Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P25/00—Drugs for disorders of the nervous system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
  • A01K—ANIMAL HUSBANDRY; CARE OF BIRDS, FISHES, INSECTS; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
  • A01K2217/00—Genetically modified animals
  • A01K2217/07—Animals genetically altered by homologous recombination
  • A01K2217/075—Animals genetically altered by homologous recombination inducing loss of function, i.e. knock out
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides

Definitions

• the present invention is directed to a peptide, and its encoding nucleic acids, of the toporythmic protein Delta that contains a sequence which is cleaved by the metalloprotease-disintegrin Kuzbanian (Kuz) ("Delta cleavage peptide”), as well as derivatives and analogs thereof.
• the present invention is also directed to an extracellular
• the present invention is also directed to methods for detecting or measuring Delta activation by observing or measuring Delta cleavage products that are indicative of Delta activation.
• the present invention is also directed to methods for detecting a molecule that modulates Delta activation by observing or measuring a change in the amount or pattern of Delta cleavage 25 products.
• the present invention is further directed to methods for detecting or measuring Kuz function by observing or measuring Delta cleavage products that are indicative of Kuz function.
• the present invention is also directed to methods for detecting a molecule that modulates Kuz function
• the present invention is also directed to certain protein complexes of Delta and Kuz and of D1 EC and Notch, and methods for their use in screening, diagnosis and therapy.
• Figure 1 depicts the molecular relationships between the known Notch pathway elements as well as their subcellular localization (Artavanis-Tsakonas et al . , 1995, Science
• the Drosophila Notch gene encodes an -300 kD transmembrane protein that acts as a receptor in a cell-cell signaling mechanism controlling cell fate decisions throughout development (reviewed, e.g., in Artavanis-Tsakonas et al., 1995, Science 268:225-232).
• Closely related homologs of Drosophila Notch have been isolated from a number of vertebrate species, including humans, with multiple paralogs representing the single Drosophila gene in vertebrate genomes.
• the encoded protein is designated human Notch2 because of its close relationship to the Notch2 proteins found in other species (Weinmaster et al . , 1992, Development 116:931- 941) .
• the hallmark Notch2 structures are common to all the
• Notch-related proteins including, in the extracellular domain, a stretch of 34 to 36 tandem Epidermal Growth Factorlike (EGF) repeats and three Lin-12/Notch repeats (LN repeats) , and, in the intracellular domain, 6 Ankyrin repeats and a PEST-containing region.
• EGF Epidermal Growth Factorlike
• LN repeats Lin-12/Notch repeats
• PEST-containing region 6 Ankyrin repeats and a PEST-containing region.
• Drosophila Notch and the related C. elegans genes lin-12 and glp-1 (Sternberg, 1993,
• EGF Epidermal Growth Factor-like
• Delta and Serrate are membrane bound ligands with EGF homologous extracellular domains, which interact physically with Notch on adjacent cells to trigger signaling.
• Deltex is a cytoplasmic protein which contains a ring zinc finger.
• Suppressor of Hairless is the Drosophila homologue of CBF1, a mammalian DNA binding protein involved in the Epstein-Barr virus-induced immortalization of B cells. It has been demonstrated that, at least in cultured cells, Suppressor of Hairless associates with the cdclO/ankyrin repeats in the cytoplasm and translocates into the nucleus upon the interaction of the Notch receptor with its ligand Delta on adjacent cells (Fortini and Artavanis, 1994, Cell 79:273-282).
• Notch protein is broadly expressed in the early embryo, and subsequently becomes restricted to uncommitted or proliferative groups of cells as development proceeds. In the adult, expression persists in the regenerating tissues of the ovaries and testes (reviewed in Fortini et al . , 1993, Cell 75:1245-1247; Jan et al . , 1993,
• Tissues with high expression levels include the developing brain, eye and neural tube (Coffman et al . , 1990, Science
• Notch homologue has been shown to be prominent in particular regions of the ventricular zone of the spinal cord, as well as in components of the peripheral nervous system, in an overlapping but non- identical pattern. Notch expression in the nervous system appears to be limited to regions of cellular proliferation, and is absent from nearby populations of recently differentiated cells (Weinmaster et al . , 1991, Development 113:199-205; Reaume et al., 1992, Dev. Biol. 154:377-387; Weinmaster et al . , 1992,
• a rat Notch ligand is also expressed within the developing spinal cord, in distinct bands of the ventricular zone that overlap with the expression domains of the Notch genes.
• Notchl is expressed in the undifferentiated cells of the central marginal zone and central retina (Coffman et al . ,
• Notchl plays a role in successive cell fate choices in this tissue (Lyman et al . , 1993, Proc. Natl. Acad. Sci. USA
• Notchl expression was instead found to be limited to subsets of non-mitotic, differentiating cells that are not subject to epithelial/mesenchymal interactions, a finding that is consistent with Notch expression elsewhere.
• Notch proteins in human 25 tissue and cell lines have also been reported.
• the aberrant expression of a truncated Notchl RNA in human T-cell leukemia results from a translocation with a breakpoint in Notchl
• Notchl and Notch2 appear to be expressed in overlapping patterns in differentiating populations of cells within squamous
• Drosophila embryo suppresses neuroblast segregation without impairing epidermal differentiation (Struhl et al . , 1993, 25
• Persistent expression of activated Notch in developing imaginal epithelia likewise results in an overproduction of epidermis at the expense of neural structures (Struhl et al . , 1993, Cell 69:331).
• ⁇ - Neuroblast segregation occurs in temporal waves that are delayed but not prevented by transient expression of activated Notch in the embryo (Struhl et al . , 1993, Cell 69:331) .
• Transient expression in well-defined cells of the Drosophila eye imaginal disc causes the cells to ignore their normal inductive cues and to adopt alternative cell fates (Fortini et al . , 1993, Nature 365:555-557).
• Notch in either the Drosophila embryo or the eye disc indicate that once Notch signaling activity has subsided, cells may recover and differentiate properly or respond to later developmental cues (Fortini et al . , 1993, Nature
• Notch signaling Ligands, cytoplasmic effectors and nuclear elements of Notch signaling have been identified in Drosophila, and vertebrate counterparts have also been cloned (reviewed in Artavanis-Tsakonas et al . , 1995, Science 268:225-232). While protein interactions between the various elements have been documented, the biochemical nature of Notch signaling remains elusive. Expression of truncated forms of Notch reveal that
• Notch proteins without transmembrane and extracellular domains are translocated to the nucleus both in transgenic flies and in transfected mammalian or Drosophila cells
• Delta is cleaved by the metalloprotease-disintegrin Kuzbanian (Kuz) into two l ⁇ 5 fragments, a soluble amino-terminal fragment consisting essentially of the extracellular domain, and a membrane-bound fragment consisting essentially of the transmembrane domain and the intracellular domain.
• the soluble fragment of Delta like the full length, membrane-bound Delta, is able to bind
• the detection or measurement of Delta activation, 25 i . e . , cleavage, is important in the study and manipulation of differentiation processes, since Delta plays a key role in cell fate (differentiation) determination, and since Delta is a ligand of Notch, Notch also playing a key role in cell fate (differentiation) determination.
• Molecules that modulate Delta and Notch function are important tools for studying and manipulating differentiation processes, e . g. , in expanding cell populations without substantial differentiation (International Publication WO 97/11716) , in cancer studies and therapy (International Publication WO 94/07474) , and differentiation studies on normal tissue.
• Molecules that allow the detection or measurement of Notch or Delta mRNA or protein levels or activity also have use in studying and manipulating differentiation processes. Accordingly, molecules that can be used to generate or detect anti-Delta antibodies or Delta nucleic acids have use in such detection or measurement .
• One embodiment of the present invention is directed to a peptide of approximately 30 amino acids, and its encoding nucleic acids, of the toporythmic protein Delta that contains a sequence which is cleaved by the metalloprotease- disintegrin Kuzbanian (Kuz) , (herein termed "cleavage peptide") as well as derivatives ⁇ e . g. , fragments) and analogs thereof.
• cleavage peptide a sequence which is cleaved by the metalloprotease- disintegrin Kuzbanian
• the Delta cleavage peptide consists of the sequence of amino acid Cys 516 to amino acid Phe 543 in human Delta (SEQ ID NO: 10) , of amino acid Cys 515 to amino acid Phe 543 in mouse Delta (SEQ ID N0:6), of amino acid C Y S 523 to amino acid Phe 551 in chick Delta (SEQ ID NO:7), of amino acid Cys 518 to amino acid Phe 544 in Xenopus Delta (SEQ ID NO:10)
• SEQ ID N0:6 mouse Delta
• SEQ ID N0:7 amino acid Cys 518 to amino acid Phe 544 in Xenopus Delta
• the Delta cleavage peptide is a portion of a mammalian Delta, preferably a human Delta. Such a peptide is believed to have the ability to modulate Kuz cleavage of Delta, and thus, Delta and Notch activation.
• the present invention is directed to a peptide comprising a fragment of a Delta protein, the amino acid sequence of the peptide consisting of the amino acid sequence Cys 515 to amino acid Phe 543 in human
• Drosophila Delta (SEQ ID NO: 9) .
• a fragment of a Delta protein of not more than 150 or 50 or 30 amino acids comprising a Delta sequence selected from the group consisting of amino acid sequence Cys 516 to amino acid
• Xenopus Delta (SEQ ID NO: 8), and Cys 564 to amino acid Ala 593 or
• the invention is directed to a peptide the amino acid sequence of which consists of amino acid sequence Cys 516 to amino acid Phe 543 in human Delta (SEQ ID NO: 10), Cys 515 to amino acid Phe 543 in mouse Delta (SEQ ID NO: 6) , Cys 523 to amino acid Phe 551 in chick Delta (SEQ ID NO:7), Cys 518 to amino acid Phe S44 in Xenopus Delta (SEQ ID NO: 8), or Cys 564 to amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• the invention is also directed to a derivative or analog of the cleavage peptide which is functionally active, i.e., capable of displaying one or more known functional activities associated with the "wild type" cleavage peptide.
• Such functional activities include but are not limited to antigenicity [ability to bind (or compete with the cleavage peptide for binding) to an anti-Delta cleavage peptide antibody] , immunogenicity (ability to generate antibody which binds to the cleavage peptide) , ability to bind (or compete with the cleavage peptide for binding) to Kuz .
• the invention is further directed to a fragment (and derivatives or analogs thereof) of the Delta cleavage peptide which is able to bind to Kuz .
• Delta cleavage peptide its derivatives and analogs
• Delta fragments that comprise the cleavage peptide sequence are also provided, as are fusion proteins comprising a Delta fragment containing a sequence of Delta that includes at least the cleavage peptide sequence, fused to a non-Delta sequence at the amino- and/or carboxy-terminal end of the
• Delta sequence Concatamers of Delta fragments containing at least the cleavage peptide sequence (e . g. , two, three, or more copies of a portion of the Delta sequence consisting of at least the cleavage peptide sequence) are also provided.
• the Delta fragments comprising the cleavage peptide sequence are not greater than 35, 50, 75,
• the present invention is directed to a chimeric protein comprising a Delta protein sequence fused to a non- Delta protein sequence, wherein the Delta protein sequence is a sequence of not more than 100 or 50 or 30 amino acids that comprises the amino acid sequence Cys 516 to amino acid Phe 543 in human Delta (SEQ ID NO:10), Cys 515 to amino acid Phe 543 in mouse Delta (SEQ ID NO:6), Cys 523 -to amino acid Phe 551 in chick Delta (SEQ ID NO:7), Cys 518 to amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) , or Cys 564 to amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• the present invention is directed to a peptide comprising an amino-terminal fragment of a full length Delta protein, which fragment is cleaved from the full length Delta protein by two proteolytic processing events, the cleavage of the signal peptide and the cleavage by Kuz, (herein termed "soluble Delta peptide” or “Dl EC ”) as well as derivatives and analogs thereof.
• the soluble Delta peptide amino acid sequence begins at amino acid Ser 22 and terminates between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID NO: 10); begins at amino acid Ser 22 and terminates between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6); begins at amino acid Ser 24 and terminates between amino acid Cys 523 and amino acid Phe S51 in chick Delta (SEQ ID NO:7), begins at amino acid Ser 22 and terminates between amino acid Cys sl8 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8), or begins at amino acid Ser 23 and terminates between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• Such a peptide is believed to have the ability to bind Notch, and thus modulate Delta and Notch activation.
• the invention is also directed to a derivative or analog of the soluble Delta peptide which is functionally active, i.e., capable of displaying one or more known functional activities associated with the "wild type" soluble peptide.
• functional activities include but are not limited to antigenicity [ability to bind (or compete with the soluble peptide for binding) to an anti-Delta soluble peptide antibody] , immunogenicity (ability to generate antibody which binds to the soluble peptide) , ability to bind (or compete with the soluble peptide for binding) to Notch.
• Antibodies to the Delta soluble peptide, its derivatives and analogs are additionally provided. Methods of production of the Delta cleavage peptide, derivatives and analogs, e . g. , by recombinant means, are also provided. Methods of production of the soluble peptide
• Delta peptide, derivatives and analogs, e . g. , by recombinant means, are also provided.
• the present invention is also directed to certain compositions comprising and methods for production of protein complexes of Delta and Kuz.
• the invention is directed to complexes of Delta, and derivatives, fragments and analogs of Delta, with Kuz, and its derivatives, fragments and analogs (a complex of
• Delta and Kuz is designated as "Delta:Kuz" herein) .
• Methods of production of a Delta: Kuz complex, and a derivative or analog thereof, e . g. , by recombinant means, are also provided.
• the present invention is also directed to certain compositions comprising and methods for production of protein complexes of Notch and a soluble fragment of Delta consisting essentially of the extracellular domain that is liberated by the proteolytic processing of Delta by Kuz ("soluble Delta peptide" or "Dl EC ").
• the invention is directed to complexes of the soluble Delta peptide, and derivatives, fragments and analogs of the soluble Delta peptide, with Notch, and its derivatives, fragments and analogs (a complex of the soluble fragment of
• Delta and Notch is designated as "Dl EC :Notch” herein) .
• the invention is further directed to methods for modulating (i.e., inhibiting or enhancing) the activity of Notch or Delta or Kuz by contacting a cell expressing Notch or Delta or Kuz, or an organism comprising a cell expressing Notch or Delta or Kuz, a peptide comprising a fragment of
• Delta having the amino acid sequence of about amino acid c Y s 5 i 6 to about amino acid Phe 543 in human Delta (SEQ ID NO:
• the peptide comprises 25,
• the invention is further directed to methods for modulating (i.e., inhibiting or enhancing) the activity of Notch or Delta or Kuz or at least one of their signalling pathways by contacting a cell or organism expressing Notch or
• the invention is further directed to methods for modulating (i.e., inhibiting or enhancing) the activity of a Delta: Kuz complex or a Dl EC :Notch complex.
• the protein components of a Delta:Kuz complex or a Dl EC :Notch complex have been implicated in cell fate and differentiation. Accordingly, the present invention is directed to methods for screening a Delta: Kuz complex, as well as a derivative or analog of the complex, for the ability to alter cell fate or differentiation.
• the present invention is also directed to methods for screening a D1 EC :Notch complex, as well as a derivative or analog of the complex, for the ability to alter cell fate or differentiation.
• the present invention is also directed to therapeutic and diagnostic methods and compositions based on the Delta cleavage peptide and encoding nucleic acids, as well as on soluble Delta peptide and encoding nucleic acids.
• the invention provides for the treatment of disorders of cell fate and differentiation by administration of a therapeutic compound of the invention.
• a therapeutic compound of the invention Such therapeutic compounds
• Therapeutics include: Delta cleavage peptides and derivative and analogs (including fragments) thereof, antibodies thereto, nucleic acids encoding the Delta cleavage peptide, derivatives, or analogs, Delta cleavage peptide antisense nucleic acids, Delta: Kuz complexes and 5 antibodies thereto, and Dl EC :Notch complexes and antibodies thereto.
• Therapeutics include soluble Delta peptides and derivatives and analogs thereof, antibodies thereto, nucleic acids encoding the soluble Delta peptides, derivatives, or analogs, and soluble Delta peptide antisense nucleic acids.
• Therapeutic of the invention is administered to treat a cancerous condition, or to prevent progression from a pre- neoplastic or non-malignant state into a neoplastic or a malignant state.
• a Therapeutic of the invention is administered to treat a 5 nervous system disorder or to promote tissue regeneration and repair.
• Therapeutics which antagonize, or inhibit, Notch, Delta cleavage peptide and/or Kuz function are administered for o therapeutic effect.
• Therapeutics which promote Notch, Delta cleavage peptide and/or Kuz function are administered for therapeutic effect.
• disorders of cell fate in particular hyperproliterative (e . g. , cancer) or hypoproliferative 5 disorders, involving aberrant or undesirable levels of expression or activity or localization of Notch, Delta cleavage peptide and or Kuz protein can be diagnosed by detecting such levels, as described more fully infra .
• Yet another embodiment of the present invention is 0 directed to methods for detecting or measuring Delta activation by observing or measuring Delta cleavage products that are indicative of Delta activation.
• the method for detecting or measuring Delta activation in a cell comprises detecting or measuring the expression of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM.
• the method comprises detecting or measuring an amino-terminal fragment of full-length Delta terminating between amino acid Cys 564 and amino acid Ala 593 or
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 kilodaltons (Dl EC ) .
