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WO1999067397A1 - Genes a cytosine methyltransferase d'adn adventif, polypeptides et leur utilisation - Google Patents

Genes a cytosine methyltransferase d'adn adventif, polypeptides et leur utilisation Download PDF

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WO1999067397A1
WO1999067397A1 PCT/US1999/014373 US9914373W WO9967397A1 WO 1999067397 A1 WO1999067397 A1 WO 1999067397A1 US 9914373 W US9914373 W US 9914373W WO 9967397 A1 WO9967397 A1 WO 9967397A1
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seq
polypeptide
dna
cytosine methyltransferase
dna cytosine
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Inventor
En Li
Masaki Okano
Shaoping Xie
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General Hospital Corp
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General Hospital Corp
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Priority to US09/720,086 priority Critical patent/US7342108B2/en
Priority to CA002331781A priority patent/CA2331781C/fr
Publication of WO1999067397A1 publication Critical patent/WO1999067397A1/fr
Anticipated expiration legal-status Critical
Priority to US10/623,813 priority patent/US7368551B2/en
Priority to US11/980,427 priority patent/US20080131901A1/en
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1003—Transferases (2.) transferring one-carbon groups (2.1)
    • C12N9/1007—Methyltransferases (general) (2.1.1.)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2799/00—Uses of viruses
    • C12N2799/02—Uses of viruses as vector
    • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid
    • C12N2799/026—Uses of viruses as vector for the expression of a heterologous nucleic acid where the vector is derived from a baculovirus

Definitions

  • the present invention relates generally to the fields of molecular biology, developmental biology, cancer biology and medical therapeutics. Specifically, the present invention relates to novel DNA cytosine methyltransferases. More specifically, isolated nucleic acid molecules are provided encoding mouse Dnmt3a and Dnmt3b and human DNMT3A and DNMT3B de novo DNA cytosine methyltransferase genes. Dnmt3a and Dnmt3b mouse and DNMT3A and DNMT3B human polypeptides are also provided, as are vectors, host cells and recombinant methods for producing the same. The invention further relates to an in vitro method for cytosine C5 methylation. Also provided is a diagnostic method for neoplastic disorders, and methods of gene therapy using the polynucleotides of the invention.
  • Methylation at the C-5 position of cytosine predominantly in CpG dinucleotides is the major form of DNA modification in vertebrate and invertebrate animals, plants, and fungi. Two distinctive enzymatic activities have been shown to be present in these organisms.
  • the de novo DNA cytosine methyltransferase whose expression is tightly regulated in development, methylates unmodified CpG sites to establish tissue or gene-specific methylation patterns.
  • the maintenance methyltransferase transfers a methyl group to cytosine in hemi-methylated CpG sites in newly replicated DNA, thus functioning to maintain clonal inheritance of the existing methylation patterns.
  • C5 methylation is a tightly regulated biological process important in the control of gene regulation.
  • aberrant de novo methylation can lead to undesirable consequences.
  • de novo methylation of growth regulatory genes in somatic tissues is associated with tumorigenesis in humans (Laird, P. W. and Jaenisch, R. Ann. Rev. Genet. 50:441-464 (1996); Baylin, S. B. et al, Adv. Cancer. Res. 72:141-196 (1998); and Jones, P. A. and Gonzalgo, M. L. Proc. Natl. Acad. Sci. USA 94:2X02-2X05 (1997)).
  • DnmtX The gene encoding the major maintenance methyltransferase , DnmtX , was first cloned in mice (Bestor, T. H. et al, J. Mol. Biol. 203:971-983 (1988), and the homologous genes were subsequently cloned from a number of organisms, including Arabidoposis, sea urchin, chick, and human. DnmtX is expressed ubiquitously in human and mouse tissues. Targeted disruption of DnmtX results in a genome- wide loss of cytosine methylation and embryonic lethality (Li et al. , 1992).
  • DnmtX is dispensable for the survival and growth of the embryonic stem cells, but appears to be required for the proliferation of differentiated somatic cells (Lei et al, 1996). Although it has been shown that the enzyme encoded by DnmtX can methylate DNA de novo in vitro (Bestor, 1992), there is no evidence that DnmtX is directly involved in de novo methylation in normal development. DnmtX appears to function primarily as a maintenance methyltransferase because of its strong preference for hemi-methylated DNA and direct association with newly replicated DNA (Leonhardt, H. et al, Cell 77:865- 873 (1992)).
  • ES cells homozygous for a null mutation of DnmtX can methylate newly integrated retroviral DNA, suggesting that DnmtX is not required for de novo methylation and an independently encoded de novo DNA cytosine methyltransferase is present in mammalian cells (Lei et al, 1996).
  • a first aspect of the invention provides novel de novo DNA cytosine methyltransferase nucleic acids and polypeptides that are not available in the art.
  • a second aspect of the invention relates to de novo DNA cytosine methyltransferase recombinant materials and methods for their production.
  • a third aspect of the invention relates to the production of recombinant de novo DNA cytosine methyltransferase polypeptides.
  • a fourth aspect of the invention relates to methods for using such de novo DNA cytosine methyltransferase polypeptides and polynucleotides. Such uses include the treatment of neoplastic disorders, among others.
  • Yet another aspect of the invention relates to diagnostic assays for the detection of diseases associated with inappropriate de novo DNA cytosine methyltransferase activity or levels and mutations in de novo DNA cytosine methyltransferases that might lead to neoplastic disorders.
  • Figure 1A-1D shows the nucleotide sequences of mouse Dnmt3a and
  • Figure 2A-2D shows the deduced amino acid sequence of mouse Dnmt3a and Dnmt3b and human DNMT3 A and DNMT3B genes, respectively. Sequences are presented in single letter amino acid code.
  • Figure 3 A shows a comparison of mouse Dnmt3a and Dnmt3b amino acid sequences
  • Figure 3B presents a comparison of the protein sequences of human DNMT3 A and DNMT3B 1.
