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WO2003006479A1 - Compositions et procedes pour diagnostiquer et traiter des affections, des troubles ou des maladies impliquant la mort cellulaire - Google Patents

Compositions et procedes pour diagnostiquer et traiter des affections, des troubles ou des maladies impliquant la mort cellulaire Download PDF

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Publication number
WO2003006479A1
WO2003006479A1 PCT/US2002/021938 US0221938W WO03006479A1 WO 2003006479 A1 WO2003006479 A1 WO 2003006479A1 US 0221938 W US0221938 W US 0221938W WO 03006479 A1 WO03006479 A1 WO 03006479A1
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Prior art keywords
protective
protective sequence
sequence
nucleic acid
sequences
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PCT/US2002/021938
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English (en)
Inventor
Shawn Barney
Mary Beth Thomas
Stuart D. Portbury
Kasturi Puranam
Lawrence C. Katz
Donald C. Lo
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Cogent Neuroscience, Inc.
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Publication of WO2003006479A1 publication Critical patent/WO2003006479A1/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
    • 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)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy

Definitions

  • the present invention relates to compositions and methods for the treatment and diagnosis of conditions, disorders, or diseases involving cell death, including, but not limited to, neurological disorders such as stroke.
  • Nucleic acids are described herein that, when introduced into a cell either predisposed to undergo cell death or in the process of undergoing cell death, prevent, delay, or rescue the cell from death relative to a corresponding cell into which no exogenous nucleic acids have been introduced. Such nucleic acids are referred to as "protective sequences".
  • Protective sequences or their products are identified by their ability to prevent, delay, or rescue a cell, cells, tissues, organs, or organisms from dying. Protective sequences or their products are also identified via their ability to interact with other genes or gene products involved in conditions or disorders involving cell death.
  • the invention further includes recombinant DNA molecules and cloning vectors comprising protective sequences, and host cells and host organisms engineered to contain such DNA molecules and cloning vectors.
  • the present invention further relates to protective sequence products and to antibodies directed against such protective sequence products.
  • the protective sequences identified, their products, or antibodies may be used diagnostically, prophylactically, therapeutically or as targets for therapeutic intervention.
  • the present invention provides methods for the identification and prophylactic or therapeutic use of compounds in the treatment and diagnosis of conditions, disorders, or diseases involving cell death.
  • necrosis plays an important physiologic role in signaling the presence of certain conditions.
  • the dying cells release substances that activate the body's immune response in a local, and in some cases widespread, reaction to the necrosis-inducing condition. This response is important in, for example, bacterial infection.
  • preventing, delaying, or rescuing cells from death would either alleviate the disease or allow more time for definitive treatment to be administered to the patient.
  • An example of this situation is brain cell death caused by ischemic stroke: preventing, delaying, or rescuing cells from death until the blood supply to the brain could be restored would greatly reduce, if not eliminate, the possibility of a person's death and/or long-term disability from stroke (Lee JM, et al. Nature 1999, 399(supp): A7- A14; Tarkowski E, et al. Stroke 1999, 30(2): 321-7; Pulera MR, et al. Stroke 1998, 29(12): 2622-30).
  • apoptosis When the mechanism of apoptosis does not function properly and normal cell death does not occur, the resulting disease is characterized by unregulated cellular proliferation, as occurs in a neoplastic disease or an autoimmune disease (Hetts SW. JAMA 1998, 297(4): 300-7; Yachida M, et al. Clin Exp Immunol 1999, 116(1): 140-5).
  • One method for regulating cell death involves manipulating the threshold at which the process of cell death begins. This threshold varies significantly by cell type, tissue type, the type of injury or insult suffered by the cell, cellular maturity, and the physiologic conditions in the cell's environment (Steller H, Science 1995, 267(5203): 1445-9). Although it is probable that certain cellular injuries or insults irrevocably induce death, lesser injuries or insults may begin the dying process without inducing irreversible cell death. What constitutes a lesser injury or insult may vary tremendously with changes in the factors influencing that cell's death threshold. The ability to alter a cell's threshold for responding to an injury or insult, that is, to either promote or discourage cell death, would be a desirable goal for the treatment of conditions involving cell death. The ability to better control cell death, by either discouraging or promoting the mechanisms of cell death, would be an important invention for ameliorating disease (US Patents 5,925,640; 5,786,173; 5,858,715; 5,856,171).
  • bcl-2 is believed to regulate apoptotic death in neurons, kidney, heart, liver, blood and skin cells under experimental conditions. In addition to regulating death by apoptosis, bcl-2 is believed to regulate death caused by non-apoptotic mechanisms. Factors related to bcl-2 have been shown to be over-expressed in cancer and autoimmune conditions, disorders, or diseases (US Patent 5,856,171 and references cited therein). Other related factors acting on the same pathway as bcl-2 also delay or prevent cell death.
  • bcl-2 prevented cell death in a brain ischemia model (Guegan et al, Neurobiol. Dis. 1999, 6(3): 180-9; Linnik et al., Stroke 1995, 26(9): 1670-4). It was shown that the activity of bcl-2 to prevent neuronal death was consistently demonstrated across several different physiologic insults. It also has been demonstrated that the distinction between apoptotic death and necrotic death is open to question, so the possibility exists that bcl-2 can prevent or delay the necrotic cell death pathway, the apoptotic cell death pathway or perhaps an as yet undemonstrated cell death pathway. [0016] Preventing cell death is an important medical goal.
  • the present invention relates to the discovery, identification and characterization of protective sequences and to compositions and methods for the treatment and diagnosis of conditions, disorders, or diseases involving cell death.
  • Protective sequences refer to nucleic acid molecules comprising nucleic acid sequences that, when introduced into a cell either predisposed to undergo cell death or in the process of undergoing cell death, prevent, delay, or rescue the cell from death relative to a corresponding cell into which no exogenous nucleic acids have been introduced.
  • protective sequences may act to prevent, delay, ameliorate, inhibit, reduce, or rescue neuronal cell death (e.g. apoptosis, necrosis and related cellular events).
  • the invention further relates to the discovery, identification and characterization of gene products encoded by such nucleic acid molecules, or by degenerate, e.g. , allelic or homologous, variants thereof.
  • Protective sequences also can be regulatory nucleic acids.
  • Protective sequences further can be both coding sequences and regulatory sequences.
  • the invention further relates to target sequences.
  • Target sequences include, but are not limited to, upstream and downstream regulatory sequences, upstream and downstream complete or partial gene or gene product sequences, antibodies, antisense molecules or sequences, ribozyme molecules, and other inhibitors or modulators directed against such protective sequences and protective sequence products.
  • Protective sequences and protective sequence products can be utilized prophylactically and/or therapeutically to prevent, delay ameliorate, inhibit, reduce, or rescue conditions of cell death or symptoms of conditions, disorders, or diseases involving cell death.
  • the modulation of the expression of protective sequences, e.g., endogenous protective sequences, and/or the activity of the protective sequence products, e.g. , endogenous protective sequence products can also be utilized prophylactically or therapeutically to prevent, delay, ameliorate, inhibit, reduce, or rescue conditions of cell death or symptoms of conditions, disorders, or diseases involving cell death.
  • protective sequences and protective sequence products can be used to diagnose individuals exhibiting or predisposed to such conditions, disorders, or diseases involving cell death.
  • compositions of the present invention include, in particular, nucleic acid molecules that comprise the following sequences: (a) nucleic acids of protective sequences, as well as allelic variants, homologs, mutants and fragments thereof; (b) nucleic acids that encode protective sequence products; (c) nucleic acids that encode protective sequence regulatory elements; (d) nucleic acids that encode fusion proteins comprising protective sequence products or one or more protective sequence product domains fused to a heterologous polypeptide; (e) nucleic acids that encode fusion proteins comprising protective sequence regulatory elements fused to a heterologous polypeptide; (f) nucleic acids that hybridize to the above described sequences under highly stringent or moderately stringent conditions, including, but not limited to, human homologs; and (g) complementary (e.g., antisense) nucleic acids of the sequences described in (a) through (f), above.
  • nucleic acid molecules that comprise the following sequences: (a) nucleic acids of protective sequences, as well as allelic variant
  • the nucleic acid molecules of the invention include, but are not limited to, cDNA, genomic DNA and RNA sequences.
  • the present invention also encompasses expression gene products of the protective sequences listed above; i.e., proteins and/or polypeptides that are encoded by the above protective sequences.
  • Mimics, agonists and antagonists of the protective sequences, protective sequence products, genes, gene products, or their regulatory elements are also included in the present invention.
  • Such mimics, agonists and antagonists will include, for example, small molecules, large molecules (e.g., protective sequence product fragments or protective sequence product ligands) and antibodies directed against a protective sequence product.
  • Mimics, agonists and antagonists of the invention also include nucleic acids, such as antisense and ribozyme molecules, and gene or regulatory sequence replacement constructs, which can be used to modulate, inhibit or enhance expression of a protective sequence.
  • the present invention further encompasses cloning and expression vectors, which may include, but are not limited to, bacterial, fungal, insect, plant, and mammalian vectors, which contain the protective nucleic acid sequences of the invention, which can be used as probes or to express those protective nucleic acid sequences, protective sequence products, genes and/or gene products in host cells or organisms.
  • the present invention also relates to cells that have been transformed, transfected, or infected with such vectors, and to cells engineered to contain or express the protective nucleic acid sequences, protective sequence products, genes, gene products, and/or regulatory elements of the invention.
  • non-human host organisms that have been transformed, transfected, or infected with these protective nucleic acid sequences, or their regulatory elements, are also encompassed in the present invention.
  • Host organisms of the invention include organisms transformed, transfected, or infected with the cloning vectors described above, including, but not limited to, non-human transgenic animals, and particularly transgenic non-human mammals that have been engineered to express a protective sequence, protective sequence product, gene, gene product, or regulatory element of the invention, or "knock-outs" that have been engineered to not express the protective sequence, protective sequence product, gene, gene product, or regulatory element of the invention.
  • the transgenic animals of the invention include animals that express a mutant variant or polymo ⁇ hism of a protective sequence, protective sequence product, gene, gene product, or regulatory element, particularly a mutant variant or polymo ⁇ hism of a protective sequence, protective sequence product, gene, gene product, or regulatory element that is associated with a condition, disorder, or disease involving cell death.
  • the transgenic animals of the invention further include those that express a protective sequence transgene at higher or lower levels than normal.
  • the transgenic animals of the invention further include those that express the protective sequence, protective sequence product, gene, gene product, or regulatory element in all their cells, "mosaic” animals that express the protective sequence, protective sequence product, gene, gene product, or regulatory element in only some of their cells, and those in which the protective sequence, protective sequence product, gene, gene product, or regulatory element is selectively introduced into and expressed in a specific cell type(s).
  • the transgenic animals of the invention also include "knock-out" animals. Knock-out animals comprise animals that have been engineered to no longer express the protective sequence, protective sequence product, gene, gene product, or regulatory element.
  • the present invention also relates to methods and compositions for the diagnosis of conditions, disorders, or diseases involving cell death, as well as for the identification of subjects susceptible to such conditions, disorders, or diseases.
  • Such methods comprise, for example, measuring expression of the protective sequence, protective sequence product, gene, gene product, or regulatory element in a patient sample, or detecting a mutation in the protective sequence, protective sequence product, gene, gene product, or regulatory element in the genome of a mammal, including a human, suspected of exhibiting such a condition, disorder, or disease.
  • the protective nucleic acid molecules of the invention can be used also as diagnostic hybridization probes, or as primers for diagnostic PCR analysis to identify protective sequences, protective sequence products, genes, gene products, or regulatory element mutations, allelic variations or regulatory defects, such as defects in the expression of the protective sequence, protective sequence product, gene, gene product, or regulatory element.
  • diagnostic PCR analyses can be used to diagnose individuals with a condition, disorder, or disease involving cell death associated with a particular protective sequence, protective sequence product, gene, gene product, or regulatory element mutation, allelic variation or regulatory defect.
  • Such diagnostic PCR analyses can be used also to identify individuals susceptible to such conditions, disorders, or diseases involving cell death.
  • Methods and compositions, including pharmaceutical compositions, for the treatment of conditions, disorders, or diseases involving cell death also are included in the invention.
  • Such methods and compositions can increase, decrease or otherwise modulate the level of protective sequences, protective sequence products, genes, gene products, or their regulatory elements in a patient in need of such treatment.
  • Such methods and compositions can also modulate the level of protective sequence expression (e.g., endogenous protective sequence expression) and or the level of activity of a protective sequence product, (e.g., endogenous protective sequence product).
  • such methods include, for example, modulating the expression of the protective sequence and/or the activity of the protective sequence product for the treatment of conditions, disorders, or diseases involving cell death that are normally mediated by some other gene.
  • such methods and compositions are utilized for the treatment of the types of conditions, disorders, or diseases, which can be prevented, delayed or rescued from cell death and include, but are not limited to, those associated with the central nervous system including neurological and psychiatric conditions, disorders, or diseases; those of the peripheral nervous system; conditions, disorders, or diseases caused by physical injury; conditions, disorders, or diseases of the blood vessels or heart; conditions, disorders, or diseases of the respiratory system; neoplastic conditions, disorders, or diseases; conditions, disorders, or diseases of blood cells; conditions, disorders, or diseases of the gastrointestinal tract; conditions, disorders, or diseases of the liver; conditions, disorders, or diseases of the pancreas; conditions, disorders, or diseases of the kidney; conditions, disorders, or diseases of the ureters, urethra or bladder; conditions, disorders, or diseases of the male genital system; conditions, disorders, or diseases of the female genital tract; conditions, disorders, or diseases of the breast; conditions, disorders, or diseases of the endocrine system; conditions,
  • the methods and compositions of the invention are utilized for the prevention, or delay, of cell death in the event of one or more infections that may be caused by bacteria; viruses; members of the family rickettsiae or chlamydia; fungi, yeast, hyphae or pseudohyphae; prions; protozoans; or metazoans.
  • the compounds and methods of the invention can be used to treat infections or conditions, disorders, or diseases that cause cell death in organ systems including, but not limited to, blood vessels, heart, red blood cells, white blood cells, lymph nodes, spleen, respiratory system, oral cavity, gastrointestinal tract, liver and biliary tract, pancreas, kidney, lower urinary tract, upper urinary tract and bladder, male sexual organs and genitalia, female sexual organs and genitalia, breast, thyroid gland, adrenal gland, parathyroid gland, skin, musculoskeletal system, bone marrow or bones.
  • organ systems including, but not limited to, blood vessels, heart, red blood cells, white blood cells, lymph nodes, spleen, respiratory system, oral cavity, gastrointestinal tract, liver and biliary tract, pancreas, kidney, lower urinary tract, upper urinary tract and bladder, male sexual organs and genitalia, female sexual organs and genitalia, breast, thyroid gland, adrenal gland, parathyroid gland, skin, musculoskeletal system,
  • the compounds and methods of the invention can be used to treat further physiological impacts on organs caused by the infections that induce cell death including, but not limited to, fever equal to or greater than 101.5 degrees Fahrenheit, a decrease or increase in pulse rate by more than 20 beats per minute, a decrease or increase in supine systolic blood pressure by more than 30 millimeters of mercury, an increase or decrease in respiratory rate by more than 8 breaths per minute, an increase or decrease in blood pH by more than 0.10 pH units, an increase or decrease in one or more serum electrolytes outside of the clinical laboratory's usual reference range, an increase or decrease in the partial pressure of arterial oxygen or carbon dioxide outside of the clinical laboratory's usual reference range, an increase or decrease in white or red blood cells outside of the laboratory's usual reference range, an acute confusional state such as delirium where delirium is defined by the American Psychiatric Association's DSM-IV Manual or a diminished level of consciousness or attention.
  • fever equal to or greater than 101.5 degrees Fahrenheit a decrease or increase in pulse
  • the compounds and methods of the invention can be used to promote cell death. These compounds could be useful for treating and/or ameliorating conditions caused by, for example, cancer and autoimmune diseases, both of which are manifested by an uncontrolled growth of cells.
  • the invention still further relates to methods for identifying compounds that modulate the expression of a protective sequence and/or the synthesis or activity of a protective sequence product. Such compounds include therapeutic compounds that can be used as pharmaceutical compositions to reduce or eliminate the symptoms of conditions, disorders, or diseases involving cell death.
  • Cellular and non-cellular assays are described that can be used to identify compounds that interact with a protective sequence, protective sequence product, gene, gene product, and/or regulatory element, e.g., modulate the activity of a protective sequence and/or bind to a protective sequence product.
  • Such cell-based assays of the invention utilize cells, cell lines, or engineered cells or cell lines that express the protective sequence, protective sequence product, gene, gene product, and/or regulatory element.
  • such methods comprise contacting a compound to a cell that expresses a protective sequence, protective sequence product, gene, gene product, and/or regulatory element, measuring the level of protective sequence expression, gene product expression or gene product activity, and comparing this level to the level of protective sequence expression, gene product expression or gene product activity produced by the cell in the absence of the compound, such that if the level obtained in the presence of the compound differs from that obtained in its absence, a compound that modulates the expression of the protective sequence and/or the synthesis or activity of protective sequence products has been identified.
  • such methods comprise administering a compound to a host, e.g. , a transgenic animal that expresses a protective sequence transgene or a mutant protective sequence transgene, and measuring the level of protective sequence expression, gene product expression or gene product activity.
  • the measured level is compared to the level of protective sequence expression, gene product expression or gene product activity in a host that is not exposed to the compound, such that if the level obtained when the host is exposed to the compound differs from that obtained when the host is not exposed to the compound, a compound that modulates the expression of the protective sequence and/or the synthesis or activity of protective sequence products, and/or the symptoms of conditions, disorders, or diseases involving cell death, has been identified.
  • Protective sequence refers to nucleic acid molecules comprising nucleic acid sequences that, when introduced into a cell predisposed to either undergo cell death or in the process of undergoing cell death, prevent, delay, or rescue the cell from death relative to a corresponding cell into which no exogenous protective nucleic acids have been introduced.
  • a protective sequence encodes a protective sequence product.
  • protective sequences are any transcriptional products of the sequences disclosed herein.
  • protective sequences comprise regulatory elements of the sequences disclosed herein that modulate the expression of a nucleic acid within a cell.
  • protective sequences, their products, or their regulatory elements may act to prevent, delay, or rescue a cell, cells, tissues, organs, or organisms from dying.
  • Compounds that modulate protective sequence expression or activity of the protective sequence product can be used in the treatment of conditions, disorders or diseases associated with cell death processes. It is to be understood that the protective sequences described above can act to ameliorate or delay symptoms related to cell death.
