed in culture medium. Cells are then ready to use in assays.


EXAMPLE 9
Analysis of ‘off-target’ Knock Down Effect

SiRNAs exert knock-down of gene expression through a recently discovered and partially understood mechanism. It is generally accepted that the specific annealing of the siRNA sequence to mRNA is responsible for a gene-specific ‘on-target’ knock-down. However, it cannot be excluded yet that limited mismatching between the siRNA and another mRNA can induce ‘off-target’ down-regulation of gene expression.


In order to exclude that the knock-down of (an) ‘off-target’ mRNA(s) was responsible for the observed osteogenic effect, additional siRNAs/shRNAs are designed for 38 targets that induced mineralization (Example 6) using stringent design criteria. The additional Ad-shRNAs are then tested in the BAP assay.


To address the question of possible ‘off-target’ effects, additional siRNA sequences are designed that align perfectly with the mRNA targeted by the original siRNA. Preferred siRNA sequences do not align to other mRNAs. However, in some cases only siRNAs could be designed that showed some overlap to other mRNAs. For siRNAs that aligned to a minimal number of ‘off-target’ mRNAs (maximum of 2 basepairs non-identity checked for every position of the 19mer) the following rules are applied: the putative ‘off-target’ mRNAs must be different from the putative ‘off-target’ mRNAs identified for the original siRNA; and putative ‘off-target’ mRNAs must be different from the putative ‘off-target’ mRNAs identified for all original target siRNAs. The only exception to these rules made during the course of these experiments are siRNAs designed for PPIA.


For each of the 38 selected target genes, 7 additional siRNAs were designed and processed to derive recombinant adenoviruses. All siRNAs are sequenced upon cloning, to verify their identity and exclude errors due to the oligonucleotide synthesis.


261 Ad-shRNAS were successfully generated and tested in the BAP assay at 3 MOIs in 2 independent experiments, in parallel with the original 38 Ad-shRNAs.


Recombinant adenoviruses encoding the designed shRNAs (Ad-shRNAs) are produced, titered, aliquoted in 96 well plates and stored at −80° C. These plates were processed in the primary BAP assay as follows:


MPC cells wearere seeded with a Multidrop 384 (Labsystems) in black 384 well plates with clear bottom (Costar or Nunc) in 60 μl MSC medium containing 10% fetal calf serum (Progentix, The Netherlands), at a density of 500 cells per well. One day later, a 96 well plate containing aliquoted Ad-shRNAs and another containing negative and positive control viruses (knock-down control plate) are thawed and virus aliquots transferred to the MPC plate using a 96-channel dispenser (Tecan Freedom 200 equipped with a TeMO96 and a RoMa plate handler, Tecan AG, Switzerland). For the control plate, 1 μL virus stock (average titer of of 2×109 viral particles per ml) is transferred to the 384 well screening plates. On the control plate (see FIG. 3), negative (N1, N2, N3) and positive (P1, P2) control viruses are diagonally distributed over the plate. N1, N2, N3: Ad-siRNAs targeting the eGFP, mannose-6-phosphate-receptor and luciferase mRNAs, respectively. P1 and P2: Ad-siRNAs targeting the PRKCN (H24-010) and MPP6 (H24-011) mRNAs. P3: Ad-eGFP: overexpression of eGFP allows monitoring of infection efficiency.


The Ad-shRNAs are screened at 3 multiplicities of infection (MOIs): 12,000, 4,000 and 1,333. Ad-shRNAs are aliquotted into the inner wells of a 96 well plate at a titer of 1.5×109/4 μl and 1/3 and 1/9 dilutions are derived of this plate (FIG. 11). The resulting 3 plates are used to infect 3×384 well plates seeded with MSCs, in the A1 and B2 positions of each quadrant using robotics. The viruses from the control plate are pipetted in the A2 and B1 positions.


Next, 5 μl of adenovirus expressing the human coxsackie and adenovirus receptor (hCAR) (AdC15-hCAR/AdC20-hCAR) is transferred into these wells (final MOI of 155) from a 96 well V-bottom plate with the aid of the 96-channel dispenser.