  • Figure 4A presents a schematic comparison of mouse Dnmtl, Dnmt2,
  • Figure 4B presents a schematic of the DNMT3A, DNMT3B and zebrafish Zmt3 proteins.
  • Figure 4C and 4D present a schematic of the human DNMT3B gene organization and exon/intron junction sequences.
  • Figure 5 A presents a comparison of highly conserved protein structural motifs for eukaryotic and prokaryotic C5 methyltransferase.
  • Figure 5B presents a sequence alignment of the C-rich domain of vertebrate DNMT3 proteins and the
  • Figure 5C presents a non-rooted phylogenic tree of methyltransferase proteins.
  • Figure 6A-6C demonstrates the expression of Dnmt3a and Dnmt3b in mouse adult tissues, embryos, and ES cells by northern blot.
  • Figure 7 A-7D demonstrates in vitro methyltransferase activities of mouse Dnm ⁇ a and Dnmt3b proteins.
  • Figure 8 demonstrates in vitro analysis of de novo and maintenance activities of Dnmt3a, Dnmt3bl and Dnmt3b2 proteins.
  • Figure 9 presents Northern blot expression analysis of DNMT3 A and DNMT3B.
  • Figure 10 presents DNMT3 Northern Blot expression analysis of DNMT3A and DNMT3B in human tumor cell lines.
  • Cloning vector A plasmid or phage DNA or other DNA sequence which is able to replicate autonomously in a host cell, and which is characterized by one or a small number of restriction endonuclease recognition sites at which such DNA sequences may be cut in a determinable fashion without loss of an essential biological function of the vector, and into which a DNA fragment may be spliced in order to bring about its replication and cloning.
  • the cloning vector may further contain a marker suitable for use in the identification of cells transformed with the cloning vector. Markers, for example, provide tetracycline resistance or ampicillin resistance.
  • Expression vector A vector similar to a cloning vector but which is capable of enhancing the expression of a gene which has been cloned into it, after
  • RECTIFIED SHEET (RULE 91) transformation into a host.
  • the cloned gene is usually placed under the control of (i.e., operably linked to) certain control sequences such as promoter sequences.
  • Promoter sequences may be either constitutive or inducible.
  • a recombinant host may be any prokaryotic or eukaryotic host cell which contains the desired cloned genes on an expression vector or cloning vector. This term is also meant to include those prokaryotic or eukaryotic cells that have been genetically engineered to contain the desired gene(s) in the chromosome or genome of that organism. For examples of such hosts, see Sambrook et al, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor,
  • Preferred recombinant hosts are eukaryotic cells transformed with the DNA construct of the invention. More specifically, mammalian cells are preferred.
  • Recombinant vector Any cloning vector or expression vector which contains the desired cloned gene(s).
  • Host Animal Transgenic animals, all of whose germ and somatic cells contain the DNA construct of the invention. Such transgenic animals are in general vertebrates. Preferred Host Animals are mammals such as non-human primates, mice, sheep, pigs, cattle, goats, guinea pigs, rodents, e.g. rats, and the like. The term Host Animal also includes animals in all stages of development, including embryonic and fetal stages.
  • Promoter A DNA sequence generally described as the 5 ' region of a gene, located proximal to the start codon. The transcription of an adjacent gene(s) is initiated at the promoter region. If a promoter is an inducible promoter, then the rate of transcription increases in response to an inducing agent. In contrast, the rate of transcription is not regulated by an inducing agent if the promoter is a constitutive promoter. According to the invention, preferred promoters are heterologous to the de novo DNA cytosine methyltransferase genes, that is, the promoters do not drive expression of the gene in a mouse or human.
  • Such promoters include the CMV promoter (InVitrogen, San Diego, CA), the SV40, MMTV, and hMTIIa promoters (U.S.5,457,034), the HSV-1 4/5 promoter (U.S. 5,501 ,979), and the early intermediate HCMV promoter (WO92/17581).
  • the promoter is tissue-specific, that is, it is induced selectively in a specific tissue.
  • tissue-specific enhancer elements may be employed.
  • such promoters may include tissue and cell- specific promoters of an organism.
  • Gene A DNA sequence that contains information needed for expressing a polypeptide or protein.
  • Structural gene A DNA sequence that is transcribed into messenger RNA (mRNA) that is then translated into a sequence of amino acids characteristic of a specific polypeptide.
  • mRNA messenger RNA
  • cDNA Complementary DNA
  • cDNA Complementary DNA
  • a "complementary DNA,” or “cDNA” gene includes recombinant genes synthesized by reverse transcription of mRNA and from which intervening sequences (introns) have been removed.
  • Expression is the process by which a polypeptide is produced from a structural gene. The process involves transcription of the gene into mRNA and the translation of such mRNA into polypeptide(s).
  • Homologous/Nonhomologous Two nucleic acid molecules are considered to be "homologous" if their nucleotide sequences share a similarity of greater than 40%, as determined by HASH-coding algorithms (Wilber, W.J. and
  • nucleic acid molecules are considered to be "nonhomologous" if their nucleotide sequences share a similarity of less than 40%.
  • Polynucleotide This term generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified
  • RNA or DNA include, without limitation single- and double- stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double- stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or. more typically, double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • polynucleotide embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells.
  • Polynucleotide also embraces relatively short polynucleotides, often referred to as oligonucleotides.
  • Polypeptide This term refers to any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres.
  • Polypeptide refers to both short chains, commonly referred to as peptides, oligopeptides or oligomers, and to longer chains, generally referred to as proteins. Polypeptides may contain amino acids other than the 20 gene-encoded amino acids.
  • Polypeptides include amino acid sequences modified either by natural processes, such as post-translational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature.
  • Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Polypeptides may be branched as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched and branched cyclic polypeptides may result from post-translation natural processes or may be made by synthetic methods.
  • Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cystine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. See, for instance, Proteins-Structure
  • Variant The term used herein is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties.
  • a typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below.