• the method comprises detecting or measuring a soluble Delta peptide having the amino acid sequence beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID NO:10); beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO: 6); beginning at amino acid Ser 24 and terminating between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO: 7); beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8); and the sequence beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 8) .
• the present invention is also directed to methods for detecting or measuring Kuz function by observing or measuring Delta cleavage products that are indicative of Kuz function.
• the method for detecting or measuring Kuz function in a cell comprises detecting or measuring the expression of one or more Delta cleavage products selected from the group consisting of Dl E and DlTM.
• the method comprises detecting or measuring an amino-terminal fragment of full-length Delta which terminates between amino acid c y s 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta, between amino acid Cys 516 and amino acid Phe 543 in human Delta, between amino acid Cys 515 and amino acid Phe 543 in mouse Delta, between amino acid Cys S23 and amino acid Phe 551 in chick Delta, or terminates between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta.
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 kilodaltons.
• the method comprises detecting or measuring a soluble Delta peptide having the amino acid sequence beginning at amino acid Ser 22 and terminating between amino acid Cys s ⁇ 6 and amino acid Phe 543 in human Delta (SEQ ID NO:10); beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6); beginning at amino acid Ser 24 and terminating between amino acid Cys S23 and amino acid Phe 551 in chick Delta (SEQ ID NO:7); beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) ; and the sequence beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• the present invention is also directed to methods for identifying a molecule that modulates Delta activation by detecting or measuring a change in the amount or pattern of Delta cleavage products .
• the method for identifying a modulator of Delta activation comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate c molecule indicates that the molecule modulates Delta activity.
• the method for identifying a modulator of Delta activation comprises contacting a candidate modulator molecule with a full length
• Delta in the presence of a composition comprising Kuz and 0 optionally other cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition and detecting or measuring the amount of Delta cleavage products Dl EC and DlTM that result, in which a difference in the 5 presence or amount of said Delta cleavage products compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the present invention is 0 also directed to methods for identifying a molecule that modulates Kuz function by detecting or measuring a change in the amount of Delta cleavage products that are necessary for
• the method for identifying a modulator of Kuz function comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates
• the present invention is also directed to methods for identifying a molecule that modulates Kuz function by detecting or measuring a change in the amount of Delta cleavage products that are indicative of Kuz function.
• the method for identifying a modulator of Kuz function comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates
• the present invention is also directed to therapeutic and prophylactic, as well as diagnostic, prognostic, and screening methods and compositions based upon the Delta: Kuz complex or the Dl EC :Notch complex (and the nucleic acids encoding the individual proteins that participate in the complex) .
• Therapeutic compounds of the invention include, but are not limited to, a Delta:Kuz complex, and a complex where one or both members of the complex is a derivative, fragment, ho olog or analog of Delta or Kuz; antibodies to and nucleic acids encoding the foregoing; and antisense nucleic acids to the nucleotide sequences encoding the complex components. Diagnostic, prognostic and screening kits are also provided.
• Figure 1 is a schematic diagram of the Notch signaling pathway.
• the Notch receptor can bind to either
• Figure 2 is a Notch homolog sequence comparison.
• the human Notch2 (humN2) (SEQ ID NO:l), human Notchl (humNl)
• SEQ ID NO:2 Xenopus Notch/Xotch (XenN) (SEQ ID NO:3), and Drosophila Notch (DrosN) (SEQ ID NO:4) protein sequences are aligned, with names indicated to the left and numbering to the right (Wharton et al . , 1985, Cell 43:567-581; Coffman et al., 1990, Science 249:1438-1441; Ellisen et al . , 1991, Cell
• Notch protein motifs are enclosed in boxes. Starting from the N-terminal, the boxed regions indicate: EGF repeats,
• Lin-12/Notch (LN) repeats Lin-12/Notch (TM) repeats, transmembrane domain (TM) , Ankyrin repeats, and PEST-containing region. Also indicated are the putative CcN motif components (Stifani et al . , 1992, Nature
• Figure 3 is a Delta homolog sequence comparison.
• the human Delta (HDL) (SEQ ID N0:5), mouse Delta (MDL) (SEQ ID N0:6), chick Delta (CDL) (SEQ ID NO:7), Xenopus Delta (XDL) (SEQ ID N0:8), and Drosophila Delta (DDL) (SEQ ID NO:9) protein sequences are aligned, with names indicated to the left and numbering to the right.
• Major Delta protein motifs are labeled.
• Figure 4A and 4B is the amino acid sequence (SEQ ID NO:10) and the nucleic acid sequence (SEQ ID NO:ll), respectfully, of human Delta.
• Figure 5A and 5B is the amino acid sequence (SEQ ID NO:12) and the nucleic acid sequence (SEQ ID NO:13), respectfully, of the human Kuz homolog.
• Figures 6A-6F shows results of a genetic modifier screen that was carried out to identify genes that genetically interact with kuz .
• a strain constitutively expressing a KuzDN construct in developing imaginal discs was used in the screen (expression of a KuzDN construct lacking the proprotein and metalloprotease domains was driven by a
• GAL4 line 32B which causes adult mutant phenotypes, including extra wing vein materials, mostly notably deltas at the ends of the longitudinal veins (denoted by arrowheads in Figure 6A) , small and rough eyes, and extra bristles on the notum (denoted by arrowheads in Figure 6E) .
• More than 2400 lethal P-element insertions were screened for phenotypic modification effects on KuzDN. Seven P- insertions were found to cause significant reduction of the viability (semi-lethal) of the KuzDN flies when they are also heterozygous for each of the P-insertion.
• Figure 7C Affinity purified Dl EC migrates at MW ⁇ 62,000 Daltons under reducing conditions and at MW ⁇ 67,000 Daltons under non- reducing conditions on a coomassie blue-stained SDS-PAGE gel.
• Figure 7D Schematic of the Drosophila Delta protein demonstrates the DSL domain (DSL) , the epidermal growth factor like repeats (EGF) and the transmembrane domain (TM) . Amino acid numbering of N-terminus, the beginning of the TM domain and the C-terminus is shown.
• Figure 7E Thirteen cycles of N-terminal amino acid sequence analysis of Dl EC is shown with alignment to the Drosophila (dDl) , Xenopus (xDl) and human (hDl) Delta amino acid sequences. The arrow indicates the conserved serine residue in the position of the N-terminus of Dl EC and the potential site of signal peptide processing for Dl .
• Figures 8A-8D shows that Kuz plays a direct role in
• FIG. 8A The first two panels (-) : Expression of Delta and Dl EC are apparent by western blotting with the 9B antibody in the cell pellet (c) and the medium (m) in S2 cells transiently transfected with full length Delta (Fehon, et al . , 1990, Cell 61:523-534).
• Kuz and Delta results in an increase in the Dl EC fragment in the cell culture media (m) which correlates with an apparent decrease in Delta in the cell pellet (c) .
• the third two panels (KuzDN) Cotransfection with dominant negative Kuz dramatically decreases the Dl EC observed in the media (m) and corresponds with greater amounts of full length Delta in the cell pellet (c) .
• Figure 8B Cotransfection of Kuz and KuzDN with Notch was done under identical experimental conditions as for Delta and western blotted with the 9C6 Notch intracellular domain antibody (Fehon, et al .
• FIG. 8C The metalloprotease inhibitors EDTA and 1 , 10-phenanthroline inhibit the endogenous S2 cell proteolytic activity yielding Dl EC .
• the left panel demonstrates the accumulation of Dl EC at various time points up to 60 minutes in the medium of S2 cells stably expressing full length Delta (Rebay, et al . , 1991, Cell
• the right panel shows the accumulation of D1 EC at 60 minutes in the presence of EDTA (5, 10, 15 mM) and
• Figures 9A-9C shows that Dl EC binds to Notch
• FIG. 10 competes for Notch-Delta interaction and acts as an agonist of the Notch pathway.
• Figure 9A The Dl EC fragment specifically binds to Notch expressing S2 cells and does not bind to S2 cells alone. Notch expressing S2 cells (lane 1, 2) incubated in the absence (lane 1) or presence (lane 2) of
• D1 EC 15 D1 EC (lane 6) were sedimented through a sucrose cushion and the extract was western blotted with antibody 9B.
• Dl EC was prepared as a 5X concentrate of 16 hour culture media (Sang's M3) of 0.7mM CuS0 4 induced Delta-S2 cells. Notch-S2 and nontransfected S2 cells were induced with 0.7 mM CuS0 4 for
• Delta-S2 cells as measured turbidimetrically with transmitted light at 320nm. At the concentration shown (IX Dl EC , closed circles) , a 60% inhibition in the initial rate of aggregation was seen compared to control media concentrate (IX ⁇ ECN, 0 closed squares) . The error bars show the standard deviation of the mean of triplicate determinations.
• Figure 9C shows the effect of D1 EC on primary cultured cortical neurons in the representative images as labeled: (I) seven to ten days in vi tro cortical neurons before treatment, (II) cultured in the.
• the graph represents the mean length of neurites per neuron. Each bar represents the mean ⁇ SEM of three separate experimental trials. Primary cortical neurons o exhibit multipolar morphology and the extensive neurite network in control cultures (I) , cultures in the presence of
• Figure 10 is a schematic diagram comparing the soluble fragment of Delta (Dl EC ) that is clipped by Kuz with
• FIG. 11 shows the amino acid sequence of the
• Delta cleavage peptide of Drosophila Delta (SEQ ID NO: 9) .
• Bold arrows indicate potential cleavage sites identified by data from both C-terminal sequence analysis and LC/MS; dashed arrows indicate potential cleavage sites identified by only one of the analyses.
• (A) indicates the alanine instead of the threonine reported by Vassin et al.,1987, EMBO J. 6:3431- 3440.
• Delta is cleaved by the metalloprotease-disintegrin Kuzbanian (Kuz) into two fragments, a soluble amino-terminal fragment consisting essentially of the extracellular domain, and a membrane-bound fragment consisting essentially of the transmembrane domain and the intracellular domain.
• the soluble fragment of Delta like the full length, membrane-bound Delta, is able to bind to Notch.
• Applicants believe that even though full length Delta is able to bind to Notch, it is the soluble fragment of Delta that is the actual ligand for Notch in vivo .
• Delta activation i.e., cleavage
• cleavage a ligand of Notch
• Molecules that modulate Delta and Notch function are important tools for studying and manipulating differentiation processes, e . g. , in expanding cell populations without substantial differentiation
• One embodiment of the present invention is directed to a peptide of approximately 30 amino acids, and its 5 encoding nucleic acids, of the toporythmic protein Delta that contains a sequence which is cleaved by the metalloprotease- disintegrin Kuzbanian (Kuz) , (herein termed "cleavage peptide") as well as derivatives (e.g., fragments) and analogs thereof.
• cleavage peptide consists of the sequence of amino acid Cys 516 to amino acid
• the Delta cleavage peptide is a portion of a mammalian Delta, preferably a human Delta. Such a peptide is believed to have the ability to modulate Kuz cleavage of
• the invention is also directed to a derivative or analog of the cleavage peptide which is functionally active, i . e . , capable of displaying one or more known functional activities associated with the "wild type" cleavage peptide.
• Such functional activities include but are not limited to 25 antigenicity [ability to bind (or compete with the cleavage peptide for binding) to an anti-Delta cleavage peptide antibody] , immunogenicity (ability to generate antibody which binds to the cleavage peptide) , ability to bind (or compete with the cleavage peptide for binding) to Kuz.
• Delta fragments that comprise the cleavage peptide sequence are also provided, as are fusion proteins comprising c a Delta fragment containing a sequence of Delta that includes at least the cleavage peptide sequence, fused to a non-Delta sequence at the amino- and/or carboxy-terminal end of the
• Delta sequence Concatamers of Delta fragments containing at least the cleavage peptide sequence (e . g. , two, three, or more copies of a portion of the Delta sequence consisting of 0 at least the cleavage peptide sequence) are also provided.
• the Delta fragments comprising the cleavage peptide sequence are not greater than 35, 50, 75,
• the present invention is directed to a peptide comprising an amino-terminal fragment of a full length Delta protein, which fragment is cleaved 0 from the full length Delta protein by two proteolytic processing events, the cleavage of the signal peptide and the cleavage by Kuz (herein termed "soluble Delta peptide" or
• the soluble Delta peptide amino acid sequence begins at amino acid Ser wound and terminates between amino acid Cys-,, 5 and amino acid Phe 543 in human Delta (SEQ ID NO: 10) ; begins at amino acid Ser 22 and terminates between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6); begins at amino acid Ser 24 and terminates between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO:7), begins at ⁇ amino acid Ser 22 and terminates between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO:8), or begins at amino acid Ser 23 and terminates between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• Such a peptide is believed to have the ability to bind Notch, and thus modulate Delta and Notch activation.
• the invention is also directed to a derivative or
• soluble Delta peptide which is functionally active, i.e., capable of displaying one or more known functional activities associated with the "wild type" soluble peptide.
• functional activities include but are not limited to antigenicity [ability to bind (or compete with the soluble peptide for binding) to an anti-Delta soluble peptide 10 antibody] , immunogenicity (ability to generate antibody which binds to the soluble peptide) , ability to bind (or compete with the soluble peptide for binding) to Notch.
• Antibodies to the Delta soluble peptide, its derivatives and analogs are additionally provided. 15 Methods of production of the soluble Delta peptide, derivatives and analogs, e . g. , by recombinant means, are also provided .
• the present invention is also directed to certain compositions comprising and methods for production of protein 20 complexes of Delta and Kuz.
• the invention is directed to complexes of Delta, and derivatives, fragments and analogs of Delta, with Kuz, and its derivatives, fragments and analogs (a complex of Delta and Kuz is designated as "Delta:Kuz" herein) .
• Methods of production of a Delta: Kuz complex, and a derivative or analog thereof, e . g. , by recombinant means, are also provided.
• the present invention is also directed to certain compositions and methods for production of protein complexes with Notch of the soluble fragment of Delta liberated by Kuz.
• the invention is directed to complexes of the soluble Delta peptide, and derivatives, fragments and analogs of the soluble fragment, with Notch, and its derivatives, fragments and analogs (a complex of the soluble fragment of Delta and Notch is designated as "D1 EC :Notch” herein) .
• D1 EC :Notch a complex of the soluble fragment of Delta and Notch.
• the invention is further directed to methods for modulating (i.e., inhibiting or enhancing) the activity of Notch or Delta or Kuz by contacting a cell expressing Notch or Delta or Kuz, or an organism comprising a cell expressing Notch or Delta or Kuz, a peptide comprising a fragment of Delta having the amino acid sequence of about amino acid c y 5 i 6 to about amino acid Phe 543 in human Delta (SEQ ID NO:10), of about amino acid Cys 51s to about amino acid Phe 543 in mouse Delta (SEQ ID NO: 6), of about amino acid Cys 523 to about amino acid Phe 551 in chick Delta (SEQ ID NO:7), of about amino acid Cys 518 to about amino acid Phe 544 in Xenopus Delta (SEQ ID N0:8), and the sequence of about amino acid Cys 564 to about amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO:9).
• the peptide comprises 25, 30, 35, 40
• the invention is further directed to methods for modulating (i.e., inhibiting or enhancing) the activity of a
• D1 EC :Notch complex have been implicated in cell fate and differentiation. Accordingly, the present invention is directed to methods for screening a Delta: Kuz complex, as well as a derivative or analog of the complex, for the ability to alter cell fate or differentiation. The present invention is also directed to methods for screening a
• D1 EC :Notch complex as well as a derivative or analog of the complex, for the ability to alter cell fate or differentiation.
• the present invention is also directed to therapeutic and diagnostic methods and compositions based on the Delta cleavage peptide and encoding nucleic acids, as well as on soluble Delta peptides and encoding nucleic acids.
• the invention provides for the treatment of disorders of cell fate and differentiation by administration of a therapeutic compound of the invention. Such therapeutic compounds
• Therapeutics include: Delta cleavage peptides and derivative and analogs (including fragments) thereof, antibodies thereto, nucleic acids encoding the Delta cleavage peptide, derivatives, or analogs, Delta cleavage peptide antisense nucleic acids, Delta: Kuz complexes and antibodies thereto, and Dl EC :Notch complexes and antibodies thereto.
• Therapeutics include soluble
• a Therapeutic of the invention is administered to treat a cancerous condition, or to prevent progression from a pre- neoplastic or non-malignant state into a neoplastic or a malignant state.
• a Therapeutic of the invention is administered to treat a nervous system disorder or to promote tissue regeneration and repair.
• Therapeutics which antagonize, or inhibit, Notch, Delta cleavage peptide and/or Kuz function
• Antagonist Therapeutics are administered for therapeutic effect.
• Ant Therapeutics which promote Notch, Delta cleavage peptide and/or Kuz function (hereinafter “Agonist Therapeutics”) are administered for therapeutic effect.
• disorders of cell fate in particular hyperproliterative (e. g. , cancer) or hypoproliterative disorders, involving aberrant or undesirable levels of expression or activity or localization of Notch, Delta cleavage peptide and or Kuz protein can be diagnosed by detecting such levels, as described more fully infra .
• Yet another embodiment of the present invention is directed to methods for detecting or measuring Delta activation by observing or measuring Delta cleavage products that are indicative of Delta activation.
• the method for detecting or measuring Delta activation in a cell comprises detecting or measuring the expression of one or more Delta cleavage products selected from the group consisting of Dl E and DlTM.