  • the protective sequences may be involved directly in such cell death related conditions or disorders, in certain cases, the protective sequences will not normally be involved in such conditions or disorders, but will be effective for the treatment and/or prevention of such disorders.
  • Cell death refers to the irreversible cessation of the normal biochemical function(s) of a cell.
  • hallmarks of cell death include, but are not limited to, cessation of biochemical activity; cessation of production of polypeptide products normally produced; loss of electrical activity; degradation of organelles and/or chromosomes; lysis, detachment from a surface, where a cell normally attaches to a surface; and failure of cell membranes.
  • Cell death also refers to any mechanism and/or pathway whereby a cell undergoes a series of events that ultimately would lead to the death of the cell.
  • cell death may be caused by various processes including, but not limited to, apoptosis or programmed cell death, necrosis, or an as yet unidentified cell death pathway.
  • Cell death may be induced in individual cells as a consequence of numerous internal and external stimuli including, but not limited to, genetic predisposition, toxic chemicals or processes, heat, cold, rapid environmental changes, radiation, viruses, prions, bacteria, disruption of nutrient balance, or exposure to bi-products and signaling from other cells undergoing cell death.
  • the protective sequences disclosed herein, when introduced into a cell e.g.
  • a neuronal cell that has undergone an event that would ultimately lead to cell death (e.g. ischemia), are capable of rescuing the cell from cell death.
  • a protective sequence in combination with a reporter gene (e.g. green fluorescent protein), is introduced into a cell that has undergone an event that would ultimately lead to cell death, expression of the reporter gene is an indication that the protective sequence is capable of rescuing the cell from cell death.
  • a reporter gene e.g. green fluorescent protein
  • Figure 1 Protective nucleic acid CNI-00713. See Table 1 for the identity, the sequence identifier number, the length in base pairs and the Accession Number for
  • FIG. 1 Restriction map and diagram of plasmid pCMV-SPORT2, used as the cloning vector for the protective sequences. Each clone was ligated into the Sall- Notl restriction sites. The entire nucleotide sequence depicted is SEQ ID NO: 58.
  • Figures 3 A and 3B represent non-stroked, positive control samples.
  • Figure 3C represents a positive control, stroked sample using Bcl-2.
  • Figure 3D represents a stroked, negative control sample.
  • Figure 3E represents a stroked sample protected by CNI-00713.
  • compositions of the invention further include protective sequence products (e.g. proteins or RNA) that are encoded or produced by the nucleic acid molecules of the invention, and the modulation of protective sequence expression and/or gene product activity in the treatment of conditions, disorders, or diseases involving cell death.
  • protective sequence products e.g. proteins or RNA
  • antibodies directed against the protective sequence products, or conserved variants or fragments thereof, and viral-, cell-, plant-, and animal-based models by which the protective sequences may be further characterized and utilized are also discussed in this section.
  • Protective sequence CNI-00713 (SEQ TD NO: 1) and the protective sequences based on CNI-00713 are described in this section. Specifically, these protective sequences have been shown to prevent, delay, or rescue cell death in a cell predisposed for undergoing cell death, whether the pathway that leads to the cell death involves apoptosis, necrosis or an as yet undefined pathway.
  • Protective sequence CNI-00713 may be obtained using cloning methods well known to those skilled in the art, including but not limited to the use of appropriate probes to detect the protective sequences within an appropriate cDNA or gDNA (genomic DNA) library.
  • probes for the novel sequences reported herein may be obtained directly from CNI-NPP3-CNI00713, which represents a deposit containing the isolated clone, which was deposited with the NRRL as Accession No. B-30241.
  • oligonucleotide probes for the novel protective sequences may be synthesized based on the DNA sequences disclosed herein.
  • the isolated protective nucleic acid molecules of the invention include, in particular, nucleic acid molecules that comprise the following sequences: (a) nucleic acids of protective sequences, as well as allelic variants, homologs, mutants and fragments thereof; (b) nucleic acids that encode protective sequence products and/or their regulatory elements, or fragments thereof; (c) nucleic acids that encode fusion proteins comprising protective sequence products and/or their regulatory elements, or one or more protective sequence product domains and/or their regulatory elements fused to a heterologous polypeptide; (d) nucleic acids that hybridize to the above described sequences under highly stringent or moderately stringent conditions, including, but not limited to human homologs; and (e) complementary (e.g., antisense) nucleic acids of the sequences described in (a) through (d), above.
  • nucleic acid molecules that comprise the following sequences: (a) nucleic acids of protective sequences, as well as allelic variants, homologs, mutants and fragments thereof; (b)
  • the nucleic acid molecules of the invention include, but are not limited to, cDNA, genomic DNA and RNA sequences.
  • the nucleic acids of the invention also include nucleic acids that have at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more nucleic acid identity to the protective nucleic acids of (a)-(d) above.
  • the nucleic acids of the invention further include nucleic acids that encode polypeptides having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or higher amino acid sequence identity to the polypeptides encoded by the protective nucleic acids of (a)-(d).
  • the sequences are aligned for optimal comparison pu ⁇ oses (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 corresponding position in the second sequence, then the molecules are identical at that position.
  • the determination of percent identity between two sequences also can be accomplished using a mathematical algorithm.
  • a preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 57:2264-2268, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
  • Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res.25: 3389-3402.
  • PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules (Id.).
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, (1988) CABIOS 4: ⁇ 1-17. Such an algorithm is inco ⁇ orated into the ALIGN program (version 2.0) that is part of the GCG sequence alignment software package.
  • the nucleic acids of the invention further include: (a) any nucleic acid that hybridizes to a nucleic acid molecule of the invention under moderately stringent conditions, e.g.
  • nucleic acid molecule that hybridizes to the nucleic acid of (a) and (b), above is one that comprises the complement of a nucleic acid molecule that encodes a protective sequence product.
  • nucleic acid molecules comprising the nucleic acids of (a) and (b), above encode protective sequence products.
  • Functionally equivalent protective sequence products include naturally occurring protective sequence products present in the same or different species. Functionally equivalent protective sequence products also include gene products that retain at least one of the biological activities of the protective sequence products, and/or that are recognized by and bind to antibodies (polyclonal or monoclonal) directed against the protective sequence products.
  • nucleic acid molecules of the invention are deoxyoligonucleotides (“oligos") that hybridize under highly stringent or moderately stringent conditions to the nucleic acid molecules described above.
  • T m melting temperature
  • T m (°C) 81.5+16.6(log[monovalent cations (molar)])+0.41(% G+C)-(0.61% formamide)- (500/N) where N is the length of the probe.
  • hybridization is carried out at about 20-25 degrees below T m (for DNA-DNA hybrids) or 10-15 degrees below T m (for RNA-DNA hybrids).
  • Exemplary highly stringent conditions may refer, e.g., to washing in 6xSSC/0.05% sodium pyrophosphate at 37°C (for about 14-base oligos), 48 °C (for about 17-base oligos), 55 °C (for about 20-base oligos) and 60 °C (for about 23-base oligos).
  • Fragments of the nucleic acid molecules can be at least 10 nucleotides in length. Such fragments may be used as probes or primers. Fragments of the nucleic acid molecules can refer also to exons or introns, and, further, can refer to portions of coding regions that encode domains of protective sequence products.
  • the invention also encompasses (a) DNA vectors that contain any of the foregoing coding sequences and or their complements (i.e., antisense); (b) DNA expression vectors that contain any of the foregoing coding sequences operatively associated with a regulatory element that directs the expression of the coding sequences; and (c) genetically engineered host cells that contain such vectors or have been engineered to contain and/or express a nucleic acid sequence of the invention, e.g., any of the foregoing coding sequences operatively associated with a regulatory element that directs the expression of the coding sequences in the host cell.
  • regulatory elements include but are not limited to inducible and non-inducible promoters, enhancers, operators and other elements known to those skilled in the art that drive and regulate expression.
  • the invention further includes fragments of any of the DNA sequences disclosed herein.
  • the nucleic acid molecules may encode or act as antisense molecules, useful, for example, in protective sequence regulation, and/or as hybridization probes and/or as primers in amplification reactions of protective nucleic acid sequences. Further, such sequences may be used as part of ribozyme and/or triple helix sequences, also useful for protective sequence regulation.
  • Such molecules may be used as components of diagnostic methods whereby, for example, the presence of a particular allele involved in a condition, disorder, or disease involving cell death may be detected.
  • the protective nucleic acids of the invention can be readily obtained, for example, by standard sequencing and the sequences provided herein.
  • DNA sequence polymo ⁇ hisms of a protective sequence will exist within a population of individual organisms (e.g., within a human population). Such polymo ⁇ hisms may exist, for example, among individuals within a population due to natural allelic variation. Such polymo ⁇ hisms include ones that lead to changes in amino acid sequence.
  • An allele is one of a group of alternative forms of a gene that occur at a given genetic locus.
  • allelic variant refers to a nucleic acid that occurs at a given locus or to a gene product encoded by that nucleic acid. Such natural allelic variations can typically result in 1-5% variance in the nucleic acid of a given gene. Sequencing the gene of interest in a number of different individuals can identify alternative alleles. Using hybridization probes to identify the same genetic locus in a variety of individuals can readily carry this out.
  • the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising any of up to six open reading frames that may or may not encode a polypeptide of the invention.
  • the terms “gene” and “recombinant gene” refer to nucleic acid molecules encoding any of the open reading frames shown in Figure 4, and described in Table 2, respectively.
  • the term can further include nucleic acid molecules comprising upstream and/or exon/intron sequences and structures.
  • the nucleic acid molecules comprise nucleic acids that encode an open reading frame of at least 3 contiguous amino acid residues from a full-length protein. In alternate embodiments, the nucleic acid molecules comprise an open reading frame that encodes at least about 5, 8, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450 or more contiguous amino acid residues of a protein.
  • the sequence of SEQ ID NO: 1 can be used to derive the sequence of oligonucleotides useful for the detection and/or amplification of the genomic sequence or allelic variants thereof, which fragments may encode a protective sequence product or not.
  • Such fragments may be restriction fragments of SEQ ID NO: 1. Such fragments may also be discrete segments of the full-length sequences disclosed. For example, in a more specific embodiment, such fragment is at least about 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1300, 11400, 1500, 1600 or 1700 contiguous nucleotides of SEQ TD NO: 1 or the reverse complement thereof.
  • such a fragment of the invention may be, but is not limited to, the nucleotide sequence nn ⁇ -nn 50 , mmsi-nmoo, nn 10 ⁇ -nni 50 , nni 51 -nn 20 o, nn 2 o ⁇ -nn 250 , nn 251 -nn 3 oo, nn 3 o ⁇ -nn 35 o, nn 35 ⁇ -nn 4 oo, nrusi-nnsoo, nn 5 o ⁇ -nn 550 , nn 5 5i-nn 600 , nn 60 ⁇ -nn 650 , nn 65 ⁇ -nn 70 o, nn 701 -nn 750 , nn 75 ⁇ -nn 8 o 0 , nn 8 o ⁇ -nn 850 , nn 8 5i-nn 9 oo, nn9 0 ⁇
  • nn x -nn y means nucleotide X to nucleotide Y of SEQ DD NO: 1
  • nn ⁇ -nn 5 o of SEQ ED NO: 1 means contiguous nucleotides 1-50 of SEQ ED NO: 1. Longer fragments, and fragments starting at other nucleotide positions, may be generated or derived in the same manner.
  • the sequence obtained from clones containing partial coding sequences or non-coding sequences can be used to obtain the entire coding region by using the RACE method, for example (Chenchik et al, 1995, CLONTECHniques (X) 1 : 5-8; Barnes, 1994, Proc. Natl. Acad. Sci. USA 91 : 2216-2220; and Cheng et al, Proc. Natl. Acad. Sci. USA 91 : 5695-5699).
  • Oligonucleotides can be designed based on the sequence obtained from the partial clone that can amplify a reverse transcribed mRNA encoding the entire coding sequence.
  • probes can be used to screen cDNA libraries prepared from an appropriate cell or cell line in which the protective sequence is transcribed.
  • allelic variants of protective sequences associated with a condition, disorder, or disease involving cell death any and all such nucleotide variations and resulting amino acid polymo ⁇ hisms or variations that are the result of natural allelic variation of the protective sequence are intended to be within the scope of the present invention.
  • allelic variants include, but are not limited to, ones that do not alter the functional activity of the protective sequence product.
  • the isolated protective sequences disclosed herein may be labeled and used to screen a cDNA library constructed from mRNA obtained from appropriate cells or tissues (e.g., brain) derived from the organism (e.g., guinea pig, cow and mouse) of interest.
  • the hybridization conditions used generally should be of a lower stringency when the cDNA library is derived from an organism different from the type of organism from which the labeled sequence was derived, and can routinely be determined based on, e.g., relative relatedness of the target and reference organisms.
  • the labeled fragment may be used to screen a genomic library derived from the organism of interest, again, using appropriately stringent conditions.
  • Appropriate stringency conditions are well known to those of skill in the art as discussed above, and will vary predictably depending on the specific organisms from which the library and the labeled sequences are derived. For guidance regarding such conditions, see, for example, Sambrook, et al, 1989, MOLECULAR CLONING, A LABORATORY MANUAL, Second Edition, Cold Spring Harbor Press, N.Y.; and Ausubel, et al, 1989-1999, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y., both of which are inco ⁇ orated herein by reference in their entirety.
  • syntenic genes are genes that are believed to be located on the same chromosome because they are lost along with a marker gene that is known to be located on that chromosome.
  • markers gene that is known to be located on that chromosome.
  • a protective sequence allelic variant may be isolated from, for example, human nucleic acid, by performing PCR using two degenerate oligonucleotide primer pools designed on the basis of amino acid sequences within the protective sequence product of interest.
  • the template for the reaction may be cDNA obtained by reverse transcription of mRNA prepared from, for example, human or non-human cell lines or tissue known or suspected to express a wild type or mutant protective sequence allele.
  • the allelic variant is isolated from an individual who has a condition, disorder, or disease involving cell death. Such variants are described in the examples below.
  • the PCR product may be subcloned and sequenced to ensure that the amplified sequences represent the sequences of a protective nucleic acid sequence.
  • the PCR fragment may then be used to isolate a full-length cDNA clone by a variety of methods.
  • the amplified fragment may be labeled and used to screen a bacteriophage cDNA library.
  • the labeled fragment may be used to isolate genomic clones via the screening of a genomic library.
  • PCR technology also may be utilized to isolate full-length cDNA sequences.
  • RNA may be isolated, following standard procedures, from an appropriate cellular or tissue source.
  • a reverse transcription reaction may be performed on the RNA using an oligonucleotide primer specific for the most 5' end of the amplified fragment for the priming of first strand synthesis.
  • the resulting RNA/DNA hybrid may then be "tailed" with guanines using a standard terminal transferase reaction.
  • the hybrid may be digested with RNAase H and second strand synthesis may then be primed with a poly-C primer.
  • cDNA sequences upstream of the amplified fragment may easily be isolated.
  • the isolated protective sequence is the normal, or wild type gene
  • this gene may be used to isolate mutant alleles of the protective sequence.
  • Such an isolation is preferable in processes and disorders that are known or suspected to have a genetic basis.
  • Mutant alleles may be isolated from individuals either known or suspected to have a genotype that contributes to symptoms of conditions, disorders, or diseases involving cell death. Mutant alleles and mutant allele products may then be utilized in the therapeutic and diagnostic assay systems described below.
  • a cDNA of the mutant protective sequence may be isolated, for example, by using PCR, a technique well known to those of skill in the art.
  • the first cDNA strand may be synthesized by hybridizing an oligo-dT oligonucleotide to mRNA isolated from tissue known or suspected to be expressed in an individual putatively carrying the mutant allele, and by extending the new strand with reverse transcriptase.
  • the second strand of the cDNA is then synthesized using an oligonucleotide that hybridizes specifically to the 5' end of the normal protective sequence.
  • the product is then amplified via PCR, cloned into a suitable vector and subjected to DNA sequence analysis through methods well known to those of skill in the art.
  • DNA sequence analysis By comparing the DNA sequence of the mutant protective sequence to that of the normal protective sequence, the mutation(s) responsible for the loss or alteration of function of the mutant gene product can be ascertained.
  • a genomic or cDNA library can be constructed and screened using DNA or RNA, respectively, from a tissue known to or suspected of expressing the protective sequence of interest in an individual suspected of or known to carry the mutant allele.
  • the normal protective sequence or any suitable fragment thereof may then be labeled and used as a probed to identify the corresponding mutant allele in the library.
  • the clone containing this protective sequence may then be purified through methods routinely practiced in the art, and subjected to sequence analysis as described above in this Section.
  • an expression library can be constructed utilizing DNA isolated from or cDNA synthesized from a tissue known to or suspected of expressing the protective sequence of interest in an individual suspected of or known to carry the mutant allele.
  • protective sequence products made by the tissue containing the putative mutant alleles may be expressed and screened using standard antibody screening techniques in conjunction with antibodies raised against the normal protective sequence product, as described, below, in Section 5.3 (For screening techniques, see, for example, Harlow, E.
  • the invention also includes nucleic acid molecules, preferably DNA molecules that are the complements of the nucleic acids of the preceding paragraphs.
  • the protective nucleic acid molecules of the invention are present as part of protective nucleic acid molecules comprising nucleic acid sequences that do not contain heterologous (e.g. , cloning vector or expression vector) sequences.
  • the protective nucleic acid molecules of the invention further comprise vector sequences, e.g., cloning vectors or expression vectors. 5.2 Protein Products of the Protective Sequences
  • Protective sequence products or fragments thereof of the invention can be prepared for a variety of uses, including but not limited to, prophylactic or therapeutic modulators of protective sequence product function, for the generation of antibodies, diagnostic assays, or for the identification of other cellular or extracellular protective sequence products involved in the regulation of conditions, disorders, or diseases involving cell death.
  • the protective sequence products of the invention include, but are not limited to, human protective sequence products and non-human protective sequence products, e.g., mammalian (such as bovine or guinea pig), protective sequence products.
  • Protective sequence products of the invention includes those gene products encoded by any of up to six translational reading frames of the protective sequence sequences depicted in Table 1 , as well as gene products encoded by other human allelic variants and non-human variants of protective sequence products that can be identified by the methods herein described.
  • protective sequence product variants are protective sequence products comprising amino acid residues encoded by polymo ⁇ hisms of such protective sequence products.
  • protective sequence products of the invention may include proteins that represent functionally equivalent gene products.