  • a typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide.
  • a variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination.
  • a substituted or inserted amino acid residue may or may not be one encoded by the genetic code.
  • a variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques or by direct synthesis.
  • Identity This term refers to a measure of the identity of nucleotide sequences or amino acid sequences. In general, the sequences are aligned so that the highest order match is obtained. "Identity" per se has an art-recognized meaning and can be calculated using published techniques. (See, e.g. : Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press,
  • identity is well known to skilled artisans (Carillo, H. & Lipton, D., SIAM J Applied Math 48:X073 (1988)). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego, 1994, and Carillo, H. & Lipton, D., SIAM J Applied Math 45:1073 (1988). Methods to determine identity and similarity are codified in computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, GCS program package (Devereux,
  • the term "identity" represents a comparison between a test and reference polynucleotide. More specifically, reference polynucleotides are identified in this invention as SEQ ID Nos: 1, 2, 3 and 4, and a test polynucleotide is defined as any polynucleotide that is 90% or more identical to a reference polynucleotide. As used herein, the term “90% or more” refers to percent identities from 90 to 99.99 relative to the reference polynucleotide.
  • Identity at a level of 90% or more is indicative of the fact that, assuming for exemplification purposes a test and reference polynucleotide length of 100 nucleotides, that no more than 10% (i.e., 10 out of 100) nucleotides in the test polynucleotide differ from that of the reference polynucleotide. Such differences may be represented as point mutations randomly distributed over the entire length of the sequence or they may be clustered in one or more locations of varying length up to the maximum allowable 10 nucleotide difference.
  • Differences are defined as nucleotide substitutions, deletions or additions of sequence. These differences may be located at any position in the sequence, including but not limited to the 5' end, 3' end, coding and non coding sequences.
  • Fragment A "fragment" of a molecule such as de novo DNA cytosine methyltransferases is meant to refer to any polypeptide subset of that molecule.
  • Functional Derivative The term “functional derivatives” is intended to include the “variants,” “analogues,” or “chemical derivatives” of the molecule.
  • a "variant" of a molecule such as de novo DNA cytosine methyltransferases is meant to refer to a naturally occurring molecule substantially similar to either the entire molecule, or a fragment thereof.
  • An "analogue” of a molecule such as de novo DNA cytosine methyltransferases is meant to refer to a non-natural molecule substantially similar to either the entire molecule or a fragment thereof.
  • a molecule is said to be "substantially similar” to another molecule if the sequence of amino acids in both molecules is substantially the same, and if both molecules possess a similar biological activity. Thus, provided that two molecules possess a similar activity, they are considered variants as that term is used herein even if one of the molecules contains additional amino acid residues not found in the other, or if the sequence of amino acid residues is not identical.
  • a molecule is said to be a "chemical derivative" of another molecule when it contains additional chemical moieties not normally a part of the molecule. Such moieties may improve the molecule's solubility, absorption, biological half-life, etc. The moieties may alternatively decrease the toxicity of the molecule, eliminate or attenuate any undesirable side effect of the molecule, etc. Examples of moieties capable of mediating such effects are disclosed in Remington's Pharmaceutical Sciences (1980) and will be apparent to those of ordinary skill in the art.
  • Protein Activity or Biological Activity of the Protein refer to the metabolic or physiologic function of de novo DNA cytosine methyltransferase protein including similar activities or improved activities or these activities with decreased undesirable side-effects. Also included are antigenic and immunogenic activities of said de novo DNA cytosine methyltransferase protein. Among the physiological or metabolic activities of said protein is the transfer of a methyl group to the cytosine C5 position of duplex DNA. Such DNA may completely lack any methylation of may be hemimethylated. As demonstrated in Example 8, de novo DNA cytosine methyltransferases methylate C5 in cytosine moieties in nonmethylated DNA.
  • Polynucleotides This term refers to a polynucleotide containing a nucleotide sequence which encodes a de novo DNA cytosine methyltransferase polypeptide or fragment thereof or that encodes a de novo DNA cytosine methyltransferase polypeptide or fragment wherein said nucleotide sequence has at least 90% identity to a nucleotide sequence encoding the polypeptide of SEQ ID Nos: 5, 6, 7 or 8, or a corresponding fragment thereof, or which has sufficient identity to a nucleotide sequence contained in SEQ ID NO:l, 2, 3 or 4.
  • Polypeptides This term refers to polypeptides with amino acid sequences sufficiently similar to the de novo DNA cytosine methyltransferase protein sequence in SEQ ID NO:5, 6, 7 or 8 and that at least one biological activity of the protein is exhibited.
  • Antibodies As used herein includes polyclonal and monoclonal antibodies, chimeric, single chain, and humanized antibodies, as well as Fab fragments, including the products of an Fab or other immunoglobulin expression library.
  • Substantially pure As used herein means that the desired purified protein is essentially free from contaminating cellular components, said components being associated with the desired protein in nature, as evidenced by a single band following polyacrylamide-sodium dodecyl sulfate gel electrophoresis. Contaminating cellular components may include, but are not limited to, proteinaceous, carbohydrate, or lipid impurities.
  • substantially pure is further meant to describe a molecule which is homogeneous by one or more purity or homogeneity characteristics used by those of skill in the art.
  • a substantially pure de novo DNA cytosine methyltransferases will show constant and reproducible characteristics within standard experimental deviations for parameters such as the following: molecular weight, chromatographic migration, amino acid composition, amino acid sequence, blocked or unblocked N-terminus, HPLC elution profile, biological activity, and other such parameters.
  • the term is not meant to exclude artificial or synthetic mixtures of the factor with other compounds.
  • the term is not meant to exclude de novo DNA cytosine methyltransferase fusion proteins isolated from a recombinant host.
  • Isolated A term meaning altered “by the hand of man” from the natural state. If an "isolated" composition or substance occurs in nature, it has been changed or removed from its original environment, or both.
  • a polynucleotide or a polypeptide naturally present in a living animal is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein.
