EP1509544A2 - Molecules card-4 et utilisations correspondantes - Google Patents

Molecules card-4 et utilisations correspondantes

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Publication number
EP1509544A2
EP1509544A2 EP03732905A EP03732905A EP1509544A2 EP 1509544 A2 EP1509544 A2 EP 1509544A2 EP 03732905 A EP03732905 A EP 03732905A EP 03732905 A EP03732905 A EP 03732905A EP 1509544 A2 EP1509544 A2 EP 1509544A2
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EP
European Patent Office
Prior art keywords
card
cell
protein
activity
expression
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EP03732905A
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German (de)
English (en)
Inventor
John Bertin
Dana Philpott
Philippe Sansonetti
Stephen Girardin
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Institut Pasteur de Lille
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Institut Pasteur de Lille
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Publication of EP1509544A2 publication Critical patent/EP1509544A2/fr
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P13/00—Drugs for disorders of the urinary system
    • A61P13/12—Drugs for disorders of the urinary system of the kidneys
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A61P17/06—Antipsoriatics
    • 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
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • 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]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P33/00—Antiparasitic agents
    • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/08—Antiallergic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)

Definitions

  • TLRs Toll/Toll-like receptors
  • R proteins disease-resistance proteins
  • the N protein of the tobacco plant for example, although being cytosolic, possesses a C-terminal TIR domain common to TLRs as well as an N-terminal leucine rich repeat (LRR) domain similar to that of the extracellular portion of the TLRs (Medzhitov et al., 1998, Curr. Opin. Immunol., 10:12-15).
  • TLRs mediate the hypersensitive response in plants resulting in metabolic alterations and localized cell death at the site of pathogen entry.
  • TLRs in mediating PAMP responsiveness in cells of the myeloid lineage
  • the role played by TLRs in pathogen recognition in epithelial cells remains poorly defined.
  • Epithelial cells may express TLRs, however, their function in innate immune detection is unclear as these cells are largely unresponsive to extracellular LPS and to non-pathogenic bacteria (Cario et al., 2000, J. Immunol., 164:966; Philpott et al., 2000, J. Immunol., 165:903).
  • NF- ⁇ B Nuclear factor- ⁇ B
  • Molecules that regulate NF- ⁇ B activation play a critical role in both apoptosis and inflammation.
  • NF- ⁇ B resides in the cytoplasm as a heterodimer of proteins referred to as p50 and p65 and is complexed with the regulatory protein I?B. NF- ⁇ B binding to I ⁇ B causes NF- ⁇ B to remain in the cytoplasm. At least two dozen stimuli that activate NF- ⁇ B are known (New England Journal of Medicine, 336:1066, 1997) and they include cytokines, protein kinase C activators, oxidants, viruses, and immune system stimuli. NF- ⁇ B activating stimuli activate specific I ⁇ B kinases that phosphorylate I ⁇ B leading to its degradation.
  • NF- ⁇ B translocates to the nucleus and activates genes with KB sites in their promoters.
  • the proinflammatory cytokines TNF- ⁇ and IL-1 induce NF- ⁇ B activation by binding their cell-surface receptors and activating the NF- ⁇ B-inducing kinase, NIK, and NF- ⁇ B.
  • NIK NF- ⁇ B-inducing kinase
  • NIK phosphorylates the I B kinases ⁇ and ⁇ which phosphorylate I ⁇ B, leading to its degradation.
  • NF- ⁇ B and the NF- ⁇ B pathway has been implicated in mediating chronic inflammation in inflammatory diseases such as asthma, ulcerative colitis, rheumatoid arthritis (Epstein, New England Journal of Medicine 336: 1066, 1997) and inhibiting NF- ⁇ B or NF- ⁇ B pathways may be an effective way of treating these diseases.
  • NF- ⁇ B and the NF- KB pathway has also been implicated in atherosclerosis (Navab et al., American Journal of Cardiology, 76:18C, 1995), especially in mediating fatty streak formation, and inhibiting NF- ⁇ B or NF- B pathways may be an effective therapy for atherosclerosis.
  • cIAP-1 a protein which includes a CARD
  • cIAP-2 a protein which includes a CARD
  • TRAF1 a protein which includes a CARD
  • CLAP activates the Apaf-l-caspase-9 pathway and activates NF- ⁇ B by acting upstream of NIK and I ⁇ B kinase (Srinivasula et al., supra).
  • the present invention is based, at least in part, on the discovery that CARD-4 is involved in innate immune responses mediated through the activation of NF- ⁇ B and JNK and that CARD-4 participates in immune responses to bacterial infections.
  • a cDNA of CARD-4 described herein (SEQ ID NO: 1) has a 2859 nucleotide open reading frame (nucleotides 245-3103 of SEQ ID NO: 1; SEQ ID NO: 3) which encodes a 953 amino acid protein (SEQ ID NO: 2).
  • CARD-4 possesses a CARD domain (amino acids
  • Human CARD-4 also has a nucleotide binding domain which extends from about amino acid 198 to about amino acid 397 of SEQ ID NO: 2; a Walker Box "A”, which extends from about amino acid 202 to about amino acid 209 of SEQ ID NO: 2; a Walker Box “B”, which extends from about amino acid 280 to about amino acid 284 of SEQ ID NO: 2; a kinase la (P-loop) subdomain, which extends from about amino acid 127 to about amino acid 212 of SEQ ID NO: 2; a kinase 2 subdomain, which extends from about amino acid 273 to about amino acid 288 of SEQ ID NO: 2; a kinase 3a subdomain, which extends from about amino acid 327 to about amino acid 338 of SEQ ID NO: 2; and ten Leucine-rich repeats which extend from about amino acid 674 to about amino acid 950 of SEQ ID NO: 2.
  • the first Leucine-rich repeat extends from about amino acid 674 to about amino acid 701 of SEQ ID NO: 2.
  • the second Leucine-rich repeat extends from about amino acid 702 to about amino acid 727 of SEQ ID NO: 2.
  • the third Leucine-rich repeat extends from about amino acid 728 to about amino acid 754 of SEQ ID NO: 2.
  • the fourth Leucine-rich repeat extends from about amino acid 755 to about amino acid 782 of SEQ ID NO: 2.
  • the fifth Leucine-rich repeat extends from about amino acid 783 to about amino acid 810 of SEQ ID NO: 2.
  • the sixth Leucine-rich repeat extends from about amino acid 811 to about amino acid 838 of SEQ ID NO: 2.
  • the seventh Leucine-rich repeat extends from about amino acid 839 to about amino acid 866 of SEQ ID NO: 2.
  • the eighth Leucine-rich repeat extends from about amino acid 867 to about amino acid 894 of SEQ ID NO: 2.
  • the ninth Leucine-rich repeat extends from about amino acid 895 to about amino acid 922 of SEQ ID NO: 2.
  • the tenth leucine-rich repeat extends from about amino acid 923 to about amino acid 950 of SEQ ID NO: 2.
  • CARD-4 amino acid or nucleotide sequences described in U.S. Patent Nos. 6,340,576 or 6,369,196 can also be used in the practice of the invention.
  • any of the CARD-4 sequences or fragments thereof e.g., a functional domain such as a CARD, NBS, or LRR domain
  • any of the CARD-4 sequences or fragments thereof e.g., a functional domain such as a CARD, NBS, or LRR domain
  • any of the CARD-4 sequences or fragments thereof e.g., a functional domain such as a CARD, NBS, or LRR domain
  • CARD-4 activates the NF- ⁇ B pathway and enhances caspase-9 activity.
  • CARD-4 associates with CARD-4, CARD-3, caspase 9, and BCLX.
  • CARD-4 likely binds a nucleotide, thus allowing CARD-4 to bind and activate a CARD- containing caspase via a CARD-CARD interaction, leading to the activation of inflammatory and/or apoptotic signaling pathways in the cell.
  • CARD-4 is described in detail in U.S. Patent Nos. 6,340,576 or 6,369,196.
  • the invention encompasses methods of diagnosing and treating individuals having a bacterial infection or a disorder of bacterial origin.
  • Bacterial pathogens include but are not limited to, bacteria of Mycobacterium species, Helicobacter species (e.g., Helicobacter pylori), Salmonella species (e.g., Salmonella typhimurium), Shigella species (e.g., Shigella flexneri), E. coli, Rickettsia species, Listeria species, Legionella species (e.g., Legionella pneumoniae), Pseudomonas species, Vibrio species, and Borellia species (e.g., Borellia burgdorferi).
  • Helicobacter species e.g., Helicobacter pylori
  • Salmonella species e.g., Salmonella typhimurium
  • Shigella species e.g., Shigella flexneri
  • E. coli Rickettsia species
  • Listeria species e.g., Legionella pneumoniae
  • Legionella species e.g., Legionella pneumoniae
  • Disorders of bacterial origin include Bacterial infections of the upper respiratory tract (e.g., nasopharyngitis, sinusitis, purulent and acute otitis media, peritonsillar abscess), chronic obstructive pulmonary disease (e.g., emphysema and bronchitis), bacterial infections of the central nervous system (e.g., bacterial meningitis, subdural empyema, and septic thrombophlebitis) sepsis, inflammatory bowel disease (e.g., bacillary dysentery, Crohn's disease, ulcerative colitis, ischemic colitis, diverticulitis or diverticulotis, and appendicitis), and sepsis and septic shock.
  • Bacterial infections of the upper respiratory tract e.g., nasopharyngitis, sinusitis, purulent and acute otitis media, peritonsillar abscess
  • immune responsiveness can be modulated (increased or decreased) by modulating (increasing or decreasing) the expression or activity of CARD-4 in a cell.
  • Bacterial LPS is a cell-wall component of gram-negative bacteria that has the ability to induce a dramatic systemic reaction known as septic shock. This syndrome is the result of overwhelming secretion of cytokines, particularly of TNF- ⁇ , often as a result of an uncontrolled systemic bacterial infection. It is expected that septic shock can be prevented or treated by interfering with LPS-induced activation of CARD-4. For example, inhibiting CARD-4 induced activation of NF- ⁇ B is expected to reduce or inhibit symptoms associated with septic shock.
  • the invention encompasses methods of treatment that modulate the CARD-4 signaling pathways described herein that are activated by LPS and bacterial infection. Also included in the invention are methods of screening for modulators (activators or inhibitors) of these CARD-4 pathways.
  • the invention also encompasses methods of diagnosing and treating patients who are suffering from a disorder associated with an abnormal level or rate (undesirably high or undesirably low) of apoptotic cell death, abnormal activity of the Fas/APO-1 receptor complex, abnormal activity of the TNF receptor complex, or abnormal activity of a caspase by administering a compound that modulates the expression of CARD-4 (at the DNA, mRNA or protein level, e.g., by altering mRNA splicing) or by altering the activity of CARD-4.
  • Examples of such compounds include small molecules, antisense nucleic acid molecules, ribozymes, and polypeptides.
  • Certain disorders are associated with an increased number of surviving cells, which are produced and continue to survive or proliferate when apoptosis is inhibited or occurs at an undesirably low rate.
  • Compounds that modulate the expression or activity of CARD-4 can be used to treat or diagnose such disorders. These disorders include cancer (particularly follicular lymphomas, chronic myelogenous leukemia, melanoma, colon cancer, lung carcinoma, carcinomas associated with mutations in p53, and hormone-dependent tumors such as breast cancer, prostate cancer, and ovarian cancer).
  • Such compounds can also be used to treat viral infections (such as those caused by herpesviruses, poxviruses, and adenoviruses).
  • autoimmune disorders can be caused by an undesirably low levels of apoptosis.
  • modulators of CARD-4 activity or expression can be used to treat autoimmune disorders (e.g., systemic lupus erythematosis, immune-mediated glomerulonephritis, and arthritis). Many diseases are associated with an undesirably high rate of apoptosis.
  • Modulators of CARD-4 expression or activity can be used to treat or diagnose such disorders.
  • populations of cells are often depleted in the event of viral infection, with perhaps the most dramatic example being the cell depletion caused by the human immunodeficiency virus (HIV).
  • HIV human immunodeficiency virus
  • most T cells that die during HIV infections do not appear to be infected with HIV.
  • stimulation of the CD4 receptor results in the enhanced susceptibility of uninfected T cells to undergo apoptosis.
  • a wide variety of neurological diseases are characterized by the gradual loss of specific sets of neurons.
  • Such disorders include Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) retinitis pigmentosa, spinal muscular atrophy, and various forms of cerebellar degeneration.
  • the cell loss in these diseases does not induce an inflammatory response, and apoptosis appears to be the mechanism of cell death.
  • a number of hematologic diseases are associated with a decreased production of blood cells.
  • These disorders include anemia associated with chronic disease, aplastic anemia, chronic neutropenia, and the myelodysplastic syndromes.
  • disorders of blood cell production such as myelodysplastic syndrome and some forms of aplastic anemia, are associated with increased apoptotic cell death within the bone marrow.
  • disorders could result from the activation of genes that promote apoptosis, acquired deficiencies in stromal cells or hematopoietic survival factors, or the direct effects of toxins and mediators of immune responses.
  • Two common disorders associated with cell death are myocardial infarctions and stroke. In both disorders, cells within the central area of ischemia, which is produced in the event of acute loss of blood flow, appear to die rapidly as a result of necrosis. However, outside the central ischemic zone, cells die over a more protracted time period and morphologically appear to die by apoptosis.
  • CARD-4 polypeptides, nucleic acids and modulators of CARD-4 expression or activity can be used to treat immune disorders.
  • immune disorders include, but are not limited to, chronic inflammatory diseases and disorders, such as inflammatory bowel disease (e.g., Crohn's disease and ulcerative colitis); arthritis, including reactive arthritis (e.g., Lyme disease) and rheumatoid arthritis; insulin-dependent diabetes; organ-specific ' autoimmunity, including multiple sclerosis, Hashimoto's thyroiditis and Grave's disease; contact dermatitis; psoriasis; graft rejection; graft versus host disease; sarcoidosis; atopic conditions, such as asthma and allergy, including allergic rhinitis; gastrointestinal allergies, including food allergies; eosinophilia; conjunctivitis; glomerular nephritis; certain pathogen susceptibilities, such as helminthic infections (e.g., leishmaniasis), certain viral
  • a CARD-4 nucleic acid includes a nucleic acid molecule which is at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 3, or a complement thereof.