  • Functionally equivalent protective sequence products may include, for example, protective sequence products encoded by one of the nucleic acid molecules described in Section 5.1, above. In preferred embodiments, such functionally equivalent protective sequence products are naturally occurring gene products. Functionally equivalent protective sequence products also include gene products that retain at least one of the biological activities of the protective sequence products described above, and/or which are recognized by and bind to antibodies (polyclonal or monoclonal) directed against protective sequence products of the invention. [0081] Equivalent protective sequence products may contain deletions, including internal deletions, additions, including additions yielding fusion proteins, or substitutions of amino acid residues within and/or adjacent to the amino acid sequence encoded by the protective sequence sequences described, above, in Section 5.1.
  • deletions will be deletions of single amino acid residues, or deletions of no more than about 2, 3, 4, 5, 10 or 20 amino acid residues, either contiguous or non-contiguous.
  • additions or substitutions, other than additions that yield fusion proteins will be additions or substitutions of single amino acid residues, or additions or substitutions of no more than about 2, 3, 4, 5, 10 or 20 amino acid residues, either contiguous or non-contiguous.
  • these modifications result in a "silent" change, in that the change produces a protective sequence product with the same activity as the original protective sequence product.
  • nucleic acid changes resulting in amino acid additions or substitutions may also be made for the pu ⁇ ose of modifying the protective sequence product in order to generally enhance their use as therapeutic agents or components for assays, such modifications to include, but not be limited to, stabilizing the product against degradation, enhancing pharmacokinetic properties, modifying site tropisms at the level of cells, tissues, organs, or organisms.
  • Nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine;
  • polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine;
  • positively charged (basic) amino acids include arginine, lysine and histidine;
  • negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
  • non-natural amino acids including, but not limited to, D-amino acids may be used.
  • addition(s), deletion(s) or non-conservative alterations can produce altered, including reduced- activity, protective sequence products.
  • Such alterations can, for example, alter one or more of the biological functions of the protective sequence product.
  • Such alterations can be selected so as to generate protective sequence products that include, but are not limited to, products that are better suited for expression, scale up, etc. in the host cells chosen.
  • cysteine residues can be deleted or substituted with another amino acid residue in order to eliminate disulfide bridges.
  • Protein fragments and/or peptides of the invention may comprise at least as many contiguous amino acid residues as necessary to represent an epitope fragment (that is to be recognized by an antibody directed to the protein). Examples of such protein fragments and/or peptides of the invention are shown by the open reading frames of the protective sequences shown in Figures 4-13, and described in Tables 2-11, respectively. In one nonlimiting embodiment of the invention, such protein fragments or peptides comprise at least about 3 contiguous amino acid residues from a full-length protein.
  • the protein fragments and peptides of the invention can comprise about 5, 8, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450 or more contiguous amino acid residues of a protein.
  • Peptides and/or proteins corresponding to one or more domains of the protein as well as fusion proteins in which a protein, or a portion of a protein such as a truncated protein or peptide or a protein domain, is fused to an unrelated protein are also within the scope of this invention.
  • Such proteins and peptides can be designed on the basis of the nucleic acids disclosed in Section 5.1, above.
  • Fusion proteins include, but are not limited to, IgFc fusions that stabilize the protein or peptide and prolong half-life in vivo; or fusions to any amino acid sequence that allows the fusion protein to be anchored to the cell membrane; or fusions to an enzyme, fluorescent protein, luminescent protein or a epitope tagged protein or peptide that provides a marker function.
  • the protein sequences described above can include a domain, that comprises a protein transduction domain that targets the protective sequence product for delivery to various tissues and more particularly across the brain blood barrier, using, for example, the protein transduction domain of human immunodeficiency virus TAT protein (Schwarze et al, 1999, Science 285: 1569-72).
  • a signal sequence includes a peptide of at least about 15 or 20 amino acid residues in length that occurs at the N-terminus of secretory and membrane-bound proteins and that contains at least about 70% hydrophobic amino acid residues such as alanine, leucine, isoleucine, phenylalanine, proline, tyrosine, tryptophan or valine.
  • a signal sequence contains at least about 10 to 40 amino acid residues, preferably about 19-34 amino acid residues and has at least about 60-80%, more preferably 65-75% and more preferably at least about 70% hydrophobic residues.
  • a signal sequence serves to direct a protein containing such a sequence to a lipid bilayer.
  • a signal sequence of a polypeptide of the invention can be used to facilitate secretion and isolation of the secreted protein or other proteins of interest. Signal sequences are typically characterized by a core of hydrophobic amino acids, which are generally cleaved from the mature protein during secretion in one or more cleavage events. Such signal peptides contain processing sites that allow cleavage of the signal sequence from the mature proteins as they pass through the secretory pathway.
  • polypeptides of the invention pertains to the described polypeptides having a signal sequence (that is, “immature” polypeptides), as well as to the signal sequences themselves and to the polypeptides in the absence of a signal sequence (i.e., the "mature” cleavage products). It is to be understood that polypeptides of the invention can further comprise polypeptides comprising any signal sequence having characteristics as described above and a mature polypeptide sequence.
  • a nucleic acid sequence encoding a signal sequence of the invention can be operably linked in an expression vector to a protein of interest, such as a protein that is ordinarily not secreted or is otherwise difficult to isolate.
  • the signal sequence directs secretion of the protein, such as from a eukaryotic host into which the expression vector is transformed, and the signal sequence is subsequently or concurrently cleaved.
  • the protein can then be readily purified from the extracellular medium by art recognized methods.
  • the signal sequence can be linked to the protein of interest using a sequence that facilitates purification, such as with a GST domain.
  • proteins of the invention also include protein sequences wherein domains encoded by any transcriptional or post-transcriptional, and/or translational or post-translational modifications, or fragments thereof, have been deleted.
  • the polypeptides of the invention can further comprise posttranslational modifications, including, but not limited to glycosylations, acetylations and myrisalations.
  • the protective sequence products, peptide fragments thereof and fusion proteins thereof may be produced by recombinant DNA technology using techniques well known in the art.
  • methods for preparing the protective sequence products, polypeptides, peptides, fusion peptide and fusion polypeptides of the invention by expressing nucleic acid containing protective sequence sequences are described herein. Methods that are well known to those skilled in the art can be used to construct expression vectors containing protective sequence product coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques and in vivo genetic recombination.
  • RNA capable of encoding protective sequence product sequences may be chemically synthesized using, for example, synthesizers. -See, for example, the techniques described in OLIGONUCLEOTIDE SYNTHESIS, 1984, Gait, ed., ERL Press, Oxford. [0092] A variety of host-expression vector systems may be utilized to express the protective sequence product coding sequences of the invention.
  • Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells that may, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the protective sequence product of the invention in situ.
  • These include, but are not limited to, microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing protective sequence product coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing the protective sequence product coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g.
  • baculovirus containing the protective sequence product coding sequences
  • plant cell systems infected with recombinant virus expression vectors e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV
  • recombinant plasmid expression vectors e.g., Ti plasmid
  • mammalian cell systems e.g., COS, CHO, BHK, 293, 3T3 harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionine promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter).
  • a number of expression vectors may be advantageously selected depending upon the use intended for the protective sequence product being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of protective sequence product or for raising antibodies to protective sequence product, for example, vectors that direct the expression of high levels of fusion protein products that are readily purified may be desirable.
  • vectors include, but are not limited to, the E. coli expression vector pUR278 (Ruther et al, 1983, EMBO J.
  • pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S -transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adso ⁇ tion to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • the pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned protective sequence product can be released from the GST moiety.
  • AcNPV is used as a vector to express foreign genes.
  • the virus grows in Spodoptera frugiperda cells.
  • the protective sequence product coding sequence may be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of protective sequence product coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene).
  • recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed, (e.g., see Smith, et al, 1983, J. Virol. 46:584; Smith, U.S. Patent No. 4,215,051).
  • a number of viral-based expression systems may be utilized.
  • the protective sequence product coding sequence of interest may be ligated to an adenovirus transcription translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination.
  • Insertion in a non-essential region of the viral genome will result in a recombinant virus that is viable and capable of expressing protective sequence products in infected hosts.
  • a recombinant virus that is viable and capable of expressing protective sequence products in infected hosts.
  • Specific initiation signals may also be required for efficient translation of inserted protective sequence product coding sequences. These signals include the ATG initiation codon and adjacent sequences. In cases where an entire protective sequence, including its own initiation codon and adjacent sequences, is inserted into the appropriate expression vector, no additional translational control signals may be needed.
  • exogenous translational control signals including, perhaps, the ATG initiation codon
  • the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert.
  • exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc (see Bittner, et al, 1987, Methods in Enzymol. 153:516-544).
  • a host cell strain may be chosen that modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein.
  • Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.
  • eukaryotic host cells that possess the cellular machinery for proper processing of the primary transcript, glycosylation and phosphorylation of the gene product may be used.
  • Such mammalian host cells include, but are not limited to, CHO, VERO, BHK, HeLa, COS, MDCK, 293, 3T3 and WI38.
  • stable expression is preferred.
  • cell lines that stably express the protective sequence product may be engineered.
  • host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells may be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media.
  • the selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci that in turn can be cloned and expanded into cell lines.
  • This method may advantageously be used to engineer cell lines that express the protective sequence product.
  • Such engineered cell lines may be particularly useful in screening and evaluation of compounds that affect the endogenous activity of the protective sequence product.
  • a number of selection systems may be used, including, but not limited to, the he ⁇ es simplex virus thymidine kinase (Wigler, et al, 1977, Cell 11 :223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska and Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48:2026), and adenine phosphoribosyltransferase (Lowy, et al, 1980, Cell 22:817) genes can be employed in tk " , hgprf or aprt " cells, respectively.
  • antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler, et al, 1980, Proc. Natl. Acad. Sci. USA 77:3567; O'Hare, et al, 1981, Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan and Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Colberre- Garapin, et al, 1981, J. Mol. Biol. 150:1); and hygro, which confers resistance to hygromycin (Santerre, et al, 1984, Gene 30: 147).
  • an endogenous protective sequence within a cell line or microorganism may be modified by inserting a heterologous DNA regulatory element into the genome of a stable cell line or cloned microorganism such that the inserted regulatory element is operatively linked with the endogenous protective sequence.
  • a heterologous DNA regulatory element for example, an endogenous protective sequence that is normally "transcriptionally silent", i.e., a protective sequence that is normally not expressed, or is expressed only at very low levels in a cell line or microorganism, may be activated by inserting a regulatory element that is capable of promoting the expression of a normally expressed protective sequence product in that cell line or microorganism.
  • a transcriptionally silent, endogenous protective sequence may be activated by insertion of a promiscuous regulatory element that works across cell types.
  • Methods which are well known to those skilled in the art, can be used to construct vectors containing the protective sequence operatively associated with appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA techniques, and synthetic techniques. See, for example, the techniques described in Sambrook, et al, 1992, MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Laboratory, N.Y. and Ausubel et al., 1989, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Greene Publishing Associates & Wiley Interscience, N.Y.
  • the protective sequences may be associated operatively with a variety of different promoter/enhancer elements.
  • the expression elements of these vectors may vary in their strength and specificities. Depending on the host/vector system utilized, any one of a number of suitable transcription and translation elements may be used.
  • the promoter may be in the form of the promoter that is associated naturally with the gene of interest.
  • the DNA may be positioned under the control of a recombinant or heterologous promoter, i.e., a promoter that is not associated normally with that gene.
  • tissue specific promoter/enhancer elements may be used to regulate the expression of the transferred DNA in specific cell types.
  • transcriptional control regions that exhibit tissue specificity that have been described and could be used, include, but are not limited to: choline acetyltransferase (ChAT) gene control region that is active in cholinergic cells in the brain (Lonnerberg et al, 1996, J. Biol. Chem. 271:33358-65; Lonnerberg et al, 1995, Proc. Natl. Acad. Sci. U.S.A. 92: 4046-50; Ibenez and Perrson, 1991 Eur. J. Neurosci.
  • ChAT choline acetyltransferase
  • mice Thy-1.2 gene control region that is active in adult neurons including hippocampus, thalamus, cerebellum, cortex, RGC, DRG, and MN in the brain (Caroni, 1997, J. Neurosci. Meth. 71 : 3-9; Vidal et al, 1990, EMBO J9: 833-40), neuron specific enolase (NSE) gene control region that is active in pan-neuronal, neuron specific, deep layers of cerebral and neocortex (not in white matter) areas of the brain (Hannas-Djebbara et al, 1997, Brain Res. Mol. Brain Res.
  • NSE neuron specific enolase
  • beta-globin gene control region that is active in myeloid cells
  • myelin basic protein gene control region that is active in oligodendrocyte cells in the brain
  • myosin light chain-2 gene control region that is active in skeletal muscle
  • gonadotropic releasing hormone gene control region that is active in the hypothalamus
  • Promoters isolated from the genome of viruses that grow in mammalian cells may be used, as well as promoters produced by recombinant DNA or synthetic techniques.
  • promoters specifically activated within bone i.e., the osteocalcin promoter, that is specifically activated within cells of osteoblastic lineage, may be used to target expression of nucleic acids within bone cells.
  • a heterologous regulatory element may be inserted into a stable cell line or cloned microorganism, such that it is operatively linked with an endogenous protective sequence, using techniques, such as targeted homologous recombination, that are well known to those of skill in the art, and described e.g., in Chappel, U.S. Patent No. 5,272,071; PCT publication No. WO 91/06667, published May 16, 1991.
  • utilizing an antibody specific for the fusion protein being expressed may readily purify any fusion protein. For example, a system described by Janknecht, et al.
  • the protective sequence products can also be expressed in transgenic animals.
  • Animals of any species including, but not limited to, mice, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, sheep, cows and non-human primates, e.g., baboons, monkeys and chimpanzees may be used to generate transgenic animals.
  • transgenic refers to animals expressing protective sequences from a different species (e.g.
  • mice expressing human protective sequences as well as animals that have been genetically engineered to overexpress endogenous (i.e., same species) sequences or animals that have been genetically engineered to no longer express endogenous protective sequences (i.e., "knock-out” animals), and their progeny.
  • Any technique known in the art may be used to introduce a protective sequence transgene into animals to produce the founder lines of transgenic animals. Such techniques include, but are not limited to, pronuclear microinjection (Hoppe and Wagner, 1989, U.S. Pat. No. 4,873,191); retrovirus mediated gene transfer into germ lines (Van der Putten, et al, 1985, Proc. Natl. Acad.
  • transgenic animal clones containing a protective sequence transgene for example, nuclear transfer into enucleated oocytes of nuclei from cultured embryonic, fetal or adult cells induced to quiescence (Campbell, et al, 1996, Nature 380:64-66; Wilmut, et al, Nature 385:810- 813).
  • the present invention provides for transgenic animals that carry a protective sequence transgene in all their cells, as well as animals that carry the transgene in some, but not all their cells, i.e., mosaic animals.
  • the transgene may be integrated as a single transgene or in concatamers, e.g., head-to-head tandems or head-to-tail tandems.
  • the transgene also may be selectively introduced into and activated in a particular cell type by following, for example, the teaching of Lasko et al. (Lasko, et al, 1992, Proc. Natl. Acad. Sci. USA 89:6232-6236).
  • the regulatory sequences required for such a cell- type specific activation will depend on the particular cell type of interest, and will be apparent to those of skill in the art.
  • gene targeting is preferred.
  • vectors containing some nucleic acids homologous to the endogenous protective sequence are designed for the pu ⁇ ose of integrating, via homologous recombination with chromosomal sequences, into and disrupting the function of the nucleic acid of the endogenous protective sequence.
  • the transgene also may be selectively introduced into a particular cell type, thus inactivating the endogenous protective sequence in only that cell type, by following, for example, the teaching of Gu, et al. (Gu, et al, 1994, Science 265, 103-106).
  • the regulatory sequences required for such a cell-type specific inactivation will depend on the particular cell type of interest, and will be apparent to those of skill in the art.
  • the expression of the recombinant protective sequence may be assayed utilizing standard techniques. Initial screening may be accomplished by Southern blot analysis or PCR techniques to analyze animal tissues to assay whether integration of the transgene has taken place.
  • the level of mRNA expression of the transgene in the tissues of the transgenic animals may also be assessed using techniques that include, but are not limited to, Northern blot analysis of tissue samples obtained from the animal, in situ hybridization analysis and RT-PCR (reverse transcriptase PCR). Samples of protective sequence-expressing tissue also may be evaluated immunocytochemically using antibodies specific for the transgene product.
  • Protective proteins can be used, e.g., to treat cell death-related conditions, disorders, or diseases.
  • Such protective sequence products include, but are not limited to, soluble derivatives such as peptides or polypeptides corresponding to one or more domains of the protective sequence product that are modified such that they are deleted for one or more hydrophobic domains.
  • nucleotide constructs encoding such protective sequence products can be used to genetically engineer host cells to express such protective sequence products in vivo; these genetically engineered cells can function as "bioreactors" in the body delivering a continuous supply of protective sequence product, peptides and soluble polypeptides.
  • Described herein are methods for the production of antibodies capable of specifically recognizing one or more protective sequence product epitopes or epitopes of conserved variants or peptide fragments of the protective sequence products of the invention. Further, antibodies that specifically recognize mutant forms of the protective sequence products of the invention are encompassed by the invention.
  • the terms “specifically bind” and “specifically recognize” refer to antibodies that bind to protective sequence product epitopes involved in conditions, disorders, or diseases involving cell death at a higher affinity than they bind to protective sequence product epitopes not involved in such conditions, disorders, or diseases (e.g., random epitopes).
  • Such antibodies may include, but are not limited to, polyclonal antibodies, monoclonal antibodies (mAbs), humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab') 2 fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies and epitope-binding fragments of any of the above.
  • mAbs monoclonal antibodies
  • Such antibodies may be used, for example, in the detection of a protective sequence product in a biological sample and may, therefore, be utilized as part of a diagnostic or prognostic technique whereby patients may be tested for abnormal levels of protective sequence products, and/or for the presence of abnormal forms of such protective sequence products.
  • Such antibodies also may be utilized in conjunction with, for example, compound screening schemes, as described, below, in Section 5.4.2, for the evaluation of the effect of test compounds on protective sequence product levels and/or activity. Additionally, such antibodies can be used in conjunction with the gene therapy techniques described below, in Section 5.4.1.3., to evaluate, for example, the normal and/or engineered cells prior to their introduction into the patient.
