Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6887—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids from muscle, cartilage or connective tissue
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
  • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/10—Musculoskeletal or connective tissue disorders
  • G01N2800/101—Diffuse connective tissue disease, e.g. Sjögren, Wegener's granulomatosis
  • G01N2800/102—Arthritis; Rheumatoid arthritis, i.e. inflammation of peripheral joints
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

• the invention relates to a method of determining the efficacy of the treatment for RA based on two to several characteristics known to correlate with negative outcomes in RA presented in a matrix.
• the invention also relates to a method of determining the efficacy of the treatment for RA based on preparing matrix table comprising two to several covariates which significantly correlate with radiological progression.
• the matrix relates this profile of characteristics or covariates to the probability (risk) of negative outcomes under each of the alternative potential treatments. This can be done for a subject, for example, prior to the manifestation of other gross measurements of clinical response.
• Physicians are confronted with individual patients and individualized decision making on a daily basis and use treatments to limit the risk of bad outcome of a disease.
• the benefit of a treatment has to be weighed against the potential harm and cost of it and, with a growing armamentarium of therapies, choosing the right treatment for the right patient is a challenge.
• a physician would like to know in advance whether a certain patient needs a treatment and whether a specific treatment will or will not be effective in that specific patient. In practice this comes down to knowing the probability (or risk) of bad outcome of a disease and the probability of successfully treating a certain patient with a certain drug.
• the most broadly used risk model in medicine is the risk chart used in cardiology, which combines gender, age, systolic blood pressure, total cholesterol and smoking status to predict the 10-year risk of death due to cardiovascular disease (www.escardio.org/Prevention).
• Incorporation of the separate risk factors of cardiovascular disease in the model makes it an ideal tool to estimate the risk of bad outcome (death) in the individual patient.
• the simplicity of this model is furthermore that it is ideal for patient education, which is broadly used for from primary to tertiary care.
• the model does not inform the user about differential effectiveness of therapy in the prevention of risk.
• Immune mediated inflammatory disorders IMID's
• IMID's are characterized by progressive irreversible damage.
• Rheumatoid arthritis is characterized by joint inflammation leading to cartilage destruction and erosion of sub-cartilaginous bone. Recently, decreasing progression of radiographic joint damage and functional disability in the RA population is seen, and seems to be largely explained by more effective use of disease modifying anti-rheumatic drugs. More effective use of DMARD's consists of more widespread and earlier use (Finkh et al. Ann Rheum Dis 2006;65:1192-1197). In a recent meta-analysis of 12 studies comparing early vs. late initiation of DMARD's, the reduction in progression rate due to earlier initiation of DMARDs was significantly different when compared to patients who started late. The effect of starting such drugs early could account for half of the total effect size of the treatment. The authors furthermore observed that patients with more aggressive disease benefited more from earlier treatment (Finkh et al. Arthritis Rheum 2006;56(6):864-872).
• infliximab IFX
• cyclosporine SSZ
• leflunomide MTX
• parenteral gold CS
• auranofin interleukin 1 receptor antagonist
• RA rheumatoid arthritis
• a method for prognostic or diagnostic assessment of treatment of at least one an rheumatoid arthritis related disorder in a subject comprising: a) preparing a matrix table comprising set of two or more covariates which significantly correlate with radiological progression in RA with the probability of a negative clinical outcome under each of the alternative treatments; b) performing a statistical comparison of said alternative treatments with the corresponding clinical outcome negative probability; and c) selecting one or more of said alternative treatments based on the lowest negative clinical outcome probability.
• the model consists of a matrix table that combines a number of characteristics known to correlate with negative outcomes in RA.
• the matrix table relates this profile of characteristics to the probability (risk) of bad outcome under each of the treatment possibilities.
• the model matrix combines several factors in easily readable fashion and predicts outcome relative to the treatment regimen a physician can choose to treat an individual patient with.
• the model is a tool for treatment guidance and patient education.
• the present invention thus relates to a method of diagnosing and/or treating RA and/or related diseases or disorders by identifying and using two to several characteristics known to correlate with negative outcomes in RA and determining the treatment that minimizes the probability of negative outcomes.
• the present invention comprises a method of determining the efficacy of the treatment for RA based on two to several characteristics known to correlate with negative outcomes in RA presented in a matrix table.
• the matrix table relates this profile of characteristics to the probability (risk) of bad outcome under each of the treatment possibilities. This can be done for a subject, for example, prior to the manifestation of other gross measurements of clinical response.
• the method of modeling a matrix of two to several characteristics known to correlate with negative outcomes in RA.