Plates are then incubated at 37° C., 10% CO2 in a humidified incubator for four days. Four days post infection, the medium containing the adenoviruses is replaced by 60 μl fresh MSC medium containing 10% FCS free of virus. After an additional nine days of incubation, medium is removed, 15 μL of a 4-methylumbelliferylphosphate solution (Sigma, #M3168) is added to each well and the fluorescence of 4-methyl-umbelliferone released by the alkaline phosphatase activity is measured after 15 min incubation at 37° C. using a fluorimeter (excitation: 360 nm; emission: 440 nm; FluoStar, BMG).


All Ad-shRNAs viruses are screened in duplicate at 3 MOIs in two independent screens. Thresholds are calculated for hit calling using either all negative controls present in one screening round (‘Global’ analysis) or using the negative controls present on one screening plate (‘Local’ analysis). Threshold is set at a BAP signal higher than the mean plus 3 times the standard deviation of negative controls. The two individual datapoints for each virus in the batch are analyzed independently. Hits are selected if one Ad-shRNAs scored at least at one MOI in duplicate in at least one of the 2 screens above the threshold (see Table 7).


A ‘Global’ analysis of the data identified 61 siRNAs targeting 32 loci and a ‘Local’ analysis' identified 84 siRNAs targeting 35 loci. The identity of the 38 selected genes is presented in Table 7 together with the final number of siRNAs that scored in the BAP assay. In this Table, the numbers indicate all siRNAs that scored in the BAP assay, including the original 38 siRNAs. Based on the ‘Global’ and ‘Local’ analysis, an average of 2.61 and 3.21 constructs respectively are identified for each of the 38 validated targets.


All original 38 Ad-shRNAs scored in the BAP assay based on both the ‘Global’ and ‘Local’ analysis.


In conclusion, additional Ad-shRNAs targeting 38 selected targets are designed and constructed. Negative controls present on the control plates are used per plate (‘Local’ analysis) or per batch of plates (‘Global’ analysis) to determine the cutoff for hit calling.


The ‘Global’ analysis results in 61 viruses that scored positive in the BAP assay, confirming 32 of the 38 validated targets. The ‘Local’ analysis results in 84 viruses that scored positive in the BAP assay, confirming 35 of the 38 validated targets. All original 38 Ad-shRNA viruses score in the BAP assay when using either the ‘Global’ or the ‘Local’ analysis. The targets LOC160662, PPIA and SLC39A4 are identified only in the ‘Local’ analysis.

TABLE 7TARGET GeneGlobal analysis-Local analysis -SymbolRedundancyRedundancyAPG4B23C13orf622C20orf12134CCR134CCR322CEL24CLIC622CSNK1G123DUSP522FLJ2295534FRK33GPR12423GPR2323GPR6445Grin2a-GRIN2A76GZMK22HRMT1L322IRAK244LOC160662 - LST-312LOC167417 - GPR15045LOC25437834MAP3K945MLNR43MMP23B -MMP23A32MNK223OR1A246PPIA13RASD145RDH1134SENP344SLC16A323SLC26A811SLC39A412SLC4A1011TAO134TAS1R323TRPM611ULK123


EXAMPLE 10
Identification of Small Molecules that Inhibit TARGET Kinase Activity

Compounds are screened for inhibition of the activity of the TARGETS that are kinase polypeptides. The affinity of the compounds to the polypeptides is determined in an experiment detecting changed reaction conditions after phosphorylation. The TARGET kinase polypeptides are incubated with its substrate and ATP in an appropriate buffer. The combination of these components results in the in vitro phosphorylation of the substrate. Sources of compounds include commercially available screening library, peptides in a phage display library or an antibody fragment library, and compounds that have been demonstrated to have binding affinity for a TARGET kinase.


The TARGET kinase polypeptides can be prepared in a number of ways depending on whether the assay will be run using cells, cell fractions or biochemically, on purified proteins. The polypeptides can be applied as complete polypeptides or as polypeptide fragments, which still comprise TARGET kinase catalytic activity.