  • a polypeptide or polynucleotide produced and/or contained within a recombinant host cell is considered isolated for purposes of the present invention.
  • isolated polypeptide ' or an "isolated polynucleotide” are polypeptides or polynucleotides that have been purified, partially or substantially, from a recombinant host cell or from a native source.
  • a recombinantly produced version of a de novo DNA cytosine methyltransferase polypeptide can be substantially purified by the one-step method described in Smith and Johnson, Gene 67 :3X-40 (1988).
  • Neoplastic disorder This term refers to a disease state which is related to the hyperproliferation of cells. Neoplastic disorders include, but are not limited to, carcinomas, sarcomas and leukemias.
  • Gene Therapy A means of therapy directed to altering the normal pattern of gene expression of an organism. Generally, a recombinant polynucleotide is introduced into cells or tissues of the organism to effect a change in gene expression.
  • Antisense RNA gene/Antisense RNA In eukaryotes, mRNA is transcribed by RNA polymerase II. However, it is also known that one may construct a gene containing a RNA polymerase II template wherein a RNA sequence is transcribed which has a sequence complementary to that of a specific mRNA but is not normally translated. Such a gene construct is herein termed an
  • antisense RNA gene and such a RNA transcript is termed an “antisense RNA.”
  • Antisense RNAs are not normally translatable due to the presence of translation stop codons in the antisense RNA sequence.
  • Antisense oligonucleotide A DNA or RNA molecule or a derivative of a DNA or RNA molecule containing a nucleotide sequence which is complementary to that of a specific mRNA.
  • An antisense oligonucleotide binds to the complementary sequence in a specific mRNA and inhibits translation of the mRNA.
  • oligonucleotide alkylphosphonothioates and arylphosphonothioates oligonucleotide alkylphosphonothioates and arylphosphonothioates
  • WO92/20697 3'-end capped oligonucleotides.
  • Particular de novo DNA cytosine methyltransferase antisense oligonucleotides of the present invention include derivatives such as S- oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press (1989)).
  • S-oligos are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom.
  • the S-oligos of the present invention may be prepared by treatment of the corresponding O-oligos with 3H- X ,2-benzodithiol-3- one- 1,1 -dioxide which is a sulfur transfer reagent. See Iyer et al, J. Org. Chem. 55:4693-4698 (1990); and Iyer et al, J. Am. Chem. Soc. 772:1253-1254 (1990).
  • Antisense Therapy A method of treatment wherein antisense oligonucleotides are administered to a patient in order to inhibit the expression of the corresponding protein.
  • the invention relates to polynucleotides encoding and polypeptides of novel de novo DNA cytosine methyltransferase proteins.
  • the invention relates especially to de novo DNA cytosine methyltransferase mouse Dnmt3a and Dnmt3b cDNAs and the human DNMT3A and DNMT3B cDNAs set out in SEQ ID NOs: 1. 2, 3 and 4, respectively.
  • the invention also relates to mouse DnmfJa and Dnmtib nd human DNMT3A and DNMTB e novo DNA cytosine methyltransferase polypeptides set out in SEQ ID NOs: 5, 6, 7, and 8, respectively.
  • the invention further relates to the de novo DNA cytosine methyltransferase nucleotide sequences of the mouse Dnmt3a cDNA (plasmid pMT3a) and Dnmt3b cDNA (plasmid pMT3b) and the human DNMTa cDNA (plasmid pMT3A) in ATCC Deposit Nos.209933 , 209934, and 98809, respectively, and the amino acid sequences encoded therein.
  • the nucleotide sequence of the human DNMT3B cDNA identified in SEQ ID NO:4 is available in a clone (ATCC Deposit No. 326637) independently deposited by the I.M.A.G.E. Consortium.
  • the invention relates to the de novo
  • ATCC deposits are believed to contain the de novo DNA cytosine methyltransferase cDNA sequences shown in SEQ ID NOs:l, 2, 3, and 4, the nucleotide sequences of the polynucleotide contained in the deposited material, as well as the amino acid sequence of the polypeptide encoded thereby, are controlling in the event of any conflict with any description of sequences herein.
  • mice Dnmt3a and Dnmt3b cDNAs and the human DNMT3A cDNA were made under the terms of the Budapest Treaty on the international recognition of the deposit of micro-organisms for purposes of patent procedure.
  • the deposits are provided merely as a convenience for those of skill in the art and are not an admission that a deposit is required for enablement, such as that required under 35 U.S.C. ⁇ 112.
  • Another aspect of the invention relates to isolated polynucleotides, and polynucleotides closely related thereto, which encode the de novo DNA cytosine methyltransferase polypeptides.
  • sequencing of the cDNAs contained in the deposited clones encoding mouse and human de novo DNA cytosine methyltransferases confirms that the de novo DNA cytosine methyltransferase proteins of the invention are structurally related to other proteins of the DNA methyltransferase family.
  • polynucleotides of the present invention encoding de novo DNA cytosine methyltransferase proteins may be obtained using standard cloning and screening procedures as described in Example 1.
  • Polynucleotides of the invention can also be obtained from natural sources such as genomic DNA libraries or can be synthesized using well known and commercially available techniques.
  • polynucleotides encoding de novo DNA cytosine methyltransferase polypeptides having the amino acid sequence set out in SEQ ID NO:5, SEQ ID NO: 6, SEQ ID NO:7, or SEQ ID NO:8, and variants thereof.
  • a particular nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide may be identical over its entire length to the coding sequence in SEQ ID NOs:l, 2, or 3.
  • a particular nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide may be an alternate form of SEQ ID NOs: l, 2, 3 and 4 due to degeneracy in the genetic code or variation in codon usage encoding the polypeptides of SEQ ID NOs:5, 6, 7. or 8.
  • the polynucleotides of the invention contain a nucleotide sequence that is highly identical, at least 90% identical, with a nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide or at least 90% identical with the encoding nucleotide sequence set forth in SEQ ID NOs:l. 2, or 3.
