Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/34—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
  • C12Q1/44—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
  • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
  • G01N2333/4701—Details
  • G01N2333/4703—Regulators; Modulating activity
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/90—Enzymes; Proenzymes
  • G01N2333/914—Hydrolases (3)
  • G01N2333/916—Hydrolases (3) acting on ester bonds (3.1), e.g. phosphatases (3.1.3), phospholipases C or phospholipases D (3.1.4)
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2500/00—Screening for compounds of potential therapeutic value
  • G01N2500/02—Screening involving studying the effect of compounds C on the interaction between interacting molecules A and B (e.g. A = enzyme and B = substrate for A, or A = receptor and B = ligand for the receptor)

Definitions

• the invention was supported, in whole or in part, by a grant O1 CA78461 to RAW; NHLBI/NIH Fellowship to SKD KO8 HL04463.
• the U.S. Government has certain rights in the invention.
• Regulation of the cell cycle is important in homeostasis of both cells and organisms (e.g., mammalian cells or mammals). Disruptions in the normal regulation of the cell cycle can occur, for example, in tumors which proliferate uncontrollably, in response to DNA damage (e.g., ionizing radiation) to the cell or organism, and under conditions of stress (e.g., oxidative stress) in the cell or organism.
• DNA damage e.g., ionizing radiation
• stress e.g., oxidative stress
• the p53 tumor suppressor protein exerts anti-proliferative effects, including growth arrest, apoptosis, and cell senescence, in response to various types of stress, e.g., DNA damage (Levine, 1997; Giaccia and Kastan, 1998; Prives and Hall, 1999; Oren, 1999; Vogelstein et al, 2000). Inactivation of p53 function appears to be critical to tumorigenesis (Hollstein et al, 1999). Mutations in the p53 gene have been shown in more than half of all human tumors (Hollstein et al, 1994).
• p53 direct targets including p21CJJPl/WAFl, Mdm2, GADD45, Cyclin G, 14-3-3F, Noxa, p53ATPl, PUMA and others (Nakano and Vousden, 2001; Yu et al, 2001; Oda et al, 2000a, 2000b; El-Deriry et al, 1993; Wu et al, 1993; Barak et al, 1993; Kastan et al, 1992; Okamoto and Beach, 1994).
• p53 is a short-lived protein whose activity is maintained at low levels in normal cells.
• Tight regulation of p53 is essential for its effect on tumorigenesis as well as maintaining normal cell growth.
• the precise mechanism by which p53 is activated by cellular stress is not completely understood. It is generally thought to involve primarily post-translational modifications of p53, including phosphorylation and acetylation (reviewed in Appella and Anderson, 2000; Giaccia and Kastan, 1998).
• CBP/p300 a histone acetyl-transferase (HAT) acts as a coactivator of p53 and potentiates its transcriptional activity as well as biological function in vivo (Gu et al, 1997; Lill et al, 1997; Avantaggiati et al, 1997).
• acetylation of p53 can dramatically stimulate its sequence-specific DNA binding activity, perhaps as a result of an acetylation- induced conformational change (Gu and Roeder, 1997; Sakaguchi et al, 1998; Liu et al, 1999).
• CBP/p300 mediated acetylation of p53 was confirmed in vivo by a number of studies (reviewed in Chao et al, 2000; Ito et al, 2001).
• p53 can be acetylated at Lys320 by another HAT cofactor, PCAF, although the in vivo functional consequence needs to be further elucidated (Sakaguchi et al, 1998; Liu et al, 1999; Liu et al, 2000). Steady-state levels of acetylated p53 are stimulated in response to various types of stress (reviewed in Ito etal, 2001). Recently, by introducing a transcription defective p53 mutant (p53Q25S26) into mice, it was found that the mutant mouse thymocytes and ES cells failed to undergo DNA damage- induced apoptosis (Chao et al, 2000; Jimenez et al, 2000).
• this mutant protein was phosphorylated normally at the N-terminus in response to DNA damage but could not be acetylated at the C-terminus (Chao et al, 2000), supporting a critical role of p53 acetylation in transactivation as well as p53-dependent apoptotic response (Chao et al, 2000; Luo et al, 2000). Furthermore, it has been found that oncogenic Ras and PML upregulate acetylated p53 in normal primary fibroblasts, and induce premature senescence in a p53-dependent manner (Pearson et al, 2000; Ferbeyre et al, 2000).
• CBP/p300-dependent acetylation of p53 may be a critical event in p53-mediated transcriptional activation, apoptosis, senescence, and chromosome fragility.
• HDAC histone deacetylase
• PID/MTA2 a component of the HDACl complex, acts as an adaptor protein to enhance HDAC 1 -mediated deacetylation of p53 which is repressed by TSA (Luo et al, 2000).
• Mdm2 a negative regulator of p53, actively suppresses CBP/p300-mediated p53 acetylation, and this inhibitory effect can be abrogated by tumor suppressor pl9ARF.
• Acetylation may have a critical role in the p53-MDM2-pl9ARF feed back loop (Ito et al, 2001 ; Kobet t ⁇ /,, 2000).
• the Silent Information Regulator (SIR) family of genes represents a highly conserved group of genes present in the genomes of organisms ranging from archaebacteria to a variety of eukaryotes (Frye, 2000).
• the encoded SIR proteins are involved in diverse processes from regulation of gene silencing to DNA repair.
• the proteins encoded by members of the S1R2 gene family show high sequence conservation in a 250 amino acid core domain.
• a well-characterized gene in this family is S. cerevisiae SIR2, which is involved in silencing HM loci that contain information specifying yeast mating type, telomere position effects and cell aging (Guarente, 1999; Kaeberlein et al, 1999; Shore, 2000).
• the yeast Sir2 protein belongs to a family of histone deacetylases (reviewed in Guarente, 2000; Shore, 2000).
• the Sir2 homolog, CobB in Salmonella typhimurium, functions as an NAD (nicotinamide adenine dinucleotide)-dependent ADP-ribosyl transferase (Tsang and Escalante-Semerena, 1998).
• the Sir2 protein is a deacetylase which uses NAD as a cofactor (Imai et al, 2000; Moazed, 2001; Smith et al, 2000; Tanner et al, 2000; Tanny and Moazed, 2001). Unlike other deacetylases, many of wliich are involved in gene silencing, Sir2 is insensitive to histone deacetylase inhibitors like trichostatin A (TSA) (Imai et al, 2000; Landry et al, 2000a; Smith et al, 2000).
• TSA histone deacetylase inhibitors
• acetylation of acetyl-lysine by Sir2 is tightly coupled to NAD hydrolysis, producing nicotinamide and a novel acetyl- ADP ribose compound (1-O-acetyl-ADP-ribose) (Tanner et al, 2000; Landry et al, 2000b; Tanny and Moazed, 2001).
• the NAD-dependent deacetylase activity of Sir2 is essential for its functions which can connect its biological role with cellular metabolism in yeast (Guarente, 2000; Imai et al, 2000; Lin et al, 2000; Smith et al, 2000).
• Sir2 homologs have NAD-dependent histone deacetylase activity (Imai et al, 2000; Smith et al, 2000). Most information about Sir2 mediated functions comes from the studies in yeast (Gartenberg, 2000; Gottschling, 2000).
• Sir2 is the only protein localized in nuclei, which is critical for both gene silencing and extension of yeast life-span (reviewed in Guarente, 2000).
• mouse Sir2 ⁇ and its human ortholog SIRT1 are the closest homologs to yeast Sir2 (Imai et al, 2000; Frye, 1999, 2000) and both exhibit nuclear localization (Figure 7C).
• Homologues of Sir2 have been identified in almost all organisms examined including bacteria, which has no histone proteins (reviewed in Gray and Ekstrom, 2001; Frye, 1999; 2000; Brachmann et al, 1995). For this reason it is likely that Sir2 also targets non-histone proteins for functional regulation (Muth et ⁇ /., 2001).
• the S. cerevisiae Sir2 is involved in DNA damage responses (Martin et al, 1999; McAinsh et al, 1999; Mills et al, 1999).
• one of the primary mediators of the DNA damage response is the p53 protein (Levine, 1997; Oren, 1999; Vogelstein et al, 2000).
• the p53 protein is protected from rapid degradation and acquires transcription-activating functions, these changes being achieved largely through post- translational modifications (Abraham et al, 2000; Cannian et al, 1998; Chehab et al, 1999; Sakaguchi et al, 1998; Shieh et al, 2000; Siliciano et al, 1997).
• Transcriptional activation of p53 protein in turn upregulates promoters of a number of genes including p21 WAFl (el-Deiry et al, 1993) that promotes cell cycle exit or death-inducing proteins like PIDD (Lin et al, 2000).
• the p53 protein is phosphorylated in response to DNA damage (Siliciano et al, 1997). There are at least 13 different residues both at the N and C terminal portions of p53 protein that are phosphorylated by various kinases (Appella and Anderson, 2000). For example, the ATM and ATR proteins phosphorylate p53 at residue Serl5 (Khanna et al, 1998; Siliciano et al, 1997; Tibbetts et al, 1999) and Chkl/2 kinases at residue Ser20 (Chehab et al, 1999; Shieh et /., 2000).
• Modification of Serl5 is important for the functional activation of the p53 protein.
• Phosphorylation of Serl5 may increase the affinity of the p300 acetylase for p53 (Dumaz and Meek, 1999; Lambert et al, 1998).
• p53 is acetylated in vitro by p300 at Lys 370-372, 381 and 382 (Gu and Roeder, 1997).
• p53 is also acetylated in vivo at Lys 373 and Lys 382 (Abraham et al, 2000; Sakaguchi et al, 1998).
• MDM2 protein which is involved in the negative regulation of p53 (Oren, 1999) and can suppress acetylation of p53 protein by p300 (Ito et al, 2001; Kobet et al, 2000). While acetylation by p300 and deacetylation by the TSA-sensitive HDAC1 complex (Luo et al, 2000) have been shown to be important in regulation of p53 protein activity, the remaining factors responsible for its regulation as a transcription factor remain elusive.
• the SIR complex in Saccharomyces cerevisiae was originally identified through its involvement in the maintenance of chromatin silencing at telomeres and at mating type loci. It is composed of four components, Sirlp, Sir2p, Sir3p, and Sir4p, that normally reside at yeast telomeres.
• the SIR complexes relocate to the site of double- stranded breaks where they participate in the repair of the lesions by non-homologous end joining. This DNA damage response is dependent on the function of the MEC1/RAD9 DNA checkpoint pathway.
• MECl is a homolog of the ATM protein that coordinates the DNA damage response in mammalian cells, in part by triggering the cascade of events that lead to the stabilization of the p53 protein (Canman et al, 1998).
• Another major function of Sir2, gene silencing, is closely tied to the regulation of lifespan in S. cerevisiae (Guarente, 1999).
• Double-strand breaks in the genome of mammals invoke a cascade of signaling events that ultimately cause phosphorylation and subsequent stabilization of p53 protein.
• these strand breaks lead to activation of p53 protein as a transcription factor. This activation may be due largely to its acetylation (Gu and Roeder, 1997; Sakaguchi et al, 1998).
• the resulting stabilized, activated p53 protein contributes to the upregulation of cyclin-dependent kinase inhibitors such as p21WAFl and hence to the cytostatic effects of p53.
• the apoptotic effects of p53 may predominate through its ability to induce expression of pro-apoptotic proteins such as PLOD (Lin et al, 2000).
• pro-apoptotic proteins such as PLOD (Lin et al, 2000).
• modulators of Sir2 and/or p53 activity would be useful in modulating various cellular processes including, e.g., repair of DNA damage, apoptosis, oncogenesis, gene silencing and senescence, inter alia.
• the present invention relates to methods and compositions employing p53 and Sir2 proteins.
• Cellular and organismal processes are regulated by modulating the activity of Sir2 and/or p53.
• the regulated processes control a program of regulated aging and/or metabolism of a cell or an organism.
• Compounds that regulate the activity of Sir2 and/or p53 can be identified, for example, by a method described herein.
• the term "Sir2" refers to a protein that is at least 25% identical to the 250 amino acid conserved Sir2 core catalytic domain, amino acids 258-451 of SEQ ID NO. 12.
• a Sir2 protein can be for example, at least 30, 40, 50, 60, 70, 80, 85, 90, 95, 99% identical to amino acids 258-451 of SEQ ID NO. 12.
• the Sir2 protein is human SIRTl, GenBank Accession No: AF083106. There are at least seven different Sir2 homologs present in mammalian cells (Frye, 1999, 2000; Imai et al, 2000; Gray and Ekstrom, 2001). The mouse Sir2 ⁇ and human SIRTl, are preferred Sir2 proteins.
• Sir2 can be aprotein (e.g., SEQ ID NOS. 8, 10, 12, 14, 16 or 18) or a fragment of the protein capable of deacetylating a substrate in the presence or NAD and/or an NAD analog and/or a fragment capable of binding to a target protein, e.g., a transcription factor. Such functions can be evaluated by a method described herein.
• a Sir2 fragment can include a "domain" which is a structurally stable folded unit of the full-length protein.
• the Sir2 protein can be encoded by the nucleic acid sequence of SEQ ID NOS. 7, 9, 11, 13, 15 or 17. In a preferred embodiment, the Sir2 is a human Sir2.
• a model of the three-dimensional structure of a Sir2 protein has been determined (see, e.g., Bedalov et al. (2001), Min et al. (2001), Finnin et al., (2001)) and provides guidance for identifying domains of Sir2.
• a “full length” Sir2 protein refers to a protein that has at least the length of a naturally- occurring Sir2 protein.
• a “full length” Sir2 protein or a fragment thereof can also include other sequences, e.g., a purification tag., or other attached compounds, e.g., an attached fluorophore, or cofactor.
• the invention includes sequences and variants that include one or more substitutions, e.g., between one and six substitutions, e.g., with respect to a naturally-occurring protein. Whether or not a particular substitution will be tolerated can be determined by a method described herein. One or more or all substitutions may be conservative.
• a "conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art.
• amino acids with basic side chains e.g., lysine, arginine, histidine
• acidic side chains e.g., aspartic acid, glutamic acid
• uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine
• nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
• beta-branched side chains e.g., threonine, valine, isoleucine
• aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
• nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 50% identity, preferably 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%o, 97%, 98%), 99%), or higher identity over a specified region (e.g., the C.
• sequence comparison methodology such as BLAST or BLAST 2.0 with default parameters described below, or by manual alignment and visual inspection.
• sequences are then said to be "substantially identical.”
• This definition also refers to, or may be applied to, the complement of a test nucleic acid sequence.
• the definition also includes sequences that have deletions and/or additions, as well as those that have substitutions.
• the preferred algorithms can account for gaps and the like.
• identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is at least 50 or 100 amino acids or nucleotides in length.
• the p53 polypeptide can have greater than or equal to 25%, 50%, 75%, 80%, 90% overall identity or greater than or equal to 30%, 50%, 75%, 80%, 90% overall similarity to SEQ ID NO. 3.
• the Sir2 or p53 polypeptide is a human protein (e.g., as described herein), although it may also be desirable to analyze Sir2 or p53 polypeptides isolated from other organisms such as yeast, worms, flies, fish, reptiles, birds, mammals (especially rodents), and primates using the methods of the invention.
• the invention features a method of screening a compound.
• the method includes providing a reaction mixture including Sir2, a transcription factor, and the compound, and determining if the compound modulates Sir2 interaction with, e.g., binding, of the transcription factor. Determining if the compound modulates Sir2binding may be accomplished by methods known in the art, including comparing the binding of Sir2 to the transcription factor at a first concentration of the compound and at a second concentration of the compound. In a further embodiment, either of the first or second concentration of the compound may be zero, e.g., as a reference or control.
• the reaction mixture also includes a Sir2 cofactor, such as NAD or an NAD analog.
• the transcription factor is p53 or a Sir-2 binding fragment thereof.
• the transcription factor, e.g., p53, or fragment thereof may be acetylated or labeled.
• the transcription factor is an acetylated p53 fragment, and the fragment includes lysine 382.
• the Sir2 included in the reaction mixture is a Sir2 variant, e.g., a variant that has reduced deacetylase activity, such as the H363 Y mutation.
• the Sir2 may be human, e.g., human SIRTl.