• the method comprises detecting or measuring an amino-terminal fragment of full-length Delta terminating between amino acid Cys s64 and amino acid Ala 593 or Gln 594 in Drosophila Delta, between amino acid Cys 5is and amino acid Phe 543 in human Delta, between amino acid Cys 515 and amino acid Phe 543 in mouse Delta, between amino acid Cys 523 and amino acid Phe 5S1 in chick Delta, or terminating between amino acid
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 kilodaltons.
• the method comprises detecting or measuring a soluble Delta peptide having the amino acid sequence beginning at amino acid Ser 22 and terminating between amino acid Cys sl6 and amino acid Phe 543 in human Delta (SEQ ID NO: 10) ; beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID N0:6); beginning at amino acid Ser 24 and terminating between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO: 7); beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) ; and the sequence beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala 593 or G
• the present invention is also directed to methods for detecting or measuring Kuz function by observing or measuring Delta cleavage products that are indicative of Kuz function.
• the method for detecting or measuring Kuz function in a cell comprises detecting or measuring the expression of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM.
• the method comprises detecting or measuring an amino-terminal fragment of full-length Delta which terminates between amino acid c y s 56 and amino acid Ala 593 or Gln 594 in Drosophila Delta, between amino acid Cys 516 and amino acid Phe 543 in human Delta, between amino acid Cys 515 and amino acid Phe 543 in mouse Delta, between amino acid Cys 523 and amino acid Phe 551 in chick Delta, or terminates between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta.
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 kilodaltons.
• the method comprises detecting or measuring a soluble Delta peptide having the amino acid sequence beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID
• the present invention is also directed to methods for identifying a molecule that modulates Delta activation by detecting or measuring a change in the amount or pattern of Delta cleavage products.
• the method for identifying a modulator of Delta activation comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the method for identifying a modulator of Delta activation comprises contacting a candidate modulator molecule with a full length Delta in the presence of a composition comprising Kuz and optionally other cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition and detecting or measuring the amount of Delta cleavage products D1 EC and DlTM that result, in which a difference in the presence or amount of said Delta cleavage products compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the present invention is also directed to methods for identifying a molecule that modulates Notch function by detecting or measuring a change in the amount of Delta cleavage products that are necessary for Notch function.
• the method for identifying a modulator of Notch function comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates
• the present invention is also directed to methods for identifying a molecule that modulates Kuz function by detecting or measuring a change in the amount of Delta cleavage products that are indicative of
• the method for identifying a modulator of Kuz function comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of D1 EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates
• the present invention is also directed to therapeutic and prophylactic, as well as diagnostic, prognostic, and screening methods and compositions based upon the Delta: Kuz complex or a D1 EC :Notch complex (and the nucleic acids encoding the individual proteins that participate in the complex) .
• Therapeutic compounds of the invention include, but are not limited to, a Delta: Kuz complex, and a complex where one or both members of the complex is a derivative, fragment, homolog or analog of Delta or Kuz; antibodies to and nucleic acids encoding the foregoing; and antisense nucleic acids to the nucleotide sequences encoding the complex components. Diagnostic, prognostic and screening kits are also provided. Animal models and methods of screening for modulators (i . e . , agonists, and antagonists) of the activity of a Delta: Kuz complex or the activity of a D1 EC : otch complex are also provided.
• a variety of host-vector systems may be utilized to express the protein-coding sequence. These include but are not limited to mammalian cell systems infected with virus (e . g. , vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e . g. , baculovirus); microorganisms such as yeast containing yeast vectors, or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA.
• the expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system utilized, any one of a number of suitable transcription and translation elements may be used. In a specific embodiment, the human Delta cleavage peptide is expressed.
• the human soluble Delta peptide is expressed. Any of the methods previously described for the insertion of DNA fragments into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vi tro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination) .
• nucleic acid sequence encoding a Delta cleavage peptide or peptide fragment thereof may be regulated by a second nucleic acid sequence so that the Delta cleavage peptide is expressed in a host transformed with the recombinant DNA molecule.
• expression of a Delta cleavage peptide may be controlled by any promoter/enhancer element known in the art . Promoters which may be used to control Del ta cleavage peptide expression include, but are not limited to, the SV40 early promoter region (Bernoist and
• prokaryotic expression vectors such as the ⁇ -lactamase promoter (Villa-Kamaroff , et al . , 1978, Proc. Natl. Acad.
• promoter of the photosynthetic enzyme ribulose biphosphate carboxylase (Herrera-Estrella et al . , 1984, Nature 310:115-120); promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter, and the following animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells (Swift et al .
• mouse mammary tumor virus control region which is active in c testicular, breast, lymphoid and mast cells (Leder et al . , 1986, Cell 45:485-495), albumin gene control region which is active in liver (Pinkert et al . , 1987, Genes and Devel . 1:268-276), alpha-fetoprotein gene control region which is active in liver (Krumlauf et al . , 1985, Mol. Cell. Biol.
• beta- globin gene control region which is active in myeloid cells
• Delta peptide can be identified by three general approaches:
• marker gene functions and (c) expression of inserted 5 sequences.
• the presence of a foreign gene inserted in an expression vector can be detected by nucleic acid hybridization using probes comprising sequences that are homologous to the inserted Delta cleavage peptide coding sequences.
• the recombinant 0 vector/host system can be identified and selected based upon the presence or absence of certain "marker" gene functions
• telomere encoding nucleic acids e. g. , thymidine kinase activity, resistance to antibiotics, transformation phenotype, occlusion body formation in baculovirus, etc.
• recombinants containing the insert can be identified by the absence of the marker gene function.
• recombinant expression vectors can be identified by assaying the foreign gene product expressed by the recombinant.
• assays can be based, for example, on the physical or functional properties of the encoded cleavage peptide in in vi tro assay systems, e . g. , binding to Kuz, binding with antibody.
• the expression vectors which can be used include, but are not limited to, the following vectors or their derivatives : human or animal viruses such as vaccinia virus or adenovirus; insect viruses such as baculovirus; yeast vectors; bacteriophage vectors (e.g., lambda) , and plasmid and cosmid DNA vectors, to name but a few.
• a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus, expression of the genetically engineered Delta cleavage peptide may be controlled.
• different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, cleavage [e.g., of signal sequence]) of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed. For example, expression in a bacterial system can be used to produce an c unglycosylated core protein product .
• Expression in yeast will produce a glycosylated product.
• Expression in mammalian cells can be used to ensure "native" glycosylation of a heterologous mammalian Delta cleavage peptide, or to ensure “native” glycosylation of a heterologous mammalian soluble
• Delta peptide may effect processing reactions to different extents.
• the Delta cleavage peptide, fragment, analog, or derivative may be expressed as a fusion, or chimeric protein product (comprising the peptide, fragment, analog, or derivative joined via a peptide 5 bond to a heterologous protein sequence (of a different protein) ) .
• a chimeric product can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other by methods known in the art, in the proper coding frame, and expressing the chimeric 0 product by methods commonly known in the art.
• such a chimeric product may be made by protein synthetic techniques, e.g., by use of a peptide synthesizer.
• cDNA and genomic sequences can be cloned and expressed.
• One embodiment of the present invention is directed 5 to a peptide of approximately 30 amino acids, and its encoding nucleic acids, of the toporythmic protein Delta that contains a sequence which is cleaved by the etalloprotease- disintegrin Kuzbanian (Kuz) , (herein termed "cleavage peptide") as well as derivatives ( e . g. , fragments) and ⁇ analogs thereof.
• the Delta cleavage peptide consists of the sequence of about amino acid Cys 516 to about amino acid Phe 543 in human Delta (SEQ ID NO: 10), of about amino acid Cys si5 to about amino acid Phe S43 in mouse Delta
• the Delta cleavage peptide is a portion of a mammalian Delta, preferably a human Delta.
• the invention further relates to Delta cleavage peptides, and derivatives (including but not limited to fragments) and analogs of Delta cleavage peptides.
• Nucleic acids encoding Delta cleavage peptide derivatives and peptide analogs are also provided.
• the peptides, derivatives, or analogs are of mouse, chicken, frog, rat, pig, cow, dog, monkey, or human Delta cleavage peptides .
• derivatives and analogs related to Delta cleavage peptides are within the scope of the present invention.
• the derivative or analog is functionally active, i.e., capable of exhibiting one or more functional activities associated with wild-type Delta cleavage peptide.
• such derivatives or analogs which have the desired immunogenicity or antigenicity can be used, for example, in immunoassays, for immunization, for inhibition of Delta activity, etc.
• Such molecules which retain, or alternatively inhibit, a desired Delta property e.g., binding to kuz or other toporythmic proteins, can be used as inducers, or inhibitors, respectively, of such property and its physiological correlates.
• Derivatives or analogs of a Delta cleavage peptide can be tested for the desired activity by procedures known in the art, including but not limited to the assays described herein.
• Delta cleavage peptide derivatives can be made by altering Delta cleavage peptide encoding sequences by substitutions, additions or deletions that provide for functionally equivalent molecules. Due to the degeneracy of nucleotide coding sequences, other DNA sequences which encode substantially the same amino acid sequence as a Delta cleavage peptide may be used in the practice of the present invention. These include but are not limited to nucleotide sequences comprising all or portions of the encoding Delta cleavage peptide genes which are altered by the substitution of different codons that encode a functionally equivalent amino acid residue within the sequence, thus producing a silent change.
• the Delta cleavage peptide derivatives of the invention include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino acid sequence of a Delta protein including altered sequences in which functionally equivalent amino acid residues are substituted t r residues within the sequence resulting in a silent change.
• one or more amino acid residues within the sequence can be substituted by another amino acid of a similar polarity which acts as a functional equivalent, resulting in a silent alteration.
• Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs.
• the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine.
• the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine.
• the positively charged (basic) amino acids include arginine, lysine and histidine.
• the negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
• fragments of Delta that comprise the cleavage peptide sequence are also provided.
• the Delta fragments comprising the cleavage peptide are not greater than 35, 50, 75, 100, 150, or 200 amino acids in length.
• a Delta fragment containing the cleavage peptide sequence comprises the cleavage peptide sequence and 35 contiguous amino-terminal amino acids.
• the fragment comprises the cleavage peptide sequence and 100 contiguous ammo-termmal amino acids.
• the fragment comprises the cleavage peptide sequence and 50 contiguous carboxy- terminal amino acids.
• the fragment comprises the cleavage peptide sequence and 50 contiguous amino-terminal amino acids and 50 contiguous carboxy-terminal amino acids.
• oncatamers of Delta fragments containing at least the cleavage peptide sequence e.g., two, three, or more copies of a portion of the Delta sequence consisting of at least the cleavage peptide sequence are also provided.
• the Delta cleavage peptide derivatives and analogs of the invention can be produced by various methods known in the art.
• the manipulations which result in their production can occur at the gene or protein level.
• the cloned Del ta gene sequence can be modified by any of numerous strategies known in the art (Maniatis, T., 1990, Molecular Cloning, A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York) .
• the sequence can be cleaved at appropriate sites with restriction endonuclease (s) , followed by further enzymatic modification if desired, isolated, and ligated in vi tro .
• the Delta cleavage peptide-encoding nucleic acid sequence can be mutated in vi tro or in vivo, to create and/or destroy translation, initiation, and/or termination sequences, or to create variations in coding regions and/or form new restriction endonuclease sites or destroy preexisting ones, to facilitate further in vi tro modification.
• Any technique for mutagenesis known in the art can be used, including but not limited to, in vi tro site- directed mutagenesis (Hutchinson, C, et al . , 1978, J. Biol. Chem 253:6551), etc.
• PCR primers containing sequence changes can be used in PCR to introduce such changes into the amplified fragments.
• Delta cleavage peptide sequence may also be made at the protein level. Included within the scope of the invention are Delta cleavage peptide fragments or other derivatives or analogs which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc.
• any of numerous chemical modifications may be carried out by known techniques, including but not limited to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH 4 ; acetylation, formylation, oxidation, reduction; metabolic synthesis in the presence of tunicamycin; etc.
• analogs and derivatives of Delta cleavage peptide can be chemically synthesized.
• nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the Delta sequence.
• Non-classical amino acids include but are not limited to the D- isomers of the common amino acids, ⁇ -amino isobutyric acid, 4-aminobutyric acid, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t- butylalanine, phenylglycine, cyclohexylalanine, ⁇ -alanine,
• 5 designer amino acids such as ⁇ -methyl amino acids, C ⁇ -methyl amino acids, and N ⁇ -methyl amino acids and amino acid analogs in general .
• the Delta cleavage peptide derivative is a chimeric, or fusion, peptide comprising a Delta cleavage peptide or fragment thereof 0 joined at its amino- or carboxy-terminus via a peptide bond to an amino acid sequence of a different protein.
• a chimeric protein is produced by recombinant expression of a nucleic acid encoding the protein
• Such a chimeric product can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other by methods known in the art, in the proper coding frame, and expressing the chimeric product by o methods commonly known in the art.
• a chimeric product may be made by protein synthetic techniques, e.g., by use of a peptide synthesizer.
• a chimeric nucleic acid encoding a Delta cleavage peptide with a heterologous signal sequence is expressed such that the chimeric protein is expressed extracellularly by the 5 cell.
• the invention is also directed to a derivative or analog of the cleavage peptide which is functionally active, i.e., capable of displaying one or more known functional activities associated with the "wild type" cleavage peptide.
• Such functional activities include but are not limited to antigenicity [ability to bind (or compete with the cleavage peptide for binding) to an anti -Delta cleavage peptide antibody] , immunogenicity (ability to generate antibody which binds to the cleavage peptide) , ability to bind (or compete with the cleavage peptide for binding) to Kuz.
• the invention is further directed to a fragment (and derivatives or analogs
• the present invention is directed to a peptide comprising an amino-terminal fragment of a full length Delta protein, which fragment is cleaved from the full length Delta protein by two proteolytic 0 processing events, the cleavage of the signal peptide and the cleavage by Kuz, (herein termed "soluble Delta peptide") as well as derivatives and analogs thereof.
• the soluble Delta peptide amino acid sequence begins at amino acid Ser 22 and terminates between amino acid Cys 516 and amino 5 acid Phe 543 in human Delta (SEQ ID NO:10); begins at amino acid Ser 22 and terminates between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6); begins at amino acid Ser 24 and terminates between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO:7), begins at amino acid Ser 22 o and terminates between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID N0:8), or begins at amino acid Ser 23 and terminates between amino acid Cys s64 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9) .
• Such a peptide is believed to have the ability to bind Notch, and thus modulate Delta and Notch activation. 5
• the invention further relates to soluble Delta peptides, and derivatives (including but not limited to fragments) and analogs of soluble Delta peptides.
• Nucleic acids encoding soluble Delta peptide derivatives and peptide analogs are also provided.
• the " peptides, derivatives, or analogs are of mouse, chicken, frog, rat, pig, cow, dog, monkey, or human soluble Delta peptides .
• the production and use of derivatives and analogs related to soluble Delta peptides are within the scope of the present invention.
• the derivative or analog is functionally active, i.e., capable of exhibiting one or more functional activities associated with wild-type soluble Delta peptide.
• such derivatives or analogs which have the desired immunogenicity or antigenicity can be used, for example, in immunoassays, for immunization, for promotion of Delta activity, etc.
• Such molecules which retain, or alternatively inhibit, a desired Delta property e.g., binding to Notch or other toporythmic proteins, can be used as inducers, or inhibitors, respectively, of such property and its physiological correlates.
• Derivatives or analogs of a soluble Delta peptide can be tested for the desired activity by procedures known in the art, including but not limited to the assays described herein.
• soluble Delta peptide derivatives can be made by altering soluble Delta peptide encoding sequences by substitutions, additions or deletions that provide for functionally equivalent molecules. Due to the degeneracy of nucleotide coding sequences, other DNA sequences which encode substantially the same amino acid sequence as a soluble Delta peptide may be used in the practice of the present invention. These include but are not limited to nucleotide sequences comprising all or portions of the encoding soluble Delta peptide genes which are altered by the substitution of different codons that encode a functionally equivalent amino acid residue within the sequence, thus producing a silent change.
• the soluble Delta peptide derivatives of the invention include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino acid sequence of a Delta protein including altered sequences in which functionally equivalent amino acid residues are substituted for residues within the sequence resulting in a silent change.
• one or more amino acid residues within the sequence can be substituted by another amino acid of a similar polarity which acts as a functional equivalent, resulting in a silent alteration.
• Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs.
• the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine .
• the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine.
• the positively charged (basic) amino acids include arginine, lysine and histidine.
• the negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
• the soluble Delta peptide derivatives and analogs of the invention can be produced by various methods known in the art. The manipulations which result in their production can occur at the gene or protein level.
• the cloned Delta gene sequence can be modified by any of numerous strategies known in the art (Maniatis, T., 1990, Molecular
• the soluble Delta peptide-encoding nucleic acid sequence can be mutated in vi tro or in vivo, to create and/or destroy translation, initiation, and/or termination sequences, or to create variations in coding regions and/or form new restriction endonuclease sites or destroy preexisting ones, to facilitate further in vi tro modification.
• Any technique for mutagenesis known in the art can be used, including but not limited to, in vi tro site- directed mutagenesis (Hutchinson, C, et al . , 1978, J. Biol. Chem 253:6551), etc.
• PCR primers containing sequence changes can be used in PCR to introduce such changes into the amplified fragments.
• soluble Delta peptide sequence may also be made at the protein level. Included within the scope of the invention are soluble Delta peptide fragments or other derivatives or analogs which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc.