• a method for for prognostic or diagnostic assessment of treatment of at least one an rheumatoid arthritis related disorder in a subject comprising: (a) preparing a set of two or more covariates which significantly correlate with radiological progression in RA with the probability of a negative clinical outcome under each of the alternative treatments;
• the RA-related characteristic profile and treatment profile is provided in a matrix for prognostic or diagnostic purposes, the method comprising:
• Such methods can include wherein the subject is a patient having, or having the potential to develop, rheumatoid arthritis and steps (a) through (c) are performed before, during, or after treatment of the patient with a therapy for rheumatoid arthritis.
• Such methods can include wherein steps (a) through (c) are performed during treatment of the patient with a therapy for the rheumatoid arthritis and about 1-30 weeks after commencement of treatment.
• Such methods can include wherein said covariate is selected from at least one of age, numbers of tender joints, numbers of swollen joints, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) positivity, or serum C-reactive protein (CRP) level, and joint damage.
• ESR erythrocyte sedimentation rate
• RF rheumatoid factor
• CRP serum C-reactive protein
• the treatment is selected from at least one of an antirheumatic, a TNF antagonist, a muscle relaxant, a narcotic, a non-steroid anti-inflammatory drug (NSAID), an analgesic, and an anesthetic.
• NSAID non-steroid anti-inflammatory drug
• Such methods can include wherein said antirheumatic is at least one selected from methotrexate, auranofin, aurothioglucose, azathioprine, gold sodium thiomalate, hydroxychloroquine sulfate, leflunomide, or sulfasalzine.
• Such methods can include wherein said TNF antagonist is selected from a small molecule or a biologic that inhibits at least one TNF biological activity.
• Such methods can include wherein said TNF antagonist biologic is an TNF-antibody or TNF receptor fusion protein.
• Such methods can include wherein wherein said TNF antagonist biologic is selected from infliximab, adalimumab, enteracept or golimumab.
• the present invention comprises a kit for diagnosing RA and/or related diseases or disorders by identifying and using candidate agents and/or targets which modulate such diseases or disorders and for determining the efficacy of the treatment for RA and/or related diseases or disorders based on two or more characteristics known to correlate with negative outcomes in RA with the probability of a negative clinical outcome under each of the alternative treatments.
• the RA-related antagonist is an antibody that specifically binds RA-related product.
• a particular advantage of such antibodies is that they are capable of binding RA- related product in a manner that prevents its action.
• the method of the present invention thus employs antibodies having the desirable neutralizing property which makes them ideally suited for therapeutic and preventative treatment of disease states associated with various RA-related disorders in human or nonhuman patients. Accordingly, the present invention is directed to a method of treating RA or a related disease or condition in a patient in need of such treatment which comprises administering to the patient an amount of a neutralizing RA-related product antibody to inhibit the RA-related disease or condition.
• the invention provides methods for modulating activity of a member of a RA- related comprising contacting a cell with an agent (e.g., antagonist or agonist) that modulates (inhibits or enhances) the activity or expression of the member of the RA-related gene panel such that activity or expression in the cell is modulated.
• an agent e.g., antagonist or agonist
• the agent is an antibody that specifically binds to the RA-related gene panel.
• the modulator is a peptide, peptidomimetic, or other small molecule.
• the present invention also provides methods of treating a subject having RA or related disorder wherein the disorder can be ameliorated by modulating the amount or activity of the RA-related gene panel.
• the present invention also provides methods of treating a subject having a disorder characterized by aberrant activity of the RA-related product or one of their encoding polynucleotide by administering to the subject an agent that is a modulator of the activity of the RA-related product or or a modulator of the expression of a RA-related gene panel.
• the modulator is a polypeptide or small molecule compound. In another embodiment, the modulator is a polynucleotide. In a particular embodiment, the RA-related antagonist is an siRNA molecule, an shRNA molecule, an antisense molecule, a ribozyme, or a DNAzyme capable of preventing the production of RA-related by cells.
• the present invention further provides any invention described herein.
• the invention relates to a method of determining the efficacy of the treatment for RA based on two to several characteristics known to correlate with negative outcomes in RA presented in a matrix.
• the invention also relates to a method of determining the efficacy of the treatment for RA based on preparing matrix table comprising two to several covariates which significantly correlate with radiological progression.
• the matrix relates this profile of characteristics or covariates to the probability (risk) of negative outcomes under each of the alternative potential treatments. This can be done for a subject, for example, prior to the manifestation of other gross measurements of clinical response.