Identification of small molecules inhibiting the activity of the TARGET kinase polypeptides is performed by measuring changes in levels of phosphorylated substrate or ATP. Since ATP is consumed during the phosphorylation of the substrate, its levels correlate with the kinase activity. Measuring ATP levels via chemiluminescent reactions therefore represents a method to measure kinase activity in vitro (Perkin Elmer). In a second type of assay, changes in the levels of phosphorylated substrate are detected with phosphospecific agents and are correlated to kinase activity. These levels are detected in solution or after immobilization of the substrate on a microtiter plate or other carrier. In solution, the phosphorylated substrate is detected via fluorescence resonance energy transfer (FRET) between the Eu labeled substrate and an APC labeled phosphospecific antibody (Perkin Elmer), via fluorescence polarization (FP) after binding of a phosphospecific antibody to the fluorescently labeled phosphorylated substrate (Panvera), via an Amplified Luminescent Proximity Homogeneous Assay (ALPHA) using the phosphorylated substrate and phosphospecific antibody, both coupled to ALPHA beads (Perkin Elmer) or using the IMAP binding reagent that specifically detects phosphate groups and thus alleviates the use of the phosphospecific antibody (Molecular Devices). Alternatively, the substrate is immobilized directly or by using biotin-streptavidin on a microtiter plate. After immobilization, the level of phosphorylated substrate is detected using a classical ELISA where binding of the phosphospecific antibody is either monitored via an enzyme such as horseradish peroxidase (HRP) or alkaline phospahtase (AP) which are either directly coupled to the phosphospecific antibody or are coupled to a secondary antibody. Enzymatic activity correlates to phosphorylated substrate levels. Alternatively, binding of the Eu-labeled phosphospecific antibody to the immobilized phosphorylated substrate is determined via time resolved fluorescence energy (TRF) (Perkin Elmer). In addition, the substrate can be coated on FLASH plates (Perkin Elmer) and phosphorylation of the substrate is detected using 33p labeled ATP or 125I labeled phosphospecific antibody.


Small molecules are randomly screened or are preselected based upon drug class, (i.e. known kinase inhibitors), or upon virtual ligand screening (VLS) results. VLS uses virtual docking technology to test large numbers of small molecules in silico for their binding to the polypeptide of the invention. Small molecules are added to the kinase reaction and their effect on levels of phosphorylated substrate is measured with one or more of the above-described technologies.


Small molecules that inhibit the kinase activity are identified and are subsequently tested at different concentrations. IC50 values are calculated from these dose response curves. Strong binders have an IC50 in the nanomolar and even picomolar range. Compounds that have an IC50 of at least 10 micromol or better (nmol to pmol) are applied in alkaline phosphatase assay or bone mineralization assay to check for their effect on the induction of osteogenesis.


EXAMPLE 11
Ligand Screens for TARGET GPCRs

Reporter Gene Screen.


Mammalian cells such as Hek293 or CHO-K1 cells are either stably transfected with a plasmid harboring the luciferase gene under the control of a cAMP dependent promoter (CRE elements) or transduced with an adenovirus harboring a luciferase gene under the control of a cAMP dependent promoter. In addition reporter constructs can be used with the luciferase gene under the control of a Ca2+ dependent promoter (NF-AT elements) or a promoter that is controlled by activated NF-κB. These cells, expressing the reporter construct, are then transduced with an adenovirus harboring the cDNA of a TARGET GPCR. Forty (40) hours after transduction the cells are treated with the following:


a) an agonist for the receptor and screened against a large collection of reference compounds comprising peptides (LOPAP, Sigma Aldrich), lipids (Biomol, TimTech), carbohydrates (Specs), natural compounds (Specs, TimTech), small chemical compounds (Tocris), commercially available screening libraries, and compounds that have been demonstrated to have binding affinity for a polypeptide comprising an amino acid sequence selected from the group consisting of the SEQ ID NOs of the TARGET GPCRs; or


b) a large collection of reference compounds comprising peptides (LOPAP, Sigma Aldrich), lipids (Biomol, TimTech), carbohydrates (Specs), natural compounds (Specs, TimTech), small chemical compounds (Tocris), commercially available screening libraries, and compounds that have been demonstrated to have binding affinity for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs of the TARGET GPCRs.