  • Polynucleotides of the invention may be 90 to 99% identical to the nucleotides sequence set forth in SEQ ID NO:4.
  • the polynucleotide may include the coding sequence for the full-length polypeptide or a fragment thereof, by itself; the coding sequence for the full-length polypeptide or fragment in reading frame with other coding sequences, such as those encoding a leader or secretory sequence, a pre-, or pro or prepro-protein sequence, or other fusion peptide portions.
  • a marker sequence that facilitates purification of the fused polypeptide can be encoded.
  • the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al., Proc Natl Acad Sci USA 56:821-824 (1989), or it may be the HA tag, which corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson, I., et al, Cell 37:767, 1984).
  • the polynucleotide may also contain non-coding 5' and 3' sequences, such as transcribed, non-translated sequences, splicing and polyadenylation signals, ribosome binding sites and sequences that stabilize mRNA.
  • Embodiments of the invention include isolated nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 90% identical, and more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to (a) a nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence in SEQ ID NO: 1 ,
  • SEQ ID NO:2 or SEQ ID NO:3;
  • an isolated nucleic acid of the invention may be a polynucleotide at least 90% but not more than 99% identical to (a) a nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence in SEQ ID NO:4; (b) a nucleotide sequence encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence encoded by the cDNA clone contained in ATCC Deposit No.326637; or (c) a nucleotide sequence complementary to any of the nucleotide sequences in (a) or (b).
  • Further preferred embodiments are polynucleotides encoding de novo DNA cytosine methyltransferases and de novo DNA cytosine methyltransferase variants that have an amino acid sequence of the de novo DNA cytosine methyltransferase protein of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ
  • ID NO:8 in which several, 1, 1-2, 1-3, 1-5 or 5-10 amino acid residues are substituted, deleted or added, in any combination.
  • polynucleotides that are at least 90% identical over their entire length to a polynucleotide encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence set out in SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, and polynucleotides which are complementary to such polynucleotides.
  • polynucleotides that comprise regions that are at least 90% identical over their entire length to a polynucleotide encoding the de novo DNA cytosine methyltransferase polypeptides of the ATCC deposited human
  • DNMT3 A cDNA clone and polynucleotides complementary thereto, and 90% to 99% identical over their entire length to a polynucleotide encoding the de novo DNA cytosine methyltransferase polypeptides of the ATCC deposited human DNMT3B cDNA clone and polynucleotides complementary thereto.
  • polynucleotides at least 95% identical over their entire length to the same are particularly preferred, and those with at least 97% identity are especially preferred.
  • those with at least 98% identity are highly preferred and with at least 99% identity being the most preferred.
  • the nucleic acid molecules of the present invention are not the sequence of nucleotides, the nucleic acid molecules (e.g. , clones), or the nucleic acid inserts identified in one or more of the below cited public EST or STS GenBank Accession Reports.
  • the following public ESTs were identified that relate to portions of SEQ
  • ID NO:l AA052791(SEQ ID NO:9); AA111043(SEQ ID NO: 10); AA154890(SEQ ID NO: 11); AA240794(SEQ ID NO:12); AA756653(SEQ ID NO:13); W58898(SEQ ID NO:14); W59299(SEQ ID NO:15); W91664(SEQ ID NO:16); W91665(SEQ ID NO:17); to portions of SEQ ID NO:2: AAl 16694 (SEQ ID NO: 18); AA119979 (SEQ ID NO: 19); AA177277 (SEQ ID NO:20);
  • AA210568 (SEQ ID NO:21); AA399749 (SEQ ID NO:22); AA407106 (SEQ ID NO:23); AA575617 (SEQ ID NO:24); to portions of SEQ ID NO:3: AA004310 (SEQ ID NO:25); AA004399 (SEQ ID NO:26); AA312013 (SEQ ID NO:27); AA355824 (SEQ ID NO:28); AA533619 (SEQ ID NO:29); AA361360 (SEQ ID NO:30); AA364876 (SEQ ID NO:31); AA503090 (SEQ ID NO:32); AA533619
  • the present invention is further directed to fragments of SEQ ID NO: 1 , 2 or 3, or to fragments of the cDNA nucleotide sequence found in ATCC Deposit Nos. 209933, 209934, or 98809.
  • a fragment may be defined to be at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about
  • fragments are useful as diagnostic probes and primers as discussed herein.
  • larger DNA fragments are also useful according to the present invention, as are fragments corresponding to most, if not all, of the nucleotide sequence of the cDNA clones contained in the plasmids deposited as ATCC Deposit No.209933 , ATCC Deposit
  • polynucleotide fragments of the invention may be defined algebraically in the following way: (a) for SEQ ID NO:l, as 15 + N, wherein N equals zero or any positive integer up to 4176; (b) for SEQ ID NO:2, as 15 + N, wherein N equals zero or any positive integer up to 4180; and (c) for
  • SEQ ID NO:3 as 15 + N, wherein N equals zero or any positive integer up to 4401.
  • N equals zero or any positive integer up to 4401.
  • the invention is directed to fragments of SEQ ID NO:4.
  • Such fragments are defined as comprising the nucleotide sequence encoding the specific amino acid residues integral and immediately adjacent to the site where DNMT3B exons are spliced together.
  • the DNMT3B sequence of SEQ ID NO:4 consists of 23 exon sequences defined accordingly: Exon 1 consists of
  • Exon 8 consists of nucleotides 928-1035 of SEQ ID NO:4; Exon 9 consists of nucleotides 1036-1180 of SEQ ID NO:4; Exon 10 consists of nucleotides 1181- 1240 of SEQ ID NO:4; Exon 11 consists of nucleotides 1241-1366 of SEQ ID NO:4; Exon 12 consists of nucleotides 1367-1411 of SEQ ID NO:4; Exon 13 consists of nucleotide 1412-1491 of SEQ ID NO:4; Exon 14 consists of nucleotides 1492-1604 of SEQ ID NO:4; Exon 15 consists of nucleotides 1605- 1788 of SEQ ID NO:4; Exon 16 consists of nucleotides 1789-1873 of SEQ ID NO:4; Exon 17 consists of nucleotides 1874-2019 of SEQ ID NO:4; Exon 18 consists of nucleotides 2020-2110 of SEQ ID NO:4;
  • Exon 1 and Exon 23 are herein defined for the purposes of the invention.