• the Sir2 maybe murine, e.g., Sir2 ⁇ .
• the Sir2 is exogenous and expressed from a heterologous nucleic acid.
• the transcription factor may be exogenous and expressed from a heterologous nucleic acid.
• the method of screening can be used to identify compounds that modulate, e.g., increase or decrease, cell growth, modulate, e.g., slow or speed, aging, modulate, e.g., increase or decrease, lifespan, modulate cellular metabolism, e.g., by increasing or decreasing a metabolic function or rate.
• the invention features a method of screening a compound by providing a reaction mixture comprising Sir2, a transcription factor, and the compound, and determining if the compound modulates Sir2-mediated deacetylation of the transcription factor.
• the step of determining if the compound modulates Sir2-mediated deacetylation of the transcription factor may be performed by methods known in the art, including comparing the binding of Sir2 to the transcription factor at a first concentration of the compound and at a second concentration of the compound.
• either of the first or second concentration of the compound may be zero, e.g., as a reference or control.
• the reaction mixture also includes a Sir2 cofactor, such as NAD or an NAD analog.
• the transcription factor is p53 or a Sir-2 binding fragment thereof.
• the p53 or fragment thereof may be acetylated or labeled.
• the transcription factor is an acetylated p53 fragment, and the fragment includes lysine 382.
• the Sir2 included in the reaction mixture is a Sir2 variant that has reduced deacetylase activity, such as the H363Y mutation.
• the Sir2 maybe human, e.g., human SIRTl.
• the Sir2 maybe murine, e.g., Sir2a.
• the Sir2 is exogenous and expressed from a heterologous nucleic acid.
• the transcription factor may be exogenous and expressed from a heterologous nucleic acid.
• the method of screening can be used to identify compounds that modulate, e.g., increase or decrease, cell growth, modulate, e.g., slow or speed, aging, modulate, e.g., increase or decrease, lifespan, modulate cellular metabolism, e.g., by increasing or decreasing a metabolic function or rate.
• the present invention also relates to a method of screening a compound by providing a compound that interacts with Sir2, e.g., a compound that binds Sir2; contacting the compound with a cell or a system; and determining if the compound modulates transcription of a p53- regulated gene. Determining if the compound modulates transcription of a p53-regulated gene may be by any of the methods known in the art, including comparing the modulation of transcription of a p53-regulated gene at a first concentration of the compound and at a second concentration of the compound. In a further embodiment, either of the first or second concentration of the compound may be zero, e.g., as a reference or control.
• the invention features a method of evaluating a compound, the method comprising: contacting Sir2 or a transcription factor, e.g., p53, with a test compound; evaluating an interaction between the test compound and the Sir2 or the transcription factor, e.g., p53; contacting a cell or organism that produces the Sir2 or transcription factor polypeptide with the test compound; and evaluating the effect of the test compound on the rate of aging on the cell or organism.
• a transcription factor e.g., p53
• the interaction can, for example, be a physical interaction, e.g., a direct binding interaction, a covalent change in one or both of the test compound or the Sir2 or transcription factor, a change in location of the test compound (e.g., a change in subcellular localization), or a functional interaction (e.g., an alteration in activity, stability, structure, or activity of the polypeptide).
• a physical interaction e.g., a direct binding interaction
• a covalent change in one or both of the test compound or the Sir2 or transcription factor e.g., a change in location of the test compound (e.g., a change in subcellular localization)
• a functional interaction e.g., an alteration in activity, stability, structure, or activity of the polypeptide.
• the method is repeated one or more times such that, e.g., a library of test compounds can be evaluated.
• the evaluating of the interaction with the test compound and the Sir2 or the transcription factor, e.g., p53 is repeated, and the evaluating of the rate of aging is selectively used for compounds for which an interaction is detected.
• Possible test compounds include, e.g., small organic molecules, peptides, antibodies, and nucleic acid molecules.
• the interaction between the test compound and the Sir2 or transcription factor, e.g., p53 is evaluated in vitro, e.g., using an isolated polypeptide.
• the Sir2 or transcription factor, e.g., p53, polypeptide can be in solution (e.g., in a micelle) or bound to a solid support, e.g., a column, agarose beads, a plastic well or dish, or a chip (e.g., a microarray).
• a solid support e.g., a column, agarose beads, a plastic well or dish, or a chip (e.g., a microarray).
• the test compound can be in solution or bound to a solid support.
• the interaction between the test compound and the Sir2 or transcription factor, e.g., p53 is evaluated using a cell-based assay.
• the cell can be a yeast cell, an invertebrate cell (e.g., a fly cell), or a vertebrate cell (e.g., aXenopus oocyte or a mammalian cell, e.g., a mouse or human cell).
• the cell-based assay measures the activity of the Sir2 or transcription factor, e.g., p53, polypeptide.
• the effect of the test compound on the rate of aging of a cell or animal is evaluated only if an interaction between the test compound and the Sir2 or transcription factor, e.g., p53, is observed.
• the cell is a transgenic cell, e.g., a cell having a transgene.
• the transgene encodes a protein that is normally exogenous to the transgenic cell, h some embodiments, the transgene encodes a human protein, e.g., a human Sir2 or transcription factor, e.g., p53, polypeptide.
• the transgene is linked to a heterologous promoter. In other embodiments, the transgene is linked to its native promoter.
• the cell is isolated from an organism that has been contacted with the test compound. In other embodiments, the cell is contacted directly with the test compound.
• the rate of aging of an organism e.g., an invertebrate (e.g., a worm or a fly) or a vertebrate (e.g., a rodent, e.g., a mouse) is determined.
• an invertebrate e.g., a worm or a fly
• a vertebrate e.g., a rodent, e.g., a mouse
• the rate of aging of an organism can be determined by a variety of methods, e.g., by one or more of: a) assessing the life span of the cell or the organism; (b) assessing the presence or abundance of a gene transcript or gene product in the cell or organism that has a biological age-dependent expression pattern; (c) evaluating resistance of the cell or organism to stress, e.g., genotoxic stress (e.g., etopicide, UV irradition, exposure to a mutagen, and so forth) or oxidative stress; (d) evaluating one or more metabolic parameters of the cell or organism; (e) evaluating the proliferative capacity of the cell or a set of cells present in the organism; (f) evaluating physical appearance or behavior of the cell or organism, and (g) assessing the presence or absence of a gene transcript or gene product in the cell or organism that has a p53-regulation-dependent expression pattern.
• stress e.g., genotoxic stress (e.g., etop
• evaluating the rate of aging includes directly measuring the average life span of a group of animals (e.g., a group of genetically matched animals) and comparing the resulting average to the average life span of a control group of animals (e.g., a group of animals that did not receive the test compound but are genetically matched to the group of animals that did receive the test compound).
• a control group of animals e.g., a group of animals that did not receive the test compound but are genetically matched to the group of animals that did receive the test compound.
• the rate of aging of an organism can be determined by measuring an age-related parameter.
• age-related parameters include: appearance, e.g., visible signs of age; the expression of one or more genes or proteins (e.g., genes or proteins that have an age-related expression pattern); resistance to oxidative stress; metabolic parameters (e.g., protein synthesis or degradation, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.); and cellular proliferation (e.g., of retinal cells, bone cells, white blood cells, etc.).
• the organism is a transgenic animal.
• the transgenic animal can include a transgene that encodes, e.g., a copy of a Sir2 or transcription factor protein, e.g., a p53 protein, e.g., the Sir2 or transcription factor, e.g., a p53 polypeptide that was evaluated for an interaction with the test compound.
• the transgene encodes a protein that is normally exogenous to the transgenic animal.
• the transgene can encode a human protein, e.g., a human Sir2 or transcription factor, e.g., p53, polypeptide.
• the transgene is linked to a heterologous promoter. In other embodiments, the transgene is linked to its native promoter.
• the transgenic animal further comprises a genetic alteration, e.g., a point mutation, insertion, or deficiency, in a gene encoding an endogenous Sir2 or transcription factor, e.g., p53, protein, such that the expression or activity of the endogenous Sir2 or transcription factor protein is reduced or eliminated.
• a genetic alteration e.g., a point mutation, insertion, or deficiency
• an endogenous Sir2 or transcription factor e.g., p53, protein
• the organism is on a calorically rich diet, while in other embodiments the organism is on a calorically restricted diet.
• the invention features a method of evaluating a protein, comprising: identifying or selecting a candidate protein, wherein the candidate protein is a Sir2 or transcription factor, e.g. p53, polypeptide; altering the sequence, expression or activity of the candidate protein in a cell or in one or more cells of an organism; and determining whether the alteration has an effect on the interaction, e.g., binding, of Sir2 with a transcription factor, e.g. p53, or on the deacetylation of transcription factor, e.g. p53.
• the candidate protein is identified by amplification of the gene or a portion tliereof encoding the candidate protein, e.g., using a method described herein, e.g., PCR amplification or the screening of a nucleic acid library.
• the candidate protein is identified by searching a database, e.g., searching a sequence database for protein sequences homologous to Sir2 or a transcription factor, e.g., p53.
• the candidate protein is a human protein.
• the candidate protein is a mammalian protein, e.g., a mouse protein, hi other embodiments, the protein is a vertebrate protein, e.g., a fish, bird or reptile protein, or an invertebrate protein, e.g., a worm or insect protein.
• the protein is a eukaryotic protein, e.g., yeast protein.
• the invention features method of evaluating a protein, the method comprising a) identifying or selecting a candidate protein, wherein the candidate protein is Sir2 or a transcription factor, e.g., p53; b) identifying one or more polymorphisms in a gene, e.g., one or more SNPs that encodes the candidate protein; and c) assessing correspondence between the presence of one or more of the polymorphisms and an interaction, e.g., binding, of Sir2 with the transcription factor, e.g., p53, or with the deacetylation of the transcription factor, e.g., p53.
• the polymorphisms can be naturally occurring or laboratory induced, hi one embodiment, the organism is an invertebrate, e.g., a fly or nematode; in another embodiment the organism is a mammal, e.g., a rodent or human.
• a variety of statistical and genetic methods can be used to assess correspondence between a polymorphism and longevity. Such correlative methods include determination of linkage disequilibrium, LOD scores, and the like.
• the invention features a method of modulating cell growth in an animal, e.g., a mammal, by modulating the Sir2-mediated deacetylation of a transcription factor in the animal.
• the method includes modulating cell growth by increasing acetylation of p53.
• the method includes inactivating Sir2, e.g., by the use of antisense, RNAi, antibodies, intrabodies, NAD depletion, a dominant negative mutant of Sir2, or by the addition of Sir2 cofactor-analogs, e.g., NAD analogs such as those described in Vaziri et al. (1997) or nicotinamide.
• the method includes introducing a deacetylation-resistant form of p53.
• the invention is a method for treating a mammal, e.g., a mammal having a disease characterized by unwanted cell proliferation, e.g., cancer, accelerated senescence-related disorders, inflammatory and autoimmune disorders, Alzheimer's disease, and aging-related disorders.
• a mammal e.g., a mammal having a disease characterized by unwanted cell proliferation, e.g., cancer, accelerated senescence-related disorders, inflammatory and autoimmune disorders, Alzheimer's disease, and aging-related disorders.
• the method includes modulating cell growth by decreasing acetylation of p53.
• the method includes increasing NAD concentrations, hi a further embodiment, the method includes increasing Sir2 concentrations, e.g. by addition of purified Sir2, by expression of Sir2 from heterologous genes, or by increasing the expression of endogenous Sir2, or by the addition of Sir2 cofactor-analogs, e.g., NAD analogs such as those described in Vaziri et al. (1997).
• the present invention also relates to a method of modulating the growth of a cell in vivo or in vitro by modulating the Sir2-mediated deacetylation of a transcription factor in the cell.
• the method includes modulating the growth of a cell by increasing acetylation of p53, thereby decreasing cell growth.
• the method includes inactivating Sir2, e.g., by the use of antisense, RNAi, antibodies, intrabodies, NAD depletion, a dominant negative mutant of Sir2, or nicotinamide, or decreasing Sir2 activity by the addition of Sir2 cofactor-analogs, e.g., NAD analogs such as those described in Vaziri et al. (1997).
• the method includes introducing a deacetylation-resistant form ofp53.
• the method includes modulating the growth of a cell by decreasing acetylation of p53, thereby increasing cell growth.
• the method includes increasing NAD concentrations
• the method includes increasing Sir2 concentrations, e.g. by addition of purified Sir2, by expression of Sir2 from heterologous genes, or by increasing the expression of endogenous Sir2, or by the addition of Sir2 cofactor-analogs, e.g., NAD analogs such as those described in Vaziri et al. (1997).
• the invention features a method of directing Sir2 to a transcription factor binding site, e.g., ap53 binding site, and thereby modifying the acetylation status of the binding site on histone or DNA.
• the method includes providing a Sir2-transcription factor complex under conditions such that the transcription factor targets Sir2 to the transcription factor binding site, allowing the Sir 2 to modify the acetylation status of histones and DNA at the transcription factor binding site.
• the method is performed in vivo or in vitro, e.g., in an animal or in a cell.
• the Sir2-transcription factor complex is provided at a different stage of development of the cell or animal or at a greater concentration than occurs naturally.
• the Sir2 or transcription factor or both is increased, e.g., by supplying exogenous Sir2 and/or transcription factor, e.g., p53, by supplying an exogenous nucleic acid encoding Sir2 or transcription factor, e.g., p53, or by inducing endogenous production of Sir2 or a transcription factor, e.g., p53.
• the present invention relates to a method of evaluating a compound, e.g., a potential modulator of Sir2 or transcription factor, e.g., p53 activity, comprising the steps of contacting the transcription factor, e.g., p53, Sir2, and NAD or an NAD analog with the compound; evaluating an interaction between the compound and one or more of the transcription factor, e.g., p53, Sir2, and a cofactor such as NAD or an NAD analog; contacting the compound with a cell or organism having transcription factor, e.g., p53 or Sir2 activity; and evaluating the rate of aging of the cell or organism.
• a compound e.g., a potential modulator of Sir2 or transcription factor, e.g., p53 activity
• evaluating the rate of aging comprises one or more of: a) assessing the life span of the cell or organism; b) assessing the presence or absence of a gene transcript or gene product in the cell or organism that has a biological age-dependent expression pattern; c) evaluating resistance of the cell or organism to stress; d) evaluating one or more metabolic parameters of the cell or organism; e) evaluating the proliferative capacity of the cell or a set of cells present in the organism; f) evaluating physical appearance, behavior, or other characteristic of the cell or organism; and g) assessing the presence or absence of a gene transcript or gene product in the cell or organism that has a p53-regulation-dependent expression pattern.
• (A) is an autoradiograph demonstrating direct interactions of Sir2 ⁇ with GST-p53.
• the GST-p53 full length protein (GST-p53) (lane 1), the N-terminus of p53 protein (1-73) (lane 2), the middle part of p53 (100-290) (lane 3), the C-terminus of ⁇ 53 (290-393) (lane 4), and GST alone (lane 6) were used in GST pull-down assay with in vitro translated 35 S-labeled full length mouse Sir2 ⁇ .
• (B) is two western blots demonstrating p53 interactions with Sir2 ⁇ in H1299 cells.
• the cells were either transfected with p53 (lanes 3, 4) or Sir2 ⁇ (lanes 7, 8) alone, or cotransfected with p53 and Sir2 ⁇ (lanes 1, 2, 5, 6).
• C is a schematic representation of the high homology regions between mouse Sir2 ⁇ and human SIRTl (hSIRTl). The core domain represents the very conserved enzymatic domain among all Sir2 family proteins (Frye, 1999, 2000).
• D is a western blot demonstrating p53 interactions with human SIRTl in H1299 cells.
• FIG. 1 P53 interacts with mammalian Sir2 ⁇ (mouse Sir2 ⁇ and hSIRTl) in normal cells.
• (A) is two western blots demonstrating the interaction between p53 and hSIRTl in H460 cells.
• (B) is two western blots demonstrating the interaction between p53 and Sir2 ⁇ in F9 cells.
• (C) The interaction between p53 and hSIRTl un HCT116 cells either at the normal condition (lanes, 1-3) or after DNA damage treatment by etoposide (lanes, 4-6).