• any of numerous chemical modifications may be carried out by known techniques, including but not limited to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH 4 ; acetylation, formylation, oxidation, reduction; metabolic synthesis in the presence of tunicamycin; etc.
• N- or C-terminal modifications are made, e.g., N-acetylation.
• analogs and derivatives of soluble Delta peptide can be chemically synthesized.
• nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the Delta sequence.
• Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, -amino isobutyric acid, 4-aminobutyric acid, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycme, t- butylalanine, phenylglycine, cyclohexylalanine, ⁇ -alanine, designer amino acids such as ⁇ -methyl amino acids, C ⁇ -methyl amino acids, and N -methyl amino acids and amino acid analogs in general .
• the soluble Delta peptide derivative is a chimeric, or fusion, peptide comprising a soluble Delta peptide or fragment thereof joined at its amino- or carboxy-terminus via a peptide bond to an amino acid sequence of a different protein.
• a chimeric protein is produced by recombinant expression of a nucleic acid encoding the protein (comprising a soluble peptide)
• Delta peptide-coding sequence joined in- frame to a coding sequence for a different protein can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other by methods known in the art, in the proper coding frame, and expressing the chimeric product by methods commonly known in the art.
• a chimeric product may be made by protein synthetic techniques, e.g., by use of a peptide synthesizer.
• a chimeric nucleic acid encoding a soluble Delta peptide with a heterologous signal sequence is expressed such that the chimeric protein is expressed extracellularly by the cell.
• the invention is also directed to a derivative or analog of the soluble peptide which is functionally active, i.e., capable of displaying one or more known functional activities associated with the "wild type" soluble peptide.
• Such functional activities include but are not limited to antigenicity [ability to bind (or compete with the soluble peptide for binding) to an anti-soluble Delta peptide antibody] , immunogenicity (ability to generate antibody which binds to the soluble peptide) , ability to bind (or compete with the soluble peptide for binding) to Notch.
• the invention is further directed to a fragment (and derivatives or analogs thereof) of the soluble Delta peptide which is able to bind to Notch.
• the present invention is directed to a Delta: Kuz protein complex.
• the present invention is also directed to a
• D1 EC Notch protein complex. Del ta, Kuz and Notch have been cloned, see e.g., WO 92/19734, WO 97/01571 and WO 98/08933.
• Figure 2 depicts the amino acid sequences of several Notch homologs (SEQ ID NOS : 1 , 2, 3 and 4), including human Notch (SEQ ID NOS:l and 2) .
• Figure 3 depicts the amino acid sequences of several Delta homologs (SEQ ID NOS: 5, 6, 7, 8 and 9) and the nucleic acid sequence encoding human Delta is depicted in Figure 4B (SEQ ID NO: 13) .
• Dl EC is the amino-terminal fragment of full length Delta consisting of essentially the extracellular domain of wild-type Delta that is liberated when Kuz cleaves Delta.
• the Dl EC fragment is soluble and begins at amino acid Ser 23 and terminates between amino acid C Y S 56 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9), begins at amino acid Ser 22 and terminates between amino acid Cys 516 and amino acid Phe S43 in human Delta (SEQ ID NO:10), begins at amino acid Ser 22 and terminates between amino acid Cys 515 and amino acid Phe S43 in mouse Delta (SEQ ID NO: 6), begins at amino acid Ser 24 and terminates between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO:7), or begins at amino acid Ser 22 and terminates between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) .
• the Delta: Kuz complex or the Dl EC :Notch complex is a complex of human proteins.
• the invention is also directed to complexes of derivatives (including fragments) and analogs of Delta with Kuz, complexes of Delta with derivatives (including fragments) and analogs of Kuz, and complexes of derivatives (including fragments) and analogs of Delta and Kuz (as used herein, fragment, derivative, homolog or analog of a Delta: Kuz complex includes complexes where one or both 5 members of the complex are fragments, derivatives or analogs of the wild-type Delta or Kuz protein) .
• the present invention is also directed to complexes of derivatives (including fragments) and analogs of Dl EC with Notch, complexes of Dl EC with derivatives (including fragments) and analogs of Notch, and complexes of derivatives (including 0 fragments) and analogs of Dl EC and Notch (as used herein, fragment, derivative, homolog or analog of a D1 EC :Notch complex includes complexes where one or both members of the complex are fragments, derivatives or analogs of the wild- type Dl EC or Notch protein) .
• the 5 Dl E : otch complex in which one or both members of the complex is a fragment, derivative, homolog or analog of the wild type protein is a functionally-active D1 EC :Notch complex.
• the native proteins, or derivatives or analogs of Delta, Notch and/or Kuz are obtained from an o animal, e.g., mouse, rat, pig, cow, dog, monkey, human, fly, frog.
• the native proteins are obtained from plants .
• a “functionally active Delta: Kuz complex” refers to that material displaying one or more known functional attributes of a complex of wild type Delta with 5 wild type Kuz, including protein-protein binding, binding to a Delta-, a Kuz-, and/or a Delta: Kuz complex-specific antibody, or has the functional attribute (s) of Delta, Kuz, and/or a Delta: Kuz complex involved in cell fate and differentiation.
• a “functionally active Dl EC :Notch complex” refers to that material displaying one or more known functional attributes of a complex of wild type Dl EC with wild type Notch, including protein-protein binding, binding to a
• Dl EC -, a Notch-, and/or a Dl EC :Notch complex-specific antibody or has the functional attribute (s) of Dl EC , Notch, and/or a
• Dl EC Notch complex involved in cell fate and differentiation.
• the present invention is also directed to a method of screening a Delta: Kuz complex, particularly a complex of
• Delta with Kuz for the ability to alter a cell function, particularly those cell functions in which Delta and/or Kuz has been implicated, including, e.g., physiological processes such as cell fate determination and differentiation, binding to an anti-Delta : Kuz complex antibody, etc., and other activities as they are described in the art.
• the present invention is also directed to a method of screening a
• Dl EC :Notch complex particularly a complex of Dl EC with Notch for the ability to alter a cell function, particularly those cell functions in which Dl EC and/or Notch has been implicated, including, e.g., physiological processes such as cell fate determination and differentiation, binding to an anti- Dl EC :Notch complex antibody, etc., and other activities as they are described in the art .
• the present invention is also directed to a method for screening a complex of a derivative, fragment, or analog of Delta and/or Kuz for the ability to alter a cell function such as differentiation.
• such derivatives or analogs which have the desired immunogenicity or antigenicity can be used in immunoassays, for immunization, for inhibition of Delta: Kuz complex activity, etc.
• Derivatives or analogs that retain, or alternatively lack or inhibit, a property of interest e.g., participation in a Delta:Kuz complex
• the present invention is also directed to a method for screening a complex of a derivative, fragment, or analog of Dl EC and/or
• Dl EC :Notch complex activity etc.
• Derivatives or analogs that retain, or alternatively lack or inhibit, a property of interest can be used as an inducer, or inhibitor, respectively, of such a property and its physiological correlate.
• a specific embodiment of the present invention is directed to a Delta: Kuz complex of a fragment of Delta and/or a fragment of Kuz that can be bound by an anti -Delta antibody and/or bound by an anti-Kuz antibody, respectively, or bound by an antibody specific for a Delta: Kuz complex.
• Another specific embodiment of the present invention is directed to a
• Fragments and other derivatives or analogs of a Delta: Kuz complex or of a Dl EC :Notch complex can be tested for the desired activity by procedures known in the art, including but not limited to the assays described infra .
• the present invention is directed to a Delta: Kuz complex or to a Dl EC :Notch complex comprising a fragment of one or both members of the complex.
• these fragments consist of, but are not exclusive to fragments of Kuz, identified as interacting with Delta in a modified yeast matrix mating assay or genetic screen. Fragments, or proteins comprising fragments, lacking a region of either member of the complex, are also provided. Nucleic acids encoding the foregoing are provided in the present invention.
• Nucleic acids encoding Delta, Notch and Kuz are known, and in addition can be obtained by any method known in the art, e . g. , by PCR amplification using synthetic primers hybridizable to the 3' and 5' ends of each sequence, and/or by cloning from a cDNA or genomic library using an oligonucleotide specific for each nucleotide sequence.
• Homologs e.g., nucleic acids encoding Delta, Notch and Kuz of species other than human
• other related sequences e.g., paralogs
• nucleic acid containing all or a portion of the nucleotide sequence encoding the protein can be inserted into an appropriate expression vector, i.e., a vector that contains the necessary elements for the transcription and translation of the inserted protein coding sequence.
• the necessary transcriptional and translational signals can also be supplied by the native promoter of the Delta, Kuz and Notch genes, and/or their flanking regions.
• a variety of host-vector systems may be utilized to express the protein coding sequence. These include but are not limited to mammalian cell systems infected with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g., baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA.
• virus e.g., vaccinia virus, adenovirus, etc.
• insect cell systems infected with virus e.g., baculovirus
• microorganisms such as yeast containing yeast vectors
• bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA e.g., bacteriophage, or cosmid DNA.
• the expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system utilized, any one of a number of suitable transcription and
• a Delta: Kuz complex is obtained by expressing the entire Delta coding sequence and c the entire Kuz coding sequence in the same cell, either under the control of the same promoter or two separate promoters .
• a derivative, fragment or homolog of Delta and/or a derivative, fragment or homolog of Kuz are recombinantly expressed.
• the derivative, fragment or homolog of Delta and/or the Kuz protein forms a complex 0 with a binding partner identified by a binding assay, and more preferably forms a complex that binds to an anti-
• a SDelta:Notch complex is obtained by expressing the entire
• Dl EC coding sequence and the entire Notch coding sequence in 5 the same cell either under the control of the same promoter or two separate promoters.
• a derivative, fragment or homolog of Dl EC and/or a derivative, fragment or homolog of Notch are recombinantly expressed.
• the derivative, fragment or homolog of Dl EC and/or 0 the Notch protein forms a complex with a binding partner identified by a binding assay, and more preferably forms a complex that binds to an anti-Dl EC :Notch complex antibody.
• any method available in the art can be used for the insertion of DNA fragments into a vector to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and protein coding sequences. These methods may include in vi tro recombinant DNA and synthetic techniques and in vivo recombinant techniques (genetic recombination) . Expression of nucleic acid sequences encoding Delta, Kuz and Notch, or a derivative, fragment or homolog thereof, may be regulated by a second nucleic acid sequence so that the gene or fragment thereof is expressed in a host transformed with the recombinant DNA molecule (s) . For example, expression of the proteins may be controlled by any promoter/enhancer known in the art. In a specific embodiment, the promoter is not native to the genes for Delta, Notch or Kuz. Promoters that may be used include but are not limited to those described in
• a vector is used that comprises a promoter operably linked to nucleic acid sequences encoding Delta, Notch and/or Kuz, or a fragment, derivative or homolog thereof, one or more origins of replication, and optionally, one or more selectable markers
• a vector that comprises a promoter operably linked to nucleic acid sequences encoding both Delta and Kuz, or both Dl C and Notch, one or more origins of replication, and optionally, one or more selectable markers.
• an expression vector containing the coding sequence, or a portion thereof, of Delta and Kuz, or of D1 EC and Notch, either together or separately, is made by subcloning the gene sequences into the EcoRI restriction site of each of the three pGEX vectors
• Expression vectors containing the sequences of interest can be identified by three general approaches: (a) nucleic acid hybridization, (b) presence or absence of
• marker gene function and (c) expression of the inserted sequences.
• Delta, Notch and Kuz sequences can be detected by nucleic acid hybridization to probes comprising sequences homologous and complementary to the inserted sequences.
• the recombinant vector/host system can be identified and selected based upon the presence or absence of certain "marker” functions (e.g., resistance to antibiotics, occlusion body formation in baculovirus, etc.) caused by insertion of the sequences of interest in the vector.
• recombinants containing the Delta or Kuz fragment will be identified by the absence of the marker gene function (e.g., loss of beta-galactosidase activity) .
• recombinant expression vectors can be identified by assaying for the Delta and Kuz expressed by the recombinant vector. Such assays can be based, for example, on the physical or functional properties of the interacting species in in vi tro assay systems, e.g., formation of a Delta: Kuz complex or binding to an anti-Delta, anti-Kuz, or anti-Delta: Kuz complex antibody.
• recombinant Delta, Notch and Kuz molecules are identified and the complexes or individual proteins isolated, several methods known in the art can be used to propagate them.
• recombinant expression vectors can be propagated and amplified in quantity.
• the expression vectors or derivatives which can be used include, but are not limited to, human or animal viruses such as vaccinia virus or adenovirus; insect viruses such as baculovirus, yeast vectors; bacteriophage vectors such as lambda phage; and plasmid and cosmid vectors.
• a host cell strain may be chosen that modulates the expression of the inserted sequences, or modifies or processes the expressed proteins in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus expression of the genetically-engineered Delta, Notch and/or Kuz may be controlled.
• different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, phosphorylation, etc.) of proteins.
• Appropriate cell lines or host systems can be chosen to ensure that the desired modification and processing of the foreign protein is achieved.
• expression in a bacterial system can be used to produce an unglycosylated core protein, while expression in mammalian cells ensures
• vector/host expression systems may effect processing reactions to different extents.
• the Delta, Notch and/or Kuz protein or a fragment, homolog or derivative thereof may be expressed as fusion or chimeric protein products comprising the protein, fragment, homolog, or derivative joined via a peptide bond to a heterologous protein sequence of a different protein.
• Such chimeric products can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acids to each other by methods known in the art, in the proper coding frame, and expressing the chimeric products in a suitable host by methods commonly known in the art.
• a chimeric product can be made by protein synthetic techniques, e.g., by use of a peptide synthesizer. Chimeric genes comprising portions of Delta, Notch and/or Kuz fused to any heterologous protein-encoding sequences may be constructed.
• a specific embodiment relates to a chimeric protein comprising a fragment of Delta, Notch and/or Kuz of at least six amino acids .
• fusion proteins are provided that contain the interacting domains of the Delta protein and Kuz, or the interacting domains of Dl EC and Notch, and, optionally, a peptide linker between the two domains, where such a linker promotes the interaction of the Delta and
• Kuz binding domains or promotes the interaction of the Dl EC and Notch binding domains.
• These fusion proteins may be particularly useful where the stability of the interaction is desirable (due to the formation of the complex as an intramolecular reaction) , for example, in production of antibodies specific to the Delta: Kuz complex or specific to the 5 Dl EC :Notch complex.
• Delta, Notch and/or Kuz derivatives can be made by altering their sequences by substitutions, additions or deletions that provide for functionally equivalent molecules .
• nucleotide coding sequences Due to the degeneracy of nucleotide coding sequences, other DNA sequences that encode 0 substantially the same amino acid sequence as a Delta, Notch or Kuz gene or cDNA can be used in the practice of the present invention. These include but are not limited to nucleotide sequences comprising all or portions of the Delta, Notch or Kuz genes that are altered by the substitution of 5 different codons that encode a functionally equivalent amino acid residue within the sequence, thus producing a silent change.
• the Delta, Notch or Kuz derivatives of the invention include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino o acid sequence of Delta, Notch or Kuz, including altered sequences in which functionally equivalent amino acid residues are substituted for residues within the sequence resulting in a silent change.
• one or more amino acid residues within the sequence can be substituted by another amino acid of a similar polarity that acts as a 5 functional equivalent, resulting in a silent alteration.
• Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs.
• the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, 0 phenylalanine, tryptophan and methionine.
• the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine.
• the positively charged (basic) amino acids include arginine, lysine and histidine.
• the negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
• nucleic acids encoding proteins and proteins consisting of or comprising a fragment of Delta, Notch or Kuz consisting of at least 6 (continuous) amino acids of Delta, Notch or Kuz are provided.
• the fragment consists of at least 10, 20, 30, 40, or 50 amino acids of Delta and Kuz or
• Dl EC and Notch such fragments are not larger than 35, 100 or 200 amino acids.
• Derivatives or analogs of Delta, Notch and Kuz include, but are not limited, to molecules comprising regions that are substantially homologous to Delta, Notch or Kuz, in various embodiments, by at least 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% identity over an amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art, or whose encoding nucleic acid is capable of hybridizing to a sequence encoding Delta, Notch or Kuz under stringent, moderately stringent, or nonstringent conditions.
• the Delta, Notch and Kuz derivatives and analogs of the invention can be produced by various methods known in the art .
• the manipulations which result in their production can occur at the gene or protein level. For example, the cloned
• Delta, Notch and Kuz gene sequences can be modified by any of numerous strategies known in the art (Sambrook et al . , 1989,
• sequences can be cleaved at appropriate sites with restriction endonuclease (s) , followed by further enzymatic modification if desired, isolated, and ligated in vitro.
• s restriction endonuclease
• Delta-, Notch- and/or Kuz- encoding nucleic acid sequence can be mutated in vi tro or in vivo, to create and/or destroy translation, initiation, and/or termination sequences, or to create variations in coding regions and/or form new restriction endonuclease sites or destroy pre-existing ones, to facilitate further in vitro modification.
• Any technique for mutagenesis known in the art can be used, including but not limited to, chemical mutagenesis and in vi tro site-directed mutagenesis
• the individual gene product or complex can be isolated and analyzed. This is achieved by assays based on the physical and/or functional properties of the protein or complex, including, but not limited to, radioactive labeling of the product followed by analysis by gel electrophoresis, immunoassay, cross-linking to marker-labeled product, etc.