  • a CARD-4 nucleic acid includes a nucleic acid molecule which includes a fragment of at least 150 (300, 325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 1300, 1600 or 1931) nucleotides of the nucleotide sequence shown in SEQ ED NO: 1, SEQ ID NO: 3, or a complement thereof.
  • a CARD-4 nucleic acid includes a nucleic acid molecule which includes a nucleotide sequence encoding a protein having an amino acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the amino acid sequence of SEQ ID NO: 2.
  • a CARD-4 nucleic acid includes a nucleic acid molecule which encodes a fragment of a polypeptide having the amino acid sequence of SEQ ID NO: 2, the fragment including at least 15 (25, 30, 50, 100, 150, 300, 400 or 540, 600, 700, 800, 900) contiguous amino acids of SEQ ID NO: 2.
  • a CARD-4 nucleic acid includes a nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO: 2.
  • an allelic variant of a gene will be readily identifiable as mapping to the same chromosomal location as said gene.
  • the chromosomal location of the human CARD-4 gene is on chromosome 7 close to the SHGC-31928 genetic marker.
  • Allelic variants of human CARD-4 will be readily identifiable as mapping to the human CARD-4 locus on chromosome 7 near genetic marker SHGC-31928.
  • a CARD-4 protein includes: an isolated CARD-4 protein having an amino acid sequence that is at least about 65%, preferably 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ ID NO: 2; an isolated CARD-4 protein having an amino acid sequence that is at least about 85%, 95%, or 98% identical to the CARD domain of SEQ ID NO: 2 (e.g., about amino acid residues 15 to 114 of SEQ ID NO: 2); an isolated CARD-4 protein having an amino acid sequence that is at least about 85%, 95%, or 98% identical to the nucleotide binding domain of SEQ ID NO:2 (e.g., about amino acid residues 198 to 397 of SEQ ID NO: 2; an isolated CARD-4 protein having an amino acid sequence that is at least about 85%, 95%, or 98% identical to the kinase la (P-loop) subdomain SEQ ID NO: 2 (e.g., about amino acid 127 to about amino acid 212 of SEQ ID NO: 2);
  • CARD-4 nucleic acid molecules can be used to specifically detect CARD-4 nucleic acid molecules, relative to nucleic acid molecules encoding other members of the CARD superfamily.
  • a CARD-4 nucleic acid molecule hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1, SEQ ID NO: 3, or a complement thereof.
  • the CARD-4 nucleic acid molecule is at least 300 (350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 1300, 1600, 1900, 2100, 2400, 2700, 3000, or 3382) nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 3, or a complement thereof.
  • an isolated CARD-4 nucleic acid molecule comprises nucleotides 287 to 586 of SEQ ID NO: 1, encoding the CARD domain of CARD-4, or a complement thereof.
  • the invention provides an isolated nucleic acid molecule which is antisense to the coding strand of a CARD-4 nucleic acid.
  • a vector e.g., a recombinant expression vector, comprising a CARD-4 nucleic acid can be used in the methods of the invention.
  • the invention provides a host cell containing such a vector.
  • the invention also provides a method for producing CARD-4 protein by culturing, in a suitable medium, a host cell of the invention containing a recombinant expression vector such that a CARD-4 protein is produced.
  • CARD-4 proteins and polypeptides possess at least one biological activity possessed by naturally occurring human CARD-4, e.g., (1) the ability to form ⁇ rotein: ⁇ rotein interactions with proteins in the apoptotic signaling pathway; (2) the ability to form CARD-CARD interactions with proteins in the apoptotic signaling pathway; (3) the ability to bind a CARD-4 ligand (e.g., CARD-4, CARD-3, caspase 9, and/or BCLX); (4) the ability to bind to an intracellular target; (5) the ability to enhance caspase 9 activity; and (6) the ability to activate the NF- ⁇ B pathway.
  • Other activities include: (1) modulation of -88/6
  • a CARD-4 protein, or biologically active portions thereof can be operatively linked to a non-CARD-4 polypeptide (e.g., heterologous amino acid sequences) to form CARD-4 fusion proteins, respectively.
  • the invention further features antibodies that specifically bind CARD-4 proteins, such as monoclonal or polyclonal antibodies.
  • the CARD-4 proteins or biologically active portions thereof can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
  • the invention provides a method for detecting the presence of CARD-4 activity or expression in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of CARD-4 activity such that the presence of CARD-4 activity is detected in the biological sample.
  • the invention provides a method for modulating CARD-4 activity comprising contacting a cell with an agent that modulates (inhibits or stimulates) CARD-4 activity or expression such that CARD-4 activity or expression in the cell is modulated.
  • the agent is an antibody that specifically binds to CARD-4 protein.
  • the agent modulates expression of CARD-4 by modulating transcription of a CARD-4 gene, splicing of a CARD-4 mRNA, or translation of a CARD-4 mRNA.
  • the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of the CARD-4 mRNA or the CARD-4 gene.
  • the methods of the present invention are used to treat a subject having a disorder characterized by aberrant CARD-4 protein or nucleic acid expression or activity or related to CARD-4 expression or activity by administering an agent which is a CARD-4 modulator to the subject.
  • the CARD-4 modulator is a CARD- 4 protein.
  • the CARD-4 modulator is a CARD-4 nucleic acid molecule.
  • the CARD-4 modulator is a peptide, peptido imetic, or other small molecule.
  • the present invention also provides a diagnostic assay for identifying the presence or absence of a genetic lesion or mutation characterized by at least one of: (i) aberrant modification or mutation of a gene encoding a CARD-4 protein; (ii) mis-regulation of a gene encoding a CARD-4 protein; (iii) aberrant RNA splicing; and (iv) aben-ant post- -87/6
  • the invention provides a method for identifying a compound that binds to or modulates the activity of a CARD-4 protein.
  • such methods entail measuring a biological activity of a CARD-4 protein in the presence and absence of a test compound and identifying those compounds which alter the activity of the CARD-4 protein.
  • the invention also features methods for identifying a compound which modulates the expression of CARD-4 by measuring the expression of CARD-4 in the presence and absence of a compound.
  • the invention also features methods for identifying compounds (e.g., small molecules, peptide, etc.) that interfere with CARD-4 mediated activation of NF- ⁇ B and/or
  • NF- ⁇ B and JNK activation are described below.
  • activation can be assessed by measuring the level of phospho-c-Jun in cell nuclei using, for example, the assay described below, hi the case of NF- B activation, it can be desirable to measure TNF- ⁇ mediated activation in order to determine if the activation of NF-KB is relatively CARD-4 specific.
  • the invention features methods for identifying compounds that interfere with the response of cells, e.g., epithelial cells to LPS. Such compounds may be identified by identifying compounds which interfere with CARD-4 oligomerization (or oligomerization of the CARD domain of CARD-4) in the presence or absence of LPS. Such assays can be carried out in vivo or in vitro.
  • the invention also features methods for treating toxic shock or inflammation associated with intracellular pathogens by blocking
  • CARD-4 activation or activity For example, it can be desirable to administer a compound that interferes with nucleotide binding to the NBS domain of CARD-4.
  • CARD-4 activity can include polypeptides that act as dominant negative mutants.
  • a variant CARD-4 lacking the CARD domain can include polypeptides that act as dominant negative mutants.
  • the invention features a method for identifying a candidate compound that modulates lipopolysaccharide (LPS)-mediated activation of NF- ⁇ B, the method comprising: providing a cell that harbors LPS and expresses a polypeptide comprising a caspase recruitment domain (CARD), nucleotide binding site (NBS), or leucine rich repeat
  • LPS lipopolysaccharide
  • the cell is infected with Shigella flexneri, Salmonella typhimurium, or Helicobacter pylori.
  • the invention also features a method for identifying a candidate compound that modulates LPS-mediated activation of JNK kinase activity, the method comprising: providing a cell that harbors LPS and expresses a polypeptide comprising a CARD, NBS, or LRR domain of CARD-4; exposing the cell to a test compound; and measuring JNK kinase activity in the cell; wherein altered JNK kinase activity in the presence of the test compound compared to JNK kinase activity in the absence of the test compound indicates that the test compound is a candidate compound that modulates LPS-mediated activation of JNK kinase activity.
  • the cell is infected with Shigella flexneri, Salmonella typhimurium, ox Helicobacter pylori.
  • the invention also features a method for identifying a candidate compound that modulates an LPS-induced immune response, the method comprising: providing a cell that expresses a polypeptide comprising a CARD, NBS, or LRR domain of CARD-4; introducing LPS into the cell; exposing the cell to a test compound; and measuring oligomerization of the polypeptide in the cell; wherein altered oligomerization of the polypeptide in the presence of the test compound compared to oligomerization of the polypeptide in the absence of the test compound indicates that the test compound is a candidate compound for modulating an LPS-induced immune response.
  • the cell is infected with Shigella flexneri, Salmonella typhimurium, or Helicobacter pylori.
  • the polypeptide used in the screening methods described herein can optionally be a recombinant polypeptide.
  • the methods can optionally include an additional step of introducing into the cell a heterologous nucleic acid encoding the polypeptide.
  • the polypeptide can correspond in sequence to a naturally-occurring or a non-naturally- occurring CARD-4 sequence.
  • the invention also features a method of modulating LPS-induced activation of NF-
  • KB or JNK the method comprising: providing a cell that harbors intracellular LPS; and -85/6
  • the invention also features a method of modulating an LPS-induced immune response in an individual, the method comprising: selecting an individual comprising cells harboring intracellular LPS; and administering to the individual a compound that modulates expression or activity of CARD-4 in an amount sufficient to modulate an LPS-induced immune response in the individual.
  • the individual is diagnosed as having a bacterial infection, e.g., a Shigella flexneri infection, Salmonella typhimurium infection, ox Helicobacter pylori infection.
  • the invention also features a method of treating or preventing a bacterial infection, the method comprising: selecting an individual having or at risk of having a bacterial infection; administering to the individual a compound that modulates expression or activity of CARD-4 in an amount sufficient to treat or prevent the bacterial infection.
  • the invention also features a mouse whose genome comprises a disruption in an endogenous CARD-4 gene, wherein said disruption results in decreased expression or a lack of expression of said endogenous CARD-4 gene, thereby causing a decreased ability of the mouse to clear a Salmonella typhimurium or Helicobacter pylori infection.
  • Figs. 1A-1F depict a cDNA sequence (SEQ ID NO: 1) and predicted amino acid sequence (SEQ ID NO: 2) of human CARD-4.
  • the open reading frame of CARD-4 extends from nucleotide 245 to nucleotide 3103 of SEQ ID NO: 1 (SEQ ID NO: 3).
  • Fig. 2A depicts the results of an experiment demonstrating that S. flexneri infection leads to the phosphorylation of cJun.
  • Fig. 2B depicts the results of an experiment demonstrating that microinjection of LPS activates c-Jun phosphorylation.
  • Fig. 3A depicts the results of an experiment demonstrating that a dominant-negative form of TRAF2 does not inhibit the induction of NF- ⁇ B by invasive S. flexneri.
  • Fig. 3B depicts the results of an experiment demonstrating that a dominant-negative form of TRAF6 does not inhibit the induction of NF- ⁇ B by invasive S. flexneri. -84/6
  • Fig. 3C depicts the results of an experiment demonstrating that S. flexneri induces NF- ⁇ B in HEK293 deficient in IL-1 specific signaling components.
  • Fig. 3D depicts the results of an experiment demonstrating that the dominant- negative molecule MyD88 (DN-MyD88) does not inhibit NF- ⁇ B activation by invasive S. flexneri.
  • Fig. 4A depicts the domain structure of CARD-4 compared with plant disease resistance proteins tobacco N protein and Arabidopsis RPS2 protein.
  • Fig. 4B depicts the result of an experiment demonstrating that CARD-4 oligomerizes following S. flexneri infection.
  • Fig. 5A depicts the results of an experiment demonstrating that ⁇ CARD CARD4 inhibits NF- ⁇ B induction by S. flexneri but not TNFa.
  • Fig. 5B depicts the results of an experiment demonstrating that isolated CARD-4 LRR domain inhibits NF- ⁇ B induction by S. flexneri but not TNFa.
  • Fig. 5C depicts the result of an experiment depicting the effect of the overexpression of full-length and truncated forms of CARD-4 on JNK activation.
  • Fig. 6 depicts the bacterial load of wild type mice and CARD-4 deficient mice following infection with Salmonella typhimurium.
  • Fig. 7 depicts the bacterial load of wild type mice and CARD-4 deficient mice following infection with Helicobacter pylori. Detailed description of the invention
  • the present invention is based, in part, on the discovery that CARD-4 is involved in innate immune responses mediated through the activation of NF- ⁇ B and JNK and that CARD-4 participates in immune responses to bacterial infections.
  • CARD-4 Mediates NF- ⁇ B and JNK Activation in Response to Shigella Flexneri and
  • c-Jun N-terminal kinase JNK
  • JNK c-Jun N-terminal kinase
  • the target of JNK, c-Jun is phosphorylated by this kinase on serine 63 and 73, an event that increases its ability to activate transcription.
  • c-Jun is a component of the transcription factor AP-1, another -83/6
  • HeLa cells were infected with wild-type invasive S. flexneri strain M90T or the plasmid-cured, noninvasive strain BS176, for 2 hours as described previously (Philpott et al, 2000, J. Immunol. 165:903-14). Infected cells were then stained for both phospho-c-Jun using a monoclonal phospho-specific antibody to this protein (Lallemand et al., 1998, EMBO J., 17:5615) and LPS to label the infecting bacteria using a rabbit polyclonal anti LPS antibody. Stained cells were viewed using conventional fluorescence microscopy.
  • HeLa cells were microinjected with FITC-dextran to identify microinjected cells plus buffer alone or purified Escherichia coli LPS 0111:B4 as previously described (Philpott et al., 2000, J. Immunol., 165:903). Following a 1 hour incubation at 37°C and 5% C0 2 , cells were stained for phospho-c-Jun and examined by fluorescence microscopy.
  • the intracellular detection system present in epithelial cells for sensing LPS was investigated by examining the signal transduction pathway leading from intracellular LPS detection to NF- ⁇ B and JNK activation.
  • the signaling pathway leading from extracellular LPS detection mediated through TLRs to NF- ⁇ B and JNK is identical to that of the IL-1 pathway (O'Neill et al, 1998, J.