• A Colloidal blue staining of a SDS-PAGE gel containing protein Marker (lane 1), a control eluate from M2 loaded with untransfected cell extract (lane 2), and 100 ng of the highly purified Flag-tagged Sir2 ⁇ recombinant protein (lane 3).
• B Deacetylation of p53 by Sir2 ⁇ , 2.5 ⁇ g of 14C-labeled acetylated p53 (lane 1) was incubated with either the control eludate (lane 4), the purified 10 ng of Sir2 ⁇ (lanes 2 and 3), or the same amount of Sir2 ⁇ in the presence of 500 nM TSA (lane 5) for 60 min at 30EC.
• NAD 50 ⁇ m was also added in each reaction except lane 2.
• the proteins were analyzed by resolution on SDS-PAGE and autoradiography (upper) or Coomassie blue staining (lower). (C). Reduction of the steady-state levels of acetylated p53 by both mouse Sir2 ⁇ and human SIRTl expression.
• Figure 4 Abrogation of mammalian Sir2 ⁇ mediated deacetylation of p53 by nicotinamide.
• Figure 5 Bar graphs illustrating repression of p53-mediated transcriptional activation by mammalian Sir2 ⁇ .
• (A), (B) MEF (p53-/-) cells were transiently transfected with 10 ng of CMV-p53 alone, or in combination with indicated Sir2 ⁇ constructs together with either the PG13-Luc reporter construct (A), or a control reporter construct (TK-Luc) (B) by calcium phosphate precipitation essentially as previously described (Luo et al, 2000).
• MEF (p53-/-) cells were transiently transfected with 10 ng of CMV-p53 alone, or in combination with 5:g of either CMV- Sir2 ⁇ , or CMV-hSIRTl, or CMV-hSIRT5 (C), or CMV-Sir2 ⁇ H355A as indicated (D) together with the PG13-Luc reporter construct. All transfections were done in duplicate and representative experiments depict the average of three experiments with standard deviations indicated.
• H1299 cells were transfected with p53 alone, or cotransfected with p53 and Sir2 ⁇ , or cotransfected with p53 and Sir2 ⁇ H355A. After transfection, the cells were fixed, stained for p53 by FITC-conjugated ⁇ -p53 antibody, and analyzed by flow cymtometry for apoptotic cells (subGl) according to DNA content (PI staining).
• B The experiments were repeated at least three times; this bar graph depicts the average of three experiments with standard deviations indicated.
• Figure 7 Inhibition of p53-dependent apoptotic response to stress by mammalian Sir2 ⁇ .
• the blot was probed the anti-hSir2 antibody and a polyclonal sheep anti-p53 antibody (bottom panel).
• D p53 protein was immunoprecipitated with the Do-1 anti-p53 antibody from lysates of non-irradiated and irradiated (6Gy) BJT cells (expressing telomerase) that had been stably infected with pYESir2wt and pYESir2HY mutant vectors.
• the blot was probed with anti-hSir2 antibody and rabbit anti-p53 polyclonal antibodies (CM1+SC6243).
• Figure 9 Effect of hSir2 expression on p53 acetylation in vitro.
• B J cells expressing telomerase were stably infected with either a wild type hSir2 or a mutant hSir2HY virus.
• the hSir2-expressing mass cultures were subjected to 6Gy of ionizing radiation in presence of low concentrations of TSA (O.lmg/ml) and the p53 acetylation was measured at indicated time points by immunoblotting with Ab-1 that recognizes specifically the deacetylated K382 p53 protein. The blots were subsequently probed with anti-p53, anti-p21, anti- ⁇ actin and anti-hSir2 antibodies. Time (hrs) post 6 Gy of irradiation is shown inside the brackets.
• (A) is a bar graph depicting transcriptional activity of p53 protein, as measured in H1299 cells by co-transfection p53 with a p21 WAFl promoter-luciferase construct (p21Pluc). Transcriptional activity of p53 protein was measured upon ectopic expression of wild type hSir2, hSir2HY.
• (B) is a bar graph illustrating results from control SV40-Luciferase transfections with CMVp53 and increasing amounts of wild type hSir2 in to H1299 cells and luciferase activity was measured and expressed as Relative Light Unit (%RLU).
• (A) is a bar graph illustrating ectopic expression of hSir2wt and its influence on p53-dependent apoptosis in H1299 cells.
• H1299 cells were transfected with a wild type p53 expression construct to induce p53-dependent apoptosis.
• Annexin V positive and propidium iodide negative cells were measured.
• (B) is a line graph comparison of gamma-ray survival. Dose-response curves are shown for different types of BJ cells treated with ionizing radiation while growing exponentially and asynchronously. Twelve days after radiation the colonies were counted and survival calculated as described previously (Dhar et al, 2000). The ataxia-telangiectasia (A-T) cell line was used a positive control to indicate radiosensitivity in an exponentially growing population.
• A-T ataxia-telangiectasia
• Figures 13 A and 13B The coding nucleic acid (SEQ ID NO. 2) and deduced amino acid (SEQ ID NO. 3) of human p53.
• Figure 14 The nucleic acid (SEQ ID NO. 4) sequence of human p53 (GenBank Accession No: K03199). Figures 15 A, B, C and D. The nucleic acid (SEQ ID NO. 5) and deduced amino acid sequence (SEQ ID NO. 6) of mouse Sir2.
• Figures 16 A, B and C The nucleic acid (SEQ ID NO. 7) and deduced amino acid sequence (SEQ ID NO. 8) of mouse Sir2 GenBank Accession No: AF214646.
• Figures 17A and B The nucleic acid (SEQ ID NO. 9) and deduced amino acid sequence (SEQ ID NO. 10) of human Sir2 S1RT2 GenBank Accession No: AF083107.
• Figures 18 A, B and C The nucleic acid (SEQ ID NO. 11) and deduced amino acid sequence (SEQ ID NO. 12) of human Sir2 SIRTl GenBank Accession No: AF083106.
• FIG. 13 The nucleic acid (SEQ ID NO. 13) and deduced amino acid sequence (SEQ ID NO. 14) of human Sir2 S1RT3 GenBank Accession No: AF083108.
• Figures 20A and B The nucleic acid (SEQ ID NO. 15) and deduced amino acid sequence (SEQ ID NO. 16) of human Sir2 S1RT4 GenBank Accession No: AF083109.
• Figures 21 A and B The nucleic acid (SEQ ID NO. 17) and deduced amino acid sequence (SEQ ID NO. 18) of human Sir2 S1RT5 GenBank Accession No: AF083110.
• hSir2 directly binds the human p53 protein both in vitro and in vivo and can deacetylate p53, e.g., at the K382 residue of p53.
• a functional consequence of this deacetylation is an attenuation of the p53 protein's activity, e.g., as a transcription factor operating at a cellular promoter, e.g., the p21WAFl promoter.
• hSir2 activity attenuates the p53-dependent apoptotic response.
• hSir2 can negatively regulate a program of cellular death.
• Sir2 proteins can also deacetylate histones.
• Sir2 can deacetylate lysines 9 or 14 of histone H3. Histone deacetylation alters local chromatin structure and consequently can regulate the transcription of a gene in that vicinity.
• Sir2 proteins can bind to a number of other proteins, termed "Sir2-binding partners.”
• Sir2-binding partners For example, hSIRTl binds to p53.
• the Sir-2 binding partners are transcription factors, e.g., proteins that recognize specific DNA sites. Interaction between Sir2 and Sir2-binding partners delivers Sir2 to specific regions of a genome and can result in local modification of substrates, e.g., histones and transcription factors localized to the specific region.
• cellular processes can be regulated by compounds that alter (e.g., enhance or diminish) the ability of a Sir2 protein to interact with a Sir2-binding partner or that alter that ability of a Sir2 protein to modify a substrate.
• a Sir2-transcription factor complex may be directed to a region of DNA with a transcription factor binding site; once there, Sir2 may alter the acetylation status of the region, e.g., by deacetylating histones, non-histone proteins, and/or DNA. This would locally raise the concentration of Sir2 and may potentially result in the Sir2-mediated silencing of genes located at or near transcription-factor binding sites.
• Certain organismal programs such as aging or metabolism and disorders such as cancer can be controlled using such compounds.
• signals indicating the successful completion of DNA repair may be relayed via hSir2 to acetylated proteins like p53 that have been charged with the task of imposing a growth arrest following DNA damage.
• These signals enable hSir2 to reverse part or all of the damage-induced activation of p53 as a transcription factor by deacetylating the K382 residue of p53.
• hSir2 reduces the likelihood of subsequent apoptosis and, at the same time, makes it possible for cells to re-enter the active cell cycle, enabling them to return to the physiological state that they enjoyed prior to sustaining damage to their genomes.
• hiactivation of the p53 signaling pathway is involved in the pathogenesis of most if not all human tumors (Hollstein et al, 1994; Lohrum and Vousden, 1999). In about half of these tumors, mutation of the p53 gene itself suffices to derail function. In some of the remaining tumors, loss of pl4 ARF , which acts to down-regulate p53 protein levels, has been implicated (Lohrum and Vousden, 1999; Prives and Hall, 1999).
• the present invention is related to the discovery of a novel mode by which an incipient cancer cell attenuate at least some p53 functions via modulation of the activity of hSir2, which, like the other two genetic strategies, may result in the inactivation of both the cytostatic and pro-apoptotic functions of p53.
• the invention is thus based in part on the discovery of the existence of a p53 regulatory pathway that is regulated by mammalian Sir2 ⁇ .
• Sir2 ⁇ is involved in gene silencing and extension of life span in yeast and C. elegans (reviewed in Guarente, 2000; Shore, 2000; Kaeberlein et al, 1999; Tissenbaun and Guarente, 2001).
• p53 binds to mouse Sir2 ⁇ as well as its human ortholog hSIRTl both in vitro and in vivo.
• p53 is a substrate for the NAD-dependent deacetylase activity of mammalian Sir2 ⁇ .
• Sir2 ⁇ -mediated deacetylation antagonizes p53- dependent transcriptional activation and apoptosis.
• Sir2 ⁇ -mediated deacetylation of p53 is inhibited by nicotinamide both in vitro and in vivo.
• Sir2 ⁇ specifically inhibits p53-dependent apoptosis in response to DNA damage and/or oxidative stress, but not p53-independent, Fas- mediated cell death.
• compounds that alter can be used to regulate processes downstream of p53, e.g., apoptosis.
• Such compounds may alter the catalytic activity of Sir2 for a substrate such as p53 or may alter the interaction between Sir2 and p53.
• the present invention relates to the discovery that p53 is a binding partner of mammalian Sir2 ⁇ , which physically binds to p53 both in vitro and in vivo.
• ⁇ 53 is also a substrate of Sir2.
• Sir2 ⁇ specifically represses p53-mediated functions including p53-dependent apoptotic response to stress.
• p53 can be, for example, the mature protein (e.g., SEQ ID NO. 3) or a fragment thereof.
• the p53 protein can be encoded by the nucleic acid sequence of SEQ ID NOS. 2 and/or 4).
• p53 is the human p53.
• Deacetylation of p53 can be mediated by Sir2,e.g., in combination with a cofactor, such as NAD and/or an NAD analog.
• deacetylating p53 refers to the removal of one or more acetyl groups (e.g., CH 3 CO 2" ) from p53 that is acetylated on at least one amino acid residue.
• p53 is deacetylated at a lysine of p53 selected from the group consisting of lysine 370, lysine 371, lysine 372, lysine 381 and lysine 382 of SEQ ID NO. 3.
• p53 can be deacetylated in the presence or absence of DNA damage or oxidative cellular stress.
• the DNA damage can be caused by, for example, ionizing radiation (e.g., 6 Gy of ionizing radiation), or a tumor or some other uncontrolled cell proliferation.
• p53 is deacetylated in the presence of DNA damage or oxidative stress by combining p53, Sir2, NAD and/or an NAD analog.
• Sir2 can be the mature protein (e.g., SEQ ID NOS. 8, 10, 12, 14, 16 or 18) or a fragment of the mature protein capable of deacetylating p53 in the presence or NAD and/or an NAD analog.
• the Sir2 protein can be encoded by the nucleic acid sequence of SEQ ID NOS. 7, 9, 11, 13, 15 or 17).
• the Sir2 is human Sir2.
• the invention is a method of deacetylating p53 comprising the step of combining Sir2 and NAD and/or an NAD analog with p53.
• the combination can be performed in the presence or the absence of cells.
• Such combinations can be in tissue culture (e.g., BJT cells, MCF-7 cells) or in an organism (e.g., a mammal, e.g., as a human).
• Combination of p53, Sir2 and NAD and/or an NAD analog can be any placement of p53, Sir 2 and NAD or a NAD analog in sufficient proximity to cause Sir2 to deacetylate p53 that is acetylated on at least one amino acid residue, which deacetylation by Sir2 requires the presence of NAD and/or an NAD analog.
• NAD refers to nicotinamide adenine dinucleotide.
• An “NAD analog” as used herein refers to a compound (e.g., a synthetic or naturally occurring chemical, drug, protein, peptide, small organic molecule) which possesses structural similarity to component groups of NAD (e.g., adenine, ribose and phosphate groups) or functional similarity (e.g., deacetylates p53 in the presence of Sir2).
• component groups of NAD e.g., adenine, ribose and phosphate groups
• functional similarity e.g., deacetylates p53 in the presence of Sir2
• an NAD analog can be 3-aminobenzamide or 1,3- dihydroisoquinoline (H. Vaziri et al, EMBO J. 16:6018-6033 (1997), the entire teachings of which are hereby incorporated by reference).
• p53 activity refers to one or more activity of p53, e.g., p-53 mediated apoptosis, cell cycle arrest, and/or senescence,
• Modulating p53 activity refers to increasing or decreasing p53 activity, e.g., p-53 mediated apoptosis, cell cycle arrest, and/or senescence, e.g. by altering the acetylation or phosphorylation status of p53.
• Acetylation status refers to the presence or absence of one or more acetyl groups (e.g., CH 3 CO 2" ) at one or more lysine (K) residues, e.g., K370, K371, K372, K381, and/or K382 of SEQ ID NO. 3.
• “Altering the acetylation status” refers to adding or removing one or more acetyl groups (e.g., CH 3 CO 2" ) at one or more lysine (K) residues, e.g., K370, K371, K372, K381, and/or . K382 of SEQ ID NO. 3, e.g., by modulating Sir2 activity.
• phosphorylation status refers to the presence or absence of one or more phosphate groups (PO 3 " ) at one or more residues, e.g., serine 15 and/or serine 20 of SEQ ID NO. 3.
• Altering the phosphorylation status refers to adding or removing one or more phosphate groups (PO " ) at one or more residues, e.g., serine 15 and/or serine 20 of SEQ ID NO. 3.
• sir2 activity refers to one or more activity of Sir2, e.g., deacetylation of p53 or histone proteins.
• Modulating Sir2 activity refers to increasing or decreasing one or more activity of Sir2, e.g., deacetylation of p53 or histone proteins, e.g., by altering the binding affinity of Sir2 and p52, introducing exogenous Sir2 (e.g., by expressing or adding purified recombinant Sir2), increasing or decreasing levels of NAD and/or an NAD analog (e.g., 3-aminobenzamide, 1,3- dihydroxyisoquinoline), and/or increasing or decreasing levels of a Sir2 inhibitor, e.g., nicotinamide and/or a nicotinamide analog. Additionally or alternatively, modulating Sir2 activity can be accomplished by expressing, e.g. by transfection, a dominant negative gene of Sir2 (e.g., SirHY). The dominant negative gene can, for example, reduce the activity of endogenous Sir2 on p53 deacetylation thereby modulating the activity of Sir2.
• a dominant negative gene of Sir2 e
• nicotinamide analog refers to a compound (e.g., a synthetic or naturally occurring chemical, drug, protein, peptide, small organic molecule) which possesses structural similarity to component groups of nicotinamide or functional similarity (e.g., reduces Sir2 deacetylation activity of p53).
• the Sir2 ⁇ -mediated pathway is critical for cells under stress
• Sir2 ⁇ -mediated pathway can be critical for cell survival when the p53 negative-control mediated by Mdm2 is severely attenuated in response to DNA damage or other types of stress.