  • Antibodies derived from the protective sequence or protective sequence product including, but not limited to, antibodies and anti-idiotypic antibodies that mimic activity or function additionally may be used in methods for inhibiting abnormal protective sequence product activity. Thus, such antibodies may, therefore, be utilized as part of treatment methods for protective sequence product-mediated conditions, disorders, or diseases.
  • various host animals may be immunized with a protective sequence or protective sequence product, or a portion thereof.
  • Such host animals may include, but are not limited to, rabbits, mice and rats, to name but a few.
  • adjuvants may be used to increase the immunological response, depending on the host species, including, but not limited to, Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.
  • BCG Bacille Calmette-Guerin
  • Monoclonal antibodies which are homogeneous populations of antibodies to a particular antigen, may be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique of Kohler and Milstein, (1975, Nature 256:495-497; and U.S. Patent No. 4,376,110), the human B-cell hybridoma technique (Kosbor et al, 1983, Immunology Today 4:72; Cole et al, 1983, Proc. Natl. Acad. Sci.
  • Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof.
  • the hybridoma producing the mAb of this invention may be cultivated in vitro or in vivo. Production of high titers of mAbs in vivo makes this the presently preferred method of production.
  • chimeric antibodies In addition, techniques developed for the production of "chimeric antibodies" (Morrison, et al, 1984, Proc. Natl. Acad. Sci., 81 :6851-6855; Neuberger, et al, 1984, Nature 312:604-608; Takeda, et al, 1985, Nature, 314:452-454) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used.
  • a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region.
  • An immunoglobulin light or heavy chain variable region consists of a "framework" region interrupted by three hypervariable regions, referred to as complementarily determining regions (CDRs).
  • humanized antibodies are antibody molecules from non-human species having one or more CDRs from the non-human species and a framework region from a human immunoglobulin molecule.
  • techniques described for the production of single chain antibodies U.S. Patent 4,946,778; Bird, 1988, Science 242:423-426; Huston, et al, 1988, Proc. Natl. Acad. Sci.
  • Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide.
  • Antibody fragments that recognize specific epitopes may be generated by known techniques. For example, such fragments include, but are not limited to: the F(ab') 2 fragments, which can be produced by pepsin digestion of the antibody molecule and the Fab fragments, which can be generated by reducing the disulfide bridges of the F(ab') 2 fragments.
  • Fab expression libraries may be constructed (Huse, et al, 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. 5.4 Uses of the Protective Sequences, Protective Sequence Products and Antibodies
  • the application relates to compositions and methods for the treatment of conditions, disorders, or diseases involving cell death.
  • Such applications include, but are not limited to, the prophylactic or therapeutic use of protective sequences that, when introduced into a cell predisposed to undergo cell death or in the process of dying, to prevent, delay, or rescue a cell, cells, tissue, organs, or organisms from dying, as described below in Section 5.4.1
  • such applications include methods for the treatment of conditions, disorders, or diseases involving cell death, including, but not limited to, those associated with the central nervous system including neurological and psychiatric conditions, disorders, or diseases, and others as described below, in Section 5.4.1.1, and for the identification of compounds that modulate the expression of the protective sequence and/or the synthesis or activity of the protective sequence product, as described below, in Section 5.4.1.
  • Such compounds can include, for example, other cellular products that are involved in such processes as the regulation of cell death. These compounds can be used, for example, in the amelioration of conditions, disorders, or diseases involving cell death.
  • One example of the type of injury that can cause cell death in neuronal cells is stroke, which often is the result of ischemic injury.
  • a relatively broad time window (8 hours to perhaps several days or longer) exists between the onset of ischemic injury (i.e. cessation or marked reduction in blood flow) before most neural cells actually die.
  • These delayed biochemical intervention points represent ideal clinical intervention points as they correspond to the time period during which most stroke patients present for medical treatment.
  • vascular dementia multi-infarct dementia
  • vascular dementia a repetitive process of small blood vessel diseases induces regional brain cell death, leading to a progressive loss of cognitive abilities.
  • a partial list of other brain diseases that activate brain cell death pathways similar to those observed in stroke include, but are not limited to, Parkinson's disease, traumatic injury, Down's syndrome, Huntington's disease, HIV infection and intracranial infections.
  • One notable example from the preceding list is physical trauma to the nervous system. Although such trauma can be caused by a multitude of different physical insults to the head, neck, spine and other parts of the nervous system, all result in focal damage to, and death of, neural tissue and its component cells. Focally damaged areas behave similarly to stroke- induced infarcts in that a wider area of neural damage and death, a penumbra, is induced via biochemical and cellular mechanisms that are similar or identical to those occurring in stroke.
  • methods of the invention include, for example, modulating the expression of the protective sequence and/or the activity of the protective sequence product for the treatment of conditions, disorders, or diseases involving cell death that are normally mediated by some other gene.
  • Such diagnostic and prognostic methods may, for example, utilize reagents such as the protective nucleic acids described in Section 5.1, and antibodies directed against protective sequence products, including peptide fragments thereof, as described, above, in Section 5.3. [0131] Specifically, such reagents may be used, for example, for: [0132] (1) the detection of the presence of protective sequence mutations, or the detection of either over- or under-expression of the protective sequence relative to wild- type levels of expression;
  • Protective nucleic acids can, for example, be used to diagnose a condition, disorder, or disease involving cell death using, for example, the techniques for mutation/polymo ⁇ hism detection described above in Section 5.1.
  • Mutations at a number of different genetic loci may lead to phenotypes related to conditions, disorders, or diseases involving cell death.
  • the treatment of patients suffering from such conditions, disorders, or diseases will be designed to target the particular genetic loci containing the mutation mediating the condition, disorder, or disease.
  • Genetic polymo ⁇ hisms have been linked to differences in drug effectiveness.
  • identification of alterations in protective sequence, protein or gene flanking regions can be utilized in pharmacogenetic methods to optimize therapeutic drug treatments.
  • alterations i.e., polymo ⁇ hisms, in the protective sequence or protein encoded by genes comprising such polymo ⁇ hisms, are associated with a drug or drugs' efficacy, tolerance or toxicity, and may be used in pharmacogenomic methods to optimize therapeutic drug treatments, including therapeutic drug treatments for one of the conditions, disorders, or diseases described herein contained in Section 5.4.1.1, e.g., central nervous system conditions, disorders, or diseases.
  • Such polymo ⁇ hisms can be used, for example, to refme the design of drugs by decreasing the incidence of adverse events in drug tolerance studies, e.g., by identifying patient subpopulations of individuals who respond or do not respond to a particular drug therapy in efficacy studies, wherein the subpopulations have a polymo ⁇ hism associated with drug responsiveness or unresponsiveness.
  • the pharmacogenomic methods of the present invention also can provide tools to identify new drug targets for designing drugs and to optimize the use of already existing drugs, e.g., to increase the response rate to a drug and/or to identify and exclude non-responders from certain drug treatments (e.g., individuals having a particular polymo ⁇ hism associated with unresponsiveness or inferior responsiveness to the drug treatment) or to decrease the undesirable side effects of certain drug treatments and/or to identify and exclude individuals with marked susceptibility to such side effects (e.g., individuals having a particular polymo ⁇ hism associated with an undesirable side effect to the drug treatment).
  • certain drug treatments e.g., individuals having a particular polymo ⁇ hism associated with unresponsiveness or inferior responsiveness to the drug treatment
  • to decrease the undesirable side effects of certain drug treatments e.g., individuals having a particular polymo ⁇ hism associated with an undesirable side effect to the drug treatment.
  • polymo ⁇ hisms in the protective sequence or flanking this sequence, or variations in protective sequence expression, or activity may be utilized to identify an individual having a disease or condition resulting from a disorder involving cell death and thus define the most effective and safest drug treatment.
  • Assays such as those described herein may be used to identify such polymo ⁇ hisms or variations in protective sequence expression or activity.
  • any nucleated cell can be used as a starting source for genomic nucleic acid.
  • any cell type or tissue in which the protective sequence is expressed may be utilized.
  • kits for detecting the presence of a polypeptide or nucleic acid of the invention in a biological sample i.e., a test sample.
  • kits for detecting the presence of a polypeptide or nucleic acid of the invention in a biological sample i.e., a test sample.
  • Such kits can be used, e.g., to determine if a subject is suffering from or is at increased risk of developing a condition, disorder, or disease associated with a disorder-causing allele, or aberrant expression or activity of a polypeptide of the invention.
  • the kit can comprise a labeled compound or agent capable of detecting the polypeptide or mRNA or DNA or protective sequence sequences, e.g., encoding the polypeptide in a biological sample.
  • the kit can comprise further a means for determining the amount of the polypeptide or mRNA in the sample (e.g., an antibody that binds the polypeptide or an oligonucleotide probe that binds to DNA or mRNA encoding the polypeptide).
  • Kits can also include instructions for observing that the tested subject is suffering from, or is at risk of developing, a condition, disorder, or disease associated with aberrant expression of the polypeptide if the amount of the polypeptide or mRNA encoding the polypeptide is above or below a normal level, or if the DNA correlates with presence of an allele that causes a condition, disorder, or disease.
  • the kit can comprise, for example: (1) a first antibody (e.g., attached to a solid support) that binds to a polypeptide of the invention; and, optionally, (2) a second, different antibody that binds to either the polypeptide or to the first antibody and is conjugated to a detectable agent.
  • a first antibody e.g., attached to a solid support
  • a second, different antibody that binds to either the polypeptide or to the first antibody and is conjugated to a detectable agent.
  • the kit can comprise, for example: (1) an oligonucleotide (e.g., a detectably labeled oligonucleotide) that hybridizes to a nucleic acid sequence encoding a polypeptide of the invention, or (2) a pair of primers useful for amplifying a nucleic acid molecule encoding a polypeptide of the invention.
  • the kit also can comprise, for example, one or more buffering agents, preservatives or protein stabilizing agents.
  • the kit also can comprise components necessary for detecting the detectable agent (e.g., an enzyme or a substrate).
  • the kit can contain also a control sample or a series of control samples that can be assayed and compared to the test sample.
  • Each component of the kit usually is 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 condition, disorder, or disease associated with polymo ⁇ hisms that correlate with alleles that cause conditions, disorders, or diseases involving cell death, and/or aberrant levels of mRNA, polypeptides or activity.
  • the application relates to the compositions and methods for the development of screening assays for the identification of compounds, described in Section 5.4.2 below, which interact with or modulate protective sequences, protective sequence products, genes, gene products, and/or their regulatory elements.
  • This application relates to compositions and methods for the treatment of conditions, disorders, or diseases involving cell death.
  • Such applications include, but are not limited to, the prophylactic or therapeutic use of protective sequences, protective sequence products, genes, gene products, or the regulatory elements, target sequences, or variants of any of the aforementioned sequences or products, which, when introduced into a cell predisposed to undergo cell death or in the process of dying, prevent, delay, or rescue a cell, cells, tissue, organs, or organisms from dying.
  • the application further relates to the methods and compositions whereby a condition, disorder, or disease involving cell death, including but not limited to, the conditions, disorders, or diseases mentioned in Section 5.4.1.1, may be treated wherein such methods can comprise administering antibodies, antisense molecules or sequences, ribozyme molecules, or other inhibitors or modulators directed against such protective sequences, protective sequence products, genes, gene products, or the regulatory elements, target sequences, or variants of any of the aforementioned sequences or products.
  • compositions and methods for those instances whereby the condition, disorder, or disease involving cell death results from protective sequence mutations can comprise supplying the subject with a nucleic acid molecule encoding an unimpaired protective sequence product such that an unimpaired protective sequence product is expressed and the cell, cells, tissue, organ, organism displaying symptoms of the condition, disorder, or disease is prevented, delayed, or rescued from death.
  • such methods can comprise supplying the subject with a cell comprising a nucleic acid molecule that encodes an unimpaired protective sequence product such that the cell expresses the unimpaired protective sequence product and the cell, cells, tissue, organ, or organism displaying symptoms of the condition, disorder, or disease is prevented, delayed, or rescued from death.
  • protective sequence product activity In cases in which a loss of normal protective sequence product function results in the development of a condition, disorder, or disease involving cell death, an increase in protective sequence product activity would facilitate progress towards an asymptomatic state in individuals exhibiting a deficient level of protective sequence expression and/or gene product activity.
  • Methods for enhancing the expression or synthesis of protective sequence product can include, for example, methods such as those described below, in Section 5.4.1.3.
  • symptoms of a condition, disorder, or disease involving cell death may be prevented, delayed, or rescued by administering a compound that decreases the level of protective sequence expression and/or gene product activity.
  • Methods for inhibiting or reducing the level of protective sequence product synthesis or expression can include, for example, methods such as those described in Section 5.4.1.2.
  • modulating including but not limited to, mimicking, agonizing, or antagonizing the expression of a protective sequence and/or the activity of a protective sequence product, or their regulatory elements, can be used for the treatment of the condition, disorder, or disease involving cell death.
  • protective sequences are nucleic acid molecules comprising nucleic acid sequences that, when introduced into a cell predisposed to undergo cell death, prevent, delay, or rescue such cell death relative to a corresponding cell into which no exogenous protective sequence has been introduced.
  • the proteins and peptides that may be used in the methods of the invention include synthetic (e.g., recombinant or chemically synthesized) proteins and peptides, as well as naturally occurring proteins and peptides.
  • the proteins and peptides may have both naturally occurring and non-naturally occurring amino acid residues (e.g., D-amino acid residues) and/or one or more non-peptide bonds (e.g., imino, ester, hydrazide, semicarbazide, and azo bonds).
  • the proteins or peptides may also contain additional chemical groups (i.e., functional groups) present at the amino and/or carboxy termini, such that, for example, the stability, bioavailability, and/or inhibitory activity of the peptide is enhanced.
  • exemplary functional groups include hydrophobic groups (e.g.
  • the types of conditions, disorders, or diseases that can be prevented, delayed, or rescued by the compounds and methods of the present invention include, but are not limited to, those associated with the central nervous system including neurological and psychiatric conditions, disorders, or diseases; those of the peripheral nervous system; conditions, disorders, or diseases caused by physical injury; conditions, disorders, or diseases of the blood vessels or heart; conditions, disorders, or diseases of the respiratory system; neoplastic conditions, disorders, or diseases; conditions, disorders, or diseases of blood cells; conditions, disorders, or diseases of the gastrointestinal tract; conditions, disorders, or diseases of the liver; conditions, disorders, or diseases of the pancreas; conditions, disorders, or diseases of the kidney; conditions, disorders, or diseases of the ureters, urethra or bladder; conditions, disorders, or diseases of the male genital system; conditions, disorders, or diseases of the female genital tract; conditions, disorders, or diseases of the breast; conditions, disorders, or diseases
  • Conditions, disorders, or diseases involving the central nervous system include, but are not limited to, common pathophysiologic complications such as increased intracraneal pressure and cerebral hemiation, septic embolism, cerebral edema, suppurative endovasculitis and hydrocephalus; infections such as meningitis, acute meningitis, acute lymphocytic meningitis, chronic meningitis, purulent meningitis, syphilitic gumma, encephalitis, cerebral abscess, epidural abscess, subdural abscess, brain abscess, viral encephalitis, acute viral encephalitis, encephalomeningitis, aseptic meningitis, post-infectious encephalitis, subacute encephalitis, chronic encephalitis, chronic meningitis, chronic encephalomeningitis, slow virus diseases and unconventional agent encephalopathies; protozoal infections such as malaria, toxoplasmosis, am
  • Conditions, disorders, or diseases of the peripheral nervous system include, but are not limited to, peripheral neuropathy, acute idiopathic polyneuropathy, diabetic neuropathy and peripheral nerve tumors.
  • Conditions, disorders, or diseases caused by physical injury include, but are not limited to, the direct, indirect, immediate, or delayed effects of: changes in temperature such as frostbite and thermal bums; an increase in atmospheric pressure such as air blast or immersion blast caused by an explosion; a decrease in atmospheric pressure such as caisson disease or high-altitude hypoxia; mechanical violence from penetrating or non-penetrating traumatic injury; electromechanical energy such as radiation injury from either charged particles or electromagnetic waves; electrocution or non-ionizing radiation such as radio waves, microwaves, laser light or ultrasound.
  • Conditions, disorders, or diseases of the blood vessels or heart include, but are not limited to, hypertension (high blood pressure), heart failure; ischemic or atherosclerotic heart disease; myocardial infarction; cardiac arrest; hypertensive heart disease; cor pulmonale; valvular heart disease such as that caused by rheumatic fever, aortic valve stenosis, mitral annulus calcification, carcinoid heart disease, nonbacterial thrombotic endocarditis, or nonbacterial verrucous endocarditis; infectious endocarditis caused by organisms including, but not limited to, Streptococcus species, Staphylococcus species, enterococci, pneumococci, gram-negative rods, Candida species, Aspergillus species, or culture-negative endocarditis; congenital heart disease such as atrial septal defect, ventricular septal defect, patent ductus arteriosis, coarctation of the aorta, Tetralogy of Fall
  • Conditions, disorders, or diseases of the respiratory system include, but are not limited to, pulmonary congestion; heart failure; embolism; infarction; pulmonary hypertension; adult respiratory distress syndrome (ARDS); obstructive lung disease; restrictive lung disease; chronic obstructive pulmonary disease; asthma; sarcoidosis; diffuse interstitial or infiltrative lung diseases including, but not limited to, idiopathic pulmonary fibrosis, pneumoconiosis, hypersensitivity pneumonitis, Goodpasture's syndrome, idiopathic pulmonary hemosiderosis, collagen- vascular diseases, or pulmonary eosinophilia; serofibrinous pleuritis; suppurative pleuritis; hemorrhagic pleuritis; pleural effusions; pneumothorax; hemothorax or pneumohemothorax.