Compounds, which decrease the agonist induced increase in luciferase activity or the constitutive activity, are considered to be antagonists or inverse agonists for a TARGET GPCR. These compounds are screened again for verification and screened against their effect on osteoblast differentiation. The compounds are also screened to verify binding to the GPCR. The binding, osteogenesis and reporter activity assays can be performed in essentially any order to screen compounds.


In addition, cells expressing the NF-AT reporter gene can be transduced with an adenovirus harboring the cDNA encoding the α-subunit of G15 or chimerical Gα subunits. G15 is a promiscuous G protein of the Gq class that couples to many different GPCRs and as such re-directs their signaling towards the release of intracellular Ca2+ stores. The chimerical G alpha subunits are members of the Gs and Gi/o family by which the last 5 C-terminal residues are replaced by those of Gαq, these chimerical G-proteins also redirect cAMP signaling to Ca2+ signaling.


FLIPR Screen.


Mammalian cells such as Hek293 or CHO-K1 cells are stably transfected with an expression plasmid construct harboring the cDNA of a TARGET GPCR. Cells are seeded, grown, and selected until sufficient stable cells can be obtained. Cells are loaded with a Ca2+ dependent fluorophore such as Fura3 or Fura4. After washing away the excess of fluorophore the cells are screened against a large collection of reference compounds comprising peptides (LOPAP, Sigma Aldrich), lipids (Biomol, TimTech), carbohydrates (Specs), natural compounds (Specs, TimTech), small chemical compounds (Tocris), commercially available screening libraries, and compounds that have been demonstrated to have binding affinity for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs of the TARGET GPCRs, by simultaneously adding an agonist (alternatively no agonist need be added if the constitutive activity of the receptor is used) and a compound to the cells. Activation of the receptor is measured as an almost instantaneously increase in fluorescence due to the interaction of the fluorophore and the Ca2+ that is released. Compounds that reduce or inhibit the agonist induced increase in fluorescence (or constitutive fluorescence) are considered to be antagonists or inverse agonists for the receptor they are screened against. These compounds are screened again to measure the amount of osteoblast differentiation as well as binding to a TARGET GPCR. AequoScreen.


CHO cells, stably expressing Apoaequorin are stably transfected with a plasmid construct harboring the cDNA of a TARGET GPCR. Cells are seeded, grown, and selected until sufficient stable cells can be obtained. The cells are loaded with coelenterazine, a cofactor for apoaequorin. Upon receptor activation intracellular Ca2+ stores are emptied and the aequorin will react with the coelenterazine in a light emitting process. The emitted light is a measure for receptor activation. The CHO, stable expressing both the apoaequorin and the receptor are screened against a large collection of reference compounds comprising peptides (LOPAP, Sigma Aldrich), lipids (Biomol, TimTech), carbohydrates (Specs), natural compounds (Specs, TimTech), small chemical compounds (Tocris), commercially available screening libraries, and compounds that have been demonstrated to have binding affinity for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs of the TARGET GPCRs, by simultaneously adding an agonist (alternatively no agonist need be added if the constitutive activity of the receptor is used) and a compound to the cells. Activation of the receptor is measured as an almost instantaneously light flash due to the interaction of the apoaequorin, coelenterazine, and the Ca2+ that is released. Compounds that reduce or inhibit the agonist induced increase in light or the constitutive activity are considered to be antagonists or inverse agonists for the receptor they are screened against. These compounds are screened again to measure the amount of osteoblast differentiation as well as binding to a TARGET GPCR.


In addition, CHO cells stable expressing the apoaequorin gene are stably transfected with a plasmid construct harboring the cDNA encoding the α-subunit of G15 or chimerical Gα subunits. G15 is a promiscuous G protein of the Gq class that couples to many different GPCRs and as such redirects their signaling towards the release of intracellular Ca2+ stores. The chimerical G alpha subunits are members of the Gs and Gi/o family by which the last 5 C-terminal residues are replaced by those of Gαq, these chimerical G-proteins also redirect cAMP signaling to Ca2+ signaling.