• the Delta: Kuz or Dl EC : otch complexes may be isolated and purified by standard methods known in the art
• the amino acid sequence of the protein can be deduced from the nucleic acid sequence of the chimeric gene from which it was encoded.
• the protein or its derivative can be synthesized by standard chemical methods known in the art (e . g. , Hunkapiller et al . , 1984, Nature 310: 105-111).
• Delta: Kuz complexes whether produced by recombinant DNA techniques, chemical synthesis methods, or by purification from native sources include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino acid sequences substantially as depicted in Figures
• such Dl EC : otch complexes whether produced by recombinant DNA techniques, chemical synthesis methods, or by purification from native sources include, but are not limited to, those containing, as a primary amino acid sequence, all or part of the amino acid sequences substantially as depicted in Figures 2 and 3 (SEQ ID NOS: 5, 6, 7, 8 and 9 and SEQ ID NOS : 1 , 2, 3, and 4, respectively), as well as fragments and other analogs and derivatives thereof, including proteins homologous thereto.
• Delta, Notch and/or Kuz sequences may be made at the protein level .
• a complex of a Delta fragment or a Kuz fragment and Delta or Kuz fragments, derivatives and analogs that are differentially modified during or after translation e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc.
• Kuz amino acid sequences are modified to include a fluorescent label.
• Delta is another specific embodiment
• Notch and/or Kuz are modified to have a heterofunctional reagent; such heterofunctional reagents can be used to crosslink the members of the complex.
• complexes of analogs and derivatives of Delta and/or Kuz, or Dl EC and/or Notch can be chemically synthesized.
• a peptide corresponding to a portion of Delta and/or Kuz, which comprises the desired domain or mediates the desired activity in vi tro e . g. ,
• Delta: Kuz complex formation can be synthesized by use of a peptide synthesizer.
• non-classical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the Delta and/or Kuz.
• Non-classical amino acids include but are not limited to the
• amino acid 3 -amino propionoic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t- butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, ⁇ -alanine, fluoro-amino acids, designer amino acids such as ⁇ -methyl amino acids, C ⁇ -methyl amino acids, N ⁇ -methyl amino acids, and amino acid analogs in general.
• the amino acid can be D (dextrorotary) or L (levorotary) .
• the amino acid sequence of Delta, Notch or Kuz isolated from the natural source, as well as those expressed in vi tro, or from synthesized expression vectors in vivo or in vi tro can be determined from analysis of the DNA sequence, or alternatively, by direct sequencing of the isolated protein.
• Such analysis can be performed by manual sequencing or through use of an automated amino acid sequenator.
• the Delta: Kuz or Dl EC -.Notch complexes can also be analyzed by hydrophilicity analysis (Hopp and Woods, 1981,
• a hydrophilicity profile can be used to identify the hydrophobic and hydrophilic regions of the proteins, and help predict their orientation designing substrates for experimental manipulation, such as in binding experiments, antibody synthesis, etc. Secondary structural analysis can also be done to identify regions of Delta, Notch and/or Kuz, or their derivatives, that assume specific structures (Chou and Fasman, 1974, Biochemistry 13:222-23). Manipulation, translation, secondary structure prediction, hydrophilicity and hydrophobicity profile predictions, open reading frame prediction and plotting, and determination of sequence homologies, etc., can be accomplished using computer software programs available in the art.
• a Delta cleavage peptide may be used as an immunogen
• a soluble Delta peptide may be used as an immunogen to generate antibodies which recognize such an immunogen.
• Such antibodies include but are not limited to polyclonal, 0 monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library.
• antibodies to human Delta cleavage peptide are produced.
• antibodies to human soluble Delta peptide are produced.
• the Delta: Kuz complex or a fragment, derivative or homolog thereof, or the Dl EC :Notch complex or a fragment, derivative or homolog thereof may be used as an immunogen to generate antibodies which immunospecifically bind such 0 immunogen.
• Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library.
• Kuz are produced.
• antibodies to a complex of human Dl EC and human Notch are produced.
• a complex formed from a fragment of Delta and a fragment of Kuz, which fragments contain the protein domain that interacts with the other member of the complex are used as an immunogen for antibody production.
• mice including but not limited to rabbits, mice, rats, etc.
• adjuvants may be used to increase the immunological response, depending on the host species, and including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, 0 oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille
• any technique which provides for the production of antibody molecules by continuous cell lines in culture may be used.
• monoclonal antibodies can be produced in germ-free animals 5 utilizing recent technology (PCT/US90/02545) .
• human antibodies may be used and can be obtained by using human hybridomas (Cote et al . , 1983, Proc.
• 4,946,778 can be adapted to produce, for example, Delta 0 cleavage peptide-specific single chain antibodies.
• An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse et al . , 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for Delta proteins, derivatives, or analogs .
• Antibody fragments which contain the idiotype of the molecule can be generated by known techniques.
• such fragments include but are not limited to: the o F(ab') 2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab' fragments which can be generated by reducing the disulfide bridges of the F(ab') 2 fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent . 5
• screening for the desired antibody can be accomplished by techniques known in the art, e.g. ELISA (enzyme-linked immunosorbent assay) .
• ELISA enzyme-linked immunosorbent assay
• to select antibodies which recognize, for example, a Delta cleavage peptide one may assay generated hybridomas 0 for a product which binds to a Delta cleavage peptide.
• For selection of an antibody immunospecific to human Delta cleavage peptide one can select on the basis of positive binding to human Delta cleavage peptide and a lack of binding to Drosophila Delta cleavage peptide.
• the foregoing antibodies can be used in methods known in the art relating to the localization and activity of the protein sequences of the invention, e.g., for imaging these proteins, measuring levels thereof in appropriate physiological samples, in diagnostic methods, etc.
• anti-Delta cleavage peptide antibodies specific for the Delta cleavage peptide and fragments thereof containing the binding domain are Therapeutics.
• an anti-Delta : Kuz complex antibody or a fragment thereof containing the binding domain is a Therapeutic.
• an anti-soluble cleavage peptide antibodies specific for the Delta cleavage peptide and fragments thereof containing the binding domain are Therapeutics.
• an anti-Delta : Kuz complex antibody or a fragment thereof containing the binding domain is a Therapeutic.
• an anti-soluble cleavage peptide antibodies specific for the Delta cleavage peptide and fragments thereof containing the binding domain are Therapeutics.
• an anti-Delta : Kuz complex antibody or a fragment thereof containing the binding domain is a Therapeutic.
• an anti-soluble cleavage peptide antibodies specific for the Delta cleavage peptide and fragments thereof containing the binding domain are Therapeutics.
• Delta peptide antibody or a fragment thereof containing the binding domain is a Therapeutic.
• the present invention is directed to methods for detecting or measuring Delta activation by observing or measuring Delta cleavage products that are indicative of
• the method for detecting or measuring Delta activation in a cell comprises detecting or measuring the expression of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM.
• the method comprises detecting or measuring an amino- terminal fragment of full-length Delta beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9), beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID NO: 10), beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO: 6), beginning at amino acid Ser 24 and terminating between amino acid Cys S23 and amino acid Phe 551 in chick Delta (SEQ ID NO: 9
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 kilodaltons.
• the present invention is also directed to methods for identifying a molecule that modulates Delta activation by detecting or measuring a change in the amount or pattern of Delta cleavage products.
• the method for identifying a modulator of Notch activation comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Notch cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the method for identifying a modulator of Delta activation comprises contacting a candidate modulator molecule with a full length
• Delta in the presence of Kuz and optionally a composition comprising cellular proteins under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition and detecting or measuring the amount of Delta cleavage products Dl EC and DlTM that result, in which a difference in the presence or amount of said Notch cleavage products compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates
• Delta activity Any method known in the art for detecting or measuring the expression of Delta cleavage products indicative of Delta activation can be used. For example, and not by way of limitation, one such method of detection of the c active form of Delta by detecting one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, or by detecting an amino-terminal fragment of full-length
• the method comprises detecting or measuring under reducing conditions, a soluble Delta fragment of approximately 67 0 kilodaltons.
• cleavage products can be done, e.g., by immunoprecipitating the cleavage products with an anti-Delta antibody or binding to anti-Delta antibody on an immunoaffinity column or immobilized on a plate or in a well, or visualizing the fragments by Western blotting.
• the cleavage products can be labelled by general cell surface labeling, or, alternatively, by pulse labeling the cells by incubation in culture medium containing a radioactive label, or, alternatively, it can be anti-Delta antibody (or antibody binding partner) that is labeled rather 0 than the Delta cleavage products.
• Delta ligand or binding fragment thereof such as Notch
• binds to Delta e . g. , when the ligand is labeled
• Delta e.g., when the ligand is labeled
• recover Delta by coimmunoprecipitating with the appropriate anti-Delta ligand antibody to co- immunoprecipitate Delta cleavage products, etc.
• Similar procedures to those described supra can be used to make antibodies to domains of other proteins (particularly toporythmic proteins) that bind or otherwise interact with Delta (e.g., binding fragments of Notch) .
• the cell in which Delta activation is detected or measured can be any cell, e.g., one that endogenously or recombinantly expresses Delta.
• the cell can be vertebrate, insect (e.g., Drosophila) , C. elegans, mammalian, bovine, urine, rat, avian, fish, primate, human, etc.
• the Delta which is expressed can be vertebrate, insect, C. elegans, mammalian, bovine, murine, rat, avian, fish, primate, human, etc.
• the cell can be a cell of primary tissue, a cell line, or of an animal containing and expressing a Delta transgene.
• the transgenic animal can be a Drosophila ( e . g. , melanogaster) or a C. elegans .
• the transgene encodes a human Delta.
• Transgenic animals can be made by standard methods well known in the art (e.g., by use of P element transposons as a vector in Drosophila) .
• the method for identifying a modulator of Delta activation comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the method comprises providing a cell with a candidate modulator molecule and detecting or measuring the amount of the expression by the cell of an amino-terminal fragment of full-length Delta beginning at amino acid Ser 23 and terminating between amino acid Cys S64 and amino acid Ala 593 or Gln 594 in Drosophila Delta
• Xenopus Delta (SEQ ID NO: 8) ; in which a difference in the presence or amount of said fragment compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the method comprises providing a cell with a candidate modulator molecule and detecting or measuring the expression by the cell of a soluble Delta fragment of approximately 67 kilodaltons, in which a difference in the presence or amount of said soluble fragment compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates
• the method for identifying a modulator of Delta activation comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition, and detecting or measuring the amount of Delta cleavage c products Dl EC and/or DlTM that result, in which a difference in the presence or amount of said Delta cleavage product (s) compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the method for identifying a modulator of 0 the method for identifying a modulator of 0
• Delta activation comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition, 5 and detecting or measuring an amino-terminal fragment of full-length Delta beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala 593 or Gln 594 in Drosophila Delta (SEQ ID NO: 9), beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino 0 acid Phe 543 in human Delta (SEQ ID NO:10), beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6), beginning at amino acid Ser 24 and terminating between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO:7), or beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 5
• the method for identifying a modulator of Delta activation comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition and detecting or measuring the amount of a soluble Delta fragment of approximately 67 kilodaltons, in which a difference in the presence or amount of said soluble fragment compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Delta activity.
• the composition comprising cellular proteins is a cell lysate made from cells which recombinantly express Delta.
• the composition comprising cellular proteins is a cell lysate made from cells which endogenously express Delta.
• Detection or measurement of Delta cleavage products can be carried out by methods well known in the art and/or those methods disclosed in Section 5.1, supra .
• the cells used in the methods of this embodiment can either endogenously or recombinantly express Delta.
• Recombinant Delta expression is carried out by introducing Delta encoding nucleic acids into expression vectors and subsequently introducing the vectors into a cell to express Delta or simply introducing Delta encoding nucleic acids into a cell for expression.
• Nucleic acids encoding vertebrate and non- vertebrate Delta have been cloned and sequenced and their expression is well known in the art. See, for example, International Publication WO 97/01571, which is incorporated by reference in their entirety herein.
• Expression can be from expression vectors or intrachromosomal .
• Any method known to those of skill in the art for the insertion of Delta-DNA into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vi tro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination) .
• nucleic acid sequence encoding a Delta protein may be regulated by a second nucleic acid sequence so that the Delta protein is expressed in a host transformed with the recombinant DNA molecule.
• expression of a Delta protein may be controlled by any promoter/enhancer element known in the art . Promoters which may be used to control
• Delta gene expression include, but are not limited to, those described in Section 5.1.
• compositions comprising cellular proteins (e . g. , cell lysates or cell fractions) in the presence of candidate cleavage (and thus Delta activation) modulators the expression of Delta should be such that full length Delta is expressed and proteolytic cleavage of Delta is kept to a minimum such that Delta cleavage products are easily detected over any background proteolysis.
• Delta cleavage to a minimum is to express Delta in cells concurrently with Brefeldin A treatment. Another manner is to express Delta in cells which do not contain Kuz or to express Delta in an in vi tro transcription-translation system in the presence of a protease inhibitor such as phenylmethylsulfonylfluoride (PMSF) . 5.5 METHODS OF IDENTIFYING MODULATORS OF KUZ ACTIVATION
• the method for identifying a modulator of Kuz function comprises providing a Delta expressing cell with a candidate modulator molecule and detecting or measuring the expression by the cell of one or more Delta cleavage products selected from the group consisting of Dl EC and DlTM, in which a difference in the presence or amount of said one or more cleavage products compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Kuz function.
• the method comprises providing a Delta expressing cell with a candidate modulator molecule and detecting or measuring the amount of the expression by the cell of an amino-terminal fragment of full- length Delta beginning at amino acid Ser 23 and terminating between amino acid Cys 564 and amino acid Ala S93 or Gln 594 in Drosophila Delta (SEQ ID NO: 9), beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID NO: 10), beginning at amino acid Ser 22 and terminating between amino acid Cys 515 and amino acid Phe 543 in mouse Delta (SEQ ID NO:6), beginning at amino acid Ser 24 and terminating between amino acid Cys 523 and ammo acid Phe 551 in chick Delta (SEQ ID NO: 7), or beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) ; in which a difference in the presence or amount of said fragment compared to a
• the method comprises providing a Delta expressing cell with a candidate modulator molecule and detecting or measuring the expression by the cell of a soluble Delta fragment of approximately 67 kilodaltons, in which a difference in the presence or amount of said soluble fragment compared to a Delta cell not contacted with the candidate molecule indicates that the molecule modulates Kuz function.
• the method for identifying a modulator of Kuz function comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full-length Delta by Kuz and optionally one or more components of the composition, and detecting or measuring the amount of Delta cleavage products Dl EC and/or DlTM that result, in which a difference in the presence or amount of said Delta cleavage product (s) compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Kuz activity.
• the method for identifying a modulator of Kuz function comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full-length Delta by
• Gln 594 in Drosophila Delta (SEQ ID NO:9), beginning at amino acid Ser 22 and terminating between amino acid Cys 516 and amino acid Phe 543 in human Delta (SEQ ID NO:10), beginning at amino acid Ser 22 and terminating between amino acid Cys 51s and amino acid Phe S43 in mouse Delta (SEQ ID NO:6), beginning at amino acid Ser 24 and terminating between amino acid Cys 523 and amino acid Phe 551 in chick Delta (SEQ ID NO:7), or beginning at amino acid Ser 22 and terminating between amino acid Cys 518 and amino acid Phe 544 in Xenopus Delta (SEQ ID NO: 8) , in which a difference in the presence or amount of said fragment compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Kuz function.
• the method for identifying a modulator of Kuz function comprises contacting a candidate modulator molecule with a full length Delta in the presence of Kuz and optionally a composition comprising cellular proteins, under conditions conducive to cleavage of the full- length Delta by Kuz and optionally one or more components of the composition and detecting or measuring the amount of a soluble Delta fragment of approximately 67 kilodaltons, in which a difference in the presence or amount of said soluble fragment compared to a full-length Delta in presence of said composition not contacted with the candidate molecule indicates that the molecule modulates Kuz function.
• the composition comprising cellular proteins is a cell lysate made from cells which recombinantly express Kuz.
• the composition comprising cellular proteins is a cell lysate made from cells which endogenously express Kuz .
• Detection or measurement of Delta cleavage products can be carried out by methods well known in the art and/or those methods disclosed in Section 5.1, supra .
• the cells used in the methods of this embodiment can either endogenously or recombinantly express Kuz.
• Recombinant Kuz expression is carried out by introducing Kuz encoding nucleic acids into expression vectors and subsequently introducing the vectors into a cell to express Kuz or simply introducing Kuz encoding nucleic acids into a cell for expression.
• Expression can be from expression vectors or intrachromosomal .
• any method known to those of skill in the art for the insertion of Kuz-DNA into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vi tro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination) . Expression of nucleic acid sequence encoding a Delta or Kuz protein may be regulated by a second nucleic acid sequence so that the Kuz protein is expressed in a host transformed with the recombinant DNA molecule. For example, expression of a Kuz protein may be controlled by any promoter/enhancer element known in the art . Promoters which may be used to control Delta gene expression include, but are not limited to, those described in Section 5.1.
• the expression of Delta should be such that full length Delta is expressed and proteolytic cleavage of Delta is kept to a minimum such that Delta cleavage products are easily detected over any background proteolysis.
• proteolysis There are several methods known in the art to keep proteolysis to a minimum. For example, one manner to keep Delta cleavage to a minimum is to express Delta in cells concurrently with Brefeldin A treatment. Another manner is to express Kuz in cells which do not contain Delta or to express Kuz in an in vi tro transcription-translation system in the presence of a protease inhibitor such as phenylmethylsulfonylfluoride (PMSF) .