  • Neoplastic conditions, disorders, or diseases include, but are not limited to, benign tumors composed of one parenchymal cell type such as fibromas, myxomas, lipomas, hemangiomas, meningiomas, leiomyomas, adenomas, nevi, moles, or papillomas; benign mixed tumors derived from one germ layer such as a mixed tumor of salivary gland origin; benign mixed tumors derived from more than one germ layer such as a teratoma; primary malignant tumors or metastases of malignant tumors composed of one parenchymal cell type such as sarcomas, Ewing's tumor, leukemia, myeloma, histiocytosis X, Hodgkin's disease, lymphomas, carcinomas, melanomas, bronchial adenoma, small cell lung cancer, or seminoma; primary malignant tumors or metastases of mixed malignant tumors derived from one germ layer such as Wilms' tumor
  • Conditions, disorders, or diseases of blood cells include, but are not limited to, anemia due to one or more of the following conditions: acute blood loss, chronic blood loss, hemolytic anemia, sickle cell disease, thalassemia syndromes, autoimmune hemolytic anemia, traumatic anemia, or diminished erythropoesis from megaloblastic anemia, iron deficiency, aplastic anemia, idiopathic bone marrow failure; polycythemia; hemorrhagic diatheses related to increased vascular fragility; hemorrhagic diatheses related to a reduction in platelets; idiopathic or thrombotic thrombocytopenic pu ⁇ ura; hemorrhagic diatheses related to defective platelet function; hemorrhagic diatheses related to abnormalities in clotting factor(s); disseminated intravascular coagulation (DIC); neutropenia; agranulocytosis; leukocytosis; plasma cell dyscrasias
  • Conditions, disorders, or diseases of the gastrointestinal tract include, but are not limited to, congenital anomalies such as atresia, fistulas, or stenosis; periodontal disease; periapical disease; xerostomia; necrotizing sialometaplasia; esophageal rings or webs; hernia; Mallory- Weiss syndrome; esophagitis; diverticulosis; diverticulitis; scleroderma; esophageal varices; acute or chronic gastritis; peptic ulcer; gastric erosion or ulceration; ischemic bowel disease; infarction; embolism; Crohn's disease; obstruction from foreign bodies, hernia, adhesion, intussusception, or volvulus; ileus; megacolon; angoidysplasia; ulcerative colitis; psuedomembranous colitis; or polyps.
  • congenital anomalies such as atresi
  • Conditions, disorders, or diseases of the liver include, but are not limited to, acute hepatic failure due to one of more of metabolic, circulatory, toxic, microbial, or neoplastic causes; chronic hepatic failure due to one or more of metabolic, circulatory, toxic, microbial, or neoplastic causes; hereditary hyperbilirubinemias; infarct; embolism; hepatic circulation thrombosis or obstruction; fulminant hepatic necrosis; portal hypertension; alcoholic liver disease; post-necrotic cirrhosis; biliary cirrhosis; cirrhosis associated with alpha- 1-antitrypsin deficiency; Wilson's disease; or Reye's syndrome.
  • Conditions, disorders, or diseases of the pancreas include, but are not limited to, congenital aberrant pancreas, congenital anomalies of pancreatic ducts, stromal fatty infiltration, pancreatic atrophy, acute hemorrhagic pancreatitis, chronic pancreatitis, chronic calcifying pancreatitis, chronic obstructive pancreatitis, pancreatic psuedocyst, diabetes mellitus, or gestational diabetes.
  • Conditions, disorders, or diseases of the kidney include, but are not limited to, congenital anomalies; polycystic renal disease; dialysis-associated cystic disease; glomerular disease, including, but not limited to, acute glomerulonephritis, acute proliferative glomerulonephritis, rapidly progressive glomerulonephritis, postinfectious rapidly progressive glomerulonephritis, Goodpasture's syndrome, idiopathic rapidly progressive glomerulonephritis, nephrotic syndrome, membranous glomerulonephritis, lipoid nephrosis, focal segmental glomerulosclerosis, membranoproliferative glomerulonephritis, focal proliferative glomerulonephritis, chronic glomerulonephritis, or hereditary nephritis; acute tubular necrosis; acute renal failure; tubulointerstitial diseases including, but not limited to, pyelonep
  • Conditions, disorders, or diseases of the ureters, urethra or bladder include, but are not limited to, congenital anomalies; inflammatory diseases; physical obstruction by causes including, but not limited to calculi, strictures, neoplasia, blood clot, or pregnancy; sclerosing retroperitonitis; acute cystitis; chronic cystitis; interstitial cystitis; emphysematous cystitis; eosinophilic cystitis; encrusted cystitis; fistula; or neurogenic bladder.
  • Conditions, disorders, or diseases of the male genital system include, but are not limited to, congenital anomalies; balanoposthitis; condyloma; phimosis; paraphimosis; dysplastic epithelial lesions; nonspecific epididymitis or orchitis; granulomatous orchitis; torsion of the testis or its vascular supply; granulomatous prostatitis; acute or chronic prostatitis; or benign prostatic hype ⁇ lasia.
  • Conditions, disorders, or diseases of the female genital tract include, but are not limited to, congenital anomalies, lichen scleroses, acute cervicitis, chronic cervicitis, cervical polyps; acute endometritis; chronic endometritis; endometriosis; dysfunctional uterine bleeding; endometrial hype ⁇ lasia; senile cystic endometrial atrophy; salpingitis; polycystic ovary disease; pre-eclampsia or eclampsia (toxemia of pregnancy); placentitis; threatened abortion; or ectopic pregnancy.
  • Conditions, disorders, or diseases of the breast include, but are not limited to, congenital anomalies, acute mastitis, chronic mastitis, galactocele, granulomas, traumatic fat necrosis, mammary duct ectasia, fibrocystic disease, sclerosing adenitis, epithelial hype ⁇ lasia, hypertrophy, or gynecomastia.
  • Conditions, disorders, or diseases of the endocrine system include, but are not limited to, congenital anomalies; Sheehan's pituitary necrosis; empty sella syndrome; hyperthyroidism (thyrotoxicosis) from causes including, but not limited to, Graves' disease, toxic multinodular goiter, toxic adenoma, acute or subacute thyroiditis, TSH- secreting tumor, neonatal thyrotoxicosis, iatrogenic thyrotoxicosis; Hashimoto's thyroiditis; hypothyroidism (cretinism or myxedema) from causes including, but not limited to, surgical or radioactive ablation, primary idiopathic myxedema, iodine deficiency, goitrogenic agents, hypopituitarism, hypothalamic lesions, TSH resistance, subacute thyroiditis, or chronic thyroiditis; diffuse nontoxic simple or multinodular goiter; multiple
  • Conditions, disorders, or diseases of the skin or mucosa include, but are not limited to, melanocytic proliferative disorders; inflammatory dermatoses including, but not limited to, eczematous dermatitis, urticaria, erythema multiforme, cutaneous necrotizing vasculitis, cutaneous lupus erythematosus, graft-versus-host disease, panniculitis, acne vulgaris, rosacea, lichen planus, lichen sclerosus et atrophicus, pityriasis, psoriasis, or parapsoriasis; blistering diseases including, but not limited to, pemphigus, bullous pemphigoid, dermatitis he ⁇ etiformis, or po ⁇ hyria.
  • Conditions, disorders, or diseases of the musculoskeletal system include, but are not limited to, muscular atrophy; segmental necrosis; myo
  • Fascioscapulohumeral Limb-Girdle, myotonic dystrophy, or ocular myopathy; congenital myopathies; myasthenia gravis; traumatic myositis ossificans; nodular fasciitis; desmoid tumors; palmar fibromatosis; congenital bone disorders including, but not limited to, osteogenesis imperfecta, achondroplasia, osteopetrosis, osteochondromatosis, endochondromatosis; osteomyelitis; fractures; osteoporosis; osteomalacia; bony changes secondary to hype ⁇ arathyroidism; Paget's disease; hypertrophic osteoarthropathy; fibrous dysplasia; or nonossifying fibroma.
  • Conditions, disorders, or diseases causing a fluid or hemodynamic derangement include, but are not limited to, systemic edema; anasarca; edema from increased hydrostatic pressure including, but not limited to congestive heart failure, cirrhosis of the liver, constrictive pericarditis, venous obstruction; edema from reduced oncotic pressure including, but not limited to, cirrhosis of the liver, malnutrition, protein- losing renal disease, protein-losing gastroenteropathy, protein loss through increased vascular permeability; edema from lymphatic obstruction including, but not limited to, cancer, inflammatory injury, surgical injury, traumatic injury, or radiation injury; edema from increased osmotic tension in the interstitial fluid including, but not limited to, sodium retention from excessive salt intake or increased renal sodium retention, reduced renal perfusion, acute or chronic renal failure, acute or chronic renal insufficiency; edema from increased endothelial permeability including, but not limited to, inflammation, shock
  • Inherited conditions, disorders, or diseases include, but are not limited to,
  • Down's syndrome Edwards' syndrome, Patau's syndrome, other trisomies, Cri du Chat syndrome, Klinefelter's syndrome, XYY syndrome, Turner's syndrome, Multi-X female syndrome, hermaphrodism or pseudohermaphrodism, Marfan's syndrome, neurofibromatosis, vonHippel-Lindau disease, familial hypercholesterolemia, albinism, alkaptonuria, Fabry's disease, Fragile-X syndrome, Ehlers-Danlos syndromes, inherited neoplastic syndromes, inherited autosomal dominant conditions, Huntington's disease, Alport's disease, sickle-cell disease, thalessemia, tuberous sclerosis, vonWillebrand's disease, polycystic kidney disease, Pompe's disease, GMl-gangliosidosis; Tay-Sachs disease, Sandhoff-Jatzkewitz disease, metachromatic leukodystrophy, multiple sufatase deficiency,
  • Conditions, disorders, or diseases of the immune system or spleen include, but are not limited to, Type I hypersensitivity conditions (anaphylaxis and other basophil or mast cell mediated conditions), Type II hypersensitivity conditions (cytotoxic conditions involving phagocytosis or lysis of target cell), Type III hypersensitivity conditions (immune complex conditions involving antigen-antibody complexes), Type TV hypersensitivity conditions (cell-mediated conditions), transplant rejection, systemic lupus erythematosus, Sjogren's syndrome, CREST, scleroderma, polymyositis- dermatomyositis, mixed connective tissue disease, polyarteritis nodosa, amyloidosis, X- linked agammaglobulinemia, common variable immunodeficiency, isolated IgA deficiency, DiGeorge's syndrome, severe combined immunodeficiency, Wiscott- Aldrich syndrome, infection with HIV virus, acquired immune deficiency syndrome (AIDS), congenital anomalies
  • Conditions, disorders, or diseases caused by a nutritional disease include, but are not limited to, marasmus, kwashiorkor, fat-soluble vitamin deficiency or toxicity (Vitamins A, D, E, or K), water-soluble vitamin deficiency or toxicity (thiamine, riboflavin, niacin, pyridoxine, folate, cobalamin, Vitamin C), mineral deficiency or toxicity (iron, calcium, magnesium, sodium, potassium, chloride, zinc, copper, iodine, cobalt, chromium, selenium, nickel, vanadium, manganese, molybdenum, rickets, osteomalacia, beriberi, hypoprothrombinemia, pellagra, megaloblastic anemia, scurvy, pernicious anemia, lack of gastric intrinsic factor, removal or pathophysiological functioning in the terminal ileum, microcytic anemia, or obesity.
  • Conditions, disorders, or diseases typically occurring in infancy or childhood include, but are not limited to, preterm birth, congenital malformations from genetic causes, congenital malformations from infectious causes, congenital malformations from toxic or teratogenic causes, congenital malformations from radiation, congenital malformations from idiopathic causes, small for gestational age infants, perinatal trauma, perinatal asphyxia, perinatal ischemia or hypoxia, birth injury, intracranial hemorrhage, deformations, respiratory distress syndrome of the newborn, atelectasis, hemolytic disease of the newborn, kernicterus, hydrops fetalis, congenital anemia of the newborn, icterus gravis, phenylketonuria, galactosemia, cystic fibrosis, hamartoma, or choristoma.
  • the compounds and methods of the invention can be used to treat infections that cause cell death.
  • the infections may be caused by bacteria; viruses; members of the family rickettsiae or chlamydia; fungi, yeast, hyphae or pseudohyphae; prions; protozoas; or metazoas.
  • Examples of aerobic or anaerobic bacteria that may cause such infections include, but are not limited to, gram-positive cocci, gram-positive bacilli (gram-positive rods), gram-negative cocci, gram-negative bacilli (gram-negative rods), Mvcoplasma species, Ureaplasma species, Treponema species, Leptospira species, Borrelia species, Vibrio species, Mvcobacteria species, members of Actinomycetes or L- forms (cell- wall deficient forms).
  • DNA, RNA or both DNA and RNA viruses that may cause such infections include, but are not limited to, members of the families adenoviridae, parvoviridae, papovaviridae, he ⁇ esviridae, poxviridae, picomaviridae, orthomyxoviridae, paramyxoviridae, rhabdoviridae, bunyaviridae, arenaviridae, coronaviridae, retroviridae, reoviridae, togaviridae and caliciviridae.
  • Examples of members of the families rickettsiae or chlamydiae that may cause such infections include, but are not limited to, Rickettsia species, Rochalimaea species, Coxiella species or Chlamydia species.
  • fungi, yeast, hyphae or pseudohyphae that may cause such infections include, but are not limited to, members of Ascomycota, Basidiomycota, Zygomycota, or Deutoeromycota (Fungi Imperfecti); Candida species, Crvptococcus species, Torulopsis species, Rhodotomla species, Sporothrix species, Phialophora species, Cladosporium species, Xylohvpha species, Blastomyces species, Histoplasma species, Coccidioides species, Paracoccidioides species, Geotrichum species, Aspergillus species, Rhizopus species, Mucor species, Pseudoallescheria species or Absidia species.
  • prions that may cause such infections include, but are not limited to, the causative agent of Creutzfeldt- Jakob Disease, the causative agent of Gerstmann-Straussler-Scheinker Disease, the causative agent of fatal familial insomnia, the causative agent of kuru, and the causative agent of bovine spongiform encephalopathy.
  • Examples of protozoa at any point in their life cycle that may cause such infections include, but are not limited to, Entamoeba species, Naegleria species, Acanthamoeba species, Pneumocystis species, Balantidium species, members of order Leptomyxida, Plasmodium species, Toxoplasma species, Leishmania species and Trypanosoma species.
  • metazoa at any point in their life cycle that may cause such infections include, but are not limited to, members of Platyhelminthes such as the organisms in Cestoda (tapeworms) or Trematoda (flukes); or members of Aschelminthes such as the organisms in Acanthocephala, Chaetognatha, Cycliophora, Gastrotricha, Nematoda or Rotifera.
  • members of Platyhelminthes such as the organisms in Cestoda (tapeworms) or Trematoda (flukes); or members of Aschelminthes such as the organisms in Acanthocephala, Chaetognatha, Cycliophora, Gastrotricha, Nematoda or Rotifera.
  • the compounds and methods of the invention can be used to treat infections or disorders that cause cell death in organ systems including, but not limited to, blood vessels, heart, red blood cells, white blood cells, lymph nodes, spleen, respiratory system, oral cavity, gastrointestinal tract, liver and biliary tract, pancreas, kidney, lower urinary tract, upper urinary tract and bladder, male sexual organs and genitalia, female sexual organs and genitalia, breast, thyroid gland, adrenal gland, parathyroid gland, skin, musculoskeletal system, bone marrow or bones.
  • the compounds and methods of the invention can be used to treat further physiological impacts on organs caused by the infections that induce cell death including, but not limited to, fever equal to or greater than 101.5 degrees Fahrenheit, a decrease or increase in pulse rate by more than 20 beats per minute, a decrease or increase in supine systolic blood pressure by more than 30 millimeters of mercury, an increase or decrease in respiratory rate by more than 8 breaths per minute, an increase or decrease in blood pH by more than 0.10 pH units, an increase or decrease in one or more serum electrolytes outside of the clinical laboratory's usual reference range, an increase or decrease in the partial pressure of arterial oxygen or carbon dioxide outside of the clinical laboratory's usual reference range, an increase or decrease in white or red blood cells outside of the laboratory's usual reference range, an acute confusional state such as delirium where delirium is defined by the American Psychiatric Association's DSM-IV Manual or a diminished level of consciousness or attention.
  • fever equal to or greater than 101.5 degrees Fahrenheit a decrease or increase in pulse
  • the types of conditions, disorders, or diseases involving cell death that may be prevented, delayed, or rescued by modulating protective sequence expression, protective sequence product activity, or their regulatory elements by using protective sequences in conjunction with well-known antisense, gene "knock-out,” ribozyme and/or triple helix methods, are described.
  • the compounds that may exhibit the ability to modulate the activity, expression or synthesis of the protective sequence, the protective sequence product, or its regulatory elements, including the ability to prevent, delay, or rescue a cell, cells, tissue, organ, or organism from the symptoms of a condition, disorder, or disease involving cell death are antisense, ribozyme and triple helix molecules.
  • Antisense RNA and DNA molecules act to directly block the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation.
  • Antisense approaches involve the design of oligonucleotides that are complementary to a protective sequence mRNA. The antisense oligonucleotides will bind to the complementary protective sequence mRNA transcripts and prevent translation. Absolute complementarity, although preferred, is not required.
  • a sequence "complementary" to a portion of an RNA means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed.
  • the ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA it may contain and still form a stable duplex (or triplex, as the case may be).
  • oligonucleotides complementary to non-coding regions of the protective sequence of interest could be used in an antisense approach to inhibit translation of endogenous mRNA.
  • Antisense nucleic acids should be at least six nucleotides in length, and are preferably oligonucleotides ranging from 6 to about 50 nucleotides in length.
  • the oligonucleotide is at least 10 nucleotides, at least 17 nucleotides, at least 25 nucleotides or at least 50 nucleotides.
  • in vitro studies are first performed to quantitate the ability of the antisense oligonucleotide to inhibit protective sequence expression. It is preferred that these studies utilize controls that distinguish between antisense gene inhibition and nonspecific biological effects of oligonucleotides. It is also preferred that these studies compare levels of the cerebral RNA or protein with that of an internal control RNA or protein. Additionally, it is envisioned that results obtained using the antisense oligonucleotide are compared with those obtained using a control oligonucleotide.
  • control oligonucleotide is of approximately the same length as the test oligonucleotide and that the nucleic acid of the oligonucleotide differs from the antisense sequence no more than is necessary to prevent specific hybridization to the target sequence.
  • the oligonucleotides can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded.
  • the oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, hybridization, etc.
  • the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger, et al, 1989, Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556; Lemaitre, et al, 1987, Proc. Natl. Acad. Sci. U.S.A. 84:648-652; PCT Publication No. WO88/09810, published December 15, 1988) or the blood-brain barrier (see, e.g., PCT Publication No.
  • the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization- triggered cleavage agent, etc.
  • the antisense oligonucleotide may comprise at least one modified base moiety that is selected from the group including but not limited to 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-mannosy
  • the antisense oligonucleotide may also comprise at least one modified sugar moiety selected from the group including but not limited to arabinose, 2-fluoroarabinose, xylulose, and hexose.
  • the antisense oligonucleotide comprises at least one modified phosphate backbone selected from the group consisting of a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof.