Screening for Compounds that Bind to the GPCR Polypeptides (Displacement Experiment)


Compounds are screened for binding to the TARGET GPCR polypeptides. The affinity of the compounds to the polypeptides is determined in a displacement experiment. In brief, the GPCR polypeptides are incubated with a labeled (radiolabeled, fluorescent labeled) ligand that is known to bind to the polypeptide and with an unlabeled compound. The displacement of the labeled ligand from the polypeptide is determined by measuring the amount of labeled ligand that is still associated with the polypeptide. The amount associated with the polypeptide is plotted against the concentration of the compound to calculate IC50 values. This value reflects the binding affinity of the compound to its TARGET, i.e. the TARGET GPCR polypeptides. Strong binders have an IC50 in the nanomolar and even picomolar range. Compounds that have an IC50 of at least 10 micromol or better (nmol to pmol) are applied an osteoblast differentiation assay to check for their effect on osteogenesis. The TARGET GPCR polypeptides can be prepared in a number of ways depending on whether the assay are run on cells, cell fractions or biochemically, on purified proteins. Screening for compounds that bind to a TARGET GPCR (generic GPCR screening assay) When a G protein receptor becomes constitutively active, it binds to a G protein (Gq, Gs, Gi, Go) and stimulates the binding of GTP to the G protein. The G protein then acts as a GTPase and slowly hydrolyses the GTP to GDP, whereby the receptor, under normal conditions, becomes deactivated. However, constitutively activated receptors continue to exchange GDP to GTP. A non-hydrolyzable analog of GTP, [35S]GTPγS, can be used to monitor enhanced binding to membranes which express constitutively activated receptors. It is reported that [35S]GTPγS can be used to monitor G protein coupling to membranes in the absence and presence of ligand. Moreover, a preferred approach is the use of a GPCR-G protein fusion protein. The strategy to generate a TARGET GPCR-G protein fusion protein is well known for those known in the art. Membranes expressing TARGET GPCR-G protein fusion protein are prepared for use in the direct identification of candidate compounds such as inverse agonist. Homogenized membranes with TARGET GPCR-G protein fusion protein are transferred in a 96-well plate. A pin-tool is used to transfer a candidate compound in each well plus [35S]GTPγS, followed by incubation on a shaker for 60 minutes at room temperature. The assay is stopped by spinning of the plates at 4000 RPM for 15 minutes at 22° C. The plates are then aspirated and radioactivity is then read.


Receptor Ligand Binding Study on Cell Surface


The receptor is expressed in mammalian cells (Hek293, CHO, COS7) by adenoviral transducing the cells (see U.S. Pat. No. 6,340,595). The cells are incubated with both labeled ligand (iodinated, tritiated, or fluorescent) and the unlabeled compound at various concentrations, ranging from 10 pM to 10 μM (3 hours at 4° C.: 25 mM HEPES, 140 mM NaCl, 1 mM CaCl2, 5 mM MgCl2 and 0.2% BSA, adjusted to pH 7.4). Reactions mixtures are aspirated onto PEI-treated GF/B glass filters using a cell harvester (Packard). The filters are washed twice with ice cold wash buffer (25 mM HEPES, 500 mM NaCl, 1 mM CaCl2, 5 mM MgCl2, adjusted to pH 7.4). Scintillant (MicroScint-10; 35 μl) is added to dried filters and the filters counted in a (Packard Topcount) scintillation counter. Data are analyzed and plotted using Prism software (GraphPad Software, San Diego, Calif.). Competition curves are analyzed and IC50 values calculated. If one or more data points do not fall within the sigmoidal range of the competition curve or close to the sigmoidal range the assay is repeated and concentrations of labeled ligand and unlabeled compound adapted to have more data points close to or in the sigmoidal range of the curve.