• PMSF phenylmethylsulfonylfluoride
• Delta Kuz or D1 EC :Notch complexes, and derivatives, fragments and analogs thereof, nucleic acids encoding Delta
• Notch and Kuz as well as derivatives, fragments and analogs of the nucleic acids can be used to screen for compounds that bind to, or modulate the function of a Delta: Kuz complex or a D1 EC :Notch complex, complex member encoding nucleic acids, complex member proteins, and derivatives of the foregoing, and thus, have potential use as agonists or antagonists of Delta: Kuz or Dl EC :Notch complex activity or formation.
• the present invention is thus directed to assays for detecting molecules that specifically bind to, or modulate the function of, Delta, Notch and Kuz nucleic acids, proteins or derivatives of the nucleic acids and proteins.
• recombinant cells expressing both Delta and Kuz nucleic acids can be used to recombinantly produce the complexes or proteins in these assays, to screen for molecules that bind to, or interfere with, or promote Delta: Kuz complex formation or activity.
• a Delta: Kuz or Dl EC :Notch complex e.g., Delta and Kuz or Dl EC and Notch modified to be resistant to proteolytic degradation in the binding assay buffers, or to be resistant to oxidative degradation
• are used to screen for modulators of Delta activity or Kuz activity or Delta: Kuz complex activity or formation or are used to screen for modulators of D1 EC activity or Notch activity or Dl EC :Notch complex activity or formation.
• Such resistant molecules can be generated, e.g., by substitution of amino acids at proteolytic cleavage sites, the use of chemically derivatized amino acids at proteolytic susceptible sites, and the replacement of amino acid residues subject to oxidation, i.e. methionine and cysteine.
• a molecule e.g., a putative binding partner or modulator of Delta: Kuz or Dl EC :Notch complex activity or formation
• the Delta: Kuz or Dl EC :Notch complex, or fragment thereof, respectively under conditions conducive to binding or modulation, and then a molecule that specifically bind to or modulate Delta: Kuz or Dl EC :Notch complex activity or formation is identified.
• Similar methods can be used to screen for molecules that bind to or modulate the function of Delta: Kuz or Dl EC :Notch complex encoding nucleic acids or derivatives thereof .
• a particular aspect of the present invention relates to identifying molecules that inhibit or promote formation or degradation of a Delta: Kuz or Dl EC :Notch complex, e.g., using the method described for screening inhibitors using the modified yeast matrix mating test described in
• a molecule that modulates activity of Delta or Kuz, or a complex of Delta and Kuz is identified by contacting one or more candidate molecules with Delta in the presence of Kuz; and measuring the amount of complex that forms between Delta and Kuz; wherein an increase or decrease in the amount of complex that forms relative to the amount that forms in the absence of the candidate molecule (s) indicates that the molecule (s) modulates the activity of Delta or Kuz or said complex of c Delta and Kuz.
• a modulator is identified by administering a candidate molecule to a transgenic non-human animal expressing both Delta and Kuz from promoters that are not the native Delta or the native Kuz promoters, more preferably where the candidate molecule is also recombinantly expressed in the transgenic non-human 0 animal.
• the method for identifying such a modulator can be carried out in vi tro, preferably with purified Delta, purified Kuz, and a purified candidate molecule .
• a molecule 5 that modulates activity of Dl C or Notch, or a complex of Dl EC and Notch is identified by contacting one or more candidate molecules with Dl EC in the presence of Notch; and measuring the amount of complex that forms between Dl EC and Notch; wherein an increase or decrease in the amount of complex that o forms relative to the amount that forms in the absence of the candidate molecule (s) indicates that the molecule (s) modulates the activity of Dl EC or Notch or said complex of Dl EC and Notch.
• a modulator is identified by administering a candidate molecule to a transgenic non-human animal expressing both Dl EC and Notch from promoters that are not the native Dl EC or the native Notch promoters, more preferably where the candidate molecule is also recombinantly expressed in the transgenic non-human animal.
• Agents/molecules to be screened can be provided as mixtures of a limited number of specified compounds, or as compound libraries, peptide libraries and the like as described in Section 5.7, infra . Agents/molecules to be screened may also include all forms of antisera, antisense nucleic acids, etc., that can modulate complex activity or formation.
• Any molecule known in the art can be tested for its ability to modulate Delta activation or Kuz function as measured by the expression of one or more of the Delta cleavage products disclosed herein. Furthermore, any molecule known in the art can be tested for its ability to modulate Delta: Kuz complex function, or for its ability to modulate Dl EC :Notch complex function.
• candidate molecules can be directly provided to a cell expressing Delta or Kuz or, in the case of candidate proteins, can be provided by providing their encoding nucleic acids under conditions in which the nucleic acids are recombinantly expressed to produce the candidate proteins within the Delta or Kuz expressing cell.
• candidate molecules can also be added to a composition comprising cellular proteins (whole cell lysates, membrane fraction, etc.), preferably derived from cells endogenously or recombinantly expressing Delta.
• cellular proteins whole cell lysates, membrane fraction, etc.
• This embodiment of the invention is well suited to screen chemical libraries for molecules which modulate, e.g., inhibit, antagonize, or agonize, Delta activation or Kuz function or complex function.
• the chemical libraries can be peptide libraries, peptidomimetic libraries, other non- peptide synthetic organic libraries, etc.
• Exemplary libraries are commercially available from several sources (ArQule, Tripos/PanLabs, ChemDesign, Pharmacopoeia) .
• these chemical libraries are generated using combinatorial strategies that encode the identity of each member of the library on a substrate to which the member compound is attached, thus allowing direct and immediate identification of a molecule that is an effective modulator.
• the position on a plate of a compound specifies that compound's composition.
• a single plate position may have from 1-20 chemicals that can be screened by administration to a well containing the interactions of interest. Thus, if modulation is detected, smaller and smaller pools of interacting pairs can be assayed for the modulation activity. By such methods, many candidate molecules can be screened.
• libraries suitable for use are known in the art and can be used to provide compounds to be tested according to the present invention. Alternatively, libraries can be constructed using standard methods .
• the libraries can be constrained or semirigid
• the library can be a cDNA or genomic expression library, random peptide expression library or a chemically synthesized random peptide library, or non-peptide library.
• Expression libraries are introduced into the cells in which the assay occurs, where the nucleic acids of the library are expressed to produce their encoded proteins.
• peptide libraries that can be used in the present invention may be libraries that are chemically synthesized in vi tro . Examples of such libraries are given in Houghten et al . , 1991, Nature 354:84-86, which describes mixtures of free hexapeptides in which the first and second residues in each peptide were individually and specifically defined; Lam et al .
• a combinatorial library may be prepared for use, according to the methods of Ohlmeyer et al., 1993, Proc. Natl. Acad. Sci. USA 90:10922-10926; Erb et al., 1994, Proc. Natl. Acad. Sci. USA 91:11422-11426; Houghten et al . , 1992, Biotechniques 13:412; Jayawickreme et al., 1994, Proc. Natl. Acad. Sci. USA 91:1614-1618; or Salmon et al., 1993, Proc. Natl. Acad. Sci. USA 90:11708-11712.
• PCT PCT
• benzodiazepine library see e.g., Bunin et al . , 1994, Proc. Natl. Acad. Sci. USA 91:4708-4712 may be used.
• Conformationally constrained libraries that can be used include but are not limited to those containing invariant cysteine residues which, in an oxidizing environment, cross-link by disulfide bonds to form cystines, modified peptides (e.g., incorporating fluorine, metals, isotopic labels, are phosphorylated, etc.), peptides containing one or more non-naturally occurring amino acids, non-peptide structures, and peptides containing a significant fraction of ⁇ -carboxyglutamic acid.
• modified peptides e.g., incorporating fluorine, metals, isotopic labels, are phosphorylated, etc.
• peptides containing one or more non-naturally occurring amino acids e.g., incorporating fluorine, metals, isotopic labels, are phosphorylated, etc.
• peptides containing one or more non-naturally occurring amino acids e.g., incorporating fluorine, metals, isotopic labels, are phosphorylated
• non-peptides e.g., peptide derivatives (for example, that contain one or more non- naturally occurring amino acids) can also be used.
• peptide derivatives for example, that contain one or more non- naturally occurring amino acids
• peptoid libraries Simon et al . , 1992,
• Peptoids are polymers of non-natural amino acids that have naturally occurring side chains attached not to the alpha carbon but to the backbone amino nitrogen. Since peptoids are not easily degraded by human digestive enzymes, they are advantageously more easily adaptable to drug use.
• Another example of a library that can be used, in which the amide functionalities in peptides have been permethylated to generate a chemically transformed combinatorial library, is described by Ostresh et al., 1994, Proc. Natl. Acad. Sci. USA 91:11138-11142).
• the members of the peptide libraries that can be screened according to the invention are not limited to containing the 20 naturally occurring amino acids.
• chemically synthesized libraries and polysome based libraries allow the use of amino acids in addition to the 20 naturally occurring amino acids (by their inclusion in the precursor pool of amino acids used in library production) .
• the library members contain one or more non-natural or non-classical amino acids or cyclic peptides.
• Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid; ⁇ -Abu, e-Ahx, 6-amino hexanoic acid; Aib, 2- amino isobutyric acid; 3 -amino propionic acid; ornithine; norleucine; norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, ⁇ -alanine, designer amino acids such as ⁇ - methyl amino acids, C -methyl amino acids, N ⁇ -methyl amino acids, fluoro-amino acids and amino acid analogs in general.
• the amino acid can be D (dextrorotary) or L (levorotary) .
• toporythmic proteins, derivatives and fragments thereof can be tested for the ability to modulate
• Toporythmic proteins and more generally, members of the "Notch cascade” or the “Notch group” of genes, include Notch, Delta, Serrate, Kuz, and other members of the Delta/Serrate family, which are identified by genetic (as detected phenotypically, e.g., in Drosophila) or molecular interaction (e.g., binding in vi tro) . See, International Publications WO 92/19734, WO 97/18822, WO 96/27610, and WO 97/01571 and references therein, for examples of vertebrate and non-vertebrate members of the Notch family of genes.
• Screening the libraries can be accomplished by any of a variety of commonly known methods. See, e.g., the following references, which disclose screening of peptide libraries: Parmley and Smith, 1989, Adv. Exp. Med. Biol.
• screening can be carried out by contacting the library members with Delta or Kuz or a protein complex or the present invention (or encoding nucleic acid or derivative) immobilized on a solid phase, and harvesting those library members that bind to the protein or complex (or encoding nucleic acid or derivative) .
• panning techniques
• fragments and/or analogs of Delta or Kuz are screened for activity as competitive or non-competitive inhibitors of
• Delta Kuz complex formation, which thereby inhibit Delta: Kuz complex activity or formation.
• Methods for screening may involve labeling the proteins or complex proteins of the present invention with radioligands (e.g., 125 I or 3 H) , magnetic ligands (e.g., paramagnetic beads covalently attached to photobiotin acetate), fluorescent ligands (e.g., fluorescein or rhodamine) , or enzyme ligands (e.g., luciferase or beta- galactosidase) .
• radioligands e.g., 125 I or 3 H
• magnetic ligands e.g., paramagnetic beads covalently attached to photobiotin acetate
• fluorescent ligands e.g., fluorescein or rhodamine
• enzyme ligands e.g., luciferase or beta- galactosidase
• the reactants that bind in solution can then be isolated by one of many techniques known in the art, including but not restricted to, co-immunoprecipitation of the labeled protein or complex moiety using antisera against the unlabeled binding partner (or labeled binding partner with a distinguishable marker from that used on the second labeled protein or complex moiety) , immunoaffinity chromatography, size exclusion chromatography, and gradient density centrifugation.
• the labeled binding partner is a small fragment or peptidomimetic that is not retained by a commercially available filter. Upon binding, the labeled species is then unable to pass through the filter, providing for a simple assay of complex formation. Methods commonly known in the art are used to label proteins.
• Suitable labeling methods include, but are not limited to, radiolabeling by incorporation of radiolabeled amino acids, e.g., 3 H-leucine or 35 S-methionine, radiolabeling by post-translational iodination with 125 I or 131 I using the chloramine T method, Bolton-Hunter reagents, etc., or labeling with 32 P using phosphorylase and inorganic radiolabeled phosphorous, biotin labeling with photobiotin- acetate and sunlamp exposure, etc.
• radiolabeled amino acids e.g., 3 H-leucine or 35 S-methionine
• radiolabeling by post-translational iodination with 125 I or 131 I using the chloramine T method Bolton-Hunter reagents, etc.
• labeling with 32 P using phosphorylase and inorganic radiolabeled phosphorous biotin labeling with photobiotin- acetate and sunlamp exposure, etc.
• the invention provides for treatment of disorders of cell fate or differentiation by administration of a therapeutic compound of the invention.
• therapeutic compounds include: Delta cleavage peptides, Delta: Kuz and Dl EC :Notch protein complexes and analogs and derivatives (including fragments) thereof (e.g., as described hereinabove); antibodies thereto (as described hereinabove) ; nucleic acids encoding the Delta cleavage peptides, analogs, or derivatives (e.g., as described hereinabove) as well as the protein complexes of the present invention; and Del ta , Notch and Kuz antisense nucleic acids.
• Therapeutics include soluble Delta peptides and derivatives and analogs thereof, antibodies thereto, nucleic acids encoding the soluble Delta peptides, derivatives, or analogs, and soluble Delta peptide antisense nucleic acids.
• the Therapeutics include soluble Delta peptides and derivatives and analogs thereof, antibodies thereto, nucleic acids encoding the soluble Delta peptides, derivatives, or analogs, and soluble Delta peptide antisense nucleic acids.
• the Therapeutics include soluble Delta peptides and derivatives and analogs thereof, antibodies thereto, nucleic acids encoding the soluble Delta peptides, derivatives, or analogs, and soluble Delta peptide antisense nucleic acids.
• Therapeutic is a peptide comprising a fragment of a Delta protein of about amino acid Cys 516 to about amino acid Phe 543 in human Delta (SEQ ID NO:10), of about amino acid Cys 515 to about amino acid Phe 543 in mouse Delta (SEQ ID NO:6), of about ammo acid Cys 523 to about amino acid Phe 551 in chick Delta
• Drosophila Delta (SEQ ID NO: 9) .
• the peptide comprises 25, 30, 35, 40, 50, 100, 150, 200 or 250 contiguous amino acids of a Delta protein.
• Therapeutics of the invention are those Therapeutics which antagonize, or inhibit, Delta function and/or Notch function
• Antagonist Therapeutics are most preferably identified by use of known convenient in vi tro assays, e.g., based on their 10 ability to inhibit binding of Delta to another protein (e.g., a Notch protein or a Kuz protein) , or inhibit any known Notch or Delta or Kuz function as preferably assayed in vi tro or in cell culture, although genetic assays (e.g., in Drosophila) may also be employed.
• a Notch protein or a Kuz protein e.g., a Notch protein or a Kuz protein
• the Antagonist Therapeutics are most preferably identified by use of known convenient in vi tro assays, e.g., based on their 10 ability to inhibit binding of Delta to another protein (e.g., a Notch protein or a Kuz protein) , or inhibit any known Notch or Delta or Kuz function as preferably assayed in vi tro or in cell culture, although genetic assays (e.g., in Drosophila) may also be employed.
• Antagonist Therapeutic is a Delta cleavage peptide which mediates binding to Kuz, or an antibody thereto.
• an Antagonist Therapeutic is a nucleic acid capable of expressing a molecule comprising a
• antisense nucleic acid see Section 5.11 herein. It should be noted that preferably, suitable in vi tro or in vivo assays, as described infra, should be utilized to determine the effect of a specific Therapeutic and whether its administration is indicated for treatment of the affected
• tissue since the developmental history of the tissue may determine whether an Antagonist or Agonist Therapeutic is desired.
• the mode of administration e.g., whether administered in soluble form or administered via its encoding nucleic acid for intracellular recombinant
• Delta cleavage peptide or derivative or protein complex or derivative can affect whether it acts as an agonist or antagonist.
• the Agonist Therapeutics of the invention as described supra, promote Delta function or Notch function or
• Such Agonist Therapeutics include but are not limited to proteins and derivatives comprising the portions of Delta that mediate binding to Kuz, and nucleic acids encoding the foregoing (which can be administered to express their encoded products in vivo) .
• Molecules which retain, or alternatively inhibit, a desired Delta property can be used therapeutically as inducers, or inhibitors, respectively, of such property and its physiological correlates.
• a peptide e.g., in the range of 6-50 or 100-200 amino acids; and particularly of about 25, 30, 35, 50, 100 or 150 amino acids
• such an Antagonist Therapeutic is used to treat or prevent human or other malignancies associated with increased Notch expression (e.g., cervical cancer, colon cancer, breast cancer, squamous adenocarcimas
• Derivatives or analogs of Delta can be tested for the desired activity by procedures known in the art, including but not limited to the assays described in the examples infra .
• peptide libraries can be screened to select a peptide with the desired activity; such screening can be carried out by assaying, e.g., for binding to Kuz.
• Therapeutics include molecules that bind to a
• the invention also provides a method for identifying such molecules.
• Such molecules can be identified by a method comprising contacting a plurality of molecules (e.g., in a peptide library, or combinatorial chemical library) with the Kuz protein under conditions conducive to binding, and recovering any molecules that bind to the Kuz protein.