• p53 is often found in latent or inactive forms and the levels of p53 protein are very low in unstressed cells, mainly due to the tight regulation by Mdm2 through functional inhibition and protein degradation mechanisms (reviewed in Freedman et al, 1999).
• p53 is phosphorylated at multiple sites at the N-terminus; these phosphorylation events contribute to p53 stabilization and activation by preventing Mdm2 binding to p53 (reviewed in Appella and Anderson, 2000; Giaccia and Kastan, 1998; Shieh et al, 1997, 2000; Unger et al, 1999; Hirao et al, 2000). Mdm2 itself is also phosphorylated by ATM during DNA damage response, and this modification attenuates its inhibitory potential on p53 (Maya et al, 2001).
• Mdm2-mediated pathway is abrogated by induction of p 14 (or mouse p 19 ) in these cells (Honda and Yasuda, 1999; Weber et al, 1999; Tao et al, 1999a, 1999b; Zhang et al, 1998; Pomerantz et al, 1998). Furthermore, when primary fibroblasts undergo senescence, a progressive increase of the p53 acetylation levels was observed in serially passaged cells (Pearson et al, 2000).
• mammalian Sir2 ⁇ -mediated regulation may also play an important role in oncogene-induced premature senescence.
• p53-mediated transcriptional activation is sufficient and also absolutely required for its effect on cell growth arrest, while both transactivation-dependent and - independent pathways are involved in p53-mediated apoptosis (reviewed in Prives and Hall, 1999; Vousden, 2000).
• p53 may be effective to induce apoptosis by activating pro-apoptotic genes in vivo (reviewed in Nakano and Vousden, 2001; Yu et al, 2001).
• tight regulation of p53-mediated transactivation is critical for its effect on both cell growth and apoptosis (Chao et al, 2000; Jimenez et al, 2000).
• Sir2 appears to repress amino acid biosynthesis genes, which are not located at traditional "silenced" loci (Bernstein et al, 2000).
• silencing repression
• ribosomal DNA reviewed in Guarente, 2000; Shore, 2000
• Sir2 may also be targeted to specific endogenous genes for transcriptional regulation in yeast.
• the mouse Sir2 ⁇ protein does not colocalize with nucleoli, telomeres or centromeres by co-immunofluorescence assay, indicating that this protein is not associated with the most highly tandemly repeated DNA in the mouse genome.
• the immunostaining pattern of human SIRTl as well as mouse Sir2 ⁇ indicates that mammalian Sir2 ⁇ is, similar to HDAC1, broadly localized in the nucleus, further supporting the notion that mammalian Sir2 may be recruited to specific target genes for transcriptional regulation in vivo.
• Mammalian Sir2 ⁇ may inhibit p53-mediated functions by attenuation of the transcriptional activation potential of p53. Since deacetylation of p53 is critical, but may not be the only function mediated by this Sir2 ⁇ -p53 interaction, additional functions mediated by Sir2 ⁇ , such as histone deacetylation, may also contribute to this regulation. As one theory, not meant to be limiting, p53 and Sir2 ⁇ may strongly interact to deacetylate p53 and possibly recruit the p53- Sir2 ⁇ complex to the target promoter. The subsequent transcription repression may act both through decreasing p53 transactivation capability and through Sir2 ⁇ -mediated histone deacetylation at the target promoter region. In contrast to HDAC 1 -mediated effect, this transcriptional regulation is not affected by TSA treatment. Other cellular factors may use a similar mechanism to recruit Sir2 for TSA-insensitive transcriptional regulation in mammalian cells. Novel implications for cancer therapy
• HDAC-mediated deacetylase inhibitors including sodium butyrate, TSA, SAHA and others, have been also proposed as antitumor drugs (Butler et al, 2000; Finnin et al, 1999; Taunton et al, 1996; Yoshida et al, 1995; Buckley et al, 1996). Combining DNA damage drags, HDAC-mediated deacetylase inhibitors, and Sir2 ⁇ -mediated deacetylase inhibitors, may have synergistic effects in cancer therapy for maximally activating p53.
• the invention shows that mammalian Sir2oc-mediated effect on p53 is NAD-dependent, indicating that this type of regulation is closely linked to cellular metabolism (reviewed Guarente 2000; Alfred, 2000; Campisi, 2000; Min et al, 2001).
• null mutants of NPTl a gene that functions in NAD synthesis, show phenotypes similar to that of Sir2 mutants in gene silencing (Smith et al, 2000) and in life extension in response to caloric restriction in yeast (Lin et al, 2000).
• metabolic rate may play a role in Sir2 ⁇ -mediated regulation of p53 function and, perhaps, modulate the sensitivity of cells inp53-dependent apoptotic response.
• the invention is a method of modulating p53-mediated apoptosis by modulating Sir2 activity.
• Sir2 activity can be modulated as described herein (e.g., overexpressing Sir2, transfecting a cell with a dominant negative regulating gene).
• An increase in Sir2 activity e.g., by overexpressing Sir2
• a decrease in Sir2 activity e.g., transfecting a cell with a dominant negative gene
• the invention is a method of screening for a a small organic or inorganic molecule) which modulates (e.g., increases or decreases) Sir2- mediated deacetylation of p53.
• the method, Sir2, p53, NAD and/or an NAD analog, and the compound to be tested are combined, the Sir2-mediated deacetylation of p53 is measured and compared to the Sir2-mediated deacetylation of p53 measured in the absence of the compound.
• An increase in the Sir2-mediated deacetylation of p53 in the presence of the compound being tested compared to the Sir2 -mediated deacetylation of p53 in the absence of the compound indicates that the compound increases Sir2 deacetylation of p53.
• Sir2-mediated deacetylation refers to the NAD-dependent removal of acetyl groups which requires Sir2.
• the present invention relates to a method of screening a compound by providing an in vitro test mixture comprising a transcription factor or a fragment thereof, Sir2, and a Sir2 cofactor with the compound, evaluating an activity of a component of the test mixture in the presence of the compound, and comparing the activity in the presence of the compound to a reference obtained in the absence of the compound.
• the present invention relates to a method of screening a compound that is a potential NAD analog by providing an in vitro test mixture comprising a transcription factor or a fragment thereof, Sir2, and the compound, evaluating an activity of a component of the test mixture in the presence of the compound, and comparing the activity in the presence of the compound to a reference obtained in the absence of the compound,
• the Sir2 is human, e.g., human SIRTl. In another embodiment, the Sir2 is murine, e.g., murine Sir2 .
• the Sir2 cofactor is NAD or an NAD analog.
• the transcription factor is p53 or a fragment thereof, and it may be acetylated and/or labeled.
• the evaluated activity is Sir2 activity, e.g., deacetylation of a protein, e.g., deacetylation of a histone protein, and/or deacetylation of the transcription factor, e.g., deacetylation of p53.
• the Sir2 activity may also be binding of a protein, e.g., binding of a histone protein and/or binding of the transcription factor, e.g.,. binding of p53.
• the Sir2 activity may be evaluated by detecting production of nicotinamide.
• the evaluated activity is p53 activity.
• the p53 activity may be evaluated by detecting cell cycle arrest, apoptosis, senescence, and/or a change in the levels of transcription or translation products of a gene regulated by p53. Methods for detecting such changes and genes regulated by p53 are known in the art and include those methods and genes disclosed in U.S. Pat. No. 6,171,789, which is incorporated herein by reference in its entirety.
• the test mixture is provided in a cell-free system.
• the test mixture is provided in a cell-based system, wherein one of the components is exogenous.
• exogenous refers to a component that is either added directly, or expressed from a heterologous DNA source, such as transfected DNA. Many methods are known in the art for expression of heterologous or exogenous gene products.
• the evaluated activity is an effect on the rate of aging of a cell or organism. Such an effect may be evaluated by contacting the compound with a cell or organism having p53 or Sir2 activity, e.g., endogenous or exogenous p53 or Sir2 activity; and evaluating the rate of aging of the cell or organism.
• the rate of aging may be evaluated by several methods, including: a) assessing the life span of the cell or organism; b) assessing the presence or absence of a gene transcript or gene product in the cell or organism that has a biological age-dependent expression pattern; c) evaluating resistance of the cell or organism to stress; d) evaluating one or more metabolic parameters of the cell or organism; e) evaluating the proliferative capacity of the cell or a set of cells present in the organism; f) evaluating physical appearance, behavior, or other characteristic of the cell or organism; and
• the compounds identified by the methods of the invention can be used, for example, to treat cancer (e.g., a compound which decreases Sir2-mediated deacetylation of p53) or prevent p53-mediated apoptosis (e.g., acompound which increases Sir2-mediated deacetylation of p53).
• the compounds can be used in methods of treating a cell or an organism, e.g., a cell or organism that has been exposed to DNA-damaging ionizing radiation, by modulating Sir2 activity in the cell.
• Sir2 activity can be reduced.
• Sir2 activity is reduced by nicotinamide or a nicotinamide analog.
• the invention is a method of screening for analogs of NAD.
• Sir2, p53 and a compound to be tested as an analog of NAD are combined.
• Deacetylation of the p53 by the Sir2 is measured and compared to the measured deacetylation of p53 by Sir2 in the presence of NAD.
• a compound which, for example, promotes Sir2-mediated deacetylation of p53 when combined with Sir2 and p53 is an NAD analog and can be used in place of NAD, for example, as a cofactor with Sir2 to prevent or decrease p53-mediated apoptosis.
• the invention is a method of treating cancer in a mammal comprising the step of modulating Sir2 activity in tumor cells to cause an increase in p53 activity.
• the Sir2 activity can be modulated as described herein (e.g., overexpression of Sir2, transfection of a cell with a dominant negative regulatory gene, or nicotinamide or a nicotinamide analog).
• the invention includes a method of treating a cell that has been exposed to ionizing radiation, the method comprising modulating Sir2 activity in the cell.
• Sir2 activity in a cell which has undergone DNA damage or oxidative stress, can be modulated to reduce Sir2 activity (e.g., by transfecting a cell with a dominant negative regulatory gene, or by addition or expression of nicotinamide or a nicotinamide analog) which can result in the arrest of the growth cycle of the cell, allowing the cell to repair at least a portion of the DNA damage caused by the ionizing radiation. Once the cell has repaired a portion of the DNA damage, the reduction in Sir2 activity can be removed and the cell cycle of the cell resumed.
• the invention includes an isolated protein complex of Sir2 and acetylated p53.
• p53 can also be phosphorylated (e.g., on one or both of serine 15 or serine 20 of SEQ LD NO. 3).
• the compounds or NAD analogs identified by the methods of the invention can be used in the treatment of diseases or conditions such as cancer, or following DNA damage or oxidative stress.
• the compounds or NAD analogs can be admimstered alone or as mixtures with conventional excipients, such as pharmaceutically, or physiologically, acceptable organic, or inorganic carrier substances such as water, salt solutions (e.g., Ringer's solution), alcohols, oils and gelatins.
• Such preparations can be sterilized and, if desired, mixed with lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like which do not deleteriously react with the NAD analogs or compounds identified by the methods of the invention.
• the dosage and frequency (single or multiple doses) of the compound or NAD analog administered to a mammal can vary depending upon a variety of factors, including the duration of DNA damage, oxidative stress or cancer condition.
• the rate of aging of a cell e.g., a yeast cell, invertebrate cell (e.g., fly cell), or vertebrate cell (e.g., mammalian cell, e.g., human or mouse cell) is determined.
• the rate of aging of the cell can be evaluated by measuring the expression of one or more genes or proteins (e.g., genes or proteins that have an age-related expression pattern), by measuring the cell's resistance to stress, e.g., genotoxic stress or oxidative stress, by measuring one or more metabolic parameters (e.g., protein synthesis or degradation, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels within the cell, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.), by measuring cellular proliferation, or any combination of measurements thereof.
• stress e.g., genotoxic stress or oxidative stress
• metabolic parameters e.g., protein synthesis or degradation, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels within the cell, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.
• the rate of aging of an organism e.g., an invertebrate (e.g., a worm or a fly) or a vertebrate (e.g., a rodent, e.g., a mouse) is determined.
• the rate of aging of an organism can be determined by directly measuring the average life span of a group of animals (e.g., a group of genetically matched animals) and comparing the resulting average to the average life span of a control group of animals (e.g., a group of animals that did not receive the test compound but are genetically matched to the group of animals that did receive the test compound).
• the rate of aging of an organism can be determined visually, e.g., by looking for visible signs of age (e.g., physical appearance or behavior), by measuring the expression of one or more genes or proteins (e.g., genes or proteins that have an age-related expression pattern), by measuring the cell's resistance to genotoxic (e.g., caused by exposure to etoposide, UV irradiation, mutagens, etc.) or oxidative stress, by measuring one or more metabolic parameters (e.g., protein synthesis or degradation, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.), by measuring cellular proliferation (e.g., of retinal cells, bone cells, white blood cells, etc.), or any combination of measurements thereof.
• the visual assessment is for evidence of apoptosis, e.g., nuclear fragmentation.
• characteristics of aging can be quite obvious.
• characteristics of older humans include skin wrinkling, graying of the hair, baldness, and cataracts, as well as hypermelanosis, osteoporosis, cerebral cortical atrophy, lymphoid depletion, thymic atrophy, increased incidence of diabetes type II, atherosclerosis, cancer, and heart disease. Nehlin et al. (2000), Annals NY Acad Sci 980: 176-79.
• mammalian aging include weight loss, lordokyphosis (hunchback spine), absence of vigor, lymphoid atrophy, decreased bone density, dermal thickening and subcutaneous adipose tissue, decreased ability to tolerate stress (including heat or cold, wounding, anesthesia, and hematopoietic precursor cell ablation), liver pathology, atrophy of intestinal villi, skin ulceration, amyloid deposits, and joint diseases. Tyner et al. (2002), Nature 415:45-53.
• characteristics of aging in other eukaryotes include slow movement, flaccidity, yolk accumulation, intestinal autofluorescence (lipofuscin), loss of ability to eat food or dispel waste, necrotic cavities in tissues, and germ cell appearance.
• aging process is also manifested at the cellular level, as well as in mitochondria.
• Cellular aging is manifested in loss of doubling capacity, increased levels of apoptosis, changes in differentiated phenotype, and changes in metabolism, e.g., decreased levels of protein synthesis and turnover.
• biological age can be deduced from patterns of gene expression, resistance to stress (e.g., oxidative or genotoxic stress), rate of cellular proliferation, and the metabolic characteristics of cells (e.g., rates of protein synthesis and turnover, mitochondrial function, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels within the cell, levels of a Krebs cycle intermediate in the cell, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.).
• stress e.g., oxidative or genotoxic stress
• rate of cellular proliferation e.g., rate of cellular proliferation
• metabolic characteristics of cells e.g., rates of protein synthesis and turnover, mitochondrial function, ubiquinone biosynthesis, cholesterol biosynthesis, ATP levels within the cell, levels of a Krebs cycle intermediate in the cell, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, etc.
• biological age is a measure of the age of a cell or organism based upon the molecular characteristics of the cell or organism. Biological age is distinct from “temporal age,” which refers to the age of a cell or organism as measured by days, months, and years.
• p53 may lead to cell cycle arrest or to apoptosis; Sir2 can suppress this effect by deacetylating p53.
• the expression or activity of p53 and/or Sir2 gene products in an organism can be a determinant of the rate of aging and life span of the organism. Reduction in the level and/or activity of such gene products would reduce the rate of aging and may ameliorate (at least temporarily) the symptoms of aging.
• a variety of techniques may be utilized to inhibit the expression, synthesis, or activity of such target genes and/or proteins.
• Such molecules may include, but are not limited to small organic molecules, peptides, antibodies, antisense, ribozyme molecules, triple helix molecules, and the like.
• the following assays provide methods (also referred to herein as "evaluating a compound” or “screening a compound”) for identifying modulators, i.e., candidate or test compounds (e.g., peptides, peptidomimetics, small molecules or other drugs) wliich modulate Sir2 or p53 activity, e.g., have a stimulatory or inhibitory effect on, for example, Sir2 or p53 expression or activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a Sir2 or p53 substrate.