• a method for prognostic or diagnostic assessment of treatment of at least one an rheumatoid arthritis related disorder in a subject comprising: d) preparing a matrix table comprising set of two or more covariates which significantly correlate with radiological progression in RA with the probability of a negative clinical outcome under each of the alternative treatments; e) performing a statistical comparison of said alternative treatments with the corresponding clinical outcome negative probability; and f) selecting one or more of said alternative treatments based on the lowest negative clinical outcome probability.
• the model consists of a matrix table that combines a number of characteristics known to correlate with negative outcomes in RA.
• the matrix table relates this profile of characteristics to the probability (risk) of bad outcome under each of the treatment possibilities.
• the model matrix combines several factors in easily readable fashion and predicts outcome relative to the treatment regimen a physician can choose to treat an individual patient with.
• the model is a tool for treatment guidance and patient education.
• the present invention thus relates to a method of diagnosing and/or treating RA and/or related diseases or disorders by identifying and using two to several characteristics known to correlate with negative outcomes in RA and determining the treatment that minimizes the probability of negative outcomes.
• the present invention comprises a method of determining the efficacy of the treatment for RA based on two to several characteristics known to correlate with negative outcomes in RA presented in a matrix table.
• the matrix table relates this profile of characteristics to the probability (risk) of bad outcome under each of the treatment possibilities. This can be done for a subject, for example, prior to the manifestation of other gross measurements of clinical response.
• the method of modeling a matrix of two to several characteristics known to correlate with negative outcomes in RA is a method of modeling a matrix of two to several characteristics known to correlate with negative outcomes in RA.
• a method for for prognostic or diagnostic assessment of treatment of at least one an rheumatoid arthritis related disorder in a subject comprising: (a) preparing a set of two or more covariates which significantly correlate with radiological progression in RA with the probability of a negative clinical outcome under each of the alternative treatments;
• the RA-related characteristic profile and treatment profile is provided in a matrix for prognostic or diagnostic purposes, the method comprising:
• Such methods can include wherein the subject is a patient having, or having the potential to develop, rheumatoid arthritis and steps (a) through (c) are performed before, during, or after treatment of the patient with a therapy for rheumatoid arthritis.
• Such methods can include wherein steps (a) through (c) are performed during treatment of the patient with a therapy for the rheumatoid arthritis and about 1-30 weeks after commencement of treatment.
• Such methods can include wherein said covariate is selected from at least one of age, numbers of tender joints, numbers of swollen joints, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) positivity, or serum C-reactive protein (CRP) level, and joint damage.
• said covariate is selected from at least one of age, numbers of tender joints, numbers of swollen joints, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) positivity, or serum C-reactive protein (CRP) level, and joint damage.
• Such methods can include wherein the treatment is selected from at least one of an antirheumatic, a TNF antagonist, a muscle relaxant, a narcotic, a non-steroid anti-inflammatory drug (NSAID), an analgesic, and an anesthetic.
• the treatment is selected from at least one of an antirheumatic, a TNF antagonist, a muscle relaxant, a narcotic, a non-steroid anti-inflammatory drug (NSAID), an analgesic, and an anesthetic.
• NSAID non-steroid anti-inflammatory drug
• Such methods can include wherein said antirheumatic is at least one selected from methotrexate, auranofin, aurothioglucose, azathioprine, gold sodium thiomalate, hydroxychloroquine sulfate, leflunomide, or sulfasalzine.
• said TNF antagonist is selected from a small molecule or a biologic that inhibits at least one TNF biological activity.
• Such methods can include wherein said TNF antagonist biologic is an TNF-antibody or TNF receptor fusion protein.
• Such methods can include wherein wherein said TNF antagonist biologic is selected from infliximab, adalimumab, enteracept or golimumab.
• the present invention comprises a kit for diagnosing RA and/or related diseases or disorders by identifying and using candidate agents and/or targets which modulate such diseases or disorders and for determining the efficacy of the treatment for RA and/or related diseases or disorders based on two or more characteristics known to correlate with negative outcomes in RA with the probability of a negative clinical outcome under each of the alternative treatments.
• Another embodiment of the present invention relates to agonists and/or antagonists ofthe transcription of the genes or of the gene products of the RA-related and a method of using RA- related antagonists, including antibodies directed toward RA-related products, to treat RA or related disorders.
• the RA-related antagonist is an antibody that specifically binds RA-related product.
• a particular advantage of such antibodies is that they are capable of binding RA- related product in a manner that prevents its action.