  • the first nucleotide of Exon 1 may or may not be the transcriptional start site for the DNMT3B genomic locus, and the last nucleotide identified for Exon 23 may or may not reflect the last nucleotide transcribed in vivo.
  • fragments of SEQ ID NO:4 comprise the following exon-exon junctions of 20 nucleotides in length: the exonl/exon 2 junction of nucleotides 98-118 of SEQ ID NO:4; the exon 2/exon 3 junction of nucleotides 246-266 of SEQ ID NO:4; the exon 3 /exon 4 junction of nucleotides 308-328 of SEQ ID NO:4; the exon 4/exon 5 junction of nucleotides 410-430 of SEQ ID NO:4; the exon 5/exon 6 junction of nucleotides 536-556 of SEQ ID NO:4; the exon 6/exon 7 junction of nucleotides 758-778 of SEQ ID NO:4; the exon 7/exon 8 junction of nucleotides 917-937 of SEQ IDNO:4; the exon 8/exon 9 junction of nucleotides 1025-1045 of SEQ ID NO:4; the exon
  • exon-exon junction fragments of SEQ ID NO:4 are possible which comprise 30, 40, 50, 60, 70, 80, 90, 100, 200. 300, 400, 500, etc., nucleotides of SEQ ID NO:4.
  • exon-exon junctions are identified: the exon 1 /exon 2 junction of nucleotides 108 and 109 of SEQ ID NO:4; the exon 2/exon 3 junction of nucleotides 256 and 257 of SEQ ID NO:4; the exon 3/exon 4 junction of nucleotides 318 and 319 of SEQ ID NO:4; the exon 4/exon 5 junction of nucleotides 420 and 421 of SEQ ID NO:4; the exon 5/exon 6 junction of nucleotides 546 and 547 of SEQ ID NO:4; the exon 6/exon 7 junction of nucleotides 768 and 769 of SEQ ID NO:4; the exon 7/exon 8 junction of nucleotides 927 and 928 of SEQ ID NO:4; the exon 8/exon 9 junction of nucleotides 1035 and 1036 of SEQ ID NO:4; the exon 9/exon 10
  • the present invention further relates to polynucleotides that hybridize to the above-described sequences.
  • the present invention especially relates to polynucleotides that hybridize under stringent conditions to the above- described polynucleotides.
  • stringent conditions means hybridization will occur only if there is at least 90% and preferably at least 95% identity and more preferably at least 97%) identity between the sequences.
  • a major consideration associated with hybridization analysis of DNA or RNA sequences is the degree of relatedness the probe has with the sequences present in the specimen under study.
  • hybridization can be carried out in a solution containing 6 x SSC (10 x SSC: 1.5 M sodium chloride, 0.15 M sodium citrate, pH 7.0), 5 x Denhardt's (1 x Denhardt's: 0.2% bovine serum albumin, 0.2% polyvinylpyrrolidone, 0.02% Ficoll 400), 10 mM EDTA, 0.5% SDS and about 10 7 cpm of nick-translated DNA for 16 hours at 65 °C.
  • a washing step may be utilized wherein probe binding to polynucleotides of low homology, or nonspecific binding of the probe, may be removed.
  • a stringent wash step may involve a buffer of 0.2 x SSC and 0.5% SDS at a temperature of 65 °C. Additional information related to hybridization technology and, more particularly, the stringency of hybridization and washing conditions may be found in Sambrook et al, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York (1989), which is incorporated herein by reference.
  • Polynucleotides of the invention which are sufficiently identical to a nucleotide sequences contained in SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3 or SEQ ID NO:4, or in the cDNA inserts of ATCC Deposit No. 209933, ATCC Deposit No. 209934, ATCC Deposit No. 98809 or ATCC Deposit No. 326637, may be used as hybridization probes for cDNA and genomic DNA, to isolate full- length cDNAs and genomic clones encoding de novo DNA cytosine methyltransferase proteins and to isolate cDNA and genomic clones of other genes that have a high sequence similarity to the de novo DNA cytosine methyltransferase genes.
  • hybridization techniques are known to those of skill in the art.
  • these nucleotide sequences are at least about 90% identical, preferably at least about 95% identical, more preferably at least about
  • the probes generally will comprise at least 15 nucleotides. Preferably, such probes will have at least 30 nucleotides and may have at least 50 nucleotides. Particularly preferred probes will range between 30 and 50 nucleotides.
  • the polynucleotides and polypeptides of the present invention may be employed as research reagents and materials for discovery of treatments and diagnostics to animal and human disease.
  • the present invention also relates to vectors that comprise a polynucleotide of the present invention, host cells which are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques.
  • Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the invention .
  • host cells can be genetically engineered to incorporate expression systems for polynucleotides of the invention.
  • Introduction of polynucleotides into host cells can be effected by methods described in many standard laboratory manuals, such as Sambrook et al, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold
  • coli Streptomyces and Bacillus subtilis cells
  • fungal cells such as yeast cells and Aspergillus cells
  • inse , ⁇ cells such as Drosophila S2 and Spodoptera Sf9 cells
  • animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293 and Bowes melanoma cells
  • plant cells A great variety of expression systems can be used.
  • Such systems include, among others, chromosomal, episomal and virus-derived systems, e.g., vectors derived from bacterial plasmids, from bacteriophages, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses, and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids.
  • the expression systems may contain control regions that regulate as well as engender expression.
  • any system or vector suitable to maintain, propagate or express polynucleotides to produce a polypeptide in a host may be used.