• modulators i.e., candidate or test compounds (e.g., peptides, peptidomimetics, small molecules or other drugs)
• wliich modulate Sir2 or p53 activity e.g., have a stimulatory or inhibitory effect on, for example, Sir2 or p53 expression or activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a Sir2 or
• assays may be performed in animals, e.g., mammals, in organs, in cells, in cell extracts, e.g., purified or unpurified nuclear extracts, intracellular extracts, in purified preparations, in cell-free systems, in cell fractions enriched for certain components, e.g., organelles or compounds, or in other systems known in the art.
• animal e.g., mammals, in organs, in cells, in cell extracts, e.g., purified or unpurified nuclear extracts, intracellular extracts, in purified preparations, in cell-free systems, in cell fractions enriched for certain components, e.g., organelles or compounds, or in other systems known in the art.
• cell extracts e.g., purified or unpurified nuclear extracts, intracellular extracts, in purified preparations, in cell-free systems, in cell fractions enriched for certain components, e.g., organelles or compounds, or in other systems known in the art.
• cell extracts e.
• transgenic cell e.g., with a transgene encoding Sir2 or p53 or a mutant thereof;
• the compound is, for example, a peptide, protein, antibody or small organic molecule; e.g., the compound interferes with or disrupts an interaction between Sir2 and a transcription factor
• proximity assays that detect interaction between Sir2 and a transcription factor (e.g., p53), or fragments thereof, for example, fluorescence proximity assays.
• two hybrid assays can be evaluated in the presence of a test compound, e.g., to determine if the test compound disrupts or interferes with an interaction.
• Two hybrid assays can, for example, be conducted using yeast or bacterial systems.
• radio-labelled substrates e.g. 35 S, 3 H, 14 C, e.g., to determine acetylation status, metabolic status, rate of protein synthesis, inter alia.
• One embodiment herein accordingly comprises methods for the identification of small molecule drug candidates from large libraries of compounds that appear to have therapeutic activity to affect metabolic maintenance and/or to reverse or prevent cell death and thus exhibits potential therapeutic utility, such as the ability to enhance longevity.
• Small organic molecules and peptides having effective inhibitory activity may be designed de novo, identified through assays or screens, or obtained by a combination of the two techniques.
• Non-protein drug design may be carried out using computer graphic modeling to design non-peptide, organic molecules able to bind to p53 or Sir2.
• NMR nuclear magnetic resonance
• Small molecules may also be developed by generating a library of molecules, selecting for those molecules which act as ligands for a specified target, (using protein functional assays, for example), and identifying the selected ligands. See, e.g., Kohl et al, Science 260: 1934, 1993. Techniques for constructing and screening combinatorial libraries of small molecules or oligomeric biomolecules to identify those that specifically bind to a given receptor protein are known. Suitable oligomers include peptides, oligonucleotides, carbohydrates, nonoligonucleotides (e.g., phosphorothioate oligonucleotides; see Chem. and Engineering News, page 20, 7 Feb.
• Known screening methods may be used by those skilled in the art to screen combinatorial libraries to identify active molecules. For example, an increase (or decrease) in p53 or Sir2 activity due to contact with an agonist or antagonist can be monitored.
• assays for screening candidate or test compounds that are substrates of a Sir2 or p53 protein or polypeptide or biologically active portion thereof are provided
• assays for screening candidate or test compounds which bind to or modulate the activity of a Sir2 or p53 protein or polypeptide or biologically active portion thereof, e.g., modulate the ability of Sir2 or p53 to interact with a ligand are provided.
• assays for screening candidate or test compounds for the ability to bind to or modulate the activity of a Sir2 or p53 protein or polypeptide and to also alter the rate of aging of a cell or an organism are provided.
• the compounds tested as modulators of Sir2 or p53 can be any small chemical compound, or a biological entity, such as a protein, e.g., an antibody, a sugar, a nucleic acid, e.g., an antisense oligonucleotide or a ribozyme, or a lipid.
• modulators can be genetically altered versions of Sir2 or p53.
• test compounds will be small chemical molecules and peptides, or antibodies, antisense molecules, or ribozymes.
• any chemical compound can be used as a potential modulator or ligand in the assays of the invention, although most often compounds that can be dissolved in aqueous or organic (especially DMSO- based) solutions are used.
• the assays are designed to screen large chemical libraries by automating the assay steps and providing compounds from any convenient source to assays, which are typically run in parallel (e.g., in microtiter formats on microtiter plates in robotic assays). It will be appreciated that there are many suppliers of chemical compounds, including Sigma (St. Louis, MO), Aldrich (St. Louis, MO), Sigma- Aldrich (St. Louis, MO), Fluka Chemika-Biochemica Analytika (Buchs Switzerland) and the like.
• high throughput screening methods known to one of ordinary skill in the art involve providing a combinatorial chemical or peptide library containing a large number of potential therapeutic compounds (potential modulator or ligand compounds). Such "combinatorial chemical libraries” or “ligand libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
• a combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical "building blocks" such as reagents.
• a linear combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks (amino acids) in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks.
• a combinatorial library can be designed to sample a family of compounds based on a parental compound, e.g., based on the chemical structure of NAD or nicotinamide.
• combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent 5,010,175, Furka, / ⁇ t. J. Pept. Prot. Res. 37:487-493 (1991) and Houghton et al, Nature 354:84-88 (1991)).
• Other chemistries for generating chemical diversity libraries can also be used.
• Such chemistries include, but are not limited to: peptoids (e.g., PCT Publication No. WO 91/19735), encoded peptides (e.g., PCT Publication No.
• WO 93/20242 random bio-oligomers (e.g., PCT Publication No. WO 92/00091), benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al, Proc. Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al, J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal peptidomimetics with glucose scaffolding (Hirschmann et al, J. Amer. Chem. Soc.
• Patent 5,539,083) antibody libraries (see, e.g., Vaughn et al, Nature Biotechnology, 14(3):309-314 (1996) and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al, Science, 274:1520-1522 (1996) and U.S. Patent 5,593,853), small organic molecule libraries (see, e.g., benzodiazepines, Baum C&EN, Jan 18, page 33 (1993); isoprenoids, U.S. Patent 5,569,588; thiazolidinones and metathiazanones, U.S. Patent 5,549,974; pyrrolidines, U.S. Patents 5,525,735 and 5,519,134; morpholino compounds, U.S. Patent 5,506,337; benzodiazepines, 5,288,514, and the like).
• antibody libraries see, e.g., Vaughn et al, Nature Biotechnology, 14(3):
• the invention provides solid phase based in vitro assays in a high throughput format, e.g., where each assay includes a cell or tissue expressing Sir2 and/or p53.
• a high throughput assays it is possible to screen up to several thousand different modulators or ligands in a single day.
• each well of a microtiter plate can be used to run a separate assay against a selected potential modulator, or, if concentration or incubation time effects are to be observed, every 5-10 wells can test a single modulator.
• a single standard microtiter plate can assay about 96 modulators. If 1536 well plates are used, then a single plate can easily assay from about 100- about 1500 different compounds. It is possible to assay many plates per day; assay screens for up to about 6,000, 20,000, 50,000, or 100,000 or more different compounds are possible using the integrated systems of the invention.
• Candidate Sir2- or p53-interacting molecules encompass many chemical classes. They can be organic molecules, preferably small organic compounds having molecular weights of 50 to 2,500 Daltons.
• the candidate molecules comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, for example, carbonyl, hydroxyl, and carboxyl groups.
• the candidate molecules can comprise cyclic carbon or heterocyclic structures and aromatic or polyaromatic structures substituted with the above groups, hi one embodiment, the candidate molecules are structurally and/or chemically related to NAD or to nicotinamide.
• combinatorial library refers to collections of diverse oligomeric biomolecules of differing sequence, which can be screened simultaneously for activity as a ligand for a particular target.
• Combinatorial libraries may also be referred to as "shape libraries", i.e., a population of randomized fragments that are potential ligands.
• shape of a molecule refers to those features of a molecule that govern its interactions with other molecules, including Van der Waals, hydrophobic, electrostatic and dynamic.
• Nucleic acid molecules may also act as ligands for receptor proteins. See, e.g., Edgington, BIO /Technology 11: 285, 1993.
• U.S. P.N. 5,270,163 to Gold and Tuerk describes a method for identifying nucleic acid ligands for a given target molecule by selecting from a library of RNA molecules with randomized sequences those molecules that bind specifically to the target molecule.
• a method for the in vitro selection of RNA molecules immunologically cross-reactive with a specific peptide is disclosed in Tsai et al, Proc. Natl. Acad. Sci. USA 89: 8864, (1992); and Tsai et al. Immunology 150:1137, (1993).
• an antiserum raised against a peptide is used to select RNA molecules from a library of RNA molecules; selected RNA molecules and the peptide compete for antibody binding, indicating that the RNA epitope functions as a specific inhibitor of the antibody-antigen interaction.
• Antibodies that are both specific for a target gene protein and that interfere with its activity may be used to inhibit target gene function. Such antibodies may be generated using standard techniques, against the proteins themselves or against peptides corresponding to portions of the proteins. Such antibodies include but are not limited to polyclonal, monoclonal, Fab fragments, single chain antibodies, chimeric antibodies, and the like. Where fragments of the antibody are used, the smallest inhibitory fragment which binds to the target protein's binding domain is preferred. For example, peptides having an amino acid sequence corresponding to the domain of the variable region of the antibody that binds to the target gene protein may be used.
• Such peptides may be synthesized chemically or produced via recombinant DNA technology using methods well known in the art (e.g., see Sambrook et al, Eds., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, (1989), or Ausubel, F. M. et al, eds. Current Protocols in Molecular Biology (1994).
• single chain neutralizing antibodies that bind to intracellular target gene epitopes may also be administered.
• Such single chain antibodies may be administered, for example, by expressing nucleotide sequences encoding single-chain antibodies within the target cell population by utilizing, for example, techniques such as those described in Marasco et al, Proc. Natl. Acad. Sci. USA 90: 7889-7893 (1993).
• Sir2 or p53 can be a full- length protein or an active fragment. Additional methods include those methods that allow for the simultaneous identification of genes that encode proteins that interact with Sir2 or p53. These methods include, for example, probing expression libraries using a labeled Sir2 or p53 protein, Sir2 or p53 fragment, or Sir2 or p53 fusion protein.
• the two-hybrid system utilizes plasmids constructed to encode two hybrid proteins: one plasmid comprises the nucleotides encoding the DNA binding domain of a transcriptional activator protein fused to the Sir2 or p53 nucleotide sequence encoding the Sir2 or p53 polypeptide, and the other plasmid comprises the nucleotides encoding the transcriptional activator protein's activation domain fused to a cDNA encoding an unknown protein that has been recombined into the plasmid from a cDNA library.
• the DNA binding domain fusion plasmid and the cDNA fusion protein library plasmids are transformed into a strain of yeast that contains a reporter gene, for example lacZ, whose regulatory region contains the activator's binding site. Either hybrid protein alone cannot activate translation of the reporter gene because it is lacking either the DNA binding domain or the activator domain. Interaction of the two hybrid proteins, however, reconstitutes a functional activator protein and results in activation of the reporter gene that is detected by an assay for the reporter gene product. The colonies that reconstitute activator activity are purified and the library plasmids responsible for reporter gene activity are isolated and sequenced. The DNA sequence is then used to identify the protein encoded by the library plasmid.
• a reporter gene for example lacZ
• Macromolecules that interact with Sir2 or p53 are referred to as Sir2 or p53 binding partners.
• Sir2 or p53 binding partners are likely to be involved in the regulation of Sir2 or p53 function. Therefore, it is possible to identify compounds that interfere with the interaction between Sir2 or p53 and its binding partners.
• the basic principle of assay systems used to identify compounds that interfere with the interaction of Sir2 or ⁇ 53 and a binding partner is to prepare a reaction mixture containing Sir2 or p53 or a Sir2 or p53 fragment and the binding partner under conditions that allow complex formation.
• the reaction mixture is prepared in the presence or absence of the test compound to test for inhibitory activity.
• the test compound may be added prior to or subsequent to Sir2/ or p53/binding partner complex formation.
• the formation of a complex in a control but not with the test compound confirms that the test compound interferes with complex formation.
• the assay can be conducted either in the solid phase or in the liquid phase.
• an assay is a cell-based assay comprising contacting a cell expressing Sir2 or p53 with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of Sir2 or p53.
• a preferred activity is the deacetylation function of Sir2 on p53; a further preferred activity is the ability of p53 to cause ERU cycle arrest or apoptosis. Determining the ability of the test compound to modulate the activity of Sir2 or p53 can be accomplished, for example, by determining the ability of Sir2 or p53 to bind to or interact with the test molecule, or by determining the ability of the test molecule to stimulate or inhibit the activity of Sir2 or p53.
• Cell-based systems can be used to identify compounds that inhibit Sir2 or p53.
• Such cells can be recombinant or non-recombinant, such as cell lines that express the Sir2 or p53 gene.
• Preferred systems are mammalian or yeast cells that express Sir2 or p53.
• cells are exposed to compounds suspected of ameliorating body weight disorders or increasing lifespan. After exposure, the cells are assayed, for example, for expression of the Sir2 or p53 gene or activity of the Sir2 or p53 protein. Alternatively, the cells are assayed for phenotypes such as those resembling body weight disorders or lifespan extension.
• the cells may also be assayed for the inhibition of the deacetylation function of Sir2 on p53, or the apoptotic or cytostatic function of p53. •
• Another preferred cell for a cell-based assay comprises a yeast cell transformed with a vector comprising the Sir2 or p53 gene.
• a yeast cell expressing Sir2 or p53 is to mutagenize the yeast and screen for yeast that will survive only when the Sir2 or p53 polypeptide is functioning normally. Synthetic lethal screens are described in Holtzman et al (1993), J. Cell Bio. 122: 635-644. The yeast that require Sir2 or p53 function for survival can then be used to screen test compounds for those that inhibit Sir2 or p53 activity. Test compounds that results in a decrease in yeast survival are likely inliibitors of Sir2 or p53 in this system.
• an assay is a cell-free assay in which Sir2 or p53 protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the Sir2 or p53 protein or biologically active portion thereof is determined. Binding of the test compound to the Sir2 or p53 protein can be determined either directly or indirectly as described above.
• the assay includes contacting the Sir2 or p53 protein or biologically active portion thereof with a known compound which binds Sir2 or p53 to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an Sir2 or p53 protein, wherein determining the ability of the test compound to interact with an Sir2 or p53 protein comprises determining the ability of the test compound to preferentially bind to Sir2 or p53 or a biologically active portion thereof as compared to the known compound.
• an assay is a cell-free system in which Sir2 protein or biologically active portion thereof is contacted with p53 protein or biologically active portion thereof, to form a mixture comprising a detectable amount bound p53:Sir complex. And a test compound is contacted with the mixture, and the ability of the compound to effect the stability or formation of the p53:Sir2 complex is determined. Interaction of the test compound with he p53:Sir2 complex may be determined directly or by methods known in the art.
• the method comprises contacting p53 with Sir2 to form a mixture comprising the p53:Sir2 complex, further contacting the mixture with a compound to be tested, and evaluating the binding kinetics of p53:Sir2 complex both in the presence and the absence of the test compound to directly bind the p53:Sir2 complex is evaluated.
• the cell-free assays are amenable to use of both soluble and/or membrane-bound forms of proteins. In the case of cell-free assays in which a membrane-bound form of a protein is used it may be desirable to utilize a solubilizing agent such that the membrane-bound form of the protein is maintained in solution.
• solubilizing agents include non-ionic detergents such as n-octylglucoside, n- dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N- methylglucamide, Triton X-100, Triton X-114, Thesit, Isotridecypoly(ethylene glycol ether)n, 3- [(3-cholamidopropyl)dimethylarnmonio]-l-propane sulfonate (CHAPS), 3-[(3- cholamidopropyl)dimethylammonio]-2-hydroxy-l -propane sulfonate (CHAPSO), orN- dodecyl,N,N-dimethyl-3-amino-l-propane sulfonate.
• non-ionic detergents such as n-octylglucoside,
• binding of a test compound to an Sir2 or p53 protein, or interaction of an Sir2 or p53 protein with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes.
• a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
• glutathione-S-transferase/Sir2 or /p53 fusion proteins or glutathione-S- transferase/target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or Sir2 or p53 protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH).
• the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above.