• the method of the present invention thus employs antibodies having the desirable neutralizing property which makes them ideally suited for therapeutic and preventative treatment of disease states associated with various RA-related disorders in human or nonhuman patients. Accordingly, the present invention is directed to a method of treating RA or a related disease or condition in a patient in need of such treatment which comprises administering to the patient an amount of a neutralizing RA-related antibody to inhibit the RA-related disease or condition.
• the invention provides methods for modulating activity of a member of a RA- related comprising contacting a cell with an agent (e.g., antagonist or agonist) that modulates (inhibits or enhances) the activity or expression of the member of the RA-related gene panel such that activity or expression in the cell is modulated.
• an agent e.g., antagonist or agonist
• the agent is an antibody that specifically binds to the RA-related gene panel.
• the modulator is a peptide, peptidomimetic, or other small molecule.
• an "activity,” a biological activity, and a functional activity of a polypeptide refers to an activity exerted by a gene of the RA-related in response to its specific interaction with another protein or
• Such activities can be a direct activity, such as an association with or an enzymatic activity on a second protein, or an indirect activity, such as a cellular process mediated by interaction of the protein with a second protein or a series of interactions as in intracellular signaling or the coagulation cascade.
• an “antibody” includes any polypeptide or peptide containing molecule that comprises at least a portion of an immunoglobulin molecule, such as but not limited to, at least one complementarity determining region (CDR) of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework region, or any portion, fragment or variant thereof.
• CDR complementarity determining region
• the term “antibody” is further intended to encompass antibodies, digestion fragments, specified portions and variants thereof, including antibody mimetics or comprising portions of antibodies that mimic the structure and/or function of an antibody or specified fragment or portion thereof, including single chain antibodies and fragments thereof.
• antibody fragments include, but are not limited to, Fab (e.g., by papain digestion), Fab' (e.g., by pepsin digestion and partial reduction) and F(ab')2 (e.g., by pepsin digestion), facb (e.g., by plasmin digestion), pFc' (e.g., by pepsin or plasmin digestion), Fd (e.g., by pepsin digestion, partial reduction and reaggregation), Fv or scFv (e.g., by molecular biology techniques) fragments, and single domain antibodies (e.g., V H or V L ), are encompassed by the invention (see, e.g., Colligan, et al., eds., Current Protocols in Immunology, John Wiley & Sons, Inc., NY (1994-2007); Colligan et al., Current Protocols in Polypeptide Science, John Wiley & Sons, NY (1997-2007)).
• labeled biological molecule or “labeled with a detectable composition” or “labeled with a detectable moiety” as used herein refer to a biological molecule, e.g., a nucleic acid, comprising a detectable composition, i.e., a label, as described in detail, below.
• the label can also be another biological molecule, as a nucleic acid, e.g., a nucleic acid in the form of a stem- loop structure as a "molecular beacon,” as described below.
• labeled bases or, bases which can bind to a detectable label
• Any label can be used, e.g., chemiluminescent labels, radiolabels, enzymatic labels and the like.
• the label can be detectable by any means, e.g., visual, spectroscopic, photochemical, biochemical, immunochemical, physical, chemical and/or chemiluminescent detection.
• the invention can use arrays comprising immobilized nucleic acids comprising detectable labels.
• profile means a pattern and relates to the magnitude and direction of change of a number of features.
• the profile may be interpreted stringently, i.e., where the variation in the magnitude and/or number of features within the profile displaying the characteristic is substantially similar to a reference profile or it may be interpreted less stringently, for example, by requiring a trend rather than an absolute match of all or a subset of feature characteristics.
• protein protein
• polypeptide amino acid sequence
• peptide amino acid sequence
• polypeptide is a polymer of amino acid residues joined by peptide bonds, and a peptide generally refers to amino acid polymers of 12 or less residues. Peptide bonds can be produced naturally as directed by the nucleic acid template or synthetically by methods well known in the art.
• a “protein” is a macromolecule comprising one or more polypeptide chains.
• a protein may further comprise substituent groups attached to the side groups of the amino acids not involved in formation of the peptide bonds.
• proteins formed by eukaryotic cell expression also contain carbohydrates. Proteins are defined herein in terms of their amino acid sequence or backbone and substituents are not specified, whether known or not.
• receptor denotes a molecule having the ability to affect biological activity, in e.g., a cell, as a result of interaction with a specific ligand or binding partner.
• Cell membrane bound receptors are characterized by an extracellular ligand-binding domain, one or more membrane spanning or transmembrane domains, and an intracellular effector domain that is typically involved in signal transduction.