  • the antisense oligonucleotide is an ⁇ -anomeric oligonucleotide.
  • An ⁇ -anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -units, the strands run parallel to each other (Gautier, et al., 1987, Nucl. Acids Res. 15:6625-6641).
  • the oligonucleotide is a 2'-0-methylribonucleotide (Inoue, et al, 1987, Nucl. Acids Res.
  • Oligonucleotides of the invention may be synthesized by standard methods known in the art, e.g., by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc.). As examples, phosphorothioate oligonucleotides may be synthesized by the method of Stein, et al. (1988, Nucl. Acids Res.
  • methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports (Sarin, et al, 1988, Proc. Natl. Acad. Sci. U.S.A. 85:7448-7451), etc. [0198] While antisense nucleotides complementary to the protective sequence coding region sequence could be used, those complementary to the transcribed, untranslated region are most preferred.
  • Antisense molecules should be delivered to cells that express the protective sequence in vivo.
  • a number of methods have been developed for delivering antisense DNA or RNA to cells; e.g., antisense molecules can be injected directly into the tissue site, or modified antisense molecules, designed to target the desired cells (e.g., antisense linked to peptides or antibodies that specifically bind receptors or antigens expressed on the target cell surface) can be administered systemically.
  • a preferred approach to achieve intracellular concentrations of the antisense sufficient to suppress translation of endogenous mRNAs utilizes a recombinant DNA construct in which the antisense oligonucleotide is placed under the control of a strong pol III or pol II promoter.
  • a vector can be introduced e.g., such that it is taken up by a cell and directs the transcription of an antisense RNA.
  • a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA.
  • Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in mammalian cells.
  • Expression of the sequence encoding the antisense RNA can be by any promoter known in the art to act in mammalian, preferably human cells. Such promoters can be inducible or constitutive. Such promoters include but are not limited to: the SV40 early promoter region (Bemoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3'-long terminal repeat of Rous sarcoma virus (Yamamoto, et al, 1980, Cell 22:787-797), the he ⁇ es thymidine kinase promoter (Wagner, et al, 1981, Proc. Natl Acad. Sci. U.S.A.
  • Ribozyme molecules designed to catalytically cleave target gene mRNA transcripts can also be used to prevent translation of target gene mRNA and, therefore, expression of target gene product.
  • Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. (For a review, see Rossi, 1994, Current Biology 4:469-471). The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by an endonucleolytic cleavage event. The composition of ribozyme molecules must include one or more sequences complementary to the target gene mRNA, and must include the well known catalytic sequence responsible for mRNA cleavage.
  • the ribozyme is engineered so that the cleavage recognition site is located near the 5' end of the target gene mRNA, i.e., to increase efficiency and minimize the intracellular accumulation of non- functional mRNA transcripts.
  • the ribozymes of the present invention also include RNA endoribonucleases (hereinafter "Cech-type ribozymes”) such as the one that occurs naturally in Tetrahymena thermophila (known as the IVS, or L-19 TVS RNA) and that has been extensively described by Thomas Cech and collaborators (Zaug, et al, 1984, Science, 224:574-578; Zaug and Cech, 1986, Science, 231:470-475; Zaug, et al, 1986, Nature, 324:429-433; published International patent application No. WO 88/04300 by University Patents Inc.; Been and Cech, 1986, Cell, 47:207-216).
  • Cech-type ribozymes such as the one that occurs naturally in Tetrahymena thermophila (known as the IVS, or L-19 TVS RNA) and that has been extensively described by Thomas Cech and collaborators (Zaug, et al, 1984, Science, 224:574-578; Za
  • the Cech-type ribozymes have an eight base pair active site that hybridizes to a target RNA sequence whereafter cleavage of the target RNA takes place.
  • the invention encompasses those Cech-type ribozymes that target eight base-pair active site sequences that are present in the target gene.
  • the ribozymes can be composed of modified oligonucleotides (e.g., for improved stability, targeting, etc.) and should be delivered to cells that express the target gene in vivo.
  • a preferred method of delivery involves using a DNA construct "encoding" the ribozyme under the control of a strong constitutive pol UI or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to destroy endogenous target gene messages and inhibit translation. Because ribozymes, unlike antisense molecules, are catalytic, a lower intracellular concentration is required for efficiency.
  • Endogenous target gene expression can also be reduced by inactivating or
  • mutant, non- functional target gene flanked by DNA homologous to the endogenous target gene (either the coding regions or regulatory regions of the target gene) can be used, with or without a selectable marker and/or a negative selectable marker, to transfect cells that express the target gene in vivo.
  • Such approaches are particularly suited in the agricultural field where modifications to ES (embryonic stem) cells can be used to generate animal offspring with an inactive target gene (e.g., see Thomas and Capecchi, 1987 and Thompson, 1989, supra).
  • ES embryonic stem
  • this approach can be adapted for use in humans provided the recombinant DNA constructs are directly administered or targeted to the required site in vivo using appropriate viral vectors.
  • endogenous target gene expression can be reduced by targeting deoxyribonucleotide sequences complementary to the regulatory region of the target gene (i.e., the target gene promoter and/or enhancers) to form triple helical structures that prevent transcription of the target gene in target cells in the body.
  • deoxyribonucleotide sequences complementary to the regulatory region of the target gene i.e., the target gene promoter and/or enhancers
  • triple helical structures that prevent transcription of the target gene in target cells in the body.
  • Nucleic acid molecules to be used in triple helix formation for the inhibition of transcription should be single stranded and composed of deoxynucleotides.
  • the base composition of these oligonucleotides must be designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizable stretches of either purines or pyrimidines to be present on one strand of a duplex.
  • Nucleic acids may be pyrimidine-based, which will result in TAT and CGC + triplets across the three associated strands of the resulting triple helix.
  • the pyrimidine-rich molecules provide base complementarity to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand.
  • nucleic acid molecules may be chosen that are purine-rich, for example, contain a stretch of G residues. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex.
  • the potential sequences that can be targeted for triple helix formation may be increased by creating a so-called "switchback" nucleic acid molecule.
  • Switchback molecules are synthesized in an alternating 5'-3', 3'-5' manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizable stretch of either purines or pyrimidines to be present on one strand of a duplex.
  • the technique may so efficiently reduce or inhibit the transcription (triple helix) and/or translation (antisense, ribozyme) of mRNA produced by normal target gene alleles that the possibility may arise wherein the concentration of normal target gene product present may be lower than is necessary for a normal phenotype.
  • nucleic acid molecules that encode and express target gene polypeptides exhibiting normal target gene activity may, be introduced into cells via gene therapy methods such as those described, below, in Section 5.4.1.3 that do not contain sequences susceptible to whatever antisense, ribozyme, or triple helix treatments are being utilized.
  • the target gene encodes an extracellular protein, it may be preferable to co- administer normal target gene protein in order to maintain the requisite level of target gene activity.
  • Anti-sense RNA and DNA, ribozyme, and triple helix molecules of the invention may be prepared by any method known in the art for the synthesis of DNA and RNA molecules, as discussed above.
  • RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding the antisense RNA molecule. Such DNA sequences may be inco ⁇ orated into a wide variety of vectors that inco ⁇ orate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters.
  • antisense cDNA constructs that synthesize antisense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines.
  • Protective nucleic acid sequences described above in Section 5.1, can be utilized for transferring recombinant protective nucleic acid sequences to cells and expressing said sequences in recipient cells. Such techniques can be used, for example, in marking cells or for the treatment of a condition, disorder, or disease involving cell death. Such treatment can be in the form of gene replacement therapy. Specifically, one or more copies of a normal protective sequence or a portion of the protective sequence that directs the production of a protective sequence product exhibiting normal protective sequence function, may be inserted into the appropriate cells within a patient, using vectors that include, but are not limited to adenovirus, adeno-associated virus and retrovirus vectors, in addition to other particles that introduce DNA into cells, such as liposomes.
  • the protective sequence of the invention may be expressed in the brain, such gene replacement therapy techniques should be capable of delivering protective sequences to these cell types within patients.
  • techniques that are well known to those of skill in the art see, e.g., PCT Publication No. WO89/10134, published April 25, 1988
  • viral vectors such as, for example, those described above, are preferable.
  • techniques for delivery involve direct administration, e.g., by stereotactic delivery of such protective sequences to the site of the cells in which the protective sequences are to be expressed.
  • Methods for introducing genes for expression in mammalian cells are well known in the field. Generally, for such gene therapy methods, the nucleic acid is directly administered in vivo into a target cell or a transgenic mouse that expresses SP-10 promoter operably linked to a reporter gene.
  • a nucleic acid-ligand complex can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation.
  • the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., PCT Publications WO 92/06180 dated April 16, 1992; WO 92/22635 dated December 23, 1992; WO92/20316 dated November 26, 1992; WO93/14188 dated July 22, 1993; WO 93/20221 dated October 14, 1993).
  • Additional methods that may be utilized to increase the overall level of protective sequence expression and/or gene product activity include using targeted homologous recombination methods, discussed in Section 5.2, above, to modify the expression characteristics of an endogenous protective sequence in a cell or microorganism by inserting a heterologous DNA regulatory element such that the inserted regulatory element is operatively linked with the endogenous protective sequence in question.
  • Targeted homologous recombination can thus be used to activate transcription of an endogenous protective sequence that is "transcriptionally silent", i.e., is not normally expressed or is normally expressed at very low levels, or to enhance the expression of an endogenous protective sequence that is normally expressed.
  • the overall level of protective sequence expression and/or gene product activity may be increased by the introduction of appropriate protective sequence- expressing cells, preferably autologous cells, into a patient at positions and in numbers that are sufficient to ameliorate the symptoms of a condition, disorder, or disease involving cell death.
  • appropriate protective sequence- expressing cells preferably autologous cells
  • Such cells may be either recombinant or non-recombinant.
  • cells that can be administered to increase the overall level of protective sequence expression in a patient are normal cells, preferably brain cells, which express the protective sequence.
  • cells preferably autologous cells, can be engineered to express protective sequences, and may then be introduced into a patient in positions appropriate for the amelioration of the symptoms of a condition, disorder, or disease involving cell death.
  • cells which express an unimpaired protective sequence and that are from a MHC matched individual can be utilized, and may include, for example, brain cells.
  • the expression of the protective sequences is controlled by the appropriate gene regulatory sequences to allow such expression in the necessary cell types. Such gene regulatory sequences are well known to the skilled artisan.
  • the cells to be administered are non-autologous cells, they can be administered using well-known techniques that prevent a host immune response against the introduced cells from developing.
  • the cells may be introduced in an encapsulated form that, while allowing for an exchange of components with the immediate extracellular environment, does not allow the introduced cells to be recognized by the host immune system.
  • compounds such as those identified via techniques such as those described, in Section 5.4.2, which are capable of modulating protective sequences, protective sequence product activity, or their regulatory sequences can be administered using standard techniques that are well known to those of skill in the art.
  • the administration techniques should include well known methods that allow for a crossing of the blood-brain barrier.
  • a variety of methods can be employed to screen for the presence of protective sequence-specific mutations or polymo ⁇ hisms (including polymo ⁇ hisms flanking protective sequences) and to detect and/or assay levels of protective nucleic acid sequences.
  • Mutations or polymo ⁇ hisms within or flanking the protective sequences can be detected by utilizing a number of techniques. Nucleic acid from any nucleated cell can be used as the starting point for such assay techniques, and may be isolated according to standard nucleic acid preparation procedures that are well known to those of skill in the art.
  • Protective nucleic acid sequences may be used in hybridization or amplification assays of biological samples to detect abnormalities involving protective sequence structure, including point mutations, insertions, deletions, inversions, translocations and chromosomal rearrangements.
  • assays may include, but are not limited to, Southern analyses, single-stranded conformational polymo ⁇ hism analyses (SSCP) and PCR analyses.
  • Diagnostic methods for the detection of protective sequence-specific mutations or polymo ⁇ hisms can involve for example, contacting and incubating nucleic acids obtained from a sample, e.g., derived from a patient sample or other appropriate cellular source with one or more labeled nucleic acid reagents including recombinant DNA molecules, cloned genes or degenerate variants thereof, such as described in Section 5.1, above, under conditions favorable for the specific annealing of these reagents to their complementary sequences within or flanking the protective sequence.
  • the diagnostic methods of the present invention further encompass contacting and incubating nucleic acids for the detection of single nucleotide mutations or polymo ⁇ hisms of the protective sequence.
  • these nucleic acid reagent sequences within the protective sequence are 15 to 30 nucleotides in length.
  • nucleic acid from the cell type or tissue of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads.
  • a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads.
  • non-annealed, labeled nucleic acid reagents of the type described in Section 5.1 are easily removed. Detection of the remaining, annealed, labeled nucleic acid reagents is accomplished using standard techniques well known to those skilled in the art.
  • the protective sequences of the invention to which the nucleic acid reagents have annealed can be compared to the annealing pattern expected from a normal protective sequence of the invention in order to determine whether a protective sequence mutation is present.
  • protective sequence mutations or polymo ⁇ hisms can be detected by using a microassay of nucleic acid sequences of the invention immobilized to a substrate or "gene chip" (see, e.g. Cronin, et al., 1996, Human Mutation 7:244-255).
  • Alternative diagnostic methods for the detection of protective sequence- specific nucleic acid molecules (or flanking sequences), in patient samples or other appropriate cell sources may involve their amplification, e.g., by PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Patent No. 4,683,202), followed by the analysis of the amplified molecules using techniques well known to those of skill in the art, such as, for example, those listed above.
  • the resulting amplified sequences can be compared to those that would be expected if the nucleic acid being amplified contained only normal copies of the protective sequence in order to determine whether a protective sequence mutation or polymo ⁇ hism in linkage disequilibrium with a disease-causing allele exists.
  • oligonucleotide primers that amplify exon sequences.
  • the sequences of such oligonucleotide primers are, therefore, preferably derived from cerebral intron sequences so that the entire exon, or coding region, can be analyzed as discussed below.
  • Primer pairs useful for amplification of cerebral exons are preferably derived from adjacent introns. Appropriate primer pairs can be chosen such that each of the cerebral exons present within the gene will be amplified. Primers for the amplification of exons can be routinely designed by one of ordinary skill.
  • Additional nucleic acid sequences that are preferred for such amplification-related analyses are those that will detect the presence of a polymo ⁇ hism that differs from the sequence depicted in the Figures.
  • Such polymo ⁇ hisms include ones that represent mutations associated with a condition, disorder, or disease involving cell death.
  • Tm(°C) 81.5+16.6(log[monovalent cations])+0.41(% G+C)-(0.61% formamide)-(500/N) where N is the length of the probe.
  • well-known genotyping techniques can be performed to identify individuals carrying protective sequence mutations. Such techniques include, for example, the use of restriction fragment length polymo ⁇ hisms (RFLPs), which involve sequence variations in one of the recognition sites for the specific restriction enzyme used.
  • RFLPs restriction fragment length polymo ⁇ hisms
  • improved methods for analyzing DNA polymo ⁇ hisms which can be utilized for the identification of protective sequence-specific mutations, have been described that capitalize on the presence of variable numbers of short, tandemly repeated DNA sequences between the restriction enzyme sites. For example, Weber (U.S. Pat.
  • No. 5,075,21-7 describes a DNA marker based on length polymo ⁇ hisms in blocks of (dC- dA)n-(dG-dT)n short tandem repeats.
  • the average separation of (dC-dA)n-(dG-dT)n blocks is estimated to be 30,000-60,000 bp.
  • Markers that are so closely spaced exhibit a high frequency of co-inheritance, and are extremely useful in the identification of genetic mutations, such as, for example, mutations within the protective sequence of the invention, and the diagnosis of diseases and disorders related to mutations of the protective sequences of the invention.
  • Caskey et al. (U.S. Pat.No. 5,364,759) describe a DNA profiling assay for detecting short tri- and tetra nucleotide repeat sequences. The process includes extracting the DNA of interest, amplifying the extracted DNA and labeling the repeat sequences to form a genotypic map of the individual's DNA.
  • SNPs single nucleotide polymo ⁇ hisms
  • Conventional techniques for detecting SNPs include, e.g., conventional dot blot analysis, single stranded conformational polymo ⁇ hism (SSCP) analysis (see, e.g., Orita et al,
  • detecting and mapping SNPs involve microsequencing techniques wherein an SNP site in a target DNA is detecting by a single nucleotide primer extension reaction (see, e.g., Goelet et al, PCT Publication No. WO92/15712; Mundy, U.S.
  • RNA from a cell type or tissue known, or suspected, to express the protective sequence may be isolated and tested utilizing hybridization or PCR techniques such as are described, above.
  • the isolated cells can be derived from cell culture or from a patient.
  • the analysis of cells taken from culture may be a necessary step in the assessment of cells to be used as part of a cell-based gene therapy technique or, alternatively, to test the effect of compounds on the expression of the protective sequence. Such analyses may reveal both quantitative and qualitative aspects of the expression pattern of the protective sequence, including activation or inactivation of protective sequence expression.
  • a cDNA molecule is synthesized from an RNA molecule of interest (e.g., by reverse transcription of the RNA molecule into cDNA).
  • a sequence within the cDNA is then used as the template for a nucleic acid amplification reaction, such as a PCR amplification reaction, or the like.
  • the nucleic acid reagents used as synthesis initiation reagents (e.g., primers) in the reverse transcription and nucleic acid amplification steps of this method are chosen from among the protective sequence nucleic acid reagents described in Section 5.1.
  • the preferred lengths of such nucleic acid reagents are at least 9-30 nucleotides.
  • the nucleic acid amplification may be performed using radioactively or non-radioactively labeled nucleotides.
  • enough amplified product may be made such that the product may be visualized by standard ethidium bromide staining or by utilizing any other suitable nucleic acid staining method.
  • Protective sequence products of the invention including both wild-type and mutant protective sequence products, conserved variants and polypeptide fragments thereof, which are discussed, above, in Section 5.2, may be detected using antibodies that are directed against such gene products. Such antibodies, which are discussed in Section 5.3, above, may thereby be used as diagnostics and prognostics for a condition, disorder, or disease involving cell death. Such methods may be used to detect abnormalities in the level of protective sequence expression or of protective sequence product synthesis, or abnormalities in the structure, temporal expression and/or physical location of protective sequence product.
  • the antibodies and immunoassay methods described herein have, for example, important in vitro applications in assessing the efficacy of treatments for conditions, disorders, or diseases involving cell death.
  • Antibodies, or fragments of antibodies, such as those described below, may be used to screen potentially therapeutic compounds in vitro to determine their effects on protective sequence expression and protective sequence product production.