• the Agonist and Antagonist Therapeutics of the invention have therapeutic utility for disorders of cell fate.
• the Agonist Therapeutics are administered therapeutically (including prophylactically) : (1) in diseases or disorders involving an absence or decreased (relative to normal, or desired) levels of Notch or Delta or Kuz function, for example, in patients where Delta protein is lacking, genetically defective, biologically inactive or underactive, or underexpressed; and (2) in diseases or disorders wherein in vi tro (or in vivo) assays (see infra) indicate the utility of Delta agonist administration.
• Notch or Delta or Kuz function can be readily detected, e.g., by obtaining a patient tissue sample (e.g., from biopsy tissue) and assaying it in vi tro for protein levels, structure and/or activity of the expressed Notch or Delta or Kuz protein. Many methods standard in the art can be thus employed, including but not limited to immunoassays to detect and/or visualize Notch or Delta or Kuz protein
• Notch or Delta or Kuz expression by detecting and/or visualizing respectively Notch or Delta or Kuz mRNA (e.g.,
• vi tro assays which can be used to determine whether administration of a specific Agonist Therapeutic or Antagonist Therapeutic is indicated, include in vi tro cell culture assays in which a patient tissue sample is grown in culture, and exposed to or otherwise administered a
• a sample of cells from such malignancy is plated out or grown in culture, and the cells are then exposed to a Therapeutic.
• a Therapeutic which inhibits survival or growth of the malignant cells e . g. , by promoting terminal differentiation) is selected for therapeutic use in vivo .
• cell proliferation can be assayed by measuring 3 H-thymidine incorporation, by direct cell count, by detecting changes in transcriptional activity of known genes such as proto- oncogenes (e.g., fos, myc) or cell cycle markers; cell viability can be assessed by trypan blue staining, differentiation can be assessed visually based on changes in morphology, etc.
• the malignant cell cultures are separately exposed to (1) an Agonist Therapeutic, and (2) an Antagonist Therapeutic; the result of the assay can indicate which type of Therapeutic has therapeutic efficacy.
• a Therapeutic is indicated for use which exhibits the desired effect, inhibition or promotion of cell growth, upon a patient cell sample from tissue having or suspected of having a hyper- or hypoproliferative disorder, respectively.
• hyper- or hypoproliterative disorders include but are not limited to those described in Sections 5.8.1 through 5.8.3 infra .
• a Therapeutic is indicated for use in treating nerve injury or a nervous system degenerative disorder (see Section 5.8.2) which exhibits in vi tro promotion of nerve regeneration/neurite extension from nerve cells of the affected patient type.
• a nervous system degenerative disorder see Section 5.8.2 which exhibits in vi tro promotion of nerve regeneration/neurite extension from nerve cells of the affected patient type.
• administration of an Antagonist is indicated for use in treating nerve injury or a nervous system degenerative disorder (see Section 5.8.2) which exhibits in vi tro promotion of nerve regeneration/neurite extension from nerve cells of the affected patient type.
• Therapeutic of the invention is also indicated m diseases or disorders determined or known to involve a Notch or Delta or Kuz dominant activated phenotype ("gain of function" mutations.)
• Administration of an Agonist Therapeutic is indicated in diseases or disorders determined or known to involve a Notch or Delta or Kuz dominant negative phenotype ("loss of function" mutations).
• the functions of various structural domains of the Notch protein have been investigated in vivo, by ectopically expressing a series of Drosophila Notch deletion mutants under the hsp70 heat-shock promoter, as well as eye-specific promoters (see Rebay et al., 1993, Cell 74:319-329).
• vi tro assays in vi tro assays can be carried out with representative cells of cell types involved in a patient's disorder, to determine if a
• Therapeutic has a desired effect upon such cell types.
• cells of a patient tissue sample suspected of being pre-neoplastic are similarly plated out or grown in vi tro, and exposed to a Therapeutic.
• Therapeutic which results in a cell phenotype that is more normal (i.e., less representative of a pre-neoplastic state, neoplastic state, malignant state, or transformed phenotype) is selected for therapeutic use.
• Many assays standard in the art can be used to assess whether a pre-neoplastic state, neoplastic state, or a transformed or malignant phenotype, is present.
• characteristics associated with a transformed phenotype include a more rounded cell morphology, looser substratum attachment, loss of contact inhibition, loss of anchorage dependence, release of proteases such as plasminogen activator, increased sugar transport, decreased serum requirement, expression of fetal antigens, disappearance of the 250,000 dalton surface protein, etc. (see Luria et al . , 1978, General Virology, 3d
• the in vi tro assays described supra can be carried out using a cell line, rather than a cell sample derived from the specific patient to be treated, in which the cell line is derived from or displays characteristic (s) associated with the malignant, neoplastic or pre-neoplastic disorder desired to be treated or prevented, or is derived from the neural or other cell type upon which an effect is desired, according to the present invention.
• the Antagonist Therapeutics are administered therapeutically (including prophylactically) : (1) in diseases or disorders involving increased (relative to normal, or desired) levels of Notch or Delta or Kuz function, for example, where the Notch or Delta or Kuz protein is overexpressed or overactive; and (2) in diseases or disorders wherein in vi tro (or in vivo) assays indicate the utility of
• Notch or Delta or Kuz function can be readily detected by methods such as those described above, by quantifying protein and/or RNA.
• vi tro assays with cells of patient tissue sample or the appropriate cell line or cell type, to determine therapeutic utility can be carried out as described above . 5.8.1 MALIGNANCIES
• Malignant and pre-neoplastic conditions which can be tested as described supra for efficacy of intervention with Antagonist or Agonist Therapeutics, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to those described below in Sections 5.8.1 and 5.9.1.
• Malignancies and related disorders, cells of which type can be tested in vi tro (and/or in vivo) , and upon observing the appropriate assay result, treated according to the present invention include but are not limited to those listed in Table 1 (for a review of such disorders, see Fishman et al . , 1985, Medicine, 2d Ed., J.B. Lippincott Co., Philadelphia) :
• malignancy or dysproliferative changes are treated or prevented in epithelial tissues such as those in the cervix, esophagus, and lung.
• malignancies of the colon and cervix exhibit • j _0 increased expression of human Notch relative to such non- malignant tissue (see PCT Publication no. WO 94/07474 published April 14, 1994, incorporated by reference herein in its entirety) .
• malignancies or premalignant changes of the colon or cervix are treated or prevented by administering an effective amount of an 15
• Antagonist Therapeutic e.g., a Delta cleavage peptide, that antagonizes Notch function.
• Notch function e.g., a Delta cleavage peptide
• cancers e.g., breast cancer, squamous adenocarcinoma, seminoma, melanoma, and lung cancer, and premalignant changes therein, as well as other hyperproliferative disorders, can be treated or prevented by administration of an Antagonist
• Nervous system disorders involving cell types which can be tested as described supra for efficacy of intervention with Antagonist or Agonist Therapeutics, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to nervous system injuries, and diseases or disorders which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination.
• Nervous system lesions which may be treated in a patient (including human and non-human mammalian patients) according to the invention include but are not limited to the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems :
• traumatic lesions including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries;
• ischemic lesions in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia;
• malignant lesions in which a portion of the nervous system is destroyed or injured by malignant tissue which is either a nervous system associated malignancy or a malignancy derived from non-nervous system tissue;
• infectious lesions in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster, or herpes simplex virus or with Lyme disease, tuberculosis, syphilis;
• degenerative lesions in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson's disease, Alzheimer's disease,
• Huntington's chorea or amyotrophic lateral sclerosis; (vi) lesions associated with nutritional diseases or disorders, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia,
• Marchiafava-Bignami disease primary degeneration of the corpus callosum
• alcoholic cerebellar degeneration
• ⁇ demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including but not limited to multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multifocal leukoencephalopathy, and central pontine myelinolysis .
• Therapeutics which are useful according to the invention for treatment of a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons (see also Section
• Rev. Neurosci. 4:17-42 increased production of neuron- associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.
• motor neuron disorders that may be treated according to the invention include but are not limited to disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome) , poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot- Marie-Tooth Disease) .
• disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar pals
• Therapeutic of the invention is used for promotion of tissue regeneration and repair, including but not limited to treatment of benign dysproliferative disorders.
• Specific embodiments are directed to treatment of cirrhosis of the liver (a condition in which scarring has overtaken normal liver regeneration processes) , treatment of keloid
• a Therapeutic of the invention is used to treat degenerative or traumatic disorders of the sensory epithelium of the inner ear.
• the Therapeutics of the invention can be administered to prevent progression to a neoplastic or malignant state, including but not limited to those disorders listed in Table 1. Such administration is indicated where the Therapeutic is shown in assays, as described supra, to have utility for treatment or prevention of such disorder.
• Such prophylactic use is indicated in conditions known or suspected of preceding progression to neoplasia or cancer, in particular, where non-neoplastic cell growth consisting of hyperplasia, metaplasia, or most particularly, dysplasia has occurred (for review of such abnormal growth conditions, see Robbins and Angel1, 1976, Basic Pathology, 2d Ed., W.B.
• Hyperplasia is a form of controlled cell proliferation involving an increase in cell number in a tissue or organ, without significant alteration in structure or function. As but one example, endometrial hyperplasia often precedes endometrial cancer.
• Metaplasia is a form of controlled cell growth in which one type of adult or fully differentiated cell substitutes for another type of adult cell . Metaplasia can occur in epithelial or connective tissue cells. Atypical metaplasia involves a somewhat disorderly metaplastic epithelium.
• Dysplasia is frequently a forerunner of cancer, and is found mainly in the epithelia; it is the most disorderly form of non-neoplastic cell growth, involving a loss in individual cell uniformity and in the architectural orientation of cells.
• Dysplastic cells often have abnormally large, deeply stained nuclei, and exhibit pleomorphism.
• Dysplasia characteristically occurs where there exists chronic irritation or inflammation, and is often found in the cervix, respiratory passages, oral cavity, and gall bladder.
• the presence of one or more characteristics of a transformed phenotype, or of a malignant phenotype, displayed in vivo or displayed in vi tro by a cell sample from a patient can indicate the desirability of prophylactic/therapeutic administration of a Therapeutic of the invention.
• characteristics of a transformed phenotype include morphology changes, looser substratum attachment, loss of contact inhibition, loss of anchorage dependence, protease release, increased sugar transport, decreased serum requirement, expression of fetal antigens, disappearance of the 250,000 dalton cell surface protein, etc. (see also id. , at pp. 84-90 for characteristics associated with a transformed or malignant phenotype) .
• leukoplakia a benign- appearing hyperplastic or dysplastic lesion of the epithelium, or Bowen's disease, a carcinoma in si tu, are pre- neoplastic lesions indicative of the desirability of prophylactic intervention.
• fibrocystic disease cystic hyperplasia, mammary dysplasia, particularly adenosis (benign epithelial hyperplasia)
• adenosis benign epithelial hyperplasia
• a patient which exhibits one or more of the following predisposing factors for malignancy is treated by administration of an effective amount of a
• Therapeutic a chromosomal translocation associated with a malignancy (e.g., the Philadelphia chromosome for chronic myelogenous leukemia, t(14;18) for follicular lymphoma, etc.), familial polyposis or Gardner's syndrome (possible forerunners of colon cancer) , benign monoclonal gammopathy (a possible forerunner of multiple myeloma) , and a first degree kinship with persons having a cancer or precancerous disease showing a Mendelian (genetic) inheritance pattern (e.g., familial polyposis of the colon, Gardner's syndrome, hereditary exostosis, polyendocrine adenomatosis, medullary thyroid carcinoma with amyloid production and pheochromocytoma, Peutz-Jeghers syndrome, neurofibromatosis of Von Recklinghausen, retinoblastoma, carotid body tumor, cutaneous melanocarcinoma, intrao
• a Therapeutic of the invention can be administered to prevent a nervous system disorder described in Section 5.8.2, or other disorder (e . g. , liver cirrhosis, psoriasis, keloids, baldness) described in Section 5.8.3. 0
• the Therapeutics of the invention can be tested in vivo for the desired therapeutic or prophylactic activity.
• such compounds can be tested in suitable animal 5 model systems prior to testing in humans, including but not limited to rats, mice, chicken, cows, monkeys, rabbits, etc.
• suitable animal 5 model systems prior to testing in humans, including but not limited to rats, mice, chicken, cows, monkeys, rabbits, etc.
• any animal model system known in the art may be used.
• Delta cleavage peptide Delta, Kuz, Notch, and Delta:Kuz or
• Dl EC :Notch complex activity and/or formation is inhibited by 5 use of antisense nucleic acids for Delta, Notch and/or Kuz.
• the present invention provides the therapeutic or prophylactic use of nucleic acids of at least six nucleotides that are antisense to a gene or cDNA encoding Delta, Notch and/or Kuz, or a portion thereof.
• An "antisense" nucleic acid as used herein refers to a nucleic acid capable of 0 hybridizing to a portion of a Delta, Notch or Kuz RNA (preferably mRNA) by virtue of some sequence complementarily .
• the antisense nucleic acid may be complementary to a coding and/or noncoding region of a Delta, Notch or Kuz mRNA.
• Such antisense nucleic acids that inhibit Delta cleavage peptide activity or Delta: Kuz complex formation or activity or Dl EC :Notch complex formation or activity have utility as Therapeutics, and can be used in the treatment or prevention of disorders as described, supra .
• the antisense nucleic acids of the invention can be oligonucleotides that are double-stranded or single-stranded, RNA or DNA, or a modification or derivative thereof, which can be directly administered to a cell, or which can be produced intracellularly by transcription of exogenous, introduced sequences .
• the present invention is directed to a method for inhibiting the expression of Delta cleavage peptide nucleic acid sequences, in a prokaryotic or eukaryotic cell, comprising providing the cell with an effective amount of a composition comprising an antisense nucleic acid of Delta cleavage peptide, or a derivative thereof, of the invention.
• the antisense nucleic acids are of at least six nucleotides and are preferably oligonucleotides, ranging from
• the oligonucleotide is at least 10 nucleotides, at least 15 nucleotides, at least 100 nucleotides, or at least 200 nucleotides.
• the oligonucleotides can be DNA or RNA or chimeric mixtures, or derivatives or modified versions thereof, and either single-stranded or double-stranded.
• the oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone.
• the oligonucleotide may include other appending groups such as peptides, agents facilitating transport across the cell membrane (see, e.g., Letsinger et al . , 1989, Proc. Natl. Acad. Sci. U.S.A.
• a Delta cleavage peptide antisense oligonucleotide is provided, preferably as single-stranded DNA.
• the oligonucleotide may be modified at any position in its structure with constituents generally known in the art.
• the antisense oligonucleotides may comprise at least one modified base moiety which is selected from the group including but not limited to 5-fluorouracil ,
• 5-bromouracil 5-chlorouracil, 5-iodouracil , hypoxanthine, xanthine, 4-acetylcytosine, 5- (carboxyhydroxylmethyl) uracil , 5-carboxymethylaminomethyl-2-thio-uridine,
• 5-carboxymethylaminomethyluracil dihydrouracil , beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2 , 2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine,
• the oligonucleotide comprises at least one modified sugar moiety selected from the group including, but not limited to, arabinose, 2-fluoroarabinose, xylulose, and hexose .
• the oligonucleotide comprises at least one modified phosphate backbone selected from the group consisting of a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal, or an analog of the foregoing.
• the oligonucleotide is a 2- -anomeric oligonucleotide.
• An -anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA
• the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization-triggered cross-
• Oligonucleotides of the invention may be synthesized by standard methods known in the art, e.g., by use of an automated DNA synthesizer (such as are commercially
• phosphorothioate oligo-nucleotides may be synthesized by the method of Stein et al . (1988, Nucl. Acids
• methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports
• the antisense oligonucleotides comprise catalytic RNAs, or ribozymes (see, e.g., International Patent Publication No. WO 90/11364;
• the oligonucleotide is a 2'-0- methylribonucleotide (Inoue et al . , 1987, Nucl. Acids Res. 15:6131-6148), or a chimeric RNA-DNA analog (Inoue et al . , 1987, FEBS Lett. 215:327-330).
• the antisense nucleic acids of the invention are produced intracellularly by transcription from an exogenous sequence.
• a vector can be introduced in vivo such that it is taken up by a cell, within which cell the vector or a portion thereof is transcribed, producing an antisense nucleic acid (RNA) of the invention.
• RNA antisense nucleic acid
• Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA.
• Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art to be capable of replication and expression in mammalian cells.
• Expression of the sequences encoding the antisense RNAs can be by any promoter known in the art to act in mammalian, preferably human, cells. Such promoters can be inducible or constitutive. Such promoters include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3' long terminal repeat of Rous sarcoma virus (Yamamoto et al . , 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner et al . , 1981, Proc. Natl. Acad. Sci. U.S.A.
• the antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of an RNA transcript of a Delta, Notch or Kuz gene, preferably a human Delta, Notch or Kuz gene.
• a sequence "complementary to at least a portion of an RNA,” as referred to herein, means a sequence having sufficient complementarily to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed.
• the ability to hybridize will depend on both the degree of complementarily
• the length of the antisense nucleic acid 5 and the length of the antisense nucleic acid.
• the longer the hybridizing nucleic acid the more base mismatches with a RNA it may contain and still form a stable duplex (or triplex, as the case may be) .
• One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized 0 complex.