• Ligand binding to cell membrane receptors causes changes in the extracellular domain that are communicated across the cell membrane, direct or indirect interaction with one or more intracellular proteins, and alters cellular properties, such as enzyme activity, cell shape, or gene expression profile.
• Receptors may also be untethered to the cell surface and may be cytosolic, nuclear, or released from the cell altogether. Non-cell associated receptors are termed soluble receptors or ligands.
• Antagonists refer to substances which inhibit or neutralize the biologic activity of RA-related genes or proteins. Such antagonists accomplish this effect in a variety of ways.
• One class of antagonists will bind to the gene product protein with sufficient affinity and specificity to neutralize the biologic effects of the protein. Included in this class of molecules are antibodies and antibody fragments (such as, for example, F(ab) or F(ab') 2 molecules).
• Another class of antagonists comprises fragments of the gene product protein, muteins or small organic molecules, i.e., peptidomimetics, that will bind to the cognate binding partners or ligands of the gene product, thereby inhibiting the biologic activity of the specific interaction of the gene product with its cognate ligand or receptor.
• the RA-related gene antagonist may be of any of these classes as long as it is a substance that inhibits at least one biological activity of the gene product.
• Antagonists include antibodies directed to one or more regions of the gene product protein or fragments thereof, antibodies directed to the cognate ligand or receptor, and partial peptides of the gene product or its cognate ligand which inhibit at least one biological activity of the gene product.
• Another class of antagonists include siRNAs, shRNAs, antisense molecules and DNAzymes targeting the gene sequence as known in the art are disclosed herein.
• Suitable antibodies include those that compete for binding to RA-related gene products with monoclonal antibodies that block RA-related gene product activation or prevent RA-related gene product binding to its cognate ligand, or prevent RA-related gene product signalling.
• a "chimeric protein” or “fusion protein” comprises all or part (preferably biologically active) of a RA-related gene
• heterologous polypeptide i.e., a polypeptide other than the same RA-related gene product polypeptide.
• heterologous polypeptide i.e., a polypeptide other than the same RA-related gene product polypeptide.
• the term "operably linked" is intended to indicate that the RA-related gene product polypeptide and the heterologous polypeptide are fused in-frame to each other.
• the heterologous polypeptide can be fused to the amino-terminus or the carboxyl-terminus of the RA-related gene product polypeptide.
• a RA-related gene product polypeptide or a domain or active fragment thereof can be fused with a heterologous protein sequence or fragment thereof to form a chimeric protein, where the polypeptides, domains or fragments are not fused end to end but are interposed within the heterologous protein framework.
• the fusion protein is an immunoglobulin fusion protein in which all or part of a RA-related gene product polypeptide is fused to sequences derived from a member of the immunoglobulin protein family.
• the immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand (soluble or membrane-bound) and a protein on the surface of a cell (receptor), to thereby suppress signal transduction in vivo.
• the immunoglobulin fusion protein can be used to affect the bioavailability of a cognate ligand of a RA-related gene product polypeptide. Inhibition of ligand/receptor interaction can be useful therapeutically, both for treating proliferative and differentiative disorders and for modulating (e.g., promoting or inhibiting) cell survival.
• an immunoglobulin chimeric protein is a C H 1 domain-deleted immunoglobulin or "mimetibody" having an active polypeptide fragment interposed within a modified framework region as taught in co-pending application PCT WO/04002417.
• the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies directed against a RA-related gene product polypeptide in a subject, to purify ligands and in screening assays to identify molecules that inhibit the interaction of receptors with ligands.
• TNF antagonists suitable for compositions, combination therapy, co-administration, devices and/or methods of the present invention include, but are not limited to, anti-TNF antibodies, antigen-binding fragments thereof, and receptor molecules which bind specifically to TNF; compounds which prevent and/or inhibit TNF synthesis, TNF release or its action on target cells, such as thalidomide, tenidap, phosphodiesterase inhibitors (e.g, pentoxifylline and rolipram), A2b adenosine receptor agonists and A2b adenosine receptor enhancers;
• TNF receptor signalling such as mitogen activated protein (MAP) kinase inhibitors; compounds which block and/or inhibit membrane TNF cleavage, such as metalloproteinase inhibitors; compounds which block and/or inhibit TNF activity, such as angiotensin converting enzyme (ACE) inhibitors (e.g., captopril); and compounds which block and/or inhibit TNF production and/or synthesis, such as MAP kinase inhibitors.
• MAP mitogen activated protein
• ACE angiotensin converting enzyme
• a "tumor necrosis factor antibody,” “TNF antibody,” “TNF ⁇ antibody,” or fragment and the like decreases, blocks, inhibits, abrogates or interferes with TNF ⁇ activity in vitro, in situ and/or preferably in vivo.