  • HEK293 cells were transfected with vector alone or incieasing amounts of DNA encoding for the dominant-negative forms of TRAF2 (DN-TRAF2) oi TRAF6 (DN- TRAF6) along with a NF- ⁇ B luciferase reporter plasmid and a ⁇ -galactosidase plasmid to normalize transfection efficiencies Following 30 hours, cells were infected with wild-type S flexneri or treated with either TNFa (100 ng/ml) or IL- 1 (10 ng/ml) for 4 hours and then assayed for luciferase activity as described previously (Philpott et al , 2000, J Immunol , 165 903-14).
  • NF- B activation after S. flexneri infection, TNFa treatment or IL-1 treatment was compared in parental HEK293 cells and the three IL-1 signaling deficient cell lines NF- ⁇ B activity was assessed following infection or cytokine treatment by the NF- ⁇ B reporter assay oi EMSA (Philpott et al , 2000, J.
  • Immunol , 165:903-14 S flexneri infection, but not IL-1 treatment, activated both NF- ⁇ B (Figure 3C) and JNK m 293 epithelial cells deficient in IRAK (11A cells) as well as m the two other IL- 1 signaling deficient cell lines.
  • IRAK2 a homologue of IRAK, has been implicated in IL-1 signaling (Muzio et al., 1997, Science, 278:1612) although its role in TLR mediated responsiveness to LPS has not been determined.
  • MyD88 is an important adaptor protein involved in TLR/IL-1 signaling to NF- ⁇ B and JNK (O'Neill et al., 1998, J. Leuko Biol., 63:650). Indeed, MyD88 is critical for LPS responsiveness since mice deficient in this factor, e.g., the TLR4 mutant C3H/HeJ mice (Poltorak et al., 1998, 282:2085) are highly resistant to LPS (Kawai et al, 1999, Immunity 11:115). The role of MyD88 in NF- ⁇ B induction by invasive S. flexneri was, therefore, investigated.
  • flexneri-mduced activation of NF- ⁇ B and JNK occurs via a pathway that is distinct from the TLR/IL-1 signaling pathway. Therefore, a distinct LPS detection and signal transduction system other than the TLRs likely exists in mammalian cells and this alternate system responds to intracellular LPS.
  • CARD-4 contains significant amino acid similarity to that of several plant disease-resistance proteins, including tobacco N protein and Arabidopsis RPS2 protein, which also contains an NBS domain ( Figure 4A). Because of its similarity to plant R proteins and its ability to activate NF- ⁇ B, it was decided to investigate the role of CARD-4 in the detection of intracellular LPS in epithelial cells infected with S. flexneri. CARD-4 has structural and functional similarities to A ⁇ af-1. For example, both proteins possess a CARD domain and an NBS domain. Moreover, both activate downstream -80/6
  • a plasmid encoding either a CARD-4 variant lacking its CARD domain ( ⁇ CARD CARD-4) or a CARD-4 variant lacking its LRR domain ( ⁇ LRR CARD-4) was transfected into HEK293 cells along with NF- ⁇ B and ⁇ -galactosidase reporter plasmids. Luciferase activity was assayed 4 hours after infection with S. flexneri or TNFa treatment, as described above. Overexpression of ⁇ CARD CARD- 4 molecule acted in a dose-dependent manner to inhibit S flexneri-mduced NF- ⁇ B activation (Figure 5A).
  • Table 1 Microinjection of LPS into transfected cells-examination for induction of NF- ⁇ B and phospho-c-Jun.
  • CARD-4 is a member of a new family of proteins that possess a C-terminal LRR and an NBS.
  • the "signaling module" domain appears to be variable. This study on CARD-4 suggests the possibility that this family of proteins represents human homologues of plant disease-resistance proteins. These cytosolic proteins may be involved in mediating defensive responses to distinct intracellular pathogens or pathogen products. As it has been shown for the TLRs, different CARD-4-like proteins may exist that are involved in the recognition of distinct bacterial products.
  • CARD-4 In infectious processes in vivo, wild-type and CARD-4-def ⁇ cient mice were infected with either Salmonella typhimurium or Helicobacter pylori and bacterial counts were assessed in various tissues following infection.
  • mice For the S. typhimurium infections, six week old wild-type or CARD-4-deficient mice were infected by the gastric route with 5 X 10 7 colony-forming units (CFUs) of virulent S. typhimurium, strain C52. Peyer's patches, spleen and liver were collected after 5 or 10 days of infection. The tissues were ground, diluted and then plated in order to assess -77/6
  • H. pylori infections CARD-4-deficient and wild-type mice were infected by the gastric route with 1 X 10 CFU of H. pylori strain SS 1, which is a human pathogenic strain adapted for mice infection. Stomachs were collected following 1 month of infection and the number of CFUs per gram of stomach tissue was assessed by plating serial diluted samples. On average, a 2 log difference was observed between the CARD-4-deficient mice compared to the wild- type mice (Fig. 7). These data further suggest a role for CARD-4 in the control of bacterial proliferation in the stomach and/or clearance of the infecting organism.
  • a nucleotide sequence encoding a human CARD-4 protein is shown in Figs.lA-lF (SEQ ID NO: 1; SEQ ID NO: 3 include the open reading frame only).
  • a predicted amino acid sequence of CARD-4 protein is also shown in Figs. lA-lF (SEQ ID NO: 2).
  • the human CARD-4 cDNA of Figs.1 A- IF has a molecular weight of approximately 108 kDa (excluding post-translational modifications).
  • a plasmid containing a cDNA encoding human CARD-4 (pC4Ll) was deposited with the American Type Culture Collection (ATCC), Manasass, VA on July 7, 1998, and assigned Accession Number 203035. This deposit will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience for those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 1 12.
  • CARD-4 has a CARD domain (amino acids 15-1 14 of SEQ ID NO: 2).
  • CARD-4 also has a nucleotide binding domain which extends from about amino acid 198 to about amino acid 397 of SEQ ID NO: 2; a predicted Walker Box "A”, which extends from about amino acid 202 to about amino acid 209 of SEQ ID NO: 2; a predicted Walker Box “B”, which extends from about amino acid 280 to about amino acid 284 of SEQ ID NO: 2; a predicted kinase la (P-loop) domain, which extends from about amino acid 197 to about -76/6
  • amino acid 212 of SEQ ID NO: 2 amino acid 212 of SEQ ID NO: 2; a predicted kinase 2 domain, which extends from about amino acid 273 to about amino acid 288 of SEQ ID NO: 2; a predicted kinase 3a subdomain, which extends from about amino acid 327 to about amino acid 338 of SEQ ID NO: 2; ten predicted Leucine-rich repeats which extend from about amino acid 674 to about amino acid 950 of SEQ ID NO: 2.
  • the first Leucine-rich repeat extends from about amino acid 674 to about amino acid 701 of SEQ ID NO: 2.
  • the second Leucine-rich repeat extends from about amino acid 702 to about amino acid 727 of SEQ ID NO: 2.
  • the third Leucine-rich repeat extends from about amino acid 728 to about amino acid 754 of SEQ ID NO: 2.
  • the fourth Leucine-rich repeat extends from about amino acid 755 to about amino acid 782 of SEQ ID NO: 2.
  • the fifth Leucine-rich repeat extends from about amino acid 783 to about amino acid 810 of SEQ ID NO: 2.
  • the sixth Leucine-rich repeat extends from about amino acid 811 to about amino acid 838 of SEQ ID NO: 2.
  • the seventh Leucine-rich repeat extends from about amino acid 839 to about amino acid 866 of SEQ ID NO: 2.
  • the eighth Leucine-rich repeat extends from about amino acid 867 to about amino acid 894 of SEQ ID NO: 2.
  • the ninth Leucine-rich repeat extends from about amino acid 895 to about amino acid 922 of SEQ ID NO:2.
  • the tenth leucine-rich repeat extends from about amino acid 923 to about amino acid 950 of SEQ ID NO: 2.
  • CARD-4 is a member of a family of molecules having certain conserved structural and functional features.
  • family when referring to the protein and nucleic acid molecules of the invention is intended to mean two or more proteins or nucleic acid molecules having a common structural domain and having sufficient amino acid or nucleotide sequence identity as defined herein.
  • family members can be naturally occurring and can be from either the same or different species.
  • a family can contain a first protein of human origin and a homologue of that protein of murine origin, as well as a second, distinct protein of human origin and a murine homologue of that protein.
  • Members of a family may also have common functional characteristics.
  • a CARD-4 protein includes a CARD domain having at least about 65%, preferably at least about 75%, and more preferably about 85%, 95%, or 98% amino acid sequence identity to the CARD domain of SEQ ID NO: 2.
  • Preferred CARD-4 polypeptides useful in the methods of the present invention have an amino acid sequence sufficiently identical to the CARD domain amino acid sequence of SEQ ID NO: 2.
  • the CARD-4 polypeptide has an amino acid sequence sufficiently identical to the -75/6
  • nucleotide binding domain of SEQ ID NO: 2 an amino acid sequence sufficiently identical to the Walker Box "A” of SEQ ID NO- 2 or Walker Box “B” of SEQ ID NO 2
  • an amino acid sequence sufficiently identical to the kinase la subdomain of SEQ ID NO: 2 an amino acid sequence sufficiently identical to the kinase 2 subdomain of SEQ ID NO: 2
  • an amino acid sequence sufficiently identical to the kinase 3a subdomain of SEQ ID NO: 2 or an amino acid sequence sufficiently identical to the Leucine-rich repeats of SEQ ID NO. 2.
  • the term "sufficiently identical" lefers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e g , an ammo acid residue which has a similar side chain) amino acid residues oi nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity
  • amino acid or nucleotide sequences which contain a common structural domain having about 65% identity, preferably 75% identity, more preferably 85%, 95%, or 98% identity are defined herein as sufficiently identical.
  • a "CARD-4 activity” biological activity of CARD-
  • CARD-4 activity refers to an activity exerted by a CARD-4 protein, polypeptide or nucleic acid molecule on a CARD-4 responsive cell as determined in vivo, or in vitro, according to standard techniques.
  • a CARD-4 activity can be a direct activity, such as an association with or an enzymatic activity on a second protein or an mdirect activity, such as a cellular signaling activity mediated by interaction of the CARD-4 protein with a second protein.
  • a CARD-4 activity mcludes at least one or more of the following activities: (1) the ability to form protei protein interactions with proteins in the apoptotic signaling pathway; (2) the ability to form CARD-CARD mteiactions with proteins in the apoptotic signaling pathway, (3) the ability to bind a CARD-4 ligand (e g., CARD-4, CARD-3, caspase 9, and/or BCLX); (4) the ability to bind to an intracellular target; (5) the ability to enhance caspase 9 activity; and (6) the ability to activate the NF- ⁇ B pathway.
  • Other activities include: (1) modulation of cellular proliferation; (2) modulation of cellular differentiation, (3) modulation of cellular death; and (4) modulation of inflammation and/or an innate immune response.
  • One aspect of the invention pertains to methods of using isolated nucleic acid molecules that encode CARD-4 proteins or biologically active portions thereof, as well as -74/6 ⁇
  • nucleic acid molecules sufficient for use as hybridization probes to identify CARD-4- encoding nucleic acids (e.g., CARD-4 mRNA) and fragments for use as PCR primers for the amplification or mutation of CARD-4 nucleic acid molecules.
  • the term "nucleic acid molecule” is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • an “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid.
  • an “isolated” nucleic acid is free of sequences (preferably protein encoding sequences) which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • the isolated CARD-4 nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
  • an "isolated" nucleic acid molecule such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • a nucleic acid molecule e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1, SEQ ID NO: 3, or a complement of any of these nucleotide sequences, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or portion of the nucleic acid sequences of SEQ ID NO: 1 or SEQ ID NO: 3 as a hybridization probe, CARD-4 nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in
  • a nucleic acid can be amplified using cDNA, mRNA or genomic DNA as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • the nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • oligonucleotides corresponding to CARD-4 nucleotide sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer. -73/6
  • an isolated nucleic acid molecule comprises a nucleic acid molecule which is a complement of the nucleotide sequence shown in SEQ ID NO- 1, SEQ ID NO: 3, or a portion theieof.
  • a nucleic acid molecule which is complementary to a given nucleotide sequence is one which is sufficiently complementary to the given nucleotide sequence that it can hybridize to the given nucleotide sequence thereby forming a stable duplex.
  • the nucleic acid molecules can comprise only a portion of a nucleic acid sequence encoding CARD-4, for example, a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of CARD-4.
  • the nucleotide sequence determined from the cloning of the human CARD-4 allows for the generation of probes and primers designed for use in identifying and/or cloning CARD-4 homologues in other cell types, e.g., from other tissues, as well as CARD-4 homologues and orthologs from other mammals.
  • the probe/primer typically comprises substantially purified oligonucleotide.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive nucleotides of the sense or anti-sense sequence of SEQ ID NO 1, SEQ ID NO: 3, or of a naturally occurring mutant of one of SEQ ID NO: 1 or SEQ ID NO. 3.
  • Probes based on the CARD-4 nucleotide sequence can be used to detect transcripts or genomic sequences encoding the same or similar protems.
  • the probe compnses a label group attached thereto, e.g , a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor
  • Such probes can be used as a part of a diagnostic test kit for identifying allelic variants and orthologs of the CARD-4 proteins of the present invention, identifying cells or tissue which mis-express a CARD-4 protein, such as by measuring a level of a CARD-4-encoding nucleic acid in a sample of cells from a subject, e.g., detecting CARD-4 mRNA levels or determining whether a genomic CARD-4 gene has been mutated or deleted.
  • a nucleic acid fragment encoding a "biologically active portion" of CARD-4 can be prepared by isolating a portion of SEQ ID NO: 1 or SEQ ID NO: 3 which encodes a polypeptide having a CARD-4 biological activity, expressing the encoded portion of CARD-4 protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of CARD-4
  • a nucleic acid fragment encoding a biologically active portion of CARD-4 can include a CARD, NBS, or leucine ⁇ ch repeat domain A -72/6
  • CARD-4 biologically active portion of CARD-4 can optionally bind caspase 9, enhance caspase 9 activity, activate the NF- ⁇ B pathway, and/or activate JNK.
  • the invention further encompasses nucleic acid molecules that differ from the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 3 due to degeneracy of the genetic code and thus encode the same CARD-4 protein as that encoded by the nucleotide sequence shown in SEQ ID NO: 1 or SEQ ID NO: 3.
  • DNA sequence polymorphisms that lead to changes in the amino acid sequences of CARD-4 may exist within a population (e.g., the human population). Such genetic polymorphism in the CARD-4 gene may exist among individuals within a population due to natural allelic variation.