• the complexes can be dissociated from the matrix, and the level of Sir2 or p53 binding or activity determined using standard techniques.
• a Sir2 or p53 protein or a Sir2 or p53 target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
• Biotinylated Sir2 or p53 protein or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, 111.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
• antibodies reactive with Sir2 or p53 protein or target molecules but which do not interfere with binding of the Sir2 or p53 protein to its target molecule can be derivatized to the wells of the plate, and unbound target Sir2 or p53 protein trapped in the wells by antibody conjugation.
• Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the Sir2 or p53 protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the Sir2 or p53 protein or target molecule.
• non-human organisms e.g., transgenic non-human organisms
• a transgenic organism is one in which a heterologous DNA sequence is chromosomally integrated into the germ cells of the animal.
• a transgenic organism will also have the transgene integrated into the chromosomes of its somatic cells.
• Organisms of any species including, but not limited to: yeast, worms, flies, fish, reptiles, birds, mammals (e.g., mice, rats, rabbits, guinea pigs, pigs, micro-pigs, and goats), and non- human primates (e.g., baboons, monkeys, chimpanzees) may be used in the methods of the invention.
• mammals e.g., mice, rats, rabbits, guinea pigs, pigs, micro-pigs, and goats
• non- human primates e.g., baboons, monkeys, chimpanzees
• the invention features a method of identifying a compound that alters the rate of aging of a cell or an organism, comprising: contacting a Sir2 or p53 polypeptide with a test compound; evaluating an interaction between the test compound and the Sir2 or p53 polypeptide; and further evaluating the effect of the test compound on the rate of aging of a cell or organism.
• the interaction between a test compound and the Sir2 or p53 polypeptide can be performed by any of the methods described herein, e.g., using cell-based assays or cell-free in vitro assays.
• test compounds include, e.g., small organic molecules, peptides, antibodies, and nucleic acid molecules, as described above.
• the rate of aging of an organism can be determined using methods known in the art.
• the rate of aging of an organism can be determined by directly measuring the life span of the organism.
• a statistical measure e.g., an average or median value
• the life span of a group of animals e.g., a group of genetically matched animals
• an equivalent statistical value e.g, an average of median value
• Such methods are suitable for organisms that have a short life span, such as worms or flies.
• test compound can be administered to test animals that have already lived for 50%, 60%, 70%, 80%, 90%, or more of their expected life span.
• the test compound can be administered to an adult organism, or even an old adult organism.
• Other possibilities include the use of genetically modified organisms.
• the organisms could harbor mutations (e.g.
• a Hyperldnetic 1 or Shaker mutation in Drosophila or a mutation in a silent information regulator gene (e.g., Sir2), or a catalase or superoxide dismutase gene) or transgenes (e.g., encoding a transporter protein (e.g., a carboxylate transport protein such as INDY) or a protein involved in insulin signaling and metabolic regulation (e.g., IGF-1)) that reduce their average life span.
• a transporter protein e.g., a carboxylate transport protein such as INDY
• IGF-1 insulin signaling and metabolic regulation
• a proxy for rate of aging of a cell or an organism can be determined using biomarkers that are indicative of the biological age of the organism (i.e., age-related parameters). Using biomarkers for determining biological age can greatly facilitate screens for compounds that alter the rate of aging, as they bypass the requirement of waiting for the animal to die in order to determine the rate of aging.
• Biomarkers suitable for use in the present invention include, but are not limited to, levels of protein modification, e.g., accumulation of glycosylated proteins, rates or levels of protein turnover, levels or composition of T-cell populations, protein activity, physical characteristics, macular degeneration, and/or increased copper and zinc concentrations in neuronal tissues.
• genes whose regulation is biological age-dependent is a particularly preferred biomarker for use in the methods of the invention.
• Numerous genes are known to be expressed in a biological age-dependent manner. In Drosophila, for example, such genes include wingless and engrailed. See Rogina and Helfand (1997), Mechanisms of Development 63:89-97.
• mice the expression of the ras oncogene is elevated in older animals. See Hass et al. (1993), Mutat. Res. 295(4-6):281-9.
• rodents and worms genes that are differentially expressed in young and old organisms have been identified by transcriptional profiling using microarrays. See, e.g., Lee et al.
• Metabolic parameters can also be used to evaluate the rate of aging of a cell or organism. For example, the rate of protein synthesis and degradation decreases in biologically aged cells, and the levels proteins having advanced glycosylation end product modifications increases. See, Lambert and Merry (2000), Exp. Gerontol 35(5):583-94; and WO 01/79842. hi addition, animals that harbor mutations conferring longer life span (and thus a reduced rate of aging) can show defects in ubiquinone biosynthesis, mitochondrial biogenesis, glucose metabolism, nucleic acid metabolism, ribosomal translation rates, and cholesterol biosynthesis. See, for example, WO 98/17823 and WO 99/10482.
• Cellular proliferation is another parameter that can be used to evaluate the biological age of a cell or organism.
• Cells from biologically aged organisms demonstrate reduced proliferative capacity as compared to the cells of a corresponding younger organism. See Li et al. (1991), Invest. Ophthalmol. 38(l):100-7; and Wolf and Pendergrass (1999), J Gerontol A Biol. Sci. Med. Sci. 54(11):B502-17. It will be understood by one skilled in the art that there are many methods for evaluating the proliferative capacity of cells that are suitable for use in the methods of the invention.
• cells can be labeled in vitro (or in vivo) with BrdU to determine the percent of dividing cells or evaluated using a colony forming assay, as described in Li et al. (1997), supra.
• Cells suitable for the analysis of proliferative capacity include cells grown in tissue culture, cells isolated from an animal that has been treated with a test compound, cells that are part of a live animal, or cells that are part of a tissue section obtained from an animal. With respect to cells present in an animal or tissue section thereof, preferable cells include lens epithelial cells, osteoblasts, osteoclasts, and lymphoid cells.
• any biomarker that is altered in a biological age-dependent manner has the potential to be used to evaluate the effect of a test compound upon the rate of aging of a cell or an organism.
• additional biomarkers include visual appearance, resistance to oxidative stress, cellular transformation (the ability to adopt a transformed (i.e., cancerous or malignant) phenotype), or DNAmethylation (e.g., of a ras oncogene). See, for example, Finkel and Holbrook (2000), Nature 408:239-47; Kari et al (1999), JNutr. Health Aging 3(2):92-101; and Hass et al. (1993), Mutat. Res. 295(4-6):281-9.
• a cell used in the methods of the invention can be from a stable cell line or a primary culture obtained from an organism, e.g., a organism treated with the test compound.
• a transgenic cell or animal used in the methods of the invention can include a transgene that encodes, e.g., a copy of a Sir2 or p53 protein, e.g., the Sir2 or p53 polypeptide that was evaluated for an interaction with the test compound.
• the transgene can encode a protein that is normally exogenous to the transgenic cell or animal, including a human protein, e.g., a human Sir2 or p53 polypeptide.
• the transgene can be linked to a heterologous or a native promoter.
• This disclosure further relates to a method of producing transgenic animals, e.g., mice or flies, hi one embodiment, the transgenic animal is engineered to express, overexpress or ectopically express Sir2 or p53, which method comprises the introduction of several copies of a segment comprising at least the polynucleotide sequence encoding SEQ ID NO. 2 with a suitable promoter into the cells of an embryo at an early stage.
• Techniques known in the art may be used to introduce the Sir2 or p53 transgene into animals to produce the founder line of animals. Such techniques include, but are not limited to: pronuclear microinjection (U.S. P.N.
• Gene targeting by homologous recombination in embryonic stem cells to produce a transgenic animal with a mutation in the Sir2 or p53 gene can also be performed .
• knock-out animals there is inactivation of the Sir2 or p53 gene or altered gene expression, such that the animals can be useful to study the function of the Sir2 or p53 gene, thus providing animals models of human disease, which are otherwise not readily available through spontaneous, chemical or irradiation mutagenesis.
• Transgenic animals such as mice, for example, may be used as test substrates for the identification of drugs, pharmaceuticals, therapies and interventions that can be used for the ameliorating or slowing the effects of aging.
• the invention features a transgenic organism that contains a transgene encoding a Sir2 or p53 polypeptide.
• the Sir2 or p53 r polypeptide is a human Sir2 or p53 polypeptide.
• the Sir2 or p53 polypeptide can be exogenous to (i.e., not naturally present in) the transgenic organism.
• the transgenic organism can be a yeast cell, an insect, e.g., a worm or a fly, a fish, a reptile, a bird, or a mammal, e.g., a rodent.
• the transgenic organism can further comprise a genetic alteration, e.g., a point mutation, insertion, or deficiency, in an endogenous gene.
• the endogenous gene harboring the genetic alteration can be a gene involved in the regulation of life span, e.g., a gene in the insulin signaling pathway, a gene encoding a Sir2 or transcription factor protein, or both.
• the genetically altered gene is a Sir2 or transcription factor, e.g., p53, polypeptide
• the invention features a method of altering the expression or activity of a Sir2 or p53 polypeptide, comprising administering to a cell or an organism a compound that increases or decreases the expression or activity of the Sir2 or p53 polypeptide in an amount effective to increase or decrease the activity of the Sir2 or p53 polypeptide.
• the Sir2 or p53 polypeptide can also be a yeast, invertebrate (e.g., worm or fly), or vertebrate (e.g., fish, reptile, bird, or mammal (e.g., mouse)) protein.
• the cell to which the compound is administered can be an invertebrate cell, e.g., a wonn cell or a fly cell, or a vertebrate cell, e.g., a fish cell (e.g., zebrafish cell), a bird cell (e.g., chicken cell), a reptile cell (e.g., amphibian cell, e.g., Xenopus cell), or a mammalian cell (e.g., mouse or human cell).
• a fish cell e.g., zebrafish cell
• a bird cell e.g., chicken cell
• a reptile cell e.g., amphibian cell, e.g., Xenopus cell
• mammalian cell e.g., mouse or human cell
• the organism to which the compound is administered can be an invertebrate, e.g., a worm or a fly, or a vertebrate, e.g., a fish (e.g., zebrafish), a bird (e.g., chicken), a reptile (e.g., amphibian, e.g., Xenopus), or a mammal (e.g., rodent or a human).
• a human it is preferred that the human is not obese or diabetic.
• the compound that is administered to the cell or organism can be an agonist that increases the expression or activity of the Sir2 or p53 polypeptide or an antagonist that decreases the expression or activity of the Sir2 or p53 polypeptide.
• the compound can be a small organic compound, an antibody, a polypeptide, or a nucleic acid molecule.
• the agonist or antagonist can alter the concentration of metabolites, e.g., Krebs Cycle intermediates, e.g., succinate, citrate, or ⁇ -keto-glutarate, within the cell or within one or more cells of the organism. Such action is expected to alter the cell's or the organism's resistance to oxidative stress. For example, an antagonist could increase the cell's or the organism's resistance to oxidative stress.
• the agonist or antagonist can alter one or more aging- related parameters, e.g., the expression of one or more genes or proteins (e.g., genes or proteins that have an age-related expression pattern), or the value of one or more metabolic parameters (e.g. , one or more metabolic parameters that reflect the rate of aging of the cell or organism). , the agonist or antagonist alters the rate of aging of the cell or organism.
• the compound reduces, e.g., partially reduces, the expression of the Sir2 or p53 polypeptide.
• anti-sense RNA, or ribozymes can be used to reduce the expression of the Sir2 or p53 polypeptide.
• Double-stranded inhibitory RNA is particularly useful as it can be used to selectively reduce the expression of one allele of a gene and not the other, thereby achieving an approximate 50%> reduction in the expression of the Sir2 or p53 polypeptide. See Garrus etal. (2001), Cell 107(l):55-65.
• treatment of aging comprises modulating the expression of a Sir2 or p53 polypeptide.
• a cell or subject can be treated with a compound that modulates the expression of a Sir2 or p53 gene.
• These compounds can be nucleic acid molecules substantially complementary to a Sir2 or p53 gene.
• Such approaches include oligonucleotide-based therapies such as antisense, ribozymes, and triple helices .
• Oligonucleotides may be designed to reduce or inhibit mutant target gene activity. Techniques for the production and use of such molecules are well known to those of ordinary skill in the art.
• Antisense RNA and DNA molecules act to directly block the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. With respect to antisense DNA, oligodeoxyribonucleotides derived from the translation initiation site, e.g., between the -10 and +10 regions of the target gene nucleotide sequence of interest, are prefened. Antisense oligonucleotides are preferably 10 to 50 nucleotides in length, and more preferably 15 to 30 nucleotides in length.
• An antisense compound is an antisense molecule corresponding to the entire Sir2 or p53 mRNA or a fragment thereof.
• Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA.
• the mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by an endonucleolytic cleavage.
• the composition of ribozyme molecules includes one or more sequences complementary to the target gene mRNA, and includes the well known catalytic sequence responsible for mRNA cleavage disclosed, for example, in U.S. P.N. 5,093,246.
• engineered hammerhead motif ribozyme molecules that specifically and efficiently catalyze endonucleolytic cleavage of RNA sequences encoding target gene proteins.
• ribozyme cleavage sites within any potential RNA target are initially identified by scanning the molecule of interest for ribozyme cleavage sites that include the sequences GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides conesponding to the region of the target gene containing the cleavage site may be evaluated for predicted structural features, such as secondary structure, that may render the oligonucleotide sequence unsuitable. The suitability of candidate sequences may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.
• Nucleic acid molecules used in triple helix fonnation for the inhibition of transcription should be single stranded and composed of deoxyribonucleotides.
• the base composition of these oligonucleotides are designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex.
• Nucleotide sequences may be pyrimidine-based, which will result in TAT and CGC triplets across the three associated strands of the resulting triple helix.
• nucleic acid molecules may be chosen that are purine-rich, for example, containing 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 targeted for triple helix formation may be increased by creating a "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 sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.
• the antisense, ribozyme, and/or triple helix molecules described herein may reduce or inhibit the transcription (triple helix) and/or translation (antisense, ribozyme) of mRNA produced by both normal and mutant target gene alleles. If it is desired to retain substantially normal levels of target gene activity, nucleic acid molecules that encode and express target gene polypeptides exhibiting normal activity may be introduced into cells via gene therapy methods that do not contain sequences susceptible to whatever antisense, ribozyme, or triple helix treatments are being utilized. Alternatively, it may be preferable to coadminister normal target gene protein into the cell or tissue in order to maintain the requisite level of cellular or tissue target gene activity.
• Antisense RNA and DNA, ribozyme, and triple helix molecules may be prepared by any method known in the art for the synthesis of DNA and RNA molecules. These include techniques for chemically synthesizing oligodeoxyribonucleotides and oligoribonucleotides, for example solid phase phosphoramidite chemical synthesis. Alternatively, 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 incorporated into a wide variety of vectors that incorporate 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.
• Various well-known modifications to the DNA molecules may be introduced as a means of increasing intracellular stability and half-life. Possible modifications include but are not limited to the addition of flanking sequences of ribonucleotides or deoxyribonucleotides of the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the oligodeoxyribonucleotide backbone.
• Modulators of Sir2 or p53 expression can be identified by a method wherein a cell is contacted with a candidate compound and the expression of Sir2 or p53 mRNA or protein in the cell is determined. The level of expression of Sir2 or p53 mRNA or protein in the presence of the candidate compound is compared to the level of expression of mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of Sir2 or p53 expression based on this comparison. For example, when expression of Sir2 or p53 mRNA or protein is greater in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of Sir2 or p53 mRNA or protein expression.
• the candidate compound when expression of Sir2 or p53 mRNA or protein is less in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of Sir2 or p53 mRNA or protein expression.
• the level of Sir2 or p53 mRNA or protein expression in the cells can be determined by methods described herein for detecting Sir2 or p53 mRNA or protein.
• viras vectors include adenovirus, herpes viras, vaccinia, and/or RNA virus such as a retrovirus.
• the retrovirus can be a derivative of a murine or avian retrovirus such as Moloney murine leukemia virus or Rous sarcoma viras. All of these vectors can transfer or incorporate a gene for a selectable marker so that transduced cells can be identified and generated.
• the specific nucleotide sequences that can be inserted into the retroviral genome to allow target specific delivery of the retroviral vector containing an antisense oligonucleotide can be determined by one of skill in the art.