• the antisense nucleic acid can be used to treat (or prevent) disorders of a cell type that expresses, or preferably overexpresses, the Delta cleavage peptide or the
• Delta Kuz complex or the Dl EC :Notch complex.
• a single-stranded Delta, Notch or Kuz DNA antisense oligonucleotide, both single-stranded Delta, Notch and Kuz antisense oligonucleotides, or a single-stranded Delta: Kuz DNA antisense fusion sequence is used.
• Cell types that express or overexpress Delta, Notch o and/or Kuz RNA can be identified by various methods known in the art. Such methods include, but are not limited to, hybridization with Delta-, Notch- and Kuz-specific nucleic acids (e.g., by Northern blot hybridization, dot blot hybridization, or in situ hybridization) , or by observing the ability of RNA from the cell type to be translated in vi tro 5 into Delta or Kuz by immunohistochemistry, Western blot analysis, ELISA, etc.
• primary tissue from a patient can be assayed for Delta, Notch and/or Kuz expression prior to treatment, e.g., by immunocytochemistry, in si tu hybridization, or any number of methods to detect 0 protein or mRNA expression.
• compositions of the invention comprising an effective amount of an antisense nucleic acid in a pharmaceutically acceptable carrier can be administered to a patient having a disease or disorder that is of a type that expresses or overexpresses, for example a Delta: Kuz complex.
• the amount of an antisense nucleic acid that will be effective in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques. Where possible, it is desirable to determine the antisense cytotoxicity in vitro, and then in useful animal model systems, prior to testing and use in humans.
• compositions comprising Delta and Kuz antisense nucleic acids are administered via liposomes, microparticles, or microcapsules .
• it may be desirable to utilize liposomes targeted via antibodies to specific identifiable central nervous system cell types Leonetti et al . , 1990, Proc. Natl. Acad. Sci. U.S.A. 87:2448-2451; Renneisen et al . , 1990, J. Biol. Chem. 265:16337-16342).
• the invention provides methods of treatment (and prophylaxis) by administration to a subject of an effective amount of a Therapeutic of the invention.
• the Therapeutic is substantially purified.
• the subject is preferably an animal, including but not limited to animals such as cows, pigs, chickens, etc., and is preferably a mammal, and most preferably human.
• a Therapeutic of the invention e.g., encapsulation in liposomes, microparticles, microcapsules, expression by recombinant cells, receptor-mediated endocytosis (see, e . g. , Wu and Wu, 1987, J. Biol. Chem.
• compositions of a Therapeutic nucleic acid as part of a retroviral or other vector etc.
• Methods of introduction include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes.
• the compounds may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local.
• intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir.
• Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent .
• compositions of the invention may be desirable to administer the pharmaceutical compositions of the invention locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
• administration can be by direct injection at the site (or former site) of a malignant tumor or neoplastic or pre- neoplastic tissue.
• the Therapeutic can be delivered in a vesicle, in particular a liposome (see Langer, 5 Science 249:1527-1533 (1990); Treat et al . , in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid. , pp. 317-327; see generally ibid.)
• the Therapeutic can be delivered in a controlled release system.
• 10 a pump may be used ( see Langer, supra; Sefton, CRC Crit . Ref .
• polymeric materials can be used (see
• a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e . g. , Goodson, in Medical
• the nucleic acid in a specific embodiment where the Therapeutic is a nucleic acid encoding a protein Therapeutic, the nucleic acid
• nucleic acid expression vector 30 can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e . g. , by use of a retroviral vector
• microparticle bombardment e.g., a gene gun
• Biolistic, Dupont or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al . , 1991, Proc. Natl. Acad.
• nucleic acid a nucleic acid
• Therapeutic can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination.
• Liver cirrhosis Oral intravenous Psoriasis Topical Keloids Topical Baldness Topical Spinal cord injury Targeted; intravenous; intrathecal Parkinson's disease Targeted; intravenous; intrathecal Motor neuron disease Targeted; intravenous; intrathecal Alzheimer's disease Targeted; intravenous; intrathecal
• compositions comprise a therapeutically effective amount of a Therapeutic, and a pharmaceutically acceptable carrier.
• pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
• carrier refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered.
• Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
• Water is a preferred carrier when the pharmaceutical composition is administered intravenously.
• Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions.
• Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
• the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
• compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like.
• the composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides .
• Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in "Remington's Pharmaceutical Sciences” by E.W. Martin. Such compositions will contain a therapeutically effective amount of the Therapeutic, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.
• the composition is formulated in accordance with routine procedures as a 5 pharmaceutical composition adapted for intravenous administration to human beings.
• compositions for intravenous administration are solutions in sterile isotonic aqueous buffer.
• the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. 0
• the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
• a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
• the 5 composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
• an ampoule of sterile water for injection or saline can be provided so that the ingredients o may be mixed prior to administration.
• the Therapeutics of the invention can be formulated as neutral or salt forms.
• Pharmaceutically acceptable salts include those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl 5 groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
• the amount of the Therapeutic of the invention 0 which will be effective in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the 5 seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. However, suitable dosage ranges for intravenous administration are generally about 20-500 micrograms of active compound per kilogram body weight.
• Suitable dosage ranges for intranasal administration are ° generally about 0.01 pg/kg body weight to 1 mg/kg body weight. Effective doses may be extrapolated from dose- response curves derived from in vi tro or animal model test systems .
• Suppositories generally contain active ingredient 5 in the range of 0.5% to 10% by weight; oral formulations preferably contain 10% to 95% active ingredient.
• the invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of 0 the invention.
• Optionally associated with such container (s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. 5
• Delta cleavage peptides soluble Delta peptides, analogs, derivatives, and subsequences thereof, Delta cleavage peptide encoding nucleic acids (and sequences 0 complementary thereto) , soluble Delta peptide encoding nucleic acids (and sequences complementary thereto) , anti- Delta cleavage peptide antibodies, anti-soluble Delta peptide antibodies, and anti-Delta: Kuz and anti-Dl EC :Notch complex antibodies have uses in diagnostics. Such molecules can be used in assays, such as immunoassays, to detect, prognose, diagnose, or monitor various conditions, diseases, and disorders affecting Delta cleavage peptide expression, or monitor the treatment thereof.
• assays such assays, such as immunoassays, to detect, prognose, diagnose, or monitor various conditions, diseases, and disorders affecting Delta cleavage peptide expression, or monitor the treatment thereof.
• such an immunoassay is carried out by a method comprising contacting a sample derived from a patient with an anti-Delta cleavage peptide antibody under conditions such that immunospecific binding can occur, and detecting or measuring 0 the amount of any immunospecific binding by the antibody.
• binding of antibody, in tissue sections, preferably in conjunction with binding of anti-Kuz or anti-Notch antibody can be used to detect aberrant Delta, Notch and/or Kuz localization or aberrant levels of Dl EC :Notch 5 or Delta-Kuz colocalization in a disease state.
• antibody to Delta cleavage peptide can be used to assay in a patient tissue or serum sample for the presence of Delta cleavage peptide where an aberrant level of Delta cleavage peptide is an indication of a diseased o condition.
• Aberrant levels of Delta binding ability in an endogenous Notch or Kuz protein, or aberrant levels of binding ability to Kuz (or other Delta ligand, e.g., Notch) in an endogenous Delta cleavage peptide may be indicative of a disorder of cell fate (e.g., cancer, etc.)
• aberrant levels is meant increased or decreased levels relative to 5 that present, or a standard level representing that present, in an analogous sample from a portion of the body or from a subject not having the disorder.
• the immunoassays which can be used include but are not limited to competitive and non-competitive assay systems 0 using techniques such as western blots, radioimmunoassays,
• ELISA enzyme linked immunosorbent assay
• "sandwich” immunoassays i munoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement- fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to name but a few.
• Delta, Notch and Kuz genes and related nucleic acid sequences and subsequences including complementary sequences, and other toporythmic gene sequences, can also be used in hybridization assays. Delta, Notch and Kuz nucleic acid sequences, or subsequences thereof comprising about at least 8 nucleotides, can be used as hybridization probes.
• Hybridization assays can be used to detect, prognose, diagnose, or monitor conditions, disorders, or disease states associated with aberrant changes in Delta expression and/or activity as described supra .
• a hybridization assay is carried out by a method comprising contacting a sample containing nucleic acid with a nucleic acid probe capable of hybridizing to Delta, Notch or Kuz D ⁇ A or R ⁇ A, under conditions such that hybridization can occur, and detecting or measuring any resulting hybridization.
• Delta binds to Notch and Kuz
• Delta or a binding portion thereof can be used to assay for the presence and/or amounts of Notch or Kuz in a sample, e.g., in screening for malignancies which exhibit increased Notch expression such as colon and cervical cancers.
• animal models for diseases and disorders involving Delta cleavage peptide, soluble Delta peptide, and Delta: Kuz and Dl EC :Notch complexes are provided. These include, but are not limited to, disorders of cell fate and differentiation such as cancer. Such animals can be initially produced by promoting homologous recombination or insertional mutagenesis between Delta, Notch and Kuz genes in the chromosome, and exogenous Delta, Notch and Kuz genes that have been rendered biologically inactive or deleted
• a heterologous sequence e. g. , an antibiotic resistance gene
• homologous recombination is carried out by transforming embryo-derived stem (ES) cells with a vector containing, e.g., the insertionally inactivated Del ta and Kuz gene, such that homologous recombination occurs, followed by injecting the transformed ES cells into a blastocyst, and implanting the blastocyst into a foster mother, followed by the birth of 10 the chimeric animal ("knockout animal”) in which a Delta and/or Kuz gene has been inactivated or deleted (Capecchi,
• the chimeric animal can be bred to produce additional knockout animals.
• Such animals can be mice, hamsters, sheep, pigs, cattle, etc., and are preferably non-human mammals.
• a knockout mouse is produced.
• knockout animals are expected to develop, or be predisposed to developing, diseases or disorders involving, but not restricted to, disorders of cell fate and
• 2 _5_ transgenic animals that have incorporated and express (or overexpress or mis-express) a functional Delta and/or Kuz gene, e.g. by introducing the Delta and Kuz genes under the control of a heterologous promoter (i . e . , a promoter that is not the native Delta or Kuz promoter) that either overexpresses the protein or proteins, or expresses them in
• a heterologous promoter i . e . , a promoter that is not the native Delta or Kuz promoter
• the present invention provides a recombinant non-human animal in which both an endogenous Delta gene and an endogenous Kuz have been deleted or inactivated by homologous recombination or insertional mutagenesis of said animal or an ancestor thereof.
• the invention provides a recombinant non- human animal containing both a Delta gene and a Kuz gene in which the Delta gene is under the control of a promoter that is not the native Kuz gene promoter and the Kuz gene is under the control of a promoter that is not the native Kuz gene promoter.
• the invention provides a recombinant non-human animal containing a transgene comprising a nucleic acid sequence encoding a chimeric protein comprising a Delta cleavage peptide of at least 6 amino acids fused via a covalent bond to a fragment of Kuz protein of at least 6 amino acids.
• the Notch signaling pathway defines an evolutionary conserved cell interaction mechanism which throughout development controls the fate of cells by modulating their response to developmental signals (Artavanis-Tsakonas et al . ,
• Notch receptor is cleaved in the trans-Golgi network as it traffics towards the plasma membrane eventually forming a ligand competent, heterodimeric molecule (Blaumueller et al . , 1997, Cell 90:281-291). Both known ligands, Delta and Serrate are thought to act as transmembrane proteins interacting via their extracellular domains with the receptor expressed on adjacent cells (Fleming et al . , 1998, Trends in Cell Biology 7:437-441;
• furin is known to act in this sub-cellular compartment, as opposed to ADAM proteases, such as Kuz, which are thought to act on the cell surface (Wolfsberg et al . , 1995, Journal of Cell Biology 131:275-278).
• KuzDN flies display extra vein material, especially deltas, at the ends of the longitudinal veins, wing notching (observed with a low penetranee) , extra bristles on the notum, and have small, rough eyes ( Figures 6A and 6E) .
• the bristle and eye phenotype are not affected (Xu et al . , unpublished observation) , nor are the vein deltas altered ( Figure 6D) .
• the KuzDN phenotypes are effectively suppressed by Delta duplications ( Figures 6B and 6F) . Indicating that a higher copy number of Delta molecules is capable of overriding the effect of the KuzDN construct.
• a monoclonal antibody was raised against an extracellular Delta epitope generated by using a fusion protein generated by using a PCR product of the the entire extracellular domain of Drosophila Delta using the primers 5' GAGTTGCGCCTGAAGTACTT 3' (SEQ ID NO: 14) and 5* GGTCGCTCCATATTGGTGGG 3' (SEQ ID NO: 15) and subsequent cloning into the Smal site of pGEX3 and Stul site of pMAL.
• a monoclonal cell line (C594.9B, designated “9B") was created by standard protocols and screening of hybridoma supernatants was done by immunostaining of Delta expressing S2 cells. Ascites fluid was made and used at 1/3000-1/10,000 dilution for western blotting followed by detection with peroxidase labelled anti-mouse antibody and chemiluminescent development with a luminol substrate (see Rand et al . , 1997, Protein
• Dl E was subsequently affinity purified from the culture medium and subjected to amino acid sequence analysis to determine the N- terminal amino acid sequence. Briefly, Drosophila S2 cells expressing Delta were induced with 0.7 mM CuS0 4 in serum free media for two days and the media was collected and precipitated with 70% ammonium sulfate. The precipitate was collected by centrifugation and subsequently resuspended and 0 dialyzed against 20 mM HEPES, 150 mM NaCl, 2 mM CaCl 2 , pH
• the amino acid sequence of Dl EC is consistent with the predicted polypeptide processing site and is conserved among the Drosophila, Xenopus and human Delta homologs o ( Figure 7E) .
• kuz mutations have multiple defects indicating an involvement in different processes (Rooke et al., 1996, Nature 273:1227-1231), its phenotype partially overlaps with that of Delta. Inactivation of kuz during embryogenesis causes a more extensive neurogenic phenotype than Delta mutations, nevertheless, it is clear that in the ventrolateral region the neural hypertrophy in the two mutations is identical. In adult mosaic clones, a small percentage of kuz mutant cells on the clone border develop into multiple bristles (Rooke et al . , 1996, Nature 273:1227-
• Delta mosaic clones present a more complicated situation. While cells on the border of the clones mutant for weak delta alleles commit to epidermal fate, it is evident that cells mutant for strong delta alleles will develop multiple bristles at a low frequency ( Figure 3 in Heitzler and Simpson, 1991, Cell, 1083-1092), the phenotype observed in kuz mutants. It is clear, however, that with strong kuz and delta alleles, all extra neurons derive from genotypically mutant cells.
• Notch/Delta interactions In order to quantify the Notch/Delta interactions we have developed a turbidimetric assay which allows us to measure aggregation in a reproducible manner.
• Expression of Notch and Delta in S2 cells are induced for 16 hours with 0.085 mM and 0.022 mM CuS0 4 , respectively. The cells are then centrifuged and 0 raised in serum free media to an equivalent density yielding between 20-30% T 320nm ( ⁇ 2xl0 6 cells/mL) in a Benchtop spectrophotometer . Blank values are set with M3 media alone. 400 ⁇ L of Notch and 400 ⁇ L of Delta cells are then pipeted into a 1.4 mL black sided, stoppered quartz cuvette and quickly inverted three times.
• T 320nm is read immediately to determine the time "zero" value.
• the cuvette is then 5 rocked horizontally on a Thermolyne vari-mixer at 20 oscillations per minute and subsequent T 320nra readings are taken at one minute intervals. Change in T 320nra (relative to time zero) is then plotted versus time. The effect of Dl EC was compared to a concentrate of media from ⁇ ECN-S2 cells
• Dl EC The biological activity of Dl EC was examined in a cell culture assay which was carried out as follows. Low density primary cultures of cortical neurons were prepared from embryonic day 15.5 to 16.5 mouse embryos. Single cell suspensions in Dulbecco's modified Eagle medium high 5 glucose/F12 (1:1), N2 Supplement, 2.5 mM L-glutamine and 5-
• Drosophila Delta juxtamembrane domain shows four of six possible alanine residues that would give a terminal sequence consistent with the C-terminal sequencing data, i.e., DA 576 , GA 581 , LA 591 , and NA 593 , ( Figure 11).
• tryptic digest peptide analysis was consistent with the C-terminal sequencing data.
• 24 tryptic digest peptides derived from Drosophila D1 EC were positively identified by LC/MS and their sequences determined. Five peptides were identified that terminated in the juxtamembrane domain. Two of the peptides terminated at residue Ala 593 and two other peptides terminated at residue Ala 581 . These data demonstrate that two prevalent forms of Dl EC terminate at amino acid residues 581 and 593. The fifth peptide terminated at amino acid position Gln 578 , which was not detected in the C-terminal analysis.
• Kuz does not appear to be responsible for the constitutive cleavage of Notch, the possibility that Kuz can cleave Notch at alternative sites remains.
• KuzDN is able to inhibit transactivation of a target gene of the Notch pathway induced by ligand binding to the receptor (Logeat, et al . , 1998, Proc. Natl. Acad. Sci. USA 95:8108-8112).
• this effect does not reflect Notch cleavage but rather the cleavage of Delta to produce an active ligand.
• Klueg et al . , 1998, Mol. Cell Biol. 9:1709-1723 (“Klueg) have recently reported the processing of Delta during normal embryogenesis demonstrating the existence of Delta fragments, one of which is consistent with Dl EC .

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