  • the terms "gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding a CARD-4 protein, preferably a mammalian CARD-4 protein.
  • Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of the CARD-4 gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in CARD-4 that are the result of natural allelic variation and that do not alter the functional activity of CARD-4 are intended to be within the scope of the invention. Thus, e.g., 1%, 2%, 3%, 4%, or 5% of the amino acids in CARD-4 are replaced by another amino acid, preferably the amino acids are replaced by conservative substitutions.
  • nucleic acid molecules encoding CARD-4 proteins from other species which have a nucleotide sequence which differs from that of a CARD-4 disclosed herein, are intended to be within the scope of the invention.
  • allelic variant of a gene will be readily identifiable as mapping to the same chromosomal location as said gene.
  • Allelic variants of human CARD-4 will be readily identifiable as mapping to the human CARD-4 locus on chromosome 7 near genetic marker SHGC-31928.
  • an isolated nucleic acid molecule is at least
  • nucleic acid molecule comprising the nucleotide sequence, preferably the coding sequence, of SEQ ID NO: 1
  • hybridizes under stringent conditions is intended to -71/6
  • stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45EC, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65EC (e.g., 50EC or 60EC or 65EC).
  • SSC 6X sodium chloride/sodium citrate
  • the isolated nucleic acid molecule of the invention that hybridizes under stringent conditions corresponds to a naturally-occurring nucleic acid molecule.
  • a "naturally- occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • a naturally-occurring allelic variants of the CARD-4 sequence that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 3 thereby leading to changes in the amino acid sequence of the encoded protein without altering the functional ability of the protein.
  • nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues are made.
  • a "non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of CARD-4 without altering the biological activity, whereas an "essential” amino acid residue is required for biological activity.
  • amino acid residues that are conserved among the CARD-4 proteins of various species are predicted to be particularly unamenable to alteration.
  • preferred CARD-4 proteins of the present invention contain at least one CARD domain.
  • a protein also contains at least one kinase domain or at least one linker domain.
  • a CARD domain contains at least one nucleotide binding domain or Leucine-rich repeats. Such conserved domains are less likely to be amenable to mutation. Other amino acid residues, however, (e.g., those that are not conserved or only semi-conserved among CARD-4 of various species) may not be essential for activity and thus are likely to be amenable to alteration. Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding CARD-4 proteins that contain changes in amino acid residues that are not essential for activity. Such CARD-4 proteins differ in amino acid sequence from SEQ ID -70/6
  • the isolated nucleic acid molecule includes a nucleotide sequence encoding a protein that includes an amino acid sequence that is at least about 45% identical, 65%, 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ ID NO: 2.
  • An isolated nucleic acid molecule encoding a CARD-4 protein having a sequence which differs from that of SEQ ID NO: 1 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of CARD-4 (SEQ ID NO: 1 or SEQ ID NO: 3) such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein.
  • Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis.
  • conservative amino acid substitutions are made at one or more predicted non- essential amino acid residues.
  • 1%, 2%, 3%, 5%, or 10% of the amino acids can be replaced by conservative substitution.
  • a "conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • a predicted nonessential amino acid residue in CARD-4 is preferably replaced with another amino acid residue from the same side chain family.
  • mutations can be introduced randomly along all or part of a CARD-4 coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for CARD-4 biological activity to identify mutants that retain activity. Following mutagenesis, the encoded protein can be expressed recombinantly and the activity of the protein can be determined.
  • Preferred mutants possess at least one biological activity possessed by naturally occurring human CARD-4, e.g., (1) the ability to form protei protein interactions with proteins in the apoptotic signaling pathway; (2) the ability to form CARD-CARD interactions with proteins in the apoptotic signaling pathway; (3) the ability to bind a CARD-4 ligand (e.g., CARD-4, CARD-3, caspase 9, and/or BCLX); (4) the ability to bind to an intracellular target; (5) the ability to enhance caspase 9 activity; and (6) the ability to activate the NF- ⁇ B -69/6
  • CARD-4 ligand e.g., CARD-4, CARD-3, caspase 9, and/or BCLX
  • Other activities include: (1) modulation of cellular proliferation; (2) modulation of cellular differentiation; (3) modulation of cellular death; and (4) modulation of inflammation and/or an innate immune response.
  • the present invention encompasses antisense nucleic acid molecules, i.e., molecules which are complementary to a sense nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid.
  • the antisense nucleic acid can be complementary to an entire CARD-4 coding strand, or to only a portion thereof, e.g., all or part of the protein coding region (or open reading frame).
  • An antisense nucleic acid molecule can be antisense to a noncoding region of the coding strand of a nucleotide sequence encoding CARD-4.
  • antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing.
  • the antisense nucleic acid molecule can be complementary to the entire coding region of CARD-4 mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of CARD-4 mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
  • an antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5- fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4- acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2- thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7- methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D- mannosylqueosine, 5'-me
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned m an antisense orientation (I e , RNA transcribed from the inserted nucleic acid will be of an antisense onentation to a target nucleic acid of interest
  • the antisense nucleic acid molecules of the invention are typically administered to a subject or generated m situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a CARD-4 protein to thereby inhibit expression of the protein, e g , by inhibiting transcription and/or translation
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix
  • An example of a route of administration of antisense nucleic acid molecules of the invention mcludes direct injection at a tissue site Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically.
  • antisense molecules can be modified such that they specifically bind to receptors oi antigens expressed on a selected cell surface, e g , by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens
  • the antisense nucleic acid molecules can also be delivered to cells using the vectors desc ⁇ bed herein
  • vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred
  • An antisense nucleic acid molecule of the invention can be an ⁇ -anomeric nucleic acid molecule.
  • An ⁇ -anome ⁇ c nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -umts, the strands run parallel to each other (Gaultier et al , 1987, Nucleic Acids Res , 15 6625-6641)
  • the antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleot ⁇ de (Inoue et al., 1987, Nucleic Acids Res , 15-6131-6148) or a chimenc RNA-DNA analogue (Inoue et al , 1987, FEBS Lett , 215.327-330)
  • Ribozymes are catalytic RNA -67/6
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach, 1 88, Nature 334:585-591) can be used to catalytically cleave CARD-4 mRNA transcripts to thereby inhibit translation of CARD-4 mRNA.
  • a ribozyme having specificity for a CARD-4- encoding nucleic acid can be designed based upon the nucleotide sequence of a CARD-4 cDNA disclosed herein.
  • a derivative of a Tetrahymena L-19 F/S RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a CARD-4-encoding mRNA.
  • CARD-4 mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel and Szostak (1993) Science 261: 1411-1418.
  • the invention also encompasses nucleic acid molecules which form triple helical structures.
  • CARD-4 gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the CARD-4 (e.g., the CARD-4 promoter and or enhancers) to form triple helical structures that prevent transcription of the CARD-4 gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the CARD-4 e.g., the CARD-4 promoter and or enhancers
  • the nucleic acid molecules of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule.
  • the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al., 1996, Bioorganic & Medicinal Chemistry, 4(l):5-23).
  • peptide nucleic acids refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained.
  • the neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength.
  • the synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al., 1996, supra; Perry-O'Keefe et al., 1996, Proc. Natl. Acad. Sci., USA, 93: 14670-675.
  • PNAs of CARD-4 can be used for therapeutic and diagnostic applications.
  • -66/6 -66/6
  • PNAs can be used as antisense oi antigene agents foi sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication
  • PNAs of CARD-4 can also be used, e g , m the analysis of single base pair mutations in a gene by, e g , PNA directed PCR clamping, as artificial restriction enzymes when used in combination with other enzymes, e.g , SI nucleases (Hyrup, 1996, supra); or as probes or primers for DNA sequence and hybridization (Hyrup, 1996, supra, Perry-O'Keefe et al , 1996, Proc Natl. Acad Sci USA, 93 14670-675).
  • PNAs of CARD-4 can be modified, e g , to enhance their stability or cellular uptake, by attaching lipophihc or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known m the art
  • PNA-DNA chimeras of CARD-4 can be generated which may combine the advantageous properties of PNA and DNA
  • Such chimeras allow DNA recogmtion enzymes, e g , RNAse H and DNA polymerases, to mtei act with the DNA portion while the PNA portion would provide high binding affinity and specificity PNA-DNA chimeras can be linked using hnkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and o ⁇ entation (Hyrup, 1996, supra)
  • the synthesis of PNA-DNA chimeras can be performed as descnbed in Hyrup, 1996, supra and Finn et
  • the oligonucleotide may include other appended groups such as peptides (e g , foi targetmg host cell receptors m vivo), or agents facilitating transport across the cell membrane (see, e , Letsinger et al , 1989, Proc Natl Acad Sci USA, 86:6553-6556, Lemaitre et al , 1987, Proc Natl Acad Sci USA, 84 648-652, PCT Publication No WO 88/09810) or the blood-brain barrier (see, e g , PCT Publication No WO 89/10134)
  • oligonucleotides can be modified with hyb ⁇ dization-t ⁇ ggered cleavage agents (see, e g , Krol et al , 1988, Bio/Techniques, 6 958-976) oi intercalating -65/6
  • the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent, etc.
  • CARD-4 proteins and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti- CARD-4 antibodies.
  • native CARD-4 proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques.
  • CARD-4 proteins are produced by recombinant DNA techniques.
  • a CARD-4 protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.
  • an “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the CARD-4 protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of CARD-4 protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • CARD-4 protein that is substantially free of cellular material includes preparations of CARD-4 protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of non-CARD-4 protein (also referred to herein as a "contaminating protein").
  • CARD-4 protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • CARD-4 protein is produced by chemical synthesis, it is preferably substantially free of chemical precursors or other chemicals, i.e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Accordingly such preparations of CARD-4 protein have less than about 30%, 20%, 10%, 5% (by dry weight) of chemical precursors or non-CARD-4 chemicals.
  • Biologically active portions of a CARD-4 protein include peptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence of the CARD-4 protein (e.g., the amino acid sequence shown in SEQ ID NO: 2), which -64/6
  • biologically active portions include less amino acids than the full length CARD-4 protein, and exhibit at least one activity of a CARD-4 protein.
  • biologically active portions comprise a domain or motif with at least one activity of the CARD-4 protein.
  • a biologically active portion of a CARD-4 protein can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acids in length.
  • Preferred biologically active polypeptides include one or more identified CARD-4 structural domains, e.g., the CARD domain, NBS domain, or leucine rich repeats.
  • Preferred biologically active polypeptides posses one or more of the following activities: 1) the ability to form proteimprotein interactions with proteins in the apoptotic signaling pathway; (2) the ability to form CARD-CARD interactions with proteins in the apoptotic signaling pathway; (3) the ability to bind a CARD-4 ligand (e.g., CARD-4, CARD-3, caspase 9, and/or BCLX); (4) the ability to bind to an intracellular target; (5) the ability to enhance caspase 9 activity; and (6) the ability to activate the NF- ⁇ B pathway.
  • Other activities include: (1) modulation of cellular proliferation; (2) modulation of cellular differentiation; (3) modulation of cellular death; and (4) modulation of inflammation and/or an innate immune response.
  • CARD-4 protein has the amino acid sequence shown of SEQ ID NO: 2.
  • Other useful CARD-4 proteins are substantially identical to SEQ ID NO: 2 and retain the functional activity of the protein of SEQ ID NO: 2, yet differ in amino acid sequence due to natural allelic variation or mutagenesis.
  • a useful CARD-4 protein is a protein which includes an amino acid sequence at least about 45%, preferably 55%, 65%, 75%, 85%, 95%, or 99% identical to the amino acid sequence of SEQ ID NO: 2 and retains the functional activity of the CARD-4 protein of SEQ ID NO: 2.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the co ⁇ esponding position in the second sequence, then the -63/6
  • % identity # of identical positions/total # of positions x 100).
  • the determination of percent homology between two sequences can be accomplished using a mathematical algorithm.
  • a prefe ⁇ ed, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Nat'l Acad. Sci. USA, 87:2264-2268, modified as in Karlin and Altschul, 1993, Proc. Nat'l Acad. Sci. USA, 90:5873-5877.
  • Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al, 1990, J. Mol. Biol., 215:403-410.
  • Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res., 25:3389-3402.
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • CARD-4 chimeric or fusion proteins As used herein, a CARD-4 "chimeric protein” or “fusion protein” comprises a CARD-4 polypeptide operatively linked to a non-CARD-4 polypeptide.
  • a "CARD-4 polypeptide” refers to a polypeptide having an amino acid sequence corresponding to all or a portion (preferably a biologically active portion) of a CARD-4, whereas a “non-CARD-4 polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not -62/6
  • the term "operatively linked" is intended to indicate that the CARD-4 polypeptide and the non-CARD-4 polypeptide are fused in-frame to each other.
  • the heterologous polypeptide can be fused to the N-terminus or C-terminus of the CARD-4 polypeptide.
  • One useful fusion protein is a GST fusion protein in which the CARD-4 sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant CARD-4.
  • the fusion protein contains a signal sequence from another protein.
  • expression and/or secretion of CARD-4 can be increased through use of a heterologous signal sequence.
  • the g ⁇ 67 secretory sequence of the baculovirus envelope protein can be used as a heterologous signal sequence (Current Protocols in Molecular Biology, Ausubel et al., eds., John Wiley & Sons, 1992).
  • eukaryotic heterologous signal sequences include the secretory sequences of melittin and human placental alkaline phosphatase (Stratagene; La Jolla, California).
  • useful prokaryotic heterologous signal sequences include the phoA secretory signal (Molecular cloning, Sambrook et al, second edition, Cold spring harbor laboratory press, 1989) and the protein A secretory signal (Pharmacia Biotech; Piscataway, New Jersey).
  • the fusion protein is a CARD-4-immunoglobulin fusion protein in which all or part of CARD-4 is fused to sequences derived from a member of the immunoglobulin protein family.
  • the CARD-4-immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a CARD-4 ligand and a CARD-4 protein on the surface of a cell, to thereby suppress CARD-4-mediated signal transduction in vivo.
  • the CARD-4-immunoglobulin fusion proteins can be used to affect the bioavailability of a CARD-4 cognate ligand.
  • Inhibition of CARD-4 ligand CARD-4 interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, as well as modulating (e.g., promoting or inhibiting) cell survival. Inhibition of the interaction may be useful for treatment of inflammatory disorders.