• colloidal dispersion systems include macromolecular complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles and liposomes.
• a prefened colloidal delivery system is a liposome, an artificial membrane vesicle useful as in vivo or in vitro delivery vehicles.
• the composition of a liposome is usually a combination of phospholipids, usually in combination with steroids, particularly cholesterol.
• the Sir2 or p53 gene may also be underexpressed.
• Methods whereby the level of Sir2 or p53 gene activity may be increased to levels wherein disease symptoms are ameliorated also include increasing the level of gene activity, for example by either increasing the level of Sir2 or p53 gene present or by increasing the level of gene product which is present.
• a target gene protein at a level sufficient to ameliorate metabolic imbalance symptoms, may be administered to a patient exhibiting such symptoms.
• concentration of effective, non-toxic doses of the normal target gene protein may be determined.
• RNA sequences encoding target gene protein may be directly administered to a patient exhibiting disease symptoms, at a concentration sufficient to produce a level of target gene protein such that the disease symptoms are ameliorated.
• Admimstration may be by a method effective to achieve intracellular administration of compounds, such as, for example, liposome administration.
• the RNA molecules may be produced, for example, by recombinant techniques such as those described above.
• patients may be treated by gene replacement therapy.
• One or more copies of a normal target gene, or a portion of the gene that directs the production of a normal target gene protein with target gene function may be inserted into cells using vectors that include, but are not limited to adenovirus, adenoma-associated virus, and retrovirus vectors, in addition to other particles that introduce DNA into cells, such as liposomes. Additionally, techniques such as those described above may be utilized for the introduction of normal target gene sequences into human cells.
• Cells preferably autologous cells, containing and expressing normal target gene sequences may then be introduced or reintroduced into the patient at positions which allow for the amelioration of metabolic disease symptoms.
• Such cell replacement techniques may be prefened, for example, when the target gene product is a secreted, extracellular gene product.
• target gene protein is extracellular, or is a transmembrane protein
• any of the administration techniques described, below which are appropriate for peptide administration may be utilized to effectively administer inhibitory target gene antibodies to their site of action.
• the identified compounds that inhibit target gene expression, synthesis and/or activity can be administered to a patient at therapeutically effective doses to treat or ameliorate or delay the symptoms of aging.
• a therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration or delay of symptoms of aging.
• 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 LD50 (the dose lethal to 50% of the population) and the ED50 (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 LD50 / ED50.
• Compounds that exhibit large therapeutic indices are prefened. 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 ED50 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 IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
• IC50 i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms
• levels in plasma may be measured, for example, by high performance liquid chromatography.
• compositions may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.
• the compounds and their physiologically acceptable salts and solvates may be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal 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, polyvinylpynolidone 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, polyvinylpynolidone 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
• 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.
• the 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.
• the dosage unit may be determined by providing a valve to deliver a metered amount.
• gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
• 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.
• a suitable vehicle e.g., sterile pyrogen- free water
• 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.
• the compounds may also be formulated as a depot preparation.
• Such long acting fonnulations 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.
• cDNA was subcloned from pET28a-Sir2 ⁇ (Imai et al, 2000) into pcDNA3 or pBabepuro vector. Site-directed mutation was generated in the plasmid pRS305-Sir2 ⁇ using the Gene Edit system (Promega).
• DNA sequences conesponding to this region were amplified by PCR and subcloned into pGEX-2T (Pharmacia).
• ⁇ -Sir2 ⁇ antisera was raised in rabbits against the purified GST-Sir2 ⁇ (480-737) fusion protein (Covance), and further affinity- purified on both protein- A and antigen columns.
• this antibody can detect both mouse Sir2 ⁇ and human SIRTl proteins.
• hSir2 expression constructs BamHI/SnaBI fragment of hSLR2SIRTl cDNA was inserted into pBabe-Y-Puro. The resulting plasmid was designated pYESir2-puro. Similarly a BamHI/SnaBI fragment of hSir2 that was mutated at residue 363 from Histidine (H) to Tyrosine (Y) by site-directed mutagenesis (Stratagene) was used to create the retroviral vector pYESir2HY.
• H Histidine
• Y Tyrosine
• pBabe-hTERT-hygro contained an EcoRI/Sall fragment of hTERT cloned into EcoRI/Sall site of pBabe-Hygro.
• pCMVwtp53, pCMVK382R and ⁇ CMVK320R were a gift from Dr. E. Appella (NTH).
• Amphotrophic viruses were produced by transient co-transfection of pCL-pCL-Ampho with the LTR containing pBabe vectors (Morgenstern and Land, 1990), pYESir2 or pYESir2HY in to 293T cell line using Fugene ⁇ (Roche). Three days post transfection supematants were collected and filtered with 0.4 micron filters. Primary BJ cells or MCF7 cells were infected with retrovirus containing media in presence of 8 mg/ml of polybrene overnight and 48 hours later cells were selected in puromycin at 1 mg/ml.
• BJT canying pYE-Puro backbone and pBabe-hTERT-hygro
• BJThSir2wt canying pYESir2 wild type hSir2 and pBabe-hTERT hygro
• BJThSir2HY pYESir2HY mutant hSir2 and pBabe-hTERT-hygro
• MCF7 cells were transfected with the vector p21P-luc (Vaziri et al, 1997) and pCMVneo, clones were selected in 500 mg/ml of G418 and the clone designated MCF73L was selected that was able to upregulate the p21WAFl promoter-luciferase in response to treatment with 6 Gy of ionizing radiation.
• MCF7 cells or MCF73L were infected with the same viruses as described before to yield the following cell lines: MCF73LP (canying pBabe Y- puro backbone), MCF73L-hSir2wt and MCF73L-hSir2HY. Cells were kept under appropriate selection throughout experiments.
• the Flag-tagged Sir2 ⁇ -expressing cells were established and expanded in DMEM medium, and cell extracts were prepared essentially as previously described (Luo et al, 2000; Gu et al, 1999; Ito et al, 1999).
• the proteins were purified under a very high stringency condition (300 mM NaCl and 0.5 % NP-40).
• the eluted proteins were resolved by a SDS-PAGE gel and analyzed by colloidal blue staining (Novex).
• Acetylated GST-p53 was prepared by p53 acetylation assay as previously described (Gu and Roeder, 1997) and further purified on glutathione-Sepharose (Luo et al, 2000).
• the 14 C-labeled acetylated p53 (2.5 ⁇ g) was incubated with purified Sir2 (10 ng) at 30 °C for 1 hr either in the presence of 50 ⁇ M NAD or as indicated.
• the reactions were performed in a buffer containing 50 mM Tris-HCl (pH 9.0), 50mM NaCl, 4 mM MgCl 2 , 0.5 mM DTT, 0.2 mM PMSF, 0.02% NP-40 and 5% glycerol.
• the reactions were resolved on SDS-PAGE and analyzed by Coomassie blue staining and autoradiography.
• H1299 cells transiently expressing p53 and hSir2 were lysed using the NP40 buffer and lysates described above and immunoprecipitated with lul of anti-hSir2 antibody overnight.
• Protein G-sepharose beads 50 ml were added to the lysates and rotated at 4°C for 3hrs. The immune complexes were collected, washed 3 times, and resolved using the Nupage gradient 4- 12%) Bis-Tris MOPS (3-N-morpholino propane sulfonic acid) protein gel (Novex) in the presence of provided anti-oxidant (Novex).
• the gels used were transfened to nitrocellulose and probed with anti-p53 antibody (pAb7 sheep anti human polyclonal antibody, Oncogene Science), signal detected using a goat anti- sheep HRP secondary antibody.
• anti-p53 antibody pAb7 sheep anti human polyclonal antibody, Oncogene Science
• signal detected using a goat anti- sheep HRP secondary antibody The membranes were subsequently washed and reprobed with anti-hSir2 antibody.
• GST fusion proteins were expressed in E. coli, extracted with buffer BC500 (20 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 20% glycerol, ImM DTT and 0.5 mM PMSF) containing 50 mM KC1 and 1% NP-40, and purified on glutathione-sepharose (Pharmacia). 35 S-labeled Sir2 ⁇ was in vitro translated by a TNT kit (Promega) using pcDNA3-Sir2 ⁇ as a template.
• the co-immunoprecipitation assay was performed essentially as described previously (Luo et al, 2000). Cells were extracted with lysis buffer (25mM HEPES-KOH, pH 8.0, 150 mM KC1, 2mM EDTA, ImM DTT, ImM PMSF, lO g/ml aprotinin, lO ⁇ g/ml leupeptin, l ⁇ g/ml pepstatin A, 20 mM NaF, 0.1%o NP-40). After centrifugation, the supematants were incubated with M2 beads (Sigma) for 4 hr at 4°C.
• M2 beads Sigma
• the M2 beads were washed five times with 0.5 ml lysis buffer, after which the associated proteins were eluted with Flag peptides to avoid the cross- reaction from the mouse IgG in western blot analysis.
• 50 million cells were extracted in the same lysis buffer.
• the supematants were incubated with 20 ⁇ g ⁇ -Sir2 ⁇ antibody or pre-immune antiserum from the same rabbit and 40 ⁇ l protein A/G plus-agarose (Santa Cruz) for overnight.
• the agarose beads were washed five times with 0.5 ml of lysis buffer, after which the associated proteins were eluted with BCIOOO (20 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 20% glycerol, ImM DTT and 0.5 mM PMSF) containing 1 M NaCl, 1% NP-40, 0.5% Deoxycholic Acid.
• BCIOOO 20 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 20% glycerol, ImM DTT and 0.5 mM PMSF
• the eluted proteins were resolved on 8% SDS PAGE and Western blot with ⁇ -Sir2 antibody and ⁇ -p53 (DO-1) for human cells and ⁇ -p53 (421) for mouse cell. Immunoblot analysis
• cell pellets were all lysed on ice at once by adding 0.5% NP40, 150 mM NaCl (in the presence of complete protease inliibitor mix, Roche), for 30 minutes and vortexing.
• Cell lysates were prepared by centrifugation for 20 minutes at 4°C. Protein content of lysates were measured using Lowry based assay (BioRad DC protein assay). Protein (300 mg) was resolved on gradient 4-20% criterion Tris-HC gels (Biorad), transferred to nitrocellulose and blocked in 10% skim milk.
• the resulting membrane was incubated overnight in 1 :400 dilution of Ab-1 (Oncogene Science, peptide based rabbit polyclonal anti K382 p53). This membrane was then washed twice in PBS(-/-) containing 0.05%oTween 20 for 15 minutes. Secondary Goat anti-rabbit antibody conjugated to HRP (Pierce) was used at a concentration of 1 :30,000 for lhr in 1% Milk. Membrane was subsequently washed twice for 30 minutes total time.
• Ab-1 Oncogene Science, peptide based rabbit polyclonal anti K382 p53
• the membrane was incubated with Supersignal west femto maximum substrate (Pierce) for 2 minutes and exposed to X-OMAT sensitive film (Kodak) for up to 30 minutes.
• the membrane was subsequently blotted with a monoclonal p21 WAFl antibody (F5, Santa Cruz Biotech), p53 antibody (SC6243, polyclonal rabbit, Santa Cruz) (Ab-6, Oncogene Science), anti-hSir2 (polyclonal rabbit), ⁇ -actin was used (Abeam) for loading control.
• 967 IS is an anti- acetyl H3 Lys9 was a monoclonal antibody (Cell Signaling).
• All MEF cells were maintained in DMEM medium supplemented with 10% fetal bovine serum, and the IMR-90 cells were maintained in Eagle's minimal essential medium supplemented with 10%o fetal bovine seram and non-essential amino acids.
• the virus infection and selection were essentially as described previously (Ferbeyre et al, 2000). After one- week selection, the cells were either frozen for stock or immediately used for further analysis. About 500,000 MEF cells were plated on a 10-cm dish 24 hr before treatment. The cells were then exposed to etoposide (20 ⁇ m) for 12 hr. After treatment, the cells were washed with PBS and fed with normal medium.
• the cells were stained with PI and analyzed by flow cytometric analysis for apoptotic cells (SubGl) according to DNA content.
• the cells were treated with actinomycin D (0.25 ⁇ g/ml) and Fas antibody (100 ng/ml) as previously described (Di Cristofano et al, 1999).
• the IMR-90 cells were treated with H 2 O (200 ⁇ M) for 24 hrs.
• H1299 cells were transfected using the Fugene ⁇ protocols (Roche) with pCMVwtp53 in presence or absence of pCMVp300 and 5 ⁇ g of p21P-Luc (containing a 2.4kb fragment of p21 linked to luciferase gene) as previously described (Vaziri et al, 1997). All experiments were performed in triplicates.
• Apoptosis was measured at approximately 48 hrs post transfection using the annexin V antigen and propidium iodide exclusion (Clontech laboratories).
• Propidum iodide (PI: 2.5 ⁇ g/ml) was added to the cells, and samples were then analyzed in a FACSCalibur (BD). A region defining high FITC fluorescence was determined, and the cells falling into this region were collected separately. The PI staining was recorded simultaneously in the red channel.
• Immunofluorescence Assay Immunofluorescence was performed essentially as the standard protocol (Guo et al, 2000). After fixation, cells were exposed to two primary antibodies: p53 monoclonal antibody DO-1 (Santa Cruz) and ⁇ -Sir2 ⁇ for 1 hr at room temperature. The cells were washed three times with 1% BSA plus 0.2%> Tween-20 in PBS and then treated with two secondary antibodies [a goat anti-rabbit IgG conjugated to Alexa 568 (Molecular Probes), and anti-mouse IgG-FITC (Santa-Cruz)]. DAPI was used for counter-staining to identify nuclei. The cells were further washed four times. Images were acquired from a Nikon Eclipse E600 fluorescent microscope (Hamamatsu Photonics).
• the cells (human lung carcinoma cell lines H460 (wild-type p53) and H1299 (p53-null), human colon carcinoma HCT116 (wild-type p53), mouse embryonal carcinoma cell line F9 (wild-type p53), mouse embryonic fibroblast MEFs or others) were maintained in DMEM medium supplemented with 10%> fetal bovine seram. For DNA damage response, about 1 million cells were plated on a 10-cm dish 24 hr before treatment. The cells were then exposed to etoposide (20 ⁇ M) and or other drugs (0.5 ⁇ M of TSA, 5 mM of nicotinamide, and 50 ⁇ M of LLNL) as indicated for 6 hr.
• etoposide 20 ⁇ M
• drugs 0.5 ⁇ M of TSA, 5 mM of nicotinamide, and 50 ⁇ M of LLNL
• This antibody recognizes the p300-mediated acetylated forms of both human and mouse p53.
• H1299 cells were transfected with 5 ⁇ g of CMV-p53 plasmid DNA, 5 ⁇ g of CMV-p300 plasmid DNA, and 10 ⁇ g of pcDNA2-Sir2 ⁇ plasmid DNA as indicated.
• the cells were lysed in a Flag-lysis buffer (50 mM Tris, 137 mM NaCl, 10 mM NaF, ImM EDTA, 1% Triton X-100 and 0.2% Sarkosyl, 1 mM DTT, 10% glycerol, pH 7.8) with fresh proteinase inhibitors, 10 ⁇ M TSA and 5mM nicotinamide (Sigma).
• the cell extracts were resolved by either 8% or 4-20% SDS-PAGE gels (Novex) and analyzed by Western blot with ⁇ -p53 (Ac)-C and ⁇ -p53 (DO-1).
• Deacetylation assay of the p53 C-terminal peptide The human p53 C-terminal peptide (residues 368-386+Cys; HLKSK(AcK)GQSTSRHK(AcK)LMFKC); (SEQ ID NO. 1) di-acetylated at positions 373 and 382 was synthesized and purified with HPLC. Deacetylation assays of this peptide by Sir2 and analyses of the reaction products were performed as described previously (Imai et al, 2000).
• Example 1 Mammalian Sir2 ⁇ interacts with p53 both in vitro and in vivo.
• the p53 protein can be divided into three distinct functional domains (Gu and Roeder, 1997): an amino-terminus that contains the transcriptional activation domain (NT: residues 1-73), a central core that contains the sequence-specific DNA- binding domain (M: residues 100-300), and the multifunctional carboxyl-terminus (CT: residues 300-393).