Receptor Ligand Binding Studies on Membrane Preparations


Membranes preparations are isolated from mammalian cells (Hek293, CHO, COS7) cells over expressing the receptor is done as follows: Medium is aspirated from the transduced cells and cells are harvested in 1× PBS by gentle scraping. Cells are pelleted (2500 rpm 5 min) and resuspended in 50 mM Tris pH 7.4 (10×106 cells/ml). The cell pellet is homogenized by sonicating 3×5 sec (UP50H; sonotrode MS1; max amplitude: 140 μm; max Sonic Power Density: 125W/cm2). Membrane fractions are prepared by centrifuging 20 min at maximal speed (13,000 rpm -15,000 to 20,000g or rcf). The resulting pellet is resuspended in 500 μl 50 mM Tris pH 7.4 and sonicated again for 3×5 sec. The membrane fraction is isolated by centrifugation and finally resuspended in PBS. Binding competition and derivation of IC50 values are determined as described above.


Internalization Screen (1)


Activation of a GPCR-associated signal transduction pathway commonly leads to translocation of specific signal transduction molecules from the cytoplasm to the plasma membrane or from the cytoplasm to the nucleus. Norak has developed their transfluor assay based on agonist-induced translocation of receptor-β-arrestin-GFP complex from the cytosol to the plasma membrane and subsequent internalization of this complex, which occurs during receptor desensitization. A similar assay uses GFP tagged receptor instead of β-arrestin. Hek293 cells are transduced with a TARGET GPCR vector that translates for a TARGET GPCR-EGFP fusion protein. 48 hours after transduction, the cells are set to fresh serum-free medium for 60 minutes and treated with a ligand for 15, 30, 60 or 120 minutes at 37° C. and 5% CO2. After indicated exposure times, cells are washed with PBS and fixed with 5% paraformaldehyde for 20 minutes at RT. GFP fluorescence is visualized with a Zeiss microscope with a digital camera. This method aims for the identification of compounds that inhibit a ligand-mediated (constitutive activity-mediated) translocation of the fusion protein to intracellular compartments.


Internalization Screen (2)


Various variations on translocation assays exists using β-arrestin and β-galactosidase enzyme complementation and BRET based assays with receptor as energy donor and β-arrestin as energy acceptor. Also the use of specific receptor antibodies labeled with pH sensitive dyes are used to detect agonist induced receptor translocation to acidic lysosomes. All of the translocation assays are used for screening for both agonistic and antagonistic acting ligands.


Melanophore Assay (Arena Pharmaceutical)


The melanophore assay is based on the ability of GPCRs to alter the distribution of melanin containing melanosomes in Xenopus melanophores. The distribution of the melanosomes depends on the exogenous receptor that is either Gi/o or Gs/q coupled. The distribution of the melanosomes (dispersed or aggregated) is easily detected by measuring light absorption. This type of assay is used for both agonist as well as antagonist compound screens.


REFERENCES

Cortez-Retamozo et al. (2004) Cancer Res 64: 2853-7.


Franceschi R T and Xiao G (2003) J Cell Biochem 8:446-454.


Lipinsky, C A, et al. (2001) Adv Drug Deliv Rev 46: 3-26.


Nakashima K, de Crombrugghe B. (2003) Trends Genet. 19(8):458-66.


Marzia M, et al. (2000) J Cell Biol 151:311.


Thirunavukkarasu et al., (2000) J Biol Chem 275: 25163-72.


Yamada et al. (2003) Blood 101: 2227-34.


Zhang et al. (2000) PNAS 97: 10549-10554.