  • the CARD-4-immunoglobulin fusion proteins of the invention can be used as immunogens to produce anti-CARD-4 antibodies in a subject, to purify CARD-4 ligands and in screening assays to identify molecules which inhibit the interaction of CARD-4 with a CARD-4 ligand.
  • a CARD-4 chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques.
  • DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
  • PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, e.g., Curcent Protocols in Molecular Biology, Ausubel et al., eds., John Wiley & Sons: 1992).
  • anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence
  • expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • a CARD-4-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the CARD- 4 protein.
  • the present invention also pertains to variants of the CARD-4 proteins which function as either CARD-4 agonists (mimetics) or as CARD-4 antagonists.
  • Variants of the CARD-4 protein can be generated by mutagenesis, e.g., discrete point mutation or truncation of the CARD-4 protein.
  • An agonist of the CARD-4 protein can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of the CARD-4 protein.
  • An antagonist of the CARD-4 protein can inhibit one or more of the activities of the naturally occurring form of the CARD-4 protein by, for example, competitively binding to a downstream or upstream member of a cellular signaling cascade which includes the CARD-4 protein.
  • CARD-4 variants can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants of the CARD-4 protein for CARD-4 protein agonist or antagonist activity.
  • a variegated library of CARD-4 variants is -60/6
  • a variegated library of CARD-4 variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential CARD-4 sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of CARD-4 sequences therein.
  • a degenerate set of potential CARD-4 sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of CARD-4 sequences therein.
  • Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector.
  • Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential CARD-4 sequences.
  • Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, 1983, Tetrahedron, 39:3; Itakura et al., 1984, Annu. Rev.
  • CARD-4 include fragments comprising or consisting of a domain or subdomain described herein, e.g., a CARD domain, NBS domain, or LRR domain.
  • libraries of fragments of the CARD-4 protein coding sequence can be used to generate a variegated population of CARD-4 fragments for screening and subsequent selection of variants of a CARD-4 protein.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a CARD-4 coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S 1 nuclease, and ligating the resulting fragment library into an expression vector.
  • an expression library can be derived which encodes N-terminal and internal fragments of various sizes of the CARD-4 protein.
  • REM Recursive ensemble mutagenesis
  • An isolated CARD-4 protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind CARD-4 using standard techniques for polyclonal and monoclonal antibody preparation.
  • the full-length CARD-4 protein can be used or, alternatively, the invention provides antigenic peptide fragments of CARD-4 for use as immunogens.
  • the antigenic peptide of CARD-4 comprises at least 8 (preferably 10, 15, 20, or 30) amino acid residues of the amino acid sequence shown in SEQ ID NO: 2 or polypeptides including amino acids 128-139 or 287-298 of SEQ ID NO: 2 and encompasses an epitope of CARD-4 such that an antibody raised against the peptide forms a specific immune complex with CARD-4.
  • Useful antibodies include antibodies which bind to a domain or subdomain of CARD-4 described herein (e.g., a kinase domain, a CARD domain, or a leucine-rich domain).
  • Preferred epitopes encompassed by the antigenic peptide are regions of CARD-4 that are located on the surface of the protein, e.g., hydrophilic regions.
  • Other important criteria include a preference for a terminal sequence, high antigenic index (e.g., as predicted by Jameson- Wolf algorithm), ease of peptide synthesis (e.g., avoidance of prolines); and high surface probability (e.g., as predicted by the Emini algorithm; Figure 8 and Figure 9).
  • a CARD-4 immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen.
  • a suitable subject e.g., rabbit, goat, mouse or other mammal
  • An appropriate immunogenic preparation can contain, for example, recombinantly expressed
  • CARD-4 protein or a chemically synthesized CARD-4 polypeptide can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent.
  • an adjuvant such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent.
  • Immunization of a suitable subject with an immunogenic CARD-4 preparation induces a polyclonal anti-CARD-4 antibody response.
  • polypeptides including amino acids 128-139 or 287-298 of human CARD-4 were -58/6
  • antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds an antigen, such as CARD-4.
  • a molecule which specifically binds to CARD-4 is a molecule which binds CARD-4, but does not substantially bind other molecules in a sample, e.g., a biological sample, which naturally contains CARD-4.
  • immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin.
  • the invention provides polyclonal and monoclonal antibodies that bind CARD-4.
  • the term "monoclonal antibody” or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of CARD-4.
  • a monoclonal antibody composition thus typically displays a single binding affinity for a particular CARD-4 protein with which it immunoreacts.
  • Polyclonal anti-CARD-4 antibodies can be prepared as described above by immunizing a suitable subject with a CARD-4 immunogen.
  • the anti-CARD-4 antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized CARD-4.
  • ELISA enzyme linked immunosorbent assay
  • the antibody molecules directed against CARD-4 can be isolated from the mammal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction.
  • antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein, 1975, Nature, 256:495-497, the human B cell hybridoma technique (Kozbor et al, 1983, Immunol. Today, 4:72), the EBV-hybridoma technique (Cole et al, 1985, Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques.
  • the technology for producing various antibodies monoclonal antibody hybridomas is well known (see generally Current Protocols in Immunology, 1994, Coligan et al, (eds.) John -57/6
  • an immortal cell line typically a myeloma
  • lymphocytes typically splenocytes
  • the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds CARD-4
  • the immortal cell line (e.g., a myeloma cell line) is derived from the same mammalian species as the lymphocytes
  • munne hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line, e.g., a myeloma cell line that is sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium").
  • HAT medium culture medium containing hypoxanthine, aminopterin and thymidine
  • any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e , the P3-NSl/l-Ag4-l, P3-x63-Ag8 653 or S ⁇ 2/0- Agl4 myeloma lines. These myeloma fines are available from ATCC.
  • HAT- sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG").
  • Hyb ⁇ doma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed).
  • Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind CARD-4, e.g., using a standard ELISA assay.
  • a monoclonal anti-CARD-4 antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with CARD-4 to thereby isolate immunoglobulin library members that bind CARD-4 Kits for generating and screening phage display libraries are commercially available (e , the Pharmacia Recombmant Phage Antibody System, Catalog No. 27-9400-01, and the Stratagene SurfZAP Phage Display Kit, Catalog No. 240612). Additionally, examples of -56/6
  • recombinant anti-CARD-4 antibodies such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
  • Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in PCT Publication No. WO 87/02671; European Patent Application EP 0 184 187; European Patent Application EP 0 171 496; European Patent Application EP 0 173 494; PCT Publication No. WO 86/01533; U.S. Patent No.
  • An anti-CARD-4 antibody (e.g., monoclonal antibody) can be used to isolate CARD-4 by standard techniques, such as affinity chromatography or immunoprecipitation.
  • An anti-CARD-4 antibody can facilitate the purification of natural CARD-4 from cells and of recombinantly produced CARD-4 expressed in host cells.
  • an anti-CARD-4 antibody can be used to detect CARD-4 protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the CARD-4 protein.
  • Anti- CARD-4 antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, -55/6
  • fluorescent materials luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, ⁇ -galactosidase, or acetylcholinesterase;
  • suitable prosthetic group complexes include streptavidin biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125 I, 131 I, 35 S or 3 H.
  • vectors preferably expression vectors, containing a nucleic acid encoding CARD-4 (or a portion thereof).
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • expression vectors are capable of directing the expression of genes to which they are operatively linked.
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids (vectors).
  • the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
  • the recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed.
  • "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the -54/6
  • regulatory sequence(s) in a mannei which allows foi expression of the nucleotide sequence (e g , in an vitro transc ⁇ ption/translation system or m a host cell when the vectoi is introduced into the host cell)
  • the term "regulatory sequence” is intended to include promoteis, enhancers and other expression control elements (e g , polyadenylation signals) Such regulatory sequences are desc ⁇ bed, for example, in Goeddel, Gene Expression Technology Methods in Enzymology 185, Academic Press, San Diego, CA (1990) Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only m certain host cells (e g, tissue-specific regulatory sequences).
  • the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc
  • the expression vectors of the invention can be introduced into host cells to thereby produce protems or peptides, including fusion proteins or peptides, encoded by nucleic acids as descnbed herein (e.g , CARD-4 protems, mutant forms of CARD-4, fusion proteins, etc.).
  • the recombinant expression vectors of the invention can be designed for expression of CARD-4 in prokaryotic or eukaryotic cells, e g , bactenal cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further m Goeddel, Gene Expression Technology Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
  • the recombmant expression vector can be transcnbed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Fusion vectors add a number of ammo acids to a protein encoded therein, usually to the ammo terminus of the recombinant protein.
  • Such fusion vectors typically serve three purposes 1) to increase expiession of recombmant protein; 2) to increase the solubility of the recombinant piotein, and 3) to aid m the punfication of the recombmant protein by acting as a ligand in affinity purification
  • a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the lecombinant protein fiom the fusion moiety subsequent to punfication of the fusion protein
  • Such enzymes, and their cognate recognition sequences clude Factor Xa, thrombin and enterokinase Typical -53/6
  • fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988, Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • GST glutathione S-transferase
  • suitable inducible non-fusion E. coli expression vectors include pTrc
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter.
  • Target gene expression from the pET l id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS 174(DE3) from a resident ⁇ prophage harboring a T7 gnl gene under the transcriptional control of the lacUV5 promoter.
  • One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California, 1990, 1 19-128).
  • Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al, 1992, Nucleic Acids Res, 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • the CARD-4 expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S. cerivisae include pYepSecl (Baldari et al, 1987, EMBO J, 6:229-234), pMFa (Kurjan and Herskowitz, 1982, Cell, 30:933-943), pJRY88 (Schultz et al, 1987, Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, CA), pGBT9 (Clontech, Palo Alto, CA), pGADIO (Clontech, Palo Alto, CA), pYADE4 and pYGAE2 and pYPGE2 (Branelli and Pall, 1993, Yeast, 9: 1299-1308), pYPGE15 (Brunelli and Pall, 1993, Yeast, 9:1309-1318), pACTII (Dr.
  • CARD-4 can be expressed in insect cells using baculovirus expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al, 1983, Mol. Cell Biol,. 3:2156-2165) and the pVL series (Lucklow and Summers, 1989, Virology, 170:31-39). -52/6
  • a nucleic acid of the invention is expressed in mammalian cells using a mammalian expiession vector
  • mammalian expression vectors include pCDM8 (Seed, 1987, Nature, 329 840), pCI (Promega), and pMT2PC (Kaufman et al , 1987, EMBO J , 6- 187-195)
  • the expression vector's contiol functions are often provided by viral regulatory elements.
  • promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Vims 40
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook et al (supra)
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially m a particular cell type (e.g, tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific piomoters include the albumin promoter (liver-specific; Pinkert et al , 1987, Genes Dev , 1.268-277), lymphoid-specific promoters (Calame and Eaton, 1988, Adv.
  • Immunol, 43.235-275 in particular promoters of T cell receptors (Winoto and Baltimore, 1989, EMBO J, 8 729-733) and immunoglobulins (Banerji et al , 1983, Cell, 33-729-740, Queen and Baltimore, 1983, Cell, 33.741-748), neuron-specific promoters (e g, the neurofilament promoter, Byrne and Ruddle, 1989, Proc Natl. Acad Sci. USA, 86 5473-5477), pancreas- specific promoters (Edlund et al , 1985, Science, 230 912-916), and mammary gland- specific promoters (e.g , milk whey promoter; U.S.
  • the invention further provides a recombmant expression vector comp ⁇ s g a DNA molecule of the invention cloned mto the expression vector an antisense o ⁇ entation That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transc ⁇ ption of the DNA molecule) of an RNA molecule which is antisense to CARD-4 mRNA Regulatory sequences operatively linked to a nucleic acid cloned m the antisense o ⁇ entation can be chosen which direct the continuous expression of the antisense RNA molecule m a variety of
  • Anolher aspect of the invention pertains to host cells into which a recombinant expression vector of the invention or isolated nucleic acid molecule of the invention has been introduced.
  • the terms "host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • a host cell can be any prokaryotic or eukaryotic cell.
  • CARD-4 protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • mammalian cells such as Chinese hamster ovary cells (CHO) or COS cells.
  • Other suitable host cells are known to those skilled in the art.
  • Vector DNA or an isolated nucleic acid molecule of the invention can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g, DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (supra), and other laboratory manuals.
  • vector DNA is retained by the host cell. In other cases the host cell does not retain vector DNA and retains only an . isolated nucleic acid molecule of the invention carried by the vector. In some cases, and isolated nucleic acid molecule of the invention is used to transform a cell without the use of a vector.
  • selectable marker e.g, resistance to antibiotics
  • Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate.
  • Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding CARD-4 or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g, cells that have incorporated the selectable marker gene will survive, while the other cells die).
  • a host cell of the invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) a CARD-4 protein.
  • the invention further provides methods for producing CARD-4 protein using the host cells of the invention.
  • the method comprises culturing the host cell of the invention (into which a recombinant expression vector or isolated nucleic acid molecule encoding CARD-4 has been introduced) in a suitable medium such that CARD-4 protein is produced.
  • the method further comprises isolating CARD-4 from the medium or the host cell.
  • the host cells of the invention can also be used to produce nonhuman transgenic animals.
  • a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which CARD-4-coding sequences have been introduced.
  • Such host cells can then be used to create non-human transgenic animals in which exogenous CARD-4 sequences have been introduced into their genome or homologous recombinant animals in which endogenous CARD-4 sequences have been altered.
  • Such animals are useful for studying the function and/or activity of CARD-4 and for identifying and/or evaluating modulators of CARD-4 activity.
  • a "transgenic animal” is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.
  • Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, etc.
  • a transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal.
  • an "homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous CARD-4 gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA -49/6
  • molecule introduced into a cell of the animal, e.g, an embryonic cell of the animal, prior to development of the animal.
  • a transgenic animal of the invention can be created by introducing CARD-4- encoding nucleic acid into the male pronuclei of a fertilized oocyte, e.g, by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal.
  • the CARD-4 cDNA sequence e.g, that of SEQ ID NO: 1 or SEQ ID NO: 3 can be introduced as a transgene into the genome of a non-human animal.
  • a nonhuman homolog or ortholog of the human CARD-4 gene such as a mouse CARD-4 gene, can be isolated based on hybridization to the human CARD-4 cDNA and used as a transgene.
  • the mouse ortholog of CARD-4 can be used to make a transgenic animal using standard methods.
  • Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene.
  • a tissue-specific regulatory sequence(s) can be operably linked to the CARD-4 transgene to direct expression of CARD-4 protein to particular cells.
  • transgenic founder animal can be identified based upon the presence of the CARD-4 transgene in its genome and/or expression of CARD-4 mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals ca ⁇ ying the transgene. Moreover, transgenic animals carrying a transgene encoding CARD-4 can further be bred to other transgenic animals carrying other transgenes.
  • a vector which contains at least a portion of a CARD-4 gene (e.g, a human or a non-human homolog of the CARD- 4 gene, e.g, a murine CARD-4 gene) into which a deletion, addition or substitution has been introduced to thereby alter, e.g, functionally disrupt, the CARD-4 gene.
  • the vector is designed such that, upon homologous recombination, the endogenous CARD-4 gene is functionally disrupted (i.e, no longer encodes a functional protein; also referred to as a "knock out" vector).
  • the vector can be designed such that, upon homologous recombination, the endogenous CARD-4 gene is mutated or otherwise altered but still encodes functional protein (e.g, the upstream regulatory region -48/6
  • the altered portion of the CARD-4 gene is flanked at its 5' and 3' ends by additional nucleic acid of the CARD-4 gene to allow for homologous recombination to occur between the exogenous CARD-4 gene carried by the vector and an endogenous CARD-4 gene in an embryonic stem cell.
  • the additional flanking CARD-4 nucleic acid is of sufficient length for successful homologous recombination with the endogenous gene.
  • flanking DNA both at the 5' and 3' ends
  • the vector is introduced into an embryonic stem cell line (e.g, by electroporation) and cells in which the introduced CARD-4 gene has homologously recombined with the endogenous CARD-4 gene are selected (see, e.g, Li et al, 1992, Cell, 69:915).
  • the selected cells are then injected into a blastocyst of an animal (e.g, a mouse) to form aggregation chimeras (see, e.g, Bradley in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed. (IRL, Oxford, 1987) pp. 113-152).
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term.
  • Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene.
  • transgenic non-humans animals can be produced which contain selected systems which allow for regulated expression of the transgene.
  • a system is the cre/loxP recombinase system of bacteriophage PI.
  • cre/loxP recombinase system of bacteriophage PI.
  • FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al, 1991, Science, 251:1351-1355.
  • mice containing transgenes encoding both the Cre recombinase and a selected protein are required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g, by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut et al, 1997, Nature, 385:810-813 and PCT Publication Nos. WO 97/07668 and WO 97/07669.
  • a cell e.g, a somatic cell
  • the quiescent cell can then be fused, e.g, through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated.
  • the reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal.
  • the offspring borne of this female foster animal will be a clone of the animal from which the cell, e.g, the somatic cell, is isolated.
  • nucleic acid encoding murine CARD-4 which can be used in the preparation of a transgenic animal or a homologous recombmant animal, is described in U.S. patent number 6,369,196, the content of which is incorporated herein by reference.
  • compositions suitable for administration can be incorporated into pharmaceutical compositions suitable for administration.
  • Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
  • the invention includes methods for preparing pharmaceutical compositions for modulating the expression or activity of a polypeptide or nucleic acid of the invention. Such methods comprise formulating a pharmaceutically acceptable carrier with an agent which modulates expression or activity of a polypeptide or nucleic acid of the invention. Such compositions can further include additional active agents. Thus, the invention further includes methods for preparing a pharmaceutical composition by formulating a -46/6
  • the agent which modulates expression or activity may, for example, be a small molecule.
  • small molecules include peptides, peptidomimetics, amino acids, amino acid analogs, polynucleotides, polynucleotide analogs, nucleotides, nucleotide analogs, organic or inorganic compounds (i.e, including heteroorganic and organometallic compounds) having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight les than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, and other pharmaceutically acceptable forms of such compounds.
  • doses of small molecule agents depends upon a number of factors within the ken of the ordinarily skilled physician, veterinarian, or researcher.
  • the dose(s) of the small molecule will vary, for example, depending upon the identity, size, and condition of the subject or sample being treated, further depending upon the route by which the composition is to be administered, if applicable, and the effect which the practitioner desires the small molecule to have upon the nucleic acid or polypeptide of the invention.
  • Exemplary doses include milligram or microgram amounts of the small molecule per kilogram of subject or sample weight (e.g, about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram.
  • appropriate doses of a small molecule depend upon the potency of the small molecule with respect to the expression or activity to modulated. Such appropriate doses may be determined using the assays described herein.
  • an animal e.g, a human
  • a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained.
  • the specific dose level for any particular subject will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and -45/6
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g, intravenous, intradermal, subcutaneous, oral (e.g, inhalation), transdermal (topical), transmucosal, and rectal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor EL? (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thfmerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin. -44/6
  • Sterile injectable solutions can be prepared by incorporating the active compound (e.g, a CARD-4 protein or anti-CARD-4 antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • the active compound e.g, a CARD-4 protein or anti-CARD-4 antibody
  • dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a suitable propellant e.g, a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art. -43/6
  • the compounds can also be prepared in the form of suppositories (e.g, with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • suppositories e.g, with conventional suppository bases such as cocoa butter and other glycerides
  • retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protected the compound against rapid elimination from the body, such as a controlled release formulation, includ ng implants and microencapsulated delivery systems.
  • a controlled release formulation include ng implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art.
  • the materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
  • the preferred dosage is 0.1 mg kg to 100 mg/kg of body weight (generally 10 mg/kg to 20 mg/kg). If the antibody is to act in the brain, a dosage of 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, lower dosages and less frequent administration are 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, 1997, J. Acquired Immune Deficiency Syndromes and Human Retrovirology, 14:193).
  • nucleic acid molecules of the invention can be inserted into vectors and used as -42/6
  • Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (U.S. Patent 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 Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g. retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
  • compositions can be included in a container, pack, or dispenser together with instructions for administration.
  • the nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: a) screening assays; b) detection assays (e.g, chromosomal mapping, tissue typing, forensic biology), c) predictive medicine (e.g, diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenomics); and d) methods of treatment (e.g, therapeutic and prophylactic).
  • a CARD-4 protein interacts with other cellular proteins and can thus be used for (i) regulation of cellular proliferation; (ii) regulation of cellular differentiation; and (iii) regulation of cell survival.
  • the isolated nucleic acid molecules of the invention can be used to express CARD-4 protein (e.g, via a recombinant expression vector in a host cell in gene therapy applications), to detect CARD-4 mRNA (e.g, in a biological sample) or a genetic lesion in a CARD-4 gene, and to modulate CARD-4 activity.
  • CARD-4 proteins can be used to screen drugs or compounds which modulate the CARD-4 activity or expression as well as to treat disorders characterized by insufficient or excessive production of CARD- 4 protein or production of CARD-4 protein forms which have decreased or abenant activity compared to CARD-4 wild type protein.
  • the anti-CARD-4 antibodies of the invention can be used to detect and isolate CARD-4 proteins and modulate CARD-4 activity.
  • Screening Assays The invention provides a method (also refe ⁇ ed to herein as a "screening assay") for -41/6
  • identifying modulators i.e, candidate or test compounds oi agents (e g , peptides, peptidomimetics, small molecules oi other drugs) which bind to CARD-4 proteins or biologically active portions thereof or have a stimulatory or inhibitory effect on, for example, CARD-4 expression or CARD-4 activity.
  • oi agents e g , peptides, peptidomimetics, small molecules oi other drugs
  • An example of a biologically active portion of human CARD-4 is amino acids 1-145 encoding the CARD domain or ammo acids 406-953 of human CARD-4 comp ⁇ smg the leucme rich repeat domain
  • screening assays are screening to identify molecules that prevent the dime ⁇ zation of a CARD-contaimng polypeptide of the invention, screening to identify molecules which block the b ding of a CARD containing polypeptide to a CARD-contaimng polypeptide of the invention (e g, CARD-4), screening to identify a competitive inhibitor of the binding of a nucleotide to the nucleotide binding site of a C ARD-conta mg polypeptide of the mvention, e , human CARD-4, screening to identify compounds which block the interaction between the leucine-rich repeat of a CARD-contaimng polypeptide of the mvention and a ligand which binds to the leucine- ⁇ ch repeat
  • the invention provides assays for screening candidate oi test compounds which bind to or modulate the activity of a CARD-4 proteins or polypeptides or biologically active portions thereof
  • the activities that can be screened for include one or more of 1) the ability to form protein protein mteractions with proteins in the apoptotic signaling pathway, (2) the ability to form CARD-CARD mteractions with protems in the apoptotic signaling pathway, (3) the ability to bind a CARD-4 ligand (e g, CARD-4, CARD-3, caspase 9, and/or BCLX), (4) the ability to bind to an intracellular target; (5) the ability to enhance caspase 9 activity, and (6) the ability to activate the NF- ⁇ B pathway.
  • Other activities include (1) modulation of cellular proliferation; (2) modulation of cellular differentiation, (3) modulation of cellular death, and (4) modulation of inflammation and or an innate immune response.
  • test compounds of the present invention can be obtained using any of the numerous approaches in combinatonal library methods known in the art, including, biological hbra ⁇ es, spatially addressable parallel solid phase or solution phase hbra ⁇ es, synthetic hbrary methods requi ⁇ ng deconvolution, the "one-bead one-compound” library method; and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to peptide hbranes, while the other four approaches are applicable to peptide, non-peptide ohgomer or small molecule hbranes of compounds -40/6
  • Determining the ability of the test compound to modulate the activity of CARD-4 oi ⁇ a biologically active portion thereof can be accomplished, for example, by determining the ability of the CARD-4 protein to bind to or interact with a CARD-4 target molecule.
  • a "target molecule” is a molecule with which a CARD-4 protem binds or interacts in nature, for example, a molecule associated with the internal surface of a cell membrane or a cytoplasmic molecule.
  • a CARD-4 target molecule can be a non-CARD-4 molecule or a CARD-4 protem or polypeptide of the present invention
  • a CARD-4 target molecule is a component of an apoptotic signal transduction pathway, e.g, CARD-4.
  • the target for example, can be a second intracellular protein which has catalytic activity or a protein which facilitates the association of downstream signaling molecules with CARD-4. Determining the ability of the test compound to modulate the activity of CARD-4 or a biologically active portion thereof can be accomplished, for example, by determining the ability of the CARD-4 protein to bind to or interact with any of the specific proteins listed in the previous paragraph as CARD-4 target molecules.
  • CARD-4 target molecules include all proteins that bind to a CARD-4 protein or a fragment thereof in a two-hybrid system binding assay which can be used without undue experimentation to isolate such proteins from cDNA or genomic two-hybrid system libraries.
  • the binding assays described in this section can be cell-based or cell free (described subsequently).
  • determining the ability of the CARD-4 protein to bind to or interact with a CARD-4 target molecule can be accomplished by determining the activity of the target molecule.
  • the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (e.g, intracellular Ca2+, diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity of the target on an appropriate substrate, detecting the induction of a reporter gene (e.g, a CARD-4-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g.
  • CARD-4 enhances caspase 9 activity, activity can be monitored by assaying the caspase 9-mediated apoptosis cellular response or caspase 9 enzymatic activity.
  • genes induced by CARD-4 expression can be identified by expressing CARD-4 in a cell fine and conducting a transcriptional profiling experiment wherein the mRNA expression patterns of the cell line transformed with an empty expression vector and the cell line transformed with a CARD-4 expression vector are compared.
  • the promoters of genes induced by CARD-4 expression can be operatively linked to reporter genes suitable for screening such as luciferase, secreted alkaline phosphatase, or beta-galactosidase and the resulting constructs could be introduced into appropriate expression vectors.
  • a recombinant cell line containing CARD-4 and transfected with an expression vector containing a CARD-4 responsive promoter operatively linked to a reporter gene can be used to identify test compounds that modulate CARD-4 activity by assaying the expression of the reporter gene in response to contacting the recombinant cell line with test compounds.
  • CARD-4 agonists can be identified as increasing the expression of the reporter gene and CARD-4 antagonists can be identified as decreasing the expression of the reporter gene.
  • the ability of a test compound to modulate the activity of CARD-4, or biologically active portions thereof can be determined by assaying the ability of the test compound to modulate CARD-4-dependent pathways or processes where the CARD-4 target proteins that mediate the CARD-4 effect are known or unknown.
  • Potential CARD-4-dependent pathways or processes include, but are not limited to, the modulation of cellular signal transduction pathways and their related second messenger molecules (e.g, intracellular Ca 2+ , diacylglycerol, IP3, cAMP etc.), cellular enzymatic activities, cellular responses (e.g, cell survival, cellular differentiation, or cell -38/6
  • CARD-4-dependent pathways or processes could be assayed by standard cell-based or cell free assays appropriate for the specific pathway or process under study.
  • cells cotransfected with CARD-4 and the NF- ⁇ B luciferase reporter gene could be contacted with a test compound and test compounds that block CARD-4 activity could be identified by their reduction of CARD-4-dependent NF- ⁇ B pathway luciferase reporter gene expression.
  • Test compounds that agonize CARD-4 would be expected to increase reporter gene expression.
  • CARD-4 could be expressed in a cell line and the recombmant CARD-4-expressing cell line could be contacted with a test compound.
  • an assay of the present invention is a cell-free assay comprising contacting a CARD-4 protein or biologically active portion thereof with a test compound and determining the ability of the test compound to bind to the CARD-4 protein or biologically active portion thereof. Binding of the test compound to the CARD-4 protein can be determined either directly or indirectly as described above.
  • a competitive binding assay includes contacting the CARD-4 protein or biologically active portion thereof with a compound known to bind CARD-4 to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a CARD-4 protein, wherein determining the ability of the test compound to interact with a CARD-4 protein comprises determining the ability of the test compound to preferentially bind to CARD-4 or biologically active portion thereof as compared to the known binding compound.
  • an assay is a cell-free assay comprising contacting CARD-4 protein or biologically active portion thereof with a test compound and determining the ability of the test compound to modulate (e.g, stimulate or inhibit) the activity of the CARD-4 protein or biologically active portion thereof. Determining the ability of the test compound to modulate the activity of CARD-4 can be accomplished, for example, by determining the ability of the CARD-4 protein to bind to a CARD-4 target molecule by one -37/6
  • determining the ability of the test compound to modulate the activity of CARD-4 can be accomplished by determining the ability of the CARD-4 protein to further modulate a CARD-4 target molecule.