• a suitable TNF human antibody of the present invention can bind TNF ⁇ and includes anti-TNF antibodies, antigen-binding fragments thereof, and specified mutants or domains thereof that bind specifically to TNF ⁇ .
• a suitable TNF anttibody or fragment can also decrease block, abrogate, interfere, prevent and/or inhibit TNF RNA, DNA or protein synthesis, TNF release, TNF receptor signaling, membrane TNF cleavage, TNF activity, TNF production and/or synthesis.
• Chimeric antibody cA2 consists of the antigen binding variable region of the high-affinity neutralizing mouse anti-human TNF ⁇ IgGI antibody, designated A2, and the constant regions of a human IgGI , kappa immunoglobulin.
• the human IgGI Fc region improves allogeneic antibody effector function, increases the circulating serum half-life and decreases the immunogenicity of the antibody.
• the avidity and epitope specificity of the chimeric antibody cA2 is derived from the variable region of the murine antibody A2.
• a preferred source for nucleic acids encoding the variable region of the murine antibody A2 is the A2 hybridoma cell line.
• Chimeric A2 (cA2) neutralizes the cytotoxic effect of both natural and recombinant human TNF ⁇ in a dose dependent manner. From binding assays of chimeric antibody cA2 and recombinant human TNF ⁇ , the affinity constant of chimeric antibody cA2 was calculated to be 1.04xl0 10 M "1 .
• murine monoclonal antibody A2 is produced by a cell line designated c134A.
• Chimeric antibody cA2 is produced by a cell line designated c168A.
• Additional examples of monoclonal anti-TNF antibodies that can be used in the present invention are described in the art (see, e.g., U.S. Patent No. 5,231 ,024; Moller, A. ef a/., Cytokine 2(3): 162-169 (1990); U.S. Application No. 07/943,852 (filed September 11 , 1992); Rathjen et al., International Publication No.
• Preferred TNF receptor molecules useful in the present invention are those that bind TNF ⁇ with high affinity (see, e.g., Feldmann ef a/., International Publication No. WO 92/07076 (published April 30, 1992); Schall ef a/., Cell 67:361-370 (1990); and Loetscher ef a/., Cell 67:351-359 (1990), which references are entirely incorporated herein by reference) and optionally possess low immunogenicity.
• the 55 kDa (p55 TNF-R) and the 75 kDa (p75 TNF-R) TNF cell surface receptors are useful in the present invention.
• Truncated forms of these receptors comprising the extracellular domains (ECD) of the receptors or functional portions thereof (see, e.g., Corcoran ef a/., Eur. J. Biochem. 223:831-840 (1994)), are also useful in the present invention.
• Truncated forms of the TNF receptors, comprising the ECD have been detected in urine and serum as 30 kDa and 40 kDa TNF ⁇ inhibitory binding proteins (Engelmann, H. ef a/., J. Biol. Chem. 265:1531-1536 (1990)).
• TNF receptor multimeric molecules and TNF immunoreceptor fusion molecules, and derivatives and fragments or portions thereof, are additional examples of TNF receptor molecules which are useful in the methods and compositions of the present invention.
• the TNF receptor molecules which can be used in the invention are characterized by their ability to treat patients for extended periods with good to excellent alleviation of symptoms and low toxicity. Low immunogenicity and/or high affinity, as well as other undefined properties, can contribute to the therapeutic results achieved.
• TNF receptor multimeric molecules useful in the present invention comprise all or a functional portion of the ECD of two or more TNF receptors linked via one or more polypeptide linkers or other nonpeptide linkers, such as polyethylene glycol (PEG).
• the multimeric molecules can further comprise a signal peptide of a secreted protein to direct expression of the multimeric molecule.
• TNF immunoreceptor fusion molecules useful in the methods and compositions of the present invention comprise at least one portion of one or more immunoglobulin molecules and all or a functional portion of one or more TNF receptors. These immunoreceptor fusion molecules can be assembled as monomers, or hetero- or homo-multimers. The immunoreceptor fusion molecules can also be monovalent or multivalent. An example of such a TNF immunoreceptor fusion molecule is TNF receptor/lgG fusion protein. TNF immunoreceptor fusion molecules and methods for their production have been described in the art (Lesslauer ef al., Eur. J. Immunol. 27:2883-2886 (1991 ); Ashkenazi et al., Proc. Natl. Acad.