Claims
  • 1. A method for identifying a compound that induces differentiation of undifferentiated vertebrate cells into osteoblasts, comprising (a) contacting a compound with a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133; and (b) measuring a compound-polypeptide property related to the differentiation of said cells.
  • 2. The method according to claim 1, wherein said polypeptide is in an in vitro cell-free preparation.
  • 3. The method according to claim 2, wherein said polypeptide is present in a mammalian cell.
  • 4. The method of claim 1, wherein said property is a binding affinity of said compound to said polypeptide.
  • 5. The method of claim 3, wherein said property is activation of a biological pathway producing a biochemical marker indicative of the differentiation of said cells.
  • 6. The method of claim 5 wherein said indicator is bone alkaline phosphatase.
  • 7. The method according to claim 1, wherein said compound is selected from the group consisting of compounds of a commercially available screening library and compounds having binding affinity for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-599, 601-606, 867-1119, 1123-1133.
  • 8. The method according to claim 2, wherein said compound is a peptide in a phage display library or an antibody fragment library.
  • 9. An agent for inducing the differentiation of undifferentiated mammalian cells into osteoblasts, selected from the group consisting of an antisense polynucleotide, a ribozyme, and a small interfering RNA (siRNA), wherein said agent comprises a nucleic acid sequence complementary to, or engineered from, a naturally-occurring polynucleotide sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133.
  • 10. The agent according to claim 9, wherein a vector in a mammalian cell expresses said agent.
  • 11. The agent according to claim 10, wherein said vector is an adenoviral, retroviral, adeno-associated viral, lentiviral, a herpes simplex viral or a sendaiviral vector.
  • 12. The agent according to claim 9, wherein said antisense polynucleotide and said siRNA comprise an antisense strand of 17-25 nucleotides complementary to a sense strand, wherein said sense strand is selected from 17-25 continuous nucleotides of a nucleic acid sequence selected from the group consisting of SEQ ID NO: 335-376, 600, 607-866, 1120-1122.
  • 13. The agent according to claim 12, wherein said siRNA further comprises said sense strand.
  • 14. The agent according to claim 13, wherein said siRNA further comprises a loop region connecting said sense and said antisense strand.
  • 15. The agent according to claim 14, wherein said loop region comprises a nucleic acid sequence defined of SEQ ID NO: 334.
  • 16. The agent according to claim 15, wherein said agent is an antisense polynucleotide, ribozyme, or siRNA comprising a nucleic acid sequence complementary to a polynucleotide selected from the group consisting of SEQ ID NO: 1-220, 247-333.
  • 17. A bone formation enhancing pharmaceutical composition comprising a therapeutically effective amount of an agent of claim 9 in admixture with a pharmaceutically acceptable carrier.
  • 18. A method of treating and/or preventing a disease involving a systemic or local decrease in mean bone density in a subject suffering from or susceptible to the disease, comprising administering to said subject a pharmaceutical composition according to claim 17.
  • 19. The method according to claim 18 wherein the disease is selected from the group consisting of osteoporosis, hypercalcemia of malignancy, multiple myelomatosis, hyperparathyroidism, and hyperthyroidism.
  • 20. The method according to claim 19, wherein the disease is osteoporosis.
  • 21. A pharmaceutical composition for the treatment and/or prevention of a disease involving a decrease in mean bone density comprising the agent according to claim 9.
  • 22. A pharmaceutical composition according to claim 21, wherein the disease is selected from the group consisting of osteoporosis, hypercalcemia of malignancy, multiple myelomatosis, hyperparathyroidism, and hyperthyroidism.
  • 23. A pharmaceutical composition according to claim 22, wherein the disease is osteoporosis.
  • 24. A method for in vitro production of bone tissue, comprising contacting undifferentiated mammalian cells with a polynucleotide sequence comprising a nucleic acid sequence complementary to a polynucleotide selected from the group consisting of SEQ ID NO: 1-220, 247-333 for a time sufficient to differentiate the undifferentiated cells into osteoblasts, thereby producing a continuous bone matrix.
  • 25. A method for diagnosing a pathological condition involving a systemic or local decrease in mean bone density or a susceptibility to the condition in a subject, comprising determining a first amount of polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 377-418, 601, 867-1119, 1123-1133 present in a biological sample obtained from said subject, and comparing said first amount with the ranges of amounts of the polypeptide determined in a population of healthy subjects, wherein an increase of the amount of polypeptide in said biological sample compared to the range of amounts determined for healthy subjects is indicative of the presence of the pathological condition.
Priority Claims (1)
Number Date Country Kind
PCT/EP03/14994 Dec 2003 WO international
CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of PCT/EP2004/014885, filed Dec. 29, 2004, which claims priority to PCT/EP03/14994, filed Dec. 29, 2003, both of which applications designate the USA, the disclosures of which are incorporated herein by reference.

Continuation in Parts (1)
Number Date Country
Parent PCT/EP04/14885 Dec 2004 US
Child 11478193 Jun 2006 US