  • the catalytic/enzymatic activity of the target molecule on an appropriate substrate can be determined as previously described.
  • the cell-free assay comprises contacting the CARD-4 protein or biologically active portion thereof with a known compound which binds CARD- 4 to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a CARD-4 protein, wherein determining the ability of the test compound to interact with a CARD-4 protein comprises determining the ability of the CARD-4 protein to preferentially bind to or modulate the activity of a CARD-4 target molecule.
  • the cell-free assays of the present invention are amenable to use of both the soluble fonn or the membrane-associated form of CARD-4.
  • a membrane-associated form of CARD-4 refers to CARD-4 that interacts with a membrane- bound target molecule.
  • a solubilizing agent such that the membrane-associated form of CARD-4 is maintained in solution.
  • non-ionic detergents such as n-octyl
  • a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
  • glutathione-S- transferase/CARD-4 fusion proteins or glutathione-S-transferase/target fusion proteins can -36/6
  • glutathione sepharose beads Sigma Chemical; St. Louis, MO
  • glutathione derivatized microtitre plates which are then combined with the test compound or the test compound and either the non-adsorbed target protein or CARD-4 protein, and the mixture incubated under conditions conducive to complex formation (e.g, at physiological conditions for salt and pH).
  • the beads or microtitre plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above.
  • the complexes can be dissociated from the matrix, and the level of CARD-4 binding or activity determined using standard techniques.
  • MYC or HA epitope tag CARD-4 fusion proteins or MYC or HA epitope tag target fusion proteins can be adsorbed onto anti-MYC or anti-HA antibody coated microbeads or onto anti-MYC or anti-HA antibody coated microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or CARD-4 protein, and the mixture incubated under conditions conducive to complex formation (e.g, at physiological conditions for salt and pH). Following incubation, the beads or microtitre plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of CARD-4 binding or activity determined using standard techniques.
  • CARD-4 or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
  • Biotinylated CARD-4 or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g, biotinylation kit, Pierce Chemicals; Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • antibodies reactive with CARD-4 or target molecules but which do not interfere with binding of the protein to its target molecule can be derivatized to the wells of the plate, and unbound target or protein trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the CARD-4 or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the -35/6
  • modulators of CARD-4 expression are identified in a method in which a cell is contacted with a candidate compound and the expression of the CARD-4 promoter, mRNA or protein in the cell is determined. The level of expression of CARD-4 mRNA or protein in the presence of the candidate compound is compared to the level of expression of CARD-4 mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of CARD-4 expression based on this comparison. For example, when expression of CARD-4 mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of CARD-4 mRNA or protein expression.
  • the candidate compound when expression of CARD-4 mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of CARD-4 mRNA or protein expression.
  • the level of CARD-4 mRNA or protein expression in the cells can be determined by methods described herein for detecting CARD-4 mRNA or protein.
  • the activity of the CARD-4 promoter can be assayed by linking the CARD-4 promoter to a reporter gene such as luciferase, secreted alkaline phosphatase, or beta-galactosidase and introducing the resulting construct into an appropriate vector, transfecting a host cell line, and measuring the activity of the reporter gene in response to test compounds.
  • the CARD-4 proteins can be used as "bait proteins" in a two-hybrid assay or three hybrid assay (see, e.g, U.S. Patent No. 5,283,317; Zervos et al, 1993, Cell, 72:223-232; Madura et al, 1993, J. Biol. Chem, 268: 12046- 12054; Bartel et al, 1993, Bio/Techniques, 14:920-924; Iwabuchi et al, 1993, Oncogene 8: 1693-1696; and PCT Publication No.
  • CARD-4-binding proteins or "CARD-4-bp”
  • CARD-4-binding proteins or "CARD-4-bp”
  • CARD-4-binding proteins are also likely to be involved in the propagation of signals by the CARD-4 proteins as, for example, upstream or downstream elements of the CARD-4 pathway.
  • the two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for CARD-4 is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g, GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an -34/6
  • unidentified protein ("prey" or “sample") is fused to a gene that codes for the activation domain of the known transcription factor. If the "bait” and the “prey” proteins are able to interact, in vivo, forming a CARD-4-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g, LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with CARD-4.
  • a reporter gene e.g, LacZ
  • the ability of a test compound to modulate the activity of CARD-4, or a biologically active portion thereof can be determined by assaying the ability of the test compound to block the binding of CARD-4 to its target proteins in a two-hybrid system assay.
  • a yeast two-hybrid screening strain coexpressing the interacting bait and prey constructs for example, a CARD-4 bait construct, is contacted with the test compound and the activity of the two-hybrid system reporter gene, usually HIS3, lacZ, or URA3 is assayed.
  • CARD-4 and their target proteins could be configured in the reverse two-hybrid system (Vidal et al, 1996, Proc. Natl. Acad. Sci. USA, 93:10321-6 and Vidal et al, 1996, Proc. Natl. Acad. Sci. USA, 93:10315-20) designed specifically for efficient drug screening.
  • CARD-4 interactors including but not limited to hNUDC and CARD-3, could be configured into two-hybrid system baits and used in two-hybrid screens to identify additional members of the CARD-4 pathway.
  • the interactors of CARD-4 interactors identified in this way could be useful targets for therapeutic intervention in CARD-4 related diseases and pathologies and an assay of their enzymatic or -33/6
  • binding activity could be useful for the identification of test compounds that modulate CARD-4 activity.
  • This invention further pertains to novel agents identified by the above-described screening assays and uses thereof for treatments as described herein.
  • cDNA sequences identified herein can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.
  • Chromosome Mapping Once the sequence (or a portion of the sequence) of a gene has been isolated, this sequence can be used to map the location of the gene on a chromosome. Accordingly, CARD-4 nucleic acid molecules described herein or fragments thereof, can be used to map the location of CARD-4 genes on a chromosome. The mapping of the CARD-4 sequences to chromosomes is an important first step in conelating these sequences with genes associated with disease.
  • CARD-4 genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the CARD-4 sequences. Computer analysis of CARD- 4 sequences can be used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene conesponding to the CARD-4 sequences will yield an amplified fragment.
  • Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g, human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes. By using media in which mouse cells cannot grow, because they lack a particular enzyme, but human cells can, the one human chromosome that contains the gene encoding the needed enzyme, will be retained. By using various media, panels of hybrid cell lines can be -32/6
  • Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. (D'Eustachio et al, 1983, Science, 220:919-924). Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.
  • PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the CARD-4 sequences to design oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map a CARD-4 sequence to its chromosome include in situ hybridization (described in Fan et al, 1990,
  • Fluorescence in situ hybridization (FISH) of a DNA sequence to a etaphase chromosomal spread can further be used to provide a precise chromosomal location in one step.
  • Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical like colcemid that disrupts the mitotic spindle. The chromosomes can be treated briefly with trypsin, and then stained with Giemsa.
  • a pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually.
  • the FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection.
  • Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to non- coding regions of the genes actually are preferred for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.
  • differences in the DNA sequences between individuals affected and unaffected with a disease associated with the CARD-4 gene can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms. 2. Tissue Typing
  • the CARD-4 sequences of the present invention can also be used to identify individuals from minute biological samples.
  • the United States military for example, is considering the use of restriction fragment length polymorphism (RFLP) for identification of its personnel.
  • RFLP restriction fragment length polymorphism
  • an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification.
  • This method does not suffer from the cu ⁇ ent limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult.
  • the sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).
  • sequences of the present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome.
  • the CARD-4 sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
  • Panels of conesponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences.
  • the sequences of the present invention can -30/6
  • the CARD-4 sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the non-coding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases.
  • Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes. Because greater numbers of polymorphisms occur in the non-coding regions, fewer sequences are necessary to differentiate individuals.
  • the non-coding sequences of SEQ ID NO: 1 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers which each yield a non-coding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ID NO: 3 are used, a more appropriate number of primers for positive individual identification would be 500-2,000.
  • a panel of reagents from CARD-4 sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual.
  • Using the unique identification database positive identification of the individual, living or dead, can be made from extremely small tissue samples.
  • DNA-based identification techniques can also be used in forensic biology.
  • Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a perpetrator of a crime.
  • PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g, hair or skin, or body fluids, e.g, blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample.
  • sequences of the present invention can be used to provide polynucleotide reagents, e.g, PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual).
  • an identification marker i.e. another DNA sequence that is unique to a particular individual.
  • actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated -29/6
  • sequences targeted to non-coding regions of SEQ ID NO: 1 are particularly appropriate for this use as greater numbers of polymorphisms occur in the non-coding regions, making it easier to differentiate individuals using this technique.
  • polynucleotide reagents include the CARD-4 sequences or portions thereof, e.g, fragments derived from the non-coding regions of SEQ ID NO: 1 which have a length of at least 20 or 30 bases.
  • sequences described herein can further be used to provide polynucleotide reagents, e.g, labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g, brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such CARD-4 probes can be used to identify tissue by species and/or by organ type.
  • these reagents e.g, CARD-4 primers or probes can be used to screen tissue culture for contamination (i.e, screen for the presence of a mixtore of different types of cells in a culture).
  • the present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials " are used for prognostic (predictive) purposes to thereby treat an individual prophylactically. Accordingly, one aspect of the present invention relates to diagnostic assays for determining CARD-4 protein and/or nucleic acid expression as well as CARD-4 activity, in the context of a biological sample (e.g, blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with abenant CARD-4 expression or activity.
  • a biological sample e.g, blood, serum, cells, tissue
  • the invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with CARD-4 protein, nucleic acid expression or activity. For example, mutations in a CARD-4 gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with CARD-4 protein, nucleic acid expression or activity.
  • Another aspect of the invention provides methods for determining CARD-4 protein, nucleic acid expression or CARD-4 activity in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (referred to herein as "pharmacogenomics").
  • Pharmacogenomics allows for the selection of agents (e.g, drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g, the genotype of the individual examined to determine the ability of the individual to respond to a particular agent).
  • Yet another aspect of the invention pertains to monitoring the influence of agents (e.g, drugs or other compounds) on the expression or activity of CARD-4 in clinical trials.
  • agents e.g, drugs or other compounds
  • An exemplary method for detecting the presence or absence of CARD-4 in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting CARD-4 protein or nucleic acid (e.g, mRNA, genomic DNA) that encodes CARD-4 protein such that the presence of CARD-4 is detected in the biological sample.
  • a compound or an agent capable of detecting CARD-4 protein or nucleic acid e.g, mRNA, genomic DNA
  • An agent for detecting CARD-4 mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to CARD-4 mRNA or genomic DNA.
  • the nucleic acid probe can be, for example, a full-length CARD- -27/6
  • nucleic acid such as the nucleic acid of SEQ ID NO: 1 or 3, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to mRNA or genomic DNA, or a human CARD-4 splice variant such as those described in U.S. Patent Nos. 6,340,576 or 6,369,196.
  • Other suitable probes for use in the diagnostic assays of the invention are described herein.
  • An agent for detecting CARD-4 protein can be an antibody capable of binding to CARD-4 protein, preferably an antibody with a detectable label.
  • Antibodies can be polyclonal, or more preferably, monoclonal.
  • polypeptides corresponding to amino acids 128-139 and 287-298 of human CARD-4 have been used to immunize rabbits and produce polyclonal antibodies that specifically recognize human CARD-4.
  • An intact antibody, or a fragment thereof e.g. Fab or F(ab')2 can be used.
  • labeled with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e, physically linking) a detectable substance to the probe oi ⁇ antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
  • indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.
  • biological sample is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject.
  • the detection method of the invention can be used to detect CARD-4 mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo.
  • in vitro techniques for detection of CARD-4 mRNA include Northern hybridizations and in situ hybridizations.
  • in vitro techniques for detection of CARD-4 protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence.
  • In vitro techniques for detection of CARD-4 genomic DNA include Southern hybridizations.
  • in vivo techniques for detection of CARD-4 protein include introducing into a subject a labeled anti-CARD-4 antibody.
  • the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
  • the biological sample contains protem molecules from the test subject.
  • the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject.
  • a biological sample is a -26/6
  • peripheral blood leukocyte sample isolated by conventional means from a subject.
  • the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting CARD-4 protein, mRNA, or genomic DNA, such that the presence of CARD-4 protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of CARD-4 protein, mRNA or genomic DNA in the control sample with the presence of CARD-4 protein, mRNA or genomic DNA in the test sample.
  • kits for detecting the presence of CARD-4 in a biological sample can be used to determine if a subject is suffering from or is at increased risk of developing a disorder associated with aberrant expression of CARD-4 (e.g, an immunological disorder).
  • the kit can comprise a labeled compound or agent capable of detecting CARD-4 protein or mRNA in a biological sample and means for determining the amount of CARD-4 in the sample (e.g, an anti-CARD-4 antibody or an oligonucleotide probe which binds to DNA encoding CARD- 4, e.g.. Kits may also include instruction for observing that the tested subject is suffering from or is at risk of developing a disorder associated with aberrant expression of CARD-4 if the amount of CARD-4 protein or mRNA is above or below a normal level.
  • the kit may comprise, for example: (1) a first antibody (e.g, attached to a solid support) which binds to CARD-4 protein; and, optionally, (2) a second, different antibody which binds to CARD-4 protein or the first antibody and is conjugated to a detectable agent.
  • a first antibody e.g, attached to a solid support
  • a second, different antibody which binds to CARD-4 protein or the first antibody and is conjugated to a detectable agent.
  • the kit may comprise, for example: (1) a oligonucleotide, e.g, a detectably labelled oligonucleotide, which hybridizes to a CARD-4 nucleic acid sequence or (2) a pah of primers useful for amplifying a CARD-4 nucleic acid molecule.
  • a oligonucleotide e.g, a detectably labelled oligonucleotide, which hybridizes to a CARD-4 nucleic acid sequence
  • a pah of primers useful for amplifying a CARD-4 nucleic acid molecule.
  • the kit may also comprise, e.g, a buffering agent, a preservative, or a protein stabilizing agent.
  • the kit may also comprise components necessary for detecting the detectable agent (e.g, an enzyme or a substrate).
  • the kit may also contain a control sample or a series of control samples which can be assayed and compared to the test sample contained.
  • Each component of the kit is usually enclosed within an individual container and all of the various containers are within a single package along with instructions for observing whether the tested subject is suffering from or is at risk of developing a disorder associated with aberrant expression of CARD-4. -25/6
  • the methods described herein can furthermore be utilized as diagnostic or prognostic assays to identify subjects having or at risk of developing a disease or disorder associated with abercant CARD-4 expression or activity.