• the GST-p53 fusion proteins containing each domain as well as the full- length protein were expressed in bacteria and purified to near homogeneity on gluthathione- agrose beads. As shown in Figure 1 A, 35 S-labeled in vitro translated Sir2 strongly bound to immobilized GST-p53 but not to immobilized GST alone (lane 1 vs. 6).
• Sir2 ⁇ was tightly bound to the C-terminal domain of p53 (GST-p53CT) (lane 4, Figure 1 A), also bound to the central DNA-binding domain (GST-p53M), but showed no binding to the N-terminal domain of p53 (GST-p53NT) (lane 3 vs. 2, Figure 1A).
• Sir2 ⁇ was detected in the immunoprecipitates obtained from H1299 cells cotransfected with constracts encoding Sir2 ⁇ and Flag-p53 (lane 6, Figure IB), but not from cells transfected with the Sir2oc constract alone (lane 8, Figure IB).
• p53 interacts similarly with human SIRTl (hSIRTl) ( Figure 1C, D), the human ortholog of mouse Sir2 (Frye, 1999; 2000), showing that p53 and mammalian Sir2 ⁇ interact.
• Example 2 Deacetylation of p53 by mammalian Sir2 ⁇ p53 was deacetylated by mammalian Sir2 ⁇ in vitro.
• Mouse Sir2 ⁇ protein was expressed with the N-terminal Flag epitope in cells and purified to near homogeneity on the M2-agrose affinity column (lane 3, Figure 3A to determine).
• the GST-p53 fusion protein was acetylated by p300 in the presence of [ 14 C]-acetyl-CoA, and the acetylated p53 protein was purified on the GST affinity column.
• These highly purified recombinant proteins were used in this assay in order to avoid possible contamination by either inhibitory factors or other types of deacetylases.
• Sir2 ⁇ -mediated deacetylase activity of p53 can be inhibited.
• Deacetylation of acetyl- lysine by Sir2 ⁇ is tightly coupled to NAD hydrolysis, producing nicotinamide and a novel acetyl- ADP-ribose compound (1-O-acetyl-ADPribose) (Landry et al, 2000b; Tanner et al, 2000; Tanny and Moazed, 2001).
• the formation of an enzyme- ADP -ribose intermediate through NAD hydrolysis may be critical for this chemical reaction (Landry et al, 2000b).
• nicotinamide is the first product from hydrolysis of the pyridinium-N-glycosidic bond of NAD, it may function as an inhibitor for its deacetylase activity (Landry et al, 2000b). Nicotinamide is able to inhibit the deacetylase activity of Sir2 on acetylated p53 in vitro.
• 3-AB 3-aminobenzamide
• PARP a strong inhibitor of PARP which is involved in another type of NAD-dependent protein modification
• Mouse embryonic fibroblast (MEF) cells which express the wild type of p53, were infected with either a pBabe-puro retrovirus empty vector or a pBabe-puro retrovirus containing Sir2 ⁇ , and cultured for a week under pharmacological selection.
• the protein levels of p53 activation in response to DNA damage in these cells was determined by Western blot analysis.
• the mild enhancement of the acetylation level of p53 by TSA during DNA damage response may be due mainly to its inhibitory effect on endogenous HDAC 1 -mediated deacetylase activity (lane 3 vs. lane 2, Figure 4C).
• a super induction of p53 acetylation was showed when the cells were treated with both TSA and nicotinamide (lane 4 vs. lane 3, Figure 4C).
• 3-AB treatment had no effect on the level of p53 acetylation (lane 5 vs. lane 3, Figure 4C), indicating that PARP-mediated poly-ADP ribosylation has no effect on p53 acetylation.
• mammalian Sir2 ⁇ -mediated deacetylation of p53 was determined by testing its effect on p53-mediated transcriptional activation.
• a mammalian p53 expression vector (CMV-p53), alone or in combination with different amounts of mouse Sir2 ⁇ expressing vector (CMV-Sir2 ⁇ ) was cotransfected into MEF (p53 ⁇ " ) cells along with a reporter construct containing synthetic p53 binding sites placed upstream of the luciferase gene (PG13- Luc).
• p53 null cells H1299 were transfected with p53 alone or cotransfected with p53 and Sir2 ⁇ . The transfected cells were fixed, stained for p53, and analyzed for apoptotic cells (SubGl) (Luo et al, 2000). As indicated in Figure 6A, overexpression of p53 alone induced significant apoptosis (32.3% SubGl). However, co-transfection of p53 with Sir2 ⁇ significantly reduced the level of apoptosis (16.4% SubGl), while the mutant Sir2 H355A was impaired in this effect (29.5% SubGl) ( Figure 6A, B).
• mammalian Sir2 ⁇ is involved in the regulation of both p53 mediated transcriptional activation and p53-dependent apoptosis, and deacetylase activity is required for these Sir2 ⁇ -mediated effects onp53.
• Example 6 The role of mammalian Sir2 ⁇ in stress induced apoptotic response
• Mammalian Sir2 ⁇ can deacetylate p53 both in vitro and in vivo (Figure 3).
• Sir2 ⁇ can block the induction of endogenous p53 acetylation levels by DNA damage ( Figure 4B, 4C).
• Figure 4B, 4C DNA damage
• IMR-90 cells were infected with either a pBabe-puro retrovirus empty vector or a pBabepuro retrovirus containing Sir2 , and cultured for a week under pharmacological selection.
• p53 in these infected cells, was induced significantly after hydrogen peroxide treatment, along with Sir2 ⁇ localized in the nuclei detected by immunostaining with specific antibodies ( Figure 7C).
• Sir2 expression significantly promotes cell survival under oxidative stress.
• the cells mock infected with the pBabe-vector were susceptible to H 2 O 2 -induced cell death, with more than 80% of the cells being killed after 24 hr exposure to 200 ⁇ M H 2 O (II vs. I).
• the pBabe-Sir2 infected cells were much more resistant to death by the same dose of H 2 O 2 , with about 70%o of the cells surviving after 24 hr of H 2 O 2 treatment (IV vs. Ill, Figure 7D).
• Mammalian Sir2 ⁇ promotes cell survival under stress by inhibiting p53-dependent apoptosis.
• the specificity of mammalian Sir2 ⁇ -mediated protection of cells from apoptosis was examined by determining whether Sir2 ⁇ has any effect of p53-independent, Fas-mediated apoptosis.
• the MEF (p53 "A ) cells were first infected with either a pBabe-puro retrovirus empty vector or a pBabe-puro retrovirus containing Sir2 ⁇ , then cultured for a week under pharmacological selection. After the treatment by anti-Fas (100 ng/ml) for 24 hrs, the cells were harvested and further analyzed for apoptotic cells (SubGl).
• Example 8 Physical interaction of hSir2 with p53 p53 protein is acetylated in response to DNA damage and the acetylation contributed to the functional activation of p53 as a transcription factor (Abraham et al, 2000; Sakaguchi et al, 1998). Sir2 is a deacetylase of p53, thereby modulating functioning of p53 as a transcription factor.
• hSir2STRTl cDNA clone obtained from the IMAGE consortium (Frye, 1999) was introduced into a pBabe-based retroviral expression vector which also canies puromycin resistance gene as a selectable marker.
• the resulting constract was termed pYESirwt.
• a retroviral construct bearing a derived, mutant allele of Sir2 and termed pYESirHY was constructed and used in parallel as control. This mutant allele encodes an amino acid substitution at residue 363, at which site the normally present histidine is replaced by tyrosine.
• hSir2 and p53 were evaluated by co-transfecting the pYESir2wt plasmid and a vector expressing wt p53 under the control of the cytomegalovirus promoter (pCMV-wtp53) transiently into H1299 human non-small cell lung carcinoma cells (Brower et al, 1986) which have a homozygous deletion of the p53 gene and produce no p53 mRNA or protein (Mitsudomi et al, 1992). Cell lysates were subsequently mixed with the rabbit anti-hSir2 antibody and resulting immune complexes were collected by protein G and analyzed by SDS-PAGE electrophoresis and immunoblotting.
• pCMV-wtp53 cytomegalovirus promoter
• the immunoblot was probed with a sheep anti-p53 antibody ( Figure 8C) and reprobed it subsequently with an anti-hSir2 antibody (top panel) to verify presence of hSir2 in the complex.
• Figure 8C immunoprecipitation of hSir2 resulted in co-precipitation of p53.
• lysates of BJT cells, human fibroblasts into which the telomerase gene has been introduced were examined.
• these cells express either the wild type hSir2 vector or the hSir2HY mutant. Two cell populations were created by infection of mass cultures of BJT cells with the respective vectors and subsequent selection in puromycin.
• the anti-p53 antibody was employed to immunoprecipitate complexes and subsequently probe the resulting immunoblot with either polyclonal anti-p53 antibodies or an anti-hSir2 antibody.
• These immunoblots demonstrated a physical interaction between hSir2 and p53 proteins ( Figure 8D). Fonnation of these complexes was unaffected by the H to Y mutation introduced into the hSir2 catalytic site ( Figure 8D).
• radiation used to increase the levels of p53 protein in BJ cells had no effect on the levels of p53:hSir2 complexes.
• Comparison of the immunoprecipitated p53 to total input ⁇ 53 resulted in an estimate of approximately 1% of the cells complement of p53 protein was present in physical complexes with hSir2.
• hSir2 forms physical complexes with p53, the ability of Sir2 to deacetylate human p53 in vitro was evaluated. Since adequate quantities of bacterially produced hSir2 were not available, bacterially expressed mouse SIR2 (mSir2a) enzyme was used in in vitro assays (Imai et al, 2000). A 20 residue-long oligopeptide that contains the sequence conesponding to residues 368-386+Cys of the human p53 protein was used as a substrate in these reactions. Lysine residues conesponding to residues 373 and 382 of the p53 protein were synthesized in acetylated form in this oligopeptide substrate.
• mSir2a mouse SIR2
• the deacetylase activity of hSir2 utilizes NAD as a co-factor (Imai etal, 2000; Moazed, 2001; Smith et al, 2000; Tanner et al, 2000; Tanny et al, 1999).
• NAD NAD
• incubation of mSir2 with p53 oligopeptide gave rise to a single prominent peak (peak 1) and a small, minor peak (peak 2) upon high pressure liquid chromatography (HPLC), conesponding to the monomeric and dimeric forms of the peptide, respectively ( Figure 9A).
• incubation in the presence of ImM NAD produced a singly deacetylated species as the major product (peak 3, Figure 9B).
• Example 10 Deacetylation of p53 by hSir2 in vivo The ability of hSir2 to deacetylate intact p53 protein in vivo was evaluated. To produce acetylated p53 in vivo, the p53 expression plasmid was co-transfected with one expressing p300. This protocol leads to acetylation of p53 in the absence of exposure to DNA-damaging agents (Luo et al, 2000). The ability of hSir2 to deacetylate the p53 protein at its K382 residue in H1299 cells that lack endogenous p53 gene was determined.
• Ab-1 rabbit polyclonal antibody
• the hSir2HY vector which expresses the mutant-catalytically inactive hSir2, was introduced into these H1299 cells.
• the mouse equivalent of this hSir2HY mutant lacks 95% of its deacetylase activity (Imai et al, 2000).
• the hSir2HY mutant failed to deacetylate wt p53 efficiently, indicating that the catalytic activity of the introduced wild type hSir2 gene product was required for specific deacetylation of p53 Lys 382 ( Figure 10 A, lane 9).
• the lysine 320 residue of p53 is also acetylated by PCAF in response to DNA damage (Sakaguchi et al, 1998). Whether the state of acetylation of residue 320 affected the ability of hSir2 to deacetylate residue 382 was determined. A mutant p53 allele that specifies a lysine-to- arginine substitution at residue 320 was expressed. This amino acid substitution did not affect the ability of hSir2 to deacetylate the K382 residue in H1299 cells, indicating that the action of hSir2 on the acetylated K382 residue is independent of the state of acetylation of the K320 residue ( Figure 10A, lanes 7, 8).
• H3 Lys9 acetylation was monitored through the use of the 967 IS monoclonal antibody.
• the 9671 S antibody specifically recognizes histone H3 that is acetylated at this position.
• Acetylation of lysine residue 382 of p53 accompanies and mediates the functional activation of p53 as a transcription factor following exposure of a cell to ionizing radiation (Sakaguchi et al, 1998).
• hSir2 could antagonize and reverse this activation of p53, by its deacetylase function, either wildtype hSir2 or the mutant form specified by the hSir2HY vector was expressed in BJT human fibroblast cells. Ectopic expression of the telomerase enzyme in these BJT cells, undertaken to extend their lifespan, had no effect on either their activation of p53 protein or their responses to DNA damage (Vaziri et al, 1999).
• TSA trichostatin A
• BJT cells do express significantly lower levels of endogenous hSir2 when compared with MCF7 cells. These lower levels of hSir2 in BJT cells may enable hSir2HY to form inhibitory complexes with endogenous wild type hSir2 or with other proteins required for its function.
• evidence in yeast suggests that H363Y mutant does indeed act as a potent dominant-negative (Tanny et al, 1999).
• hSir2 The effects of hSir2 on the transcriptional activity of p53 were determined by co- transfecting H1299 cells transiently with a p53 expression plasmid and a reporter construct in which the promoter of the p21WAFl gene (el-Deiry et al, 1993), a known target of transcriptional activity by p53, is able to drive expression of a luciferase reporter gene (Vaziri et al, 1997). As indicated in Figure 11 A, luciferase activity increased in response to increasing amount of co-transfected wtp53 expression vector. Conversely, the transcriptional activity of p53 protein was suppressed by co-expression of wild type hSir2 in a dose-dependent fashion.
• the catalytically inactive hSir2HY mutant had no effect on p53 transcriptional activity (Figure 11 A).
• the specificity of hSir2 in affecting promoter activity was determined using a constitutively active SV40 promoter linked to the luciferase gene. Expression of this control construct was not affected by increasing amounts of hSir2 expression vector at any level ( Figure IIB).
• the above observations were confirmed in a more physiologic context using a subline of MCF-7L cells.
• the subline of MCF-7 cells was stably transfected with a p21WAFl promoter- reporter construct.
• these cells were infected stably with retroviral vector constracts expressing either the wild type hSir2 or the mutant hSir2HY.
• These cells were expressed to 6 Gy of ionizing radiation and subsequently measured total p53 and p21WAFl protein levels (Figure 11C).
• p53 protein levels increased normally in all cell populations in response to inadiation of these cells.
• the levels of p21WAFl protein were reduced in cells expressing wild type hSir2 ( Figure 11C).
• MCF-7L cells expressing the mutant hSir2HY protein had a higher level of p21 WAFl when compared with the inadiated controls and with the wild type hSir2-overexpressing cells ( Figure 11C) showing that the hSir2HY mutant may act in a dominant-negative fashion in these cells.
• hSir2 can antagonize the transcriptional activities of p53 that enable it to exert cytostatic effects via transcriptional activation of the p21WAFl gene.
• Example 13 Inhibition of p53-dependent apoptosis by hSir2 hSir2 can antagonize the ability of p53 to act in a cytostatic fashion through induction of p21WAFl synthesis. The ability of hSir2 to blunt the pro-apoptotic functions of p53 was determined.
• Co-transfection of a p300 vector with the p53 gene increased this p53-dependent apoptosis ( Figure 12A).
• the p66shc adaptor protein controls oxidative stress response and life span in mammals. Nature, 402:309-313. Nakamura S., Roth J.A. and Mul hopadhyay T. (2000) Multiple lysine mutations in the C-terminal domain of p53 interfere with MDM2-dependent protein degradation and ubiquitination. Mol. Cell. Biol., 20:9391-9398.
• the Sir2 protein family A novel deacetylase for gene silencing and more. Proc. Natl. Acad. Sci. USA, 97:14030-14032.
• hSIR2SlRTl functions as an NAD-dependent p53 deacetylase. Cell, 107:149-159.
• Trichostatin A and trapoxin novel chemical probes for the role of histone acetylation in chromatin structure and function. Bioessays, 5:423-430. Yu A., Fan H., Lao D., Bailey A.D. and Weiner A.M. (2000) Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human UI, U2, and 5S genes. Mol. Cell, 5:801-810.

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