• a functional equivalent, derivative, fragment or region of TNF receptor molecule refers to the portion of the TNF receptor molecule, or the portion of the TNF receptor molecule sequence which encodes TNF receptor molecule, that is of sufficient size and sequences to functionally resemble TNF receptor molecules that can be used in the present invention (e.g., bind TNF ⁇ with high affinity and possess low immunogenicity).
• a functional equivalent of TNF receptor molecule also includes modified TNF receptor molecules that functionally resemble TNF receptor molecules that can be used in the present invention (e.g., bind TNF ⁇ with high affinity and possess low immunogenicity).
• a functional equivalent of TNF receptor molecule can contain a "SILENT" codon or one or more amino acid substitutions, deletions or additions (e.g., substitution of one acidic amino acid for another acidic amino acid; or
• the neutralizing anti-RA-related gene product antagonists such as monoclonal antibodies, described herein can be used to inhibit RA-related gene product activity. Additionally, such antagonists can be used to inhibit the pathogenesis of RA and -related inflammatory diseases amenable to such treatment, which may include, but are not limited to, rheumatic diseases.
• the individual to be treated may be any mammal and is preferably a primate, a companion animal which is a mammal and most preferably a human patient. The amount of antagonist administered will vary according to the purpose it is being used for and the method of administration.
• the RA-related gene antagonists may be administered by any number of methods that result in an effect in tissue in which pathological activity is desired to be prevented or halted. Further, the anti-RA-related gene product antagonists need not be present locally to impart an effect on the RA-related gene product activity, therefore, they may be administered wherever access to body compartments or fluids containing RA-related gene product is achieved. In the case of inflamed, malignant, or otherwise compromised tissues, these methods may include direct application of a formulation containing the antagonists. Such methods include intravenous administration of a liquid composition, transdermal administration of a liquid or solid formulation, oral, topical administration, or interstitial or inter-operative administration. Adminstration may be affected by the implantation of a device whose primary function may not be as a drug delivery vehicle.
• the preferred dosage is about 0.1 mg/kg to 100 mg/kg of body weight (generally about 10 mg/kg to 20 mg/kg). If the antibody is to act in the brain, a dosage of about 50 mg/kg to 100 mg/kg is usually appropriate. Generally, partially human antibodies and fully human antibodies have a longer half-life within the human body than other antibodies. Accordingly, the use of lower dosages and less frequent administration is often possible. Modifications, such as lipidation, can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the brain). A method for lipidation of antibodies is described by Cruikshank et al.
• the RA-related gene product antagonist nucleic acid molecules can be inserted into vectors and used as gene therapy vectors.
• Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (U.S. Pat. No. 5,328,470), or by stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91 :3054- 3057).
• the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
• the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
• the pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
• the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant expression or activity of a RA-related gene product polypeptide and/or in which the RA-related gene product polypeptide is involved.
• the present invention provides a method for modulating or treating at least one RA-related disease or condition, in a cell, tissue, organ, animal, or patient, as known in the art or as described herein, using at least one RA-related gene product antagonist.
• Compositions of RA- related gene product antagonist may find therapeutic use in the treatment of RA or related conditions. Disorders characterized by aberrant expression or activity of the RA-related gene product polypeptides are further described elsewhere in this disclosure.
• the invention provides a method for at least substantially preventing in a subject, a disease or condition associated with an aberrant expression or activity of a RA-related gene product polypeptide, by administering to the subject an agent that modulates expression or at least one activity of the polypeptide.
• Subjects at risk for a disease that is caused or contributed to by aberrant expression or activity of a RA-related gene product can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.
• Administration of a prophylactic agent can occur prior to the manifestation of symptoms
• an agonist or antagonist agent can be used for treating the subject.
• the appropriate agent can be determined based on screening assays described herein.
• the modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of the polypeptide.
• An agent that modulates activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring cognate ligand of the polypeptide, a peptide, a peptidomimetic, or other small molecule.
• the agent stimulates one or more of the biological activities of the polypeptide.
• the agent inhibits one or more of the biological activities of the RA-related gene or gene product polypeptide.
• inhibitory agents include antisense nucleic acid molecules and antibodies and other methods described herein. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject).
• the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant expression or activity of a RA-related gene product polypeptide.
• the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulate (e.g., up-regulates or down-regulates) expression or activity. Inhibition of activity is desirable in situations in which activity or expression is abnormally high or up-regulated and/or in which decreased activity is likely to have a beneficial effect.