  • the compounds that have beneficial effects on conditions, disorders, or diseases involving cell death can thereby be identified, and a therapeutically effective dose determined.
  • In vitro immunoassays may also be used, for example, to assess the efficacy of cell-based gene therapy for a condition, disorder, or disease involving cell death.
  • Antibodies directed against protective sequence products may be used in vitro to determine, for example, the level of protective sequence expression achieved in cells genetically engineered to produce the protective sequence product.
  • intracellular protective sequence products such an assessment is done, preferably, using cell lysates or extracts. Such analysis will allow for a determination of the number of transformed cells necessary to achieve therapeutic efficacy in vivo, as well as optimization of the gene replacement protocol.
  • the tissue or cell type to be analyzed generally will include those that are known, or suspected, to express the protective sequence.
  • the protein isolation methods employed herein may, for example, be such as those described in Harlow and Lane (1988, "Antibodies: A Laboratory Manual", Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York).
  • the isolated cells can be derived from cell culture or from a patient.
  • the analysis of cells taken from culture may be a necessary step in the assessment of cells to be used as part of a cell-based gene therapy technique or, alternatively, to test the effect of compounds on the expression of the protective sequence.
  • Preferred diagnostic methods for the detection of protective sequence products, conserved variants or peptide fragments thereof may involve, for example, immunoassays wherein the protective sequence products or conserved variants or peptide fragments are detected by their interaction with an anti-protective sequence product- specific antibody.
  • antibodies, or fragments of antibodies may be used to, quantitatively or qualitatively, detect the presence of protective sequence products or conserved variants or peptide fragments thereof.
  • This can be accomplished, for example, by immunofluorescence techniques employing a fluorescently labeled antibody (see below, this Section) coupled with light microscopic, flow cytometric or fluorimetric detection. Such techniques are especially preferred for protective sequence products that are expressed on the cell surface.
  • the antibodies (or fragments thereof) useful in the present invention may, additionally, be employed histologically, as in immunofluorescence or immunoelectron microscopy, for in situ detection of protective sequence products, conserved variants or peptide fragments thereof.
  • In situ detection may be accomplished by removing a histological specimen from a patient, and applying thereto a labeled antibody that binds to a protective sequence polypeptide.
  • the antibody (or fragment) is preferably applied by overlaying the labeled antibody (or fragment) onto a biological sample.
  • Immunoassays for protective sequence products, conserved variants or peptide fragments thereof will typically comprise incubating a sample, such as a biological fluid, a tissue extract, freshly harvested cells or lysates of cells in the presence of a detectably labeled antibody capable of identifying the protective sequence product, conserved variants or peptide fragments thereof, and detecting the bound antibody by any of a number of techniques well-known in the art.
  • a sample such as a biological fluid, a tissue extract, freshly harvested cells or lysates of cells
  • the biological sample may be brought in contact with and immobilized onto a solid phase support or carrier, such as nitrocellulose, which is capable of immobilizing cells, cell particles or soluble proteins.
  • a solid phase support or carrier such as nitrocellulose, which is capable of immobilizing cells, cell particles or soluble proteins.
  • the support may then be washed with suitable buffers followed by treatment with the detectably labeled protective sequence product specific antibody.
  • the solid phase support may then be washed with the buffer a second time to remove unbound antibody.
  • the amount of bound label on the solid support may then be detected by conventional means.
  • solid phase support or carrier any support capable of binding an antigen or an antibody.
  • supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite.
  • the nature of the carrier can be either soluble to some extent or insoluble for the pu ⁇ oses of the present invention.
  • the support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody.
  • the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod.
  • the surface may be flat such as a sheet, test strip, etc.
  • Preferred supports include polystyrene beads. Those skilled in the art will know many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation.
  • One of the ways in which the protective sequence product-specific antibody can be detectably labeled is by linking the same to an enzyme, such as for use in an enzyme immunoassay (EIA) (Voller, A., "The Enzyme Linked Immunosorbent Assay (ELISA)", 1978, Diagnostic Horizons 2:1-7, Microbiological Associates Quarterly Publication, Walkersville, MD); Voller, A. et al. , 1978, J. Clin. Pathol 31 :507-520; Butler, J.E., 1981, Meth. Enzymol 73:482-523; Maggio, E. (ed.), 1980, Enzyme Immunoassay, CRC Press, Boca Raton, FL,; Ishikawa, E.
  • EIA enzyme immunoassay
  • the enzyme that is bound to the antibody will react with an appropriate substrate, preferably a chromogenic substrate, in such a manner as to produce a chemical moiety that can be detected, for example, by spectrophotometric, fluorimetric or by visual means.
  • Enzymes that can be used to detectably label the antibody include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5 -steroid isomerase, yeast alcohol dehydrogenase, ⁇ -glycerophosphate, dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, ⁇ -galactosidase, ribonuclease, urease, catalase, glucose-6- phosphate dehydrogenase, glucoamylase and acetylcholinesterase.
  • the detection can be accomplished by colorimetric methods that employ a chromogenic substrate for the enzyme. Detection also may be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards. [0250] Detection may be accomplished also using any of a variety of other immunoassays. For example, by radioactively labeling the antibodies or antibody fragments, it is possible to detect protective sequence products through the use of a radioimmunoassay (RIA) (see, for example, Weintraub, B., Principles of Radioimmunoassays, Seventh Training Course on Radioligand Assay Techniques, The Endocrine Society, March, 1986). The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography. [0251] It is also possible to label the antibody with a fluorescent compound.
  • RIA radioimmunoassay
  • the fluorescently labeled antibody When the fluorescently labeled antibody is exposed to light of the proper wavelength, its presence can then be detected due to fluorescence.
  • fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.
  • the antibody can also be detectably labeled using fluorescence emitting metals such as Eu, or others of the lanthanide series. These metals can be attached to the antibody using such metal chelating groups as diethylenetriaminepentacetic acid (DTP A) or ethylenediaminetetraacetic acid (EDTA).
  • DTP A diethylenetriaminepentacetic acid
  • EDTA ethylenediaminetetraacetic acid
  • the antibody also can be detectably labeled by coupling it to a chemiluminescent compound.
  • the presence of the chemiluminescent-tagged antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction.
  • chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester.
  • a bioluminescent compound may be used to label the antibody of the present invention.
  • Bioluminescence is a type of chemiluminescence found in biological systems in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence.
  • Important bioluminescent compounds for pu ⁇ oses of labeling are luciferin, luciferase and aequorin.
  • the following assays are designed to identify compounds that bind to a protective sequence product, compounds that bind to proteins, or portions of proteins that interact with a protective sequence product, compounds that modulate, e.g., interfere with, the interaction of a protective sequence product with proteins and compounds that modulate the activity of the protective sequence (i.e., modulate the level of protective sequence expression and/or modulate the level of protective sequence product activity).
  • Assays may additionally be utilized that identify compounds that bind to protective sequence regulatory sequences (e.g., promoter sequences; see e.g., Platt, 1994, J. Biol. Chem. 269, 28558-28562), and that can modulate the level of protective sequence expression.
  • Such compounds may include, but are not limited to, small organic molecules, such as ones that are able to cross the blood-brain barrier, gain to and/or entry into an appropriate cell and affect expression of the protective sequence or some other gene involved in a protective sequence regulatory pathway.
  • Such proteins may be involved in the control and/or regulation of functions related to cell death. Further, among these compounds are compounds that affect the level of protective sequence expression and/or protective sequence product activity and that can be used in the therapeutic treatment of conditions, disorders, or diseases involving cell death as described, below, in Section 5.4.2.3.
  • Compounds may include, but are not limited to, peptides such as, for example, soluble peptides, including but not limited to, Ig-tailed fusion peptides, and members of random peptide libraries; (see, e.g., Lam, et al, 1991, Nature 354:82-84; Houghten, et al, 1991, Nature 354:84-86), and combinatorial chemistry-derived molecular library made of D- and/or L- configuration amino acids, phosphopeptides (including, but not limited to members of random or partially degenerate, directed phosphopeptide libraries; see, e.g., Songyang, et al, 1993, Cell 72:767-778), antibodies (including, but not limited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab') 2 and FAb expression library fragments, and epitope-binding fragments thereof), and small organic molecules (such
  • Such compounds include families of antidepressants such as lithium salts, carbamazepine, valproic acid, lysergic acid diethylamide (LSD), >-chlorophenylalanine, -propyldopacetamide dithiocarbamate derivatives e.g., FLA 63; anti-anxiety drugs, e.g., diazepam; monoamine oxidase (MAO) inhibitors, e.g., iproniazid, clorgyline, phenelzine and isocarboxazid; biogenic amine uptake blockers, e.g., tricyclic antidepressants such as desipramine, imipramine and amitriptyline; serotonin reuptake inhibitors e.g., fluoxetine; antipsychotic drugs such as phenothiazine derivatives (e.g.
  • chlo ⁇ romazine thorazine and trifluopromazine
  • butyrophenones e.g., haloperidol (Haldol)
  • thioxanthene derivatives e.g., chlo ⁇ rothixene
  • dibenzodiazepines e.g., clozapine
  • benzodiazepines dopaminergic agonists and antagonists e.g., L-DOPA, cocaine, amphetamine, ⁇ -methyl-tyrosine, rese ⁇ ine, tetrabenazine, benzotropine, pargyline
  • noradrenergic agonists and antagonists e.g., clonidine, phenoxybenzamine, phentolamine, tropolone.
  • Compounds identified via assays such as those described herein may be useful, for example, in elaborating the biological function of protective sequence products and for ameliorating conditions, disorders, or diseases involving cell death.
  • Assays for testing the effectiveness of compounds identified by, for example, techniques such as those described in Sections 5.4.2.1 - 5.4.2.3, are discussed, below, in Section 5.4.2.4.
  • In vitro systems may be designed to identify compounds capable of binding the protective sequence products of the invention.
  • Compounds identified may be useful, for example, in modulating the activity of unimpaired and/or mutant protective sequence products, may be useful in elaborating the biological function of the protective sequence product, may be utilized in screens for identifying compounds that disrupt normal protective sequence product interactions or may in themselves disrupt such interactions.
  • the principle of the assays used to identify compounds that bind to the protective sequence product involves preparing a reaction mixture of the protective sequence product and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex that can be removed and/or detected in the reaction mixture.
  • These assays can be conducted in a variety of ways. For example, one method to conduct such an assay involves anchoring a protective sequence product or a test substance onto a solid support and detecting protective sequence product/test compound complexes formed on the solid support at the end of the reaction.
  • the protective sequence product may be anchored onto a solid support, and the test compound, which is not anchored, may be labeled, either directly or indirectly.
  • microtiter plates are conveniently utilized as the solid support.
  • the anchored component may be immobilized by non-covalent or covalent attachments.
  • Non-covalent attachment may be accomplished by simply coating the solid surface with a solution of the protein and drying.
  • an immobilized antibody preferably a monoclonal antibody, specific for the protein to be immobilized may be used to anchor the protein to the solid surface.
  • the surfaces may be prepared in advance and stored.
  • the non-immobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface.
  • the detection of complexes anchored on the solid surface can be accomplished in a number of ways.
  • the detection of label immobilized on the surface indicates that complexes were formed.
  • an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the previously non-immobilized component (the antibody, in turn, may be directly labeled or indirectly labeled with a labeled anti-Ig antibody).
  • a reaction can be conducted in a liquid phase, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for the protective sequence product or the test compound to anchor any complexes formed in solution, and a labeled antibody specific for the other component of the possible complex to detect anchored complexes.
  • Any method suitable for detecting protein-protein interactions may be employed for identifying protective sequence product-protein interactions.
  • Among the traditional methods that may be employed are co-immunoprecipitation, cross-linking and co-purification through gradients or chromatographic columns. Utilizing procedures such as these allows for the identification of proteins, including intracellular proteins, which interact with protective sequence products. Once isolated, such a protein can be identified and can be used in conjunction with standard techniques, to identify proteins it interacts with.
  • amino acid sequence of a protein that interacts with the protective sequence product can be ascertained using techniques well known to those of skill in the art, such as via the Edman degradation technique (see, e.g., Creighton, 1983, "Proteins: Structures and Molecular Principles," W.H. Freeman & Co., N.Y., pp.34-49).
  • the amino acid sequence obtained may be used as a guide for the generation of oligonucleotide mixtures that can be used to screen for gene sequences encoding such proteins. Screening may be accomplished, for example, by standard hybridization or PCR techniques. Techniques for the generation of oligonucleotide mixtures and the screening are well known.
  • plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to the protective sequence product and the other consists of the transcription activator protein's activation domain fused to an unknown protein that is encoded by a cDNA that has been recombined into this plasmid as part of a cDNA library.
  • the DNA- binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., HBS or lacZ) whose regulatory region contains the transcription activator's binding site.
  • a reporter gene e.g., HBS or lacZ
  • the DNA-binding domain hybrid cannot because it does not provide activation function and the activation domain hybrid cannot because it cannot localize to the activator's binding sites. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product.
  • the two-hybrid system or related methodologies may be used to screen activation domain libraries for proteins that interact with the "bait" gene product.
  • protective sequence products of the invention may be used as the bait gene product. Total genomic or cDNA sequences are fused to the DNA encoding an activation domain.
  • This library and a plasmid encoding a hybrid of a bait protective sequence product fused to the DNA-binding domain are co-transformed into a yeast reporter strain, and the resulting transformants are screened for those that express the reporter gene.
  • a bait protective sequence such as the open reading frame of the gene, can be cloned into a vector such that it is translationally fused to the DNA encoding the DNA-binding domain of the GAL4 protein.
  • a cDNA library of the cell line, from which proteins that interact with bait protective sequence products are to be detected can be made using methods routinely practiced in the art. According to the particular system described herein, for example, the cDNA fragments can be inserted into a vector such that they are translationally fused to the transcriptional activation domain of GAL4. Such a library can be co-transformed along with the bait protective sequence-GAL4 fusion plasmid into a yeast strain that contains a lacZ gene driven by a promoter that contains GAL4 activation sequence. A cDNA encoded protein, fused to a GAL4 transcriptional activation domain that interacts with bait protective sequence product will reconstitute an active GAL4 protein and thereby drive expression of the HIS3 gene.
  • Colonies that express HIS3 can be detected by their growth on petri dishes containing semi-solid agar based media lacking histidine. The cDNA can then be purified from these strains, and used to produce and isolate the bait protective sequence product-interacting protein using techniques routinely practiced in the art.
  • the protective sequence products may, in vivo, interact with one or more macromolecules, including intracellular macromolecules, such as proteins.
  • macromolecules may include, but are not limited to, nucleic acid molecules and those proteins identified via methods such as those described, above, in Sections 5.4.2.1 - 5.4.2.2.
  • binding partners Compounds that disrupt protective sequence product binding to a binding partner may be useful in regulating the activity of the protective sequence product, especially mutant protective sequence products.
  • Such compounds may include, but are not limited to molecules such as peptides, and the like, as described, for example, in Section 5.4.2.1 above.
  • the basic principle of an assay system used to identify compounds that interfere with or potentiate the interaction between the protective sequence product and a binding partner or partners involves preparing a reaction mixture containing the protective sequence product and the binding partner under conditions and for a time sufficient to allow the two to interact and bind, thus forming a complex.
  • the reaction mixture is prepared in the presence and absence of the test compound.
  • the test compound may be initially included in the reaction mixture, or may be added at a time subsequent to the addition of protective sequence product and its binding partner. Control reaction mixtures are incubated without the test compound or with a compound that is known not to block complex formation. The formation of any complexes between the protective sequence product and the binding partner is then detected.
  • complex formation within reaction mixtures containing the test compound and normal protective sequence product also may be compared to complex formation within reaction mixtures containing the test compound and a mutant protective sequence product. This comparison may be important in those cases wherein it is desirable to identify compounds that disrupt interactions of mutant but not normal protective sequence product.
  • the reaction mixture is prepared in the presence and absence of the test compound.
  • the test compound may be initially included in the reaction mixture, or may be added at a time subsequent to the addition of protective sequence product and its binding partner.
  • Control reaction mixtures are incubated without the test compound or with a compound that is known not to block complex formation. The formation of any complexes between the protective sequence product and the binding partner is then detected. Increased formation of a complex in the reaction mixture containing the test compound, but not in the control reaction, indicates that the compound enhances and therefore potentiates the interaction of the protective sequence product and the binding partner.
  • complex formation within reaction mixtures containing the test compound and normal protective sequence product may also be compared to complex formation within reaction mixtures containing the test compound and a mutant protective sequence product. This comparison may be important in those cases wherein it is desirable to identify compounds that enhance interactions of mutant but not normal protective sequence product.
  • the above assays may be performed using a reaction mixture containing the protective sequence product, a binding partner and a third compound that disrupts or enhances protective sequence product binding to the binding partner. The reaction mixture is prepared and incubated in the presence and absence of the test compound, as described above, and the formation of any complexes between the protective sequence product and the binding partner is detected.
  • the formation of a complex in the reaction mixture containing the test compound, but not in the control reaction indicates that the test compound interferes with the ability of the second compound to disrupt protective sequence product binding to its binding partner.
  • the assays for compounds that interfere with or potentiate the interaction of the protective sequence products and binding partners can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring either the protective sequence product or the binding partner onto a solid support and detecting complexes formed on the solid support at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the compounds being tested.
  • test compounds that interfere with or potentiate the interaction between the protective sequence products and the binding partners can be identified by conducting the reaction in the presence of the test substance; i.e., by adding the test substance to the reaction mixture prior to or simultaneously with the protective sequence product and interactive intracellular binding partner.
  • test compounds that disrupt preformed complexes e.g., compounds with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed.
  • the various formats are described briefly below.
  • the protective sequence product or the interactive binding partner is anchored onto a solid surface, while the non-anchored species is labeled, either directly or indirectly.
  • the anchored species may be immobilized by non-covalent or covalent attachments. Non-covalent attachment may be accomplished simply by coating the solid surface with a solution of the protective sequence product or binding partner and drying. Alternatively, an immobilized antibody specific for the species to be anchored may be used to anchor the species to the solid surface. The surfaces may be prepared in advance and stored.
  • the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface.
  • the detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the non- immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre- labeled, an indirect label can be used to detect complexes anchored on the surface; e.g.
  • reaction using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, may be directly labeled or indirectly labeled with a labeled anti-Ig antibody).
  • the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes.
  • test compounds that inhibit complex formation or that disrupt preformed complexes can be identified.