  • the appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al, Molecular Cloning: A Laboratory Manual (supra).
  • RNA vectors may also be utilized for the expression of the de novo DNA cytosine methyltransferases disclosed in this invention. These vectors are based on positive or negative strand RNA viruses that naturally replicate in a wide variety of eukaryotic cells (Bredenbeek, P.J. and Rice, CM., Virology 3: 297- 310, (1992)). Unlike retroviruses, these viruses lack an intermediate DNA life- cycle phase, existing entirely in RNA form.
  • alpha viruses are used as expression vectors for foreign proteins because they can be utilized in a broad range of host cells and provide a high level of expression; examples of viruses of this type include the Sindbis virus and Semliki Forest virus (Schlesinger, S., TIBTECH 11 : 18-22, (1993); Frolov, I., et al., Proc. Natl. Acad. Sci. (USA) 93:
  • RNA form a DNA form (pSinrep5 plasmid) in the laboratory, but propagation in RNA form is feasible as well.
  • the vector containing the gene of interest exists completely in RNA form and may be continuously propagated in that state if desired.
  • secretion signals may be inco ⁇ orated into the desired polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.
  • operably linked when used in the context of a linkage between a structural gene and an expression control sequence, e.g., a promoter, refers to the position and orientation of the expression control sequence relative to the structural gene so as to permit expression of the structural gene in any host cell. For example, an operable linkage would maintain proper reading frame and would not introduce any in frame stop codons.
  • heterologous promoter refers to a promoter not normally and naturally associated with the structural gene to be expressed.
  • a heterologous promoter would be any promoter other than an endogenous promoter associated with the de novo DNA cytosine methyltransferase gene in non-recombinant mouse or human chromosomes.
  • the heterologous promoter is a prokaryotic or bacteriophage promoter, such as the lac promoter, T3 promoter, or T7 promoter.
  • the heterologous promoter is a eukaryotic promoter.
  • this invention provides an isolated nucleic acid molecule comprising a de novo DNA cytosine methyltransferase structural gene operably linked to a heterologous promoter.
  • a de novo DNA cytosine methyltransferase structural gene refers to a nucleotide sequence at least about 90% identical to one of the following nucleotide sequences:
  • nucleotide sequence encoding the de novo DNA cytosine methyltransferase polypeptide having the complete amino acid sequence encoded by the cDNA insert of ATCC Deposit No. 209933, ATCC Deposit No. 209934, or ATCC Deposit No. 98809; or (c) a nucleotide sequence complementary to any of the nucleotide sequences in (a) or (b).
  • the de novo DNA cytosine methyltransferase structural gene is 90%, and more preferably 91%, 92%, 93%, 94%, 95%, 97%, 98%), 99%), or 100% identical to one or more of nucleotide sequences (a), (b), or
  • a de novo DNA cytosine methyltransferase structural gene refers to a nucleotide sequence about 90% to 99%> identical to one of the following nucleotide sequences: (a) a nucleotide sequence encoding the de novo DNA cytosine methyltransferase polypeptide having the complete amino acid sequence in SEQ ID NO:8;
  • the de novo DNA cytosine methyltransferase structural gene is 90%, and more preferably 91%, 92%, 93%, 94%, 95%, 97%, 98%, or 99% identical to SEQ ID NO:8, ATCC Deposit No. 326637 or polynucleotides complementary thereto.
  • This invention also provides an isolated nucleic acid molecule comprising a de novo DNA cytosine methyltransferase structural gene operably linked to a heterologous promoter, wherein said isolated nucleic acid molecule does not encode a fusion protein comprising the de novo DNA cytosine methyltransferase structural gene or a fragment thereof.
  • This invention further provides an isolated nucleic acid molecule comprising a de novo DNA cytosine methyltransferase structural gene operably linked to a heterologous promoter, wherein said isolated nucleic acid molecule is capable of expressing a de novo DNA cytosine methyltransferase polypeptide when used to transform an appropriate host cell.
  • This invention also provides an isolated nucleic acid molecule comprising a polynucleotide having a nucleotide sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, wherein said isolated nucleic acid molecule does not contain a nucleotide sequence at least 90% identical to the 3' untranslated region of SEQ ID NO:l (nucleotides 2942-4191), SEQ ID NO:2 (nucleotides 2847-4174), SEQ ID NO:3
  • nucleotides 3090-4397) or SEQ IDNO:4 nucleotides 2677-4127
  • a fragment of the 3' untranslated region greater than 25, 50, 75, 100, or 125 bp in length.
  • This invention further provides an isolated nucleic acid molecule comprising a polynucleotide having a nucleotide sequence at least 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence encoding a de novo DNA cytosine methyltransferase polypeptide having the amino acid sequence of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO: 8, wherein said isolated nucleic acid molecule does not contain a nucleotide sequence at least 90% identical to the 5' untranslated region of SEQ ID NO:l (nucleotides 1-216), SEQ ID NO:2 (nucleotides 1-268), SEQ ID NO:3
  • nucleotides 1-352 or SEQ ID NO:4 (nucleotides 1-114), or a fragment of the 5' untranslated region greater than 25, 35, 45, 55, 65, 75, 85, or 90 bp.
  • Suitable known prokaryotic promoters for use in the production of proteins of the present invention include the E. coli lacX and lacZ promoters, the T3 and T7 promoters, the gpt promoter, the lambda PR and PL promoters and the trp promoter.
  • Suitable eukaryotic promoters include the CMV immediate early promoter, the HSV thymidine kinase promoter, the early and late SV40 promoters, the promoters of retroviral LTRs, such as those of the Rous Sarcoma Virus (RSV), adenovirus promoter, Herpes virus promoter, and metallothionein promoters. such as the mouse metallothionein-I promoter and tissue and organ- specific promoters known in the art.