• EXAMPLE 1 Matrix Modeling of Inflammatory-Autoimmune Disease Rheumatorid Arthritis Markers
• Radiographs of the hands and feet were obtained within 4 weeks of receiving the first dose of the study drug, at weeks 30 and 54, and upon use of a protocol-prohibited medication or study termination, as applicable. Joint damage was assessed by change in the modified Sharp/van der Heijde score (SHS) (vander Heijde Lancet 1989) from baseline to week 54.
• SHS Sharp/van der Heijde score
• 21 also incorporated the treatment regimen, i.e. MTX monotherapy or MTX + IFX, in the model. This allows the model to guide therapeutic decision making.
• treatment regimen i.e. MTX monotherapy or MTX + IFX
• the model was based on the probability of rapid radiological progression rather than on means and standard deviations or means and quartiles. Rapid progression was defined as a progression of at least 5 on the SHS score from baseline to week 54. In the SHS scoring method, a joint is considered to be destroyed if it has 4 joint space narrowing score units or 5 erosion score units (Sharp A&R 1985, Sharp A&R 1991 ). As such the radiological outcome in our model can be described as 'progression equivalent to the destruction of at least one joint per year'; a definition which is practical when trying to explain risk to patients or third party payers.
• the median age of the patients participating in this study was 51 years (range 18-76 years).
• the 1 ,004 patients included in these analyses had a female gender in 68-71 % of subjects, a mean age of 50-51 years old and disease duration of 0.8-0.9 years. 71-73% were RF positive.
• Disease activity was moderate-to-high in terms of swollen and tender joint counts (66/68 joints counted); 21-22 and 31-33 respectively, CRP and ESR; means range 2.6-3.0 mg/dl and 43-45 mm/hour respectively, pain ratings, global assessments, and Health Assessment Questionnaire scores.
• the mean and median radiographic score at baseline ranged from 11.2-11.6 and 5.1- 5.3 respectively.
• the study population was well balanced across treatment groups for baseline demographic and clinical characteristics (StClair A&R 2004). Joint damage progression.
• the change in the SHS from baseline to week 54 was significantly less among patients receiving combination therapy of MTX with infliximab at 3 mg/kg and MTX with infliximab at 6 mg/kg than among those receiving MTX alone (mean +/- SD 0.4 +/- 5.8, 0.5 +/- 5.6, and 3.7 +/- 9.6, respectively; P ⁇ 0.001 for each comparison).
• 39% of patients receiving infliximab plus MTX showed an increase in radiographic score, compared with 61 % of patients receiving MTX alone (P ⁇ 0.001 ).
• Eight percent and 23% respectively showed an increase of their radiographic score of at least 5 SHS units. 17/27 (63%) of patients who had a SHS of 0 at baseline did not progress under MTX, while this was 47/59 (80%) of the combined infliximab+MTX group.
• a matrix model was created in which the probability of rapid radiological progression at week 54 is related to the relevant disease characteristics of the individual patients at baseline.
• a color scheme ranging from blue (lowest risk of rapid progression) to red (highest risk of rapid progression) was applied for better visualization of the risk distribution, see table 1. Therapeutic guidance using the model.
• the absolute risk reduction of rapid progression ranged from 1 %-3% to 20%-35% for these respective groups. This indicates that the relative benefit of infliximab + MTX combination therapy is largest in those groups who are at the highest risk of rapid radiological progression as determined by SJC, CRP, ESR, RF-titer and age at baseline.
• Table 1 shows the differences between MTX and combined IFX+MTX groups in mean van der Waerden (VW) normal scores of the change from baseline in total SHS score at week 54 (vertical bars) and the associated 95% confidence intervals (horizontal bars) for subgroups defined by baseline disease characteristics as represented with thresholds as used in the model.
• VW van der Waerden
• the model is based on what is possibly the most broadly used model for assessing risk in a disease, i.e. the cardiovascular risk chart.
• the advantage of this model is that it combines several characteristics known to relate to outcome in a way that is easily understandable for patients and physicians.
• our model for prediction of outcome in IMID we use the same way of combining risk factors but also introduce the therapeutic regimen in the risk chart.
• the advantage of this is that risk expected in the individual is related to the treatment possibilities a physician has. As such, more than just being informative, it can be easily used for therapeutic guidance.
• patented models that combine disease characterics to predict outcome do exist (e.g. van der Helm-van Mil et al. Arthritis Rheum 2007;56(2):433-440, Drs.
• van der Helm-van Mil and Huizinga are named as investigators on the patent "Systems and methods for predicting an individual's risk of developing rheumatoid arthritis.”). These confirm the high scientific interest for them in these diseases and their patent confirms the need to protect the intellectual property of such models.

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