  • a homogeneous assay can be used. In this approach, a preformed complex of the protective sequence product and the interactive binding partner is prepared in which either the protective sequence product or its binding partners is labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Patent No. 4,109,496 by Rubenstein that utilizes this approach for immunoassays). The addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances that disrupt protective sequence product/binding partner interaction can be identified.
  • these same techniques can be employed using peptide fragments that correspond to the binding domains of the protective sequence product and/or the binding partner (in cases where the binding partner is a protein), in place of one or both of the full length proteins.
  • Any number of methods routinely practiced in the art can be used to identify and isolate the binding sites. These methods include, but are not limited to, mutagenesis of the gene encoding one of the proteins and screening for disruption of binding in a co-immunoprecipitation assay. Compensating mutations in the gene encoding the second species in the complex can then be selected. Sequence analysis of the genes encoding the respective proteins will reveal the mutations that correspond to the region of the protein involved in interactive binding.
  • one protein can be anchored to a solid surface using methods described in this Section above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide comprising the binding domain may remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the segments is engineered to express peptide fragments of the protein, it can then be tested for binding activity and purified or synthesized.
  • a proteolytic enzyme such as trypsin
  • a protective sequence product can be anchored to a solid material as described, above, in this Section by making a GST- 1 fusion protein and allowing it to bind to glutathione agarose beads.
  • the binding partner can be labeled with a radioactive isotope, such as 35 S, and cleaved with a proteolytic enzyme such as trypsin. Cleavage products can then be added to the anchored GST-1 fusion protein and allowed to bind. After washing away unbound peptides, labeled bound material, representing the binding partner binding domain, can be eluted, purified and analyzed for amino acid sequence by well-known methods. Peptides so identified can be produced synthetically or produced using recombinant DNA technology.
  • Compounds including, but not limited to, binding compounds identified via assay techniques such as those described, above, in Sections 5.4.2.1 - 5.4.2.3, can be tested for the ability to ameliorate symptoms of a condition, disorder, or disease involving cell death.
  • the assays described herein can be used to identify compounds that affect activity by either affecting protective sequence expression or by affecting the level of protective sequence product activity.
  • compounds may be identified that are involved in another step in the pathway in which the protective sequence and/or protective sequence product is involved, such as, for example, a step that is either "upstream” or "downstream” of the step in the pathway mediated by the protective sequence.
  • Such compounds may, by affecting this same pathway, modulate the effect on the development of conditions, disorders, or diseases involving cell death.
  • Such compounds can be used as part of a therapeutic method for the treatment of the condition, disorder, or disease.
  • cell-based systems can be used to identify compounds that may act to ameliorate symptoms of a condition, disorder, or disease, including, but not limited to, those described in Section 5.4.1.1.
  • Such cell systems can include, for example, recombinant or non-recombinant cell, such as cell lines, which express the protective sequence of interest.
  • cells that express the protective sequence of interest may be exposed to a compound suspected of exhibiting an ability to ameliorate symptoms of a condition, disorder, or disease involving cell death at a sufficient concentration and for a sufficient time to elicit such an amelioration of such symptoms in the exposed cells.
  • the cells can be assayed to measure alterations in the expression of the protective sequence, e.g., by assaying cell lysates for cerebral mRNA transcripts (e.g., by Northern analysis) or for protective sequence products expressed by the cell; compounds that modulate expression of the protective sequence are good candidates as therapeutics.
  • animal-based systems or models for a condition, disorder, or disease involving cell death may be used to identify compounds capable of ameliorating symptoms of the condition, disorder, or disease.
  • Such animal models may be used as test substrates for the identification of drugs, pharmaceuticals, therapies and interventions.
  • animal models may be exposed to a compound suspected of exhibiting an ability to ameliorate symptoms, at a sufficient concentration and for a sufficient time to elicit such an amelioration of symptoms of a condition, disorder, or disease involving cell death. The response of the animals to the exposure may be monitored by assessing the reversal of the symptoms of the condition, disorder, or disease.
  • any treatments that reverse any aspect of symptoms of a condition, disorder, or disease involving cell death, should be considered as candidates for human therapeutic intervention in such conditions, disorders, or diseases.
  • Dosages of test agents may be determined by deriving dose-response curves, as discussed in Section 5.5.1, below.
  • the polynucleotides of the present invention can be used for various other pu ⁇ oses.
  • they can be used to express recombinant protein for analysis, characterization or therapeutic use; as molecular weight markers on gels; as chromosome markers or tags (when labeled) to identify chromosomes or to map related gene positions; to compare with endogenous DNA sequences in patients to identify potential genetic conditions, disorders, or diseases; as probes to hybridize and thus discover novel, related DNA sequences; as a source of information to derive PCR primers for genetic fmge ⁇ rinting; as a probe to "subtract-out" known sequences in the process of discovering other novel polynucleotides; to raise anti- protein antibodies using DNA immunization techniques; and as an antigen to raise anti- DNA antibodies or elicit another immune response.
  • the proteins provided by the present invention can similarly be used to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its receptor) in biological fluids; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands.
  • the protein binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction)
  • the protein can be used to identify the other protein with which binding occurs or to identify inhibitors of the binding interaction.
  • Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.
  • Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation "Molecular Cloning: A Laboratory Manual”, 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and “Methods in Enzymology: Guide to Molecular Cloning Techniques", Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.
  • the compounds that are determined to affect protective sequence expression or gene product activity can be administered to a patient at therapeutically effective doses to treat or ameliorate a condition, disorder, or disease involving cell death or modulate a cell death-related process described herein.
  • a therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration of symptoms of such a condition, disorder, or disease.
  • Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD 50 /ED 50 .
  • Compounds that exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 (i.e., the concentration of the test compound that achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC 50 i.e., the concentration of the test compound that achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • a therapeutically effective amount of antibody, protein, or polypeptide ranges from about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25 mg/kg body weight, more preferably about 0.1 to 20 mg/kg body weight, and even more preferably about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight.
  • treatment of a subject with a therapeutically effective amount of a protein, polypeptide, or antibody can include a single treatment or, preferably, can include a series of treatments.
  • a subject is treated with antibody, protein, or polypeptide in the range of between about 0.1 to 20 mg/kg body weight, one time per week for between about 1 to 10 weeks, preferably between 2 to 8 weeks, more preferably between about 3 to 7 weeks, and even more preferably for about 4, 5, or 6 weeks.
  • the effective dosage of antibody, protein, or polypeptide used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result and become apparent from the results of diagnostic assays as described herein.
  • compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.
  • physiologically acceptable carriers or excipients may be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral rectal or topical administration.
  • the pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate).
  • binding agents e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose
  • fillers e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate
  • lubricants e.g., magnesium stearate, talc or silica
  • disintegrants e.g., potato starch
  • Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use.
  • Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid).
  • the preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.
  • Preparations for oral administration may be suitably formulated to give controlled release of the active compound.
  • compositions may take the form of tablets or lozenges formulated in conventional manner.
  • the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g. , dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g. , dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g. , dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g. , dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane
  • the compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion.
  • Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative.
  • the compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the active ingredient may be in powder form for constitution with a suitable vehicle, e.g. , sterile pyrogen-free water, before use.
  • the compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.
  • compositions of the invention may be desirable to administer locally to the area in need of treatment.
  • This may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
  • administration can be by direct injection at the site (or former site) of a malignant tumor or neoplastic or pre- neoplastic tissue.
  • the compounds may be combined with a carrier so that an effective dosage is delivered, based on the desired activity.
  • the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
  • the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • compositions may, if desired, be presented in a pack or dispenser device that may contain one or more unit dosage forms containing the active ingredient.
  • the pack may for example comprise metal or plastic foil, such as a blister pack.
  • the pack or dispenser device may be accompanied by instructions for administration.
  • a human fetal brain cDNA library (Gibco), in which individual clones were inserted into the Notl-Sall site of the pCMV-SPORT2 vector, was diluted 200,000 fold in LB broth (DEFCO Laboratories) containing 0.2 mg/ml ampicillin (Sigma). The diluted library (100-140 ⁇ l) was then plated and grown on LB agar (DEFCO Laboratories) bioassay plates with 0.2 mg/ml ampicillin. Plates were incubated at 37°C for 24 hours. Single colonies were then used to inoculate deep-well blocks containing 1.5 ml LB broth containing 0.2 mg/ml ampicillin.
  • Plasmid DNA was extracted using Promega MagneSil kits with a modified protocol. The pelleted bacteria were re-suspended and 50 ⁇ l was transferred into a round bottom plate that rests on a magnet. Cell Lysis Solution (50 ⁇ l) was added and the plate was incubated at room temperature without agitation for 30 seconds. Following lysis, 70 ⁇ l of a Neutralization Solution/MagneSil Paramagnetic Particles mixture (pre-mixed at a ratio of 6: 1) was added. The reaction was mixed by pipetting and incubated at room temperature without agitation for 5 minutes to allow the magnetic particles to be drawn to the magnet. The supernatant containing plasmid DNA was then transferred to a new plate and stored at -20°C.
  • the cDNA inserts of the clonally pure plasmids that are selected for their ability to protect cells from cell death when introduced into cells predisposed to undergo cell death are sequenced using the ABI Big Dye terminator Cycle Sequencing Ready Reaction Kit and subsequently analyzed on the ABI310 capillary sequencing machine (PE Biosystems, Foster City, CA).
  • plasmid DNA is mixed with 3.2 pmole of either the M13 forward or the Ml 3 reverse sequencing primer and 8 ⁇ l of the terminator ready reaction mix in a total volume of 20 ⁇ l.
  • the cycle sequencing reaction is carried out in a thermocycler (PCR machine) using standard methods known by those skilled in the art.
  • the extension products from the sequencing reaction are purified by precipitation using isopropanol. 80 ⁇ l of 75% isopropanol is added to the sample and after thorough mixing, the sample is incubated at room temperature (25°C) for 20 minutes. The sample is then centrifuged at 12,000 x g for 20 minutes at room temperature.
  • the supernatant is removed and the pellet is rinsed once by addition of 250 ⁇ l of 75% isopropanol followed by centrifugation as above for 5 minutes.
  • the supernatant is removed and the sample air- dried for 10 minutes.
  • the sample is then resuspended in 20 ⁇ l of TSR (template suppression reagent) and denatured by heating at 94°C for 2 minutes and rapidly cooling on ice.
  • TSR template suppression reagent
  • the subsequent electrophoresis and analysis is carried out on the ABI310 sequencer according to the manufacturer's protocol.
  • the entire cDNA clone is similarly sequenced by the use of sequence specific internal primers as required.
  • BLAST 2.0 algorithm Altschul et al, 1997, Nuc. Acids Res. 25:3389 against known sequences in the GeneBank sequence database maintained by NCBI (National Center for Biotechnology Information). This program uses the two-hit method to find homology within the database.
  • PFA phosphate buffered saline
  • PBS phosphate buffered saline
  • PFA is removed by aspiration and the fixed tissue washed consecutively four times in PBS for 15 minutes, changing the PBS solution between each wash.
  • the tissue is immersed in a blocking solution consisting of 10% goat serum, 2% bovine serum albumin (BSA), and 0.25% Triton X-100 for a duration of two hours.
  • BSA bovine serum albumin
  • Triton X-100 Triton X-100
  • the tissue is washed consecutively four times in PBS for 10 minutes, changing the PBS solution between each wash.
  • An anti-rabbit, flourescently conjugated secondary antibody diluted in PBS at a concentration of 1:500, is then added to the tissue and allowed to incubate at room temperature for four hours.
  • the secondary antibody solution is removed by aspiration and the tissue washed consecutively four times in PBS for 15 minutes, changing the PBS solution between each wash.
  • the tissue is mounted on glass slides and dried at 37°C for thirty minutes. A three-minute xylene incubation is performed before the addition of coverslips to preserve the slices.
  • Protective sequence CNI-00713 (SEQ ED NO: 1) comprises 1796 nucleotides. Twenty-eight (28) potential open reading frames (“ORFs") have been identified within the protective sequence and are depicted in Table 2. BLAST sequence comparison analysis of CNI-00713 against known sequences in the GenBank sequence database reveals 100% homology, at the nucleotide level, with human TSC-22 (Ac#
  • TSC-22 gene encodes a 144 amino acid long protein and was first described as a transcriptional target of TGF- ⁇ in mouse osteoblast cells. In these cells, TSC-22 is transiently induced by TGF- ⁇ with similar kinetics as c-jun. Other inducers of TSC-22 include phorbol ester (TPA), serum, cholera toxin and dexamethasone. These factors activate different cellular signals such as protein kinase C, cAMP-dependent kinase and glucocorticoid receptors. It is not induced by EGF or forskolin. TSC-22 has also been isolated from rat, chicken, human, and fly (Drosophila).
  • TSC-22 The interspecies homology is very high with the human TSC-22 being 99% identical to the rat, mouse or chicken protein.
  • the fly TSC-22 is 52% identical to the human protein.
  • TSC-22 encodes a putative transcriptional regulator, a member of the family of early response genes. It has a leucine zipper domain that is highly conserved but is not basic (in the upstream N terminal region) as the bZip family of transcriptional factors. (although the leucine zipper region is needed for dimerization, the upstream basic region is the DNA binding domain.)
  • TSC-22 is the target of follicle stimulating hormone (FSH) in rat Sertoli cells (derived from testis). In these cells, TSC-22 is not regulated by TGF- ⁇ .
  • FSH follicle stimulating hormone
  • TSC-22 binds to and activates the promoter of the CNP (C- type natriuretic peptide) gene.
  • CNP acts as local modulator (controls the release of growth hormone) in the pituitary system. It has been suggested that TSC-22 is responsible for the transmitting a signal from TGF- ⁇ to CNP.
  • the Drosophila homolog of TSC-22 protein, shs (shortsighted), is involved in the pathway leading to photoreceptor development. Loss-of- function mutation of shs leads to delay in neuronal differentiation in the eye.
  • the human TSC-22 transcript is 1.8 kb with an additional 5 kb transcript that is present in some tissues.
  • TSC-22 When transcribed and translated in an E.coli system and analyzed on SDS/PAGE, the size of TSC-22 protein is 18kDa.
  • Human TSC-22 is highly expressed in brain, lung and heart. In rats, the highest level of expression is in ovary, testis and lung. In mice, the highest level is in the bone, and it is relatively low in brain, lung and kidney. In humans, there is the possibility of developmental regulation of expression. This is based on the observation that the expression of TSC-22 is high in fetal kidney and drops in the adult kidney. Human TSC-22 has been mapped to 13ql4 by the FISH technique. TSC-22 is an apoptosis mediator.
  • TSC-22 expression is induced by the anticancer drug Vesnarinone. (TSC-22 was isolated as vesnarinone- inducible gene in a human cell line.)
  • CNI-NPP3-CNI00713 represents a deposit of a single strain. The deposit was made on the date indicated and assigned the indicated accession number:

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Abstract

L'invention concerne des compositions et des procédés permettant de traiter et de diagnostiquer des affections, des troubles ou des maladies impliquant la mort cellulaire, y compris des acides nucléiques protecteurs qui, une fois introduits dans une cellule prédisposée à mourir ou en train de mourir, permettent de prévenir ou de retarder la mort de la cellule ou de sauver la cellule. L'invention concerne les acides nucléiques de la séquence protectrice, l'expression de cellules hôtes et des animaux transgéniques, ainsi que des produits de séquence protectrice, des anticorps dirigés contre ces produits et des séquences cibles impliquées dans la mort cellulaire. L'invention concerne aussi des procédés et des compositions permettant de diagnostiquer et de traiter des affections, des troubles ou des maladies impliquant la mort cellulaire, y compris les affections du système nerveux central ou périphérique. L'invention concerne des procédés d'utilisation de la séquence protectrice, de produits et/ou d'éléments régulateurs en vue d'identifier des composés qui modulent l'expression de la séquence protectrice et/ou l'activité du produit de séquence protectrice.
PCT/US2002/021938 2001-07-13 2002-07-12 Compositions et procedes pour diagnostiquer et traiter des affections, des troubles ou des maladies impliquant la mort cellulaire WO2003006479A1 (fr)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008079877A3 (fr) * 2006-12-22 2008-11-20 Xenon Pharmaceuticals Inc Compositions et procédés destinés à diagnostiquer et à traiter des troubles associés au fer

Citations (4)

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US5958690A (en) * 1997-07-08 1999-09-28 Incyte Pharmaceuticals, Inc. Human TSC--22 Homolog
WO1999051727A2 (fr) * 1998-04-03 1999-10-14 Metagen Gesellschaft Für Genomforschung Mbh Sequences d'acides nucleiques humaines extraites des tissus sains d'ovaires
WO1999055913A2 (fr) * 1998-04-27 1999-11-04 Sidney Kimmel Cancer Center Cibles d'acide nucleique de moindre complexite et leurs methodes d'utilisation
WO2001064835A2 (fr) * 2000-02-28 2001-09-07 Hyseq, Inc. Nouveaux acides nucleiques et polypeptides

Patent Citations (4)

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Publication number Priority date Publication date Assignee Title
US5958690A (en) * 1997-07-08 1999-09-28 Incyte Pharmaceuticals, Inc. Human TSC--22 Homolog
WO1999051727A2 (fr) * 1998-04-03 1999-10-14 Metagen Gesellschaft Für Genomforschung Mbh Sequences d'acides nucleiques humaines extraites des tissus sains d'ovaires
WO1999055913A2 (fr) * 1998-04-27 1999-11-04 Sidney Kimmel Cancer Center Cibles d'acide nucleique de moindre complexite et leurs methodes d'utilisation
WO2001064835A2 (fr) * 2000-02-28 2001-09-07 Hyseq, Inc. Nouveaux acides nucleiques et polypeptides

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OMOTEHARA ET AL.: "In vivo enhancement of chemosensitivity of human salivary gland cancer cells by overexpression of TGF-beta stimulated clone 22", ONCOL. REP., vol. 7, no. 4, July 2000 (2000-07-01), pages 737 - 740, XP002959537 *
UCHIDA ET AL.: "Over-expression of TSC-22 (TGF-beta stimulated clone-22) markedly enhances 5-fluorouracil-induced apoptosis in a human salivary gland cancer cell line", LAB. INVEST., vol. 80, no. 6, June 2000 (2000-06-01), pages 955 - 963, XP002959538 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008079877A3 (fr) * 2006-12-22 2008-11-20 Xenon Pharmaceuticals Inc Compositions et procédés destinés à diagnostiquer et à traiter des troubles associés au fer

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