  • the assays described herein such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with CARD-4 protein, nucleic acid expression or activity.
  • the prognostic assays can be utilized to identify a subject having or at risk for developing such a disease or disorder.
  • test sample refers to a biological sample obtained from a subject of interest.
  • a test sample can be a biological fluid (e.g, serum), cell sample, or tissue.
  • the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant CARD-4 expression or activity.
  • an agent e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • agents e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • agents e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • such methods can be used to determine whether a subject can be effectively treated with a specific agent or class of agents (e.g, agents of a type which decrease CARD-4 activity).
  • the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant CARD-4 expression or activity in which a test sample is obtained and CARD-4 protein or nucleic acid is detected (e.g, wherein the presence of CARD-4 protein or nucleic acid is diagnostic for a subject that can be administered the agent to treat a disorder associated with abercant CARD-4 expression or activity).
  • the methods of the invention can also be used to detect genetic lesions or mutations in a CARD-4 gene, thereby determining if a subject with the lesioned gene is at risk for a disorder characterized by aberrant cell proliferation and or differentiation.
  • the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic lesion characterized by at least one of an alteration affecting the integrity of a gene encoding a CARD-4-protein, or the mis-expression of the CARD-4 gene.
  • such genetic lesions can be detected by ascertaining the -24/6
  • detection of the lesion involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g, U.S. Patents Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g, Landegran et al, 1988, Science, 241:1077-1080; and Nakazawa et al, 1994, Proc. Natl. Acad. Sci.
  • PCR polymerase chain reaction
  • LCR ligation chain reaction
  • This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g, genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a CARD-4 gene under conditions such that hybridization and amplification of the CARD-4-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
  • nucleic acid e.g, genomic, mRNA or both
  • Alternative amplification methods include: self sustained sequence replication (Guatelli et al, 1990, Proc. Natl. Acad. Sci. USA, 87:1874-1878), transcriptional amplification system (Kwoh et al, 1989, Proc. Natl. Acad. Sci. USA, 86:1173-1177), Q- Beta Replicase (Lizardi et al, 1988, Bio/Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially -23/6
  • nucleic acid molecules useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
  • mutations in a CARD-4 gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns.
  • sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA.
  • sequence specific ribozymes see, e.g, U.S. Patent No. 5,498,531 can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
  • genetic mutations in CARD-4 can be identified by hybridizing a sample and control nucleic acids, e.g, DNA or RNA, to high density a ⁇ ays containing hundreds or thousands of oligonucleotides probes (Cronin et al, 1996, Human Mutation, 7:244-255; Kozal et al, 1996, Nature Medicine, 2:753-759).
  • a sample and control nucleic acids e.g, DNA or RNA
  • high density a ⁇ ays containing hundreds or thousands of oligonucleotides probes e.g., DNA or RNA
  • genetic mutations in CARD-4 can be identified in two-dimensional a ⁇ ays containing light- generated DNA probes as described in Cronin et al, supra.
  • a first hybridization a ⁇ ay of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization a ⁇ ay that allows the characterization of specific mutations by using smaller, specialized probe arcays complementary to all variants or mutations detected.
  • Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
  • any of a variety of sequencing reactions known in the art can be used to directly sequence the CARD-4 gene and detect mutations by comparing the sequence of the sample CARD-4 with the corresponding wild-type (control) sequence.
  • sequencing reactions include those based on techniques developed by Maxam and Gilbert, 1977, Proc. Natl. Acad. Sci. USA, 74:560, or Sanger, 1977, Proc. Natl. Acad. Sci. USA, 74:5463. It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Bio/Techniques 19:448), including sequencing by mass spectrometry (see, e.g, PCT Publication No. WO 94/16101; Cohen et al, 1996, Adv. Chromatogr, 36:127-162; and Griffin et al, 1993, Appl. Biochem. Biotechnol, 38:147-159). -22/6
  • RNA RNA or RNA/DNA heteroduplex Other methods for detecting mutations in the CARD-4 gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA RNA or RNA/DNA heteroduplex (Myers et al, 1985, Science, 230: 1242).
  • the art technique of "mismatch cleavage" starts by providing heteroduplex of fonned by hybridizing (labeled) RNA or DNA containing the wild-type CARD-4 sequence with potentially mutant RNA or DNA obtained from a tissue sample.
  • the double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands.
  • RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with SI nuclease to enzymatically digesting the mismatched regions.
  • either DNA DNA or RNA DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, e.g, Cotton et al, 1988, Proc. Natl. Acad. Sci. USA, 85:4397; Saleeba et al, 1992, Methods Enzymol, 217:286-295.
  • the control DNA or RNA can be labeled for detection.
  • the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in CARD-4 cDNAs obtained from samples of cells.
  • DNA mismatch repair enzymes
  • the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al, 1994, Carcinogenesis, 15:1657-1662).
  • a probe based on a CARD-4 sequence e.g, a wild-type CARD-4 sequence
  • a cDNA or other DNA product from a test cell(s).
  • the duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, e.g, U.S. Patent No. 5,459,039.
  • alterations in electrophoretic mobility will be used to identify mutations in CARD-4 genes.
  • SSCP single strand conformation polymorphism
  • SSCP single strand conformation polymorphism
  • Single-stranded DNA fragments of sample and control CARD-4 nucleic acids will be denatured and allowed to renature.
  • the secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change.
  • the DNA fragments may be labeled or detected with labeled probes.
  • the sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence.
  • the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al, 1991, Trends Genet, 7:5).
  • the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al, 1985, Nature, 313:495).
  • DGGE denaturing gradient gel electrophoresis
  • DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC- rich DNA by PCR.
  • a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner, 1987, Biophys. Chem, 265:12753).
  • oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al, 1986, Nature 324: 163); Saiki et al, 1989, Proc. Natl. Acad. Sci. USA, 86:6230).
  • Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
  • Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al, 1989, Nucleic Acids Res, 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner, 1993, Tibtech, 11:238).
  • amplification may also be performed using Taq ligase for amplification (Baiany, 1991, Pioc. Natl Acad Sci. USA, 88.189). In such cases, ligation will occui only if theie is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
  • the methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits comp ⁇ sing at least one probe nucleic acid or antibody reagent descnbed herein, which may be conveniently used, e g, m clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a CARD-4 gene
  • any cell type or tissue, preferably penpheral blood leukocytes, in which CARD-4 is expressed may be utilized m the prognostic assays described herein 3.
  • Pharmacogenomics Agents, or modulators which have a stimulatory or inhibitory effect on CARD-4 activity (e , CARD 4 gene expression) as identified by a screening assay desc ⁇ bed herein can be admmistered to individuals to treat (prophylactically or therapeutically) disorders (e.g , an immunological disorder) associated with aberrant CARD-4 activity
  • the pharmacogenomics i e , the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug
  • the pharmacogenomics of the individual may be considered Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug
  • the pharmacogenomics of the individual permits the selection of effective agents (e g , drugs) for prophylactic or therapeutic treatments
  • CARD-4 protein activity of CARD-4 protein, expression of CARD-4 nucleic acid, or mutation content of CARD-4 genes in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual
  • Pharmacogenomics deals with clinically significant hereditary vanations m the response to drugs due to altered drug disposition and abnormal action in affected persons See, e g , Lmder, 1997, Clin. Chem , 43(2) 254-266.
  • two types of pharmacogenetic conditions can be differentiated Genetic conditions transmitted as a -19/6
  • G6PD glucose-6-phosphate dehydrogenase deficiency
  • the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action.
  • drug metabolizing enzymes e.g, N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19
  • NAT 2 N-acetyltransferase 2
  • CYP2D6 and CYP2C19 cytochrome P450 enzymes
  • the gene coding for CYP2D6 is highly polymorphic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C1 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite mo ⁇ hine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification.
  • CARD-4 protein expression of CARD-4 nucleic acid, or mutation content of CARD-4 genes in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual.
  • pharmacogenetic studies can be used to apply genotyping of polymo ⁇ hic alleles encoding drug-metabolizing enzymes to the identification of an individual's drug responsiveness phenotype. This knowledge, when applied to dosing or dmg selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with a CARD-4 modulator, such as a modulator identified by one of the exemplary screening assays described herein. -18/6
  • CARD-4 Monitoring the influence of agents (e.g, drugs, compounds) on the expression or activity of CARD-4 (e.g, the ability to modulate aberrant cell proliferation and/or differentiation) can be applied not only in basic drug screening, but also in clinical trials.
  • agents e.g, drugs, compounds
  • the effectiveness of an agent determined by a screening assay as described herein to increase CARD-4 gene expression, protein levels, or upregulate CARD-4 activity can be monitored in clinical trails of subjects exhibiting decreased CARD-4 gene expression, protein levels, or downregulated CARD-4 activity.
  • the effectiveness of an agent determined by a screening assay to decrease CARD-4 gene expression, protein levels, or downregulated CARD-4 activity can be monitored in clinical trials of subjects exhibiting increased CARD-4 gene expression, protein levels, or upregulated CARD-4 activity.
  • the expression or activity of CARD-4 and, preferably, other genes that have been implicated in, for example, a cellular proliferation disorder can be used as a "read out" or markers of the immune responsiveness of a particular cell.
  • genes, including CARD-4, that are modulated in cells by treatment with an agent (e.g, compound, drug or small molecule) which modulates CARD-4 activity can be identified.
  • an agent e.g, compound, drug or small molecule
  • CARD-4 activity e.g, identified in a screening assay as described herein
  • cells can be isolated and RNA prepared and analyzed for the levels of expression of CARD-4 and other genes implicated in the disorder.
  • the levels of gene expression can be quantified by Northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of CARD-4 or other genes.
  • the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent.
  • the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting -17/6
  • an agent e.g, an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein
  • the level of expression of a CARD-4 protein, mRNA, or genomic DNA in the pre- administration sample (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the CARD-4 protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the CARD-4 protein, mRNA, or genomic DNA in the pre-administration sample with the CARD-4 protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.
  • increased administration of the agent may be desirable to increase the expression or activity of CARD-4 to higher levels than detected, i.e, to increase the effectiveness of the agent.
  • decreased administration of the agent may be desirable to decrease expression or activity of CARD-4 to lower levels than detected, i.e, to decrease the effectiveness of the agent.
  • the CARD-4 nucleic acid molecules described herein, including small oligonucleotides, can be used in transcriptionally profiling.
  • these nucleic acids can be used to examine the expression of CARD-4 in normal tissue or cells and in tissue or cells subject to a disease state, e.g, tissue or cells derived from a patient having a disease of interest or cultured cells which model or reflect a disease state of interest, e.g, cells of a cultured tumor cell line.
  • a disease state of interest e.g, cells of a cultured tumor cell line.
  • a profile of expression in nonnal and disease states can be developed. This profile can be used diagnostically and to examine the effectiveness of a therapeutic regime.
  • 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 CARD-4 expression or activity, examples of which are provided herein.
  • the invention provides a method for preventing in a subject, a disease or condition associated with an abe ⁇ ant CARD-4 expression or activity, by administering to the subject an agent which modulates CARD-4 expression or at least one CARD-4 activity.
  • Subjects at risk for a disease which is caused or contributed to by abe ⁇ ant CARD- 4 expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.
  • CARD-4 agonist or CARD-4 antagonist agent can be used for treating the subject.
  • the appropriate agent can be determined based on screening assays described herein. 2.
  • the modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of CARD-4 protein activity associated with the cell.
  • An agent that modulates CARD-4 protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally- occurring cognate ligand of a CARD-4 protein, a peptide, a CARD-4 peptidomimetic, or other small molecule.
  • the agent stimulates one or more of the biological activities of CARD-4 protein. Examples of such stimulatory agents include active CARD-4 protein and a nucleic acid molecule encoding CARD-4 that has been introduced into the cell.
  • the agent inhibits one or more of the biological activities of CARD-4 protein.
  • inhibitory agents include antisense CARD-4 nucleic acid molecules and anti-CARD-4 antibodies.
  • 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 CARD-4 protem or nucleic acid molecule or a disorder related to CARD-4 expression or activity.
  • the method involves administering an agent (e.g, an agent identified by a screening assay described herein), or combination of agents that modulates (e.g, upregulates or downregulates) CARD-4 expression or activity.
  • an agent e.g, an agent identified by a screening assay described herein
  • the method involves administering a CARD-4 protein or nucleic acid molecule as therapy to compensate for reduced or aberrant CARD-4 expression or activity.
  • Activities of CARD-4 that could be modulated for therapeutic pu ⁇ oses include, but are not limited to, (1) the ability to form protein:protein interactions with proteins in the apoptotic signalling pathway; (2) the ability to form CARD-CARD interactions with proteins in the apoptotic signaling pathway; (3) the ability to bind a CARD-4 ligand (e.g, CARD-4, CARD-3, caspase 9, and/or BCLX); (4) the ability to bind to an intracellular target; (5) the ability to -15/6
  • activities that could be modulated for a therapeutic pu ⁇ ose include: (1) modulation of cellular proliferation; (2) modulation of cellular differentiation; (3) modulation of cellular death; (4) modulation of inflammation and/or an innate immune response; and (5) modulation of CARD-4 mRNA or protein expression.
  • CARD-4 activity is desirable in situations in which CARD-4 is abnormally downregulated and/or in which increased CARD-4 activity is likely to have a beneficial effect.
  • inhibition of CARD-4 activity is desirable in situations in which CARD-4 is abnormally upregulated, e.g, in myocardial infarction, and/or in which decreased CARD-4 activity is likely to have a beneficial effect. Since CARD-4 may play be involved in the processing of cytokines, inhibiting the activity or expression of CARD4 may be beneficial in patients that have abe ⁇ ant inflammation.

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Abstract

Cette invention se rapporte à des procédés d'utilisation des molécules CARD-4 pour crible les modulateurs des voies de signalisation cellulaire induites par LIPOPOLYSACCHARIDE (LPS). Cette invention concerne également des souris ayant une déficience en molécules CARD-4, des procédés de modulation des voies de signalisation cellulaire induites par LPS, et des procédés de traitement ou de prévention des infections bactériennes.
EP03732905A 2002-05-22 2003-05-22 Molecules card-4 et utilisations correspondantes Withdrawn EP1509544A2 (fr)

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