  • RSV Rous Sarcoma Virus
  • Herpes virus promoter Herpes virus promoter
  • metallothionein promoters such as the mouse metallothionein-I promoter
  • the de novo DNA cytosine methyltransferase polypeptide is to be expressed for use in screening assays, generally, it is preferred that the polypeptide be produced at the surface of the cell. In this event, the cells may be harvested prior to use in the screening assay. If de novo DNA cytosine methyltransferase polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the polypeptide; if produced intracellularly, the cells must first be lysed before the polypeptide is recovered.
  • DNA cytosine methyltransferase polypeptides can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding proteins may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification.
  • the de novo DNA cytosine methyltransferase polypeptides of the present invention include the polypeptide of SEQ ID NO:5, SEQ IDNO:6, SEQ IDNO:7 or SEQ ID NO:8, as well as polypeptides and fragments which have activity and have at least 90% identity to the polypeptide of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or the relevant portion and more preferably at least 96%. 97% or 98% identity to the polypeptide of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or the relevant portion and more preferably at least 96%. 97% or 98% identity to the polypeptide of SEQ ID NO:5, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or the relevant portion and more preferably at least 96%. 97% or 98% identity to the polypeptide of SEQ ID NO:5, SEQ ID NO:5, SEQ ID NO:6,
  • SEQ ID NO:6 SEQ ID NO:7 or SEQ ID NO:8. and still more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the polypeptide of SEQ ID NO:5, SEQ ID NO:6. SEQ ID NO:7 or SEQ ID NO:8.
  • the polypeptides of the present invention are preferably provided in an isolated form.
  • polypeptides of the present invention include the polypeptide encoded by the deposited cDNAs; a polypeptide comprising amino acids from about 1 to about 908 in SEQ ID NO:5; a polypeptide comprising amino acids from about 1 to about 859 in SEQ ID NO:6; a polypeptide comprising amino acids from about 1 to about 912 in SEQ ID NO:7 and a polypeptide comprising amino acids from about 1 to about 853 in SEQ ID NO: 8; as well as polypeptides which are at least about 90% identical, and more preferably at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the polypeptides described above and also include portions of such polypeptides with at least 30 amino acids and more preferably at least 50 amino acids.
  • Polypeptides of the invention also include alternative splicing variants of the Dnmt3 sequences disclosed herein.
  • alternative variant spliced proteins of mouse Dnmt3b include but are not limited to a polypeptide wherein, except for at least one conservative amino acid substitution, said polypeptide has a sequence selected from the group consisting of: ( 1 ) amino acid residues 1 to 362 and 383 to 859 from SEQ ID NO:2; and (2) amino acid residues 1 to 362 and 383 to 749 and 813 to 859 from SEQ ID NO:2;
  • alternative variant spliced proteins of human DNMT3B include but are not limited to a polypeptide wherein, except for at least one conservative amino acid substitution, said polypeptide has a sequence selected from the group consisting of: (1) amino acid residues 1 to 355 and 376 to 853 from SEQ ID NO:4; and (2) amino acid residues 1 to 355 and 376 to 743 and 807 to 853 from SEQ ID NO:4.
  • the de novo DNA cytosine methyltransferase polypeptides may be a part of a larger protein such as a fusion protein. It is often advantageous to include additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification such as multiple histidine residues, or additional sequence for stability during recombinant production. Biologically active fragments of the de novo DNA cytosine methyltransferase polypeptides are also included in the invention. A fragment is a polypeptide having an amino acid sequence that entirely is the same as part but not all of the amino acid sequence of one of the aforementioned de novo DNA cytosine methyltransferase polypeptides.
  • fragments may be "free-standing,” or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region.
  • a fragment may constitute from about 10 contiguous amino acids identified in SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8.
  • polypeptide fragment lengths may be defined algebraically as follows: (a) for SEQ ID NO: 5, as 10 + N, wherein N equals zero or any positive integer up to 898; (b) for SEQ ID NO:6, as 10 + N, wherein N equals zero or any positive integer up to 849; (c) for SEQ ID NO:7, as 10 + N, wherein N equals zero or any positive integer up to 902; and (d) for SEQ ID NO:8, as 10 + N, wherein N equals zero or any positive integer up to 843.
  • Preferred fragments include, for example, truncation polypeptides having the amino acid sequence of de novo DNA cytosine methyltransferase polypeptides, except for deletion of a continuous series of residues that includes the amino terminus, or a continuous series of residues that includes the carboxyl terminus or deletion of two continuous series of residues, one including the amino terminus and one including the carboxyl terminus.
  • fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet- forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions.
  • Biologically active fragments are those that mediate protein activity, including those with a similar activity or an improved activity, or with a decreased undesirable activity. Also included are those that are antigenic or immunogenic in an animal, especially in a human.
  • polypeptides of the invention include polypeptides having an amino acid sequence at least 90% identical to that of SEQ ID NO: 5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or fragments thereof with at least 90% identity to the corresponding fragment of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, all of which retain the biological activity of the de novo DNA cytosine methyltransferase protein, including antigenic activity. Included in this group are variants of the defined sequence and fragment. Preferred variants are those that vary from the reference by conservative amino acid substitutions, i.e.. those that substitute a residue with another of like characteristics.
  • Typical substitutions are among Ala, Val, Leu and He; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gin; and among the basic residues Lys and Arg, or aromatic residues Phe and Tyr. Particularly preferred are variants in which several, 5 to 10, 1 to 5, or 1 to 2 amino acids are substituted, deleted, or added in any combination.
  • the de novo DNA cytosine methyltransferase polypeptides of the invention can be prepared in any suitable manner.
  • Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
  • the starting substrate DNA may be hemimethylated (i.e., one strand of the duplex DNA is methylated) or may lack methylation completely.
  • the polypeptides of the invention being de novo
  • DNA cytosine methyltransferases are uniquely suited to the latter function, owing to the fact that, unlike maintenance methyltransferases, their preferred substrate is not hemimethylated DNA.
  • isolated polypeptides of the invention function as in vitro DNA methyltransferases when combined in an appropriately buffered solution with the appropriate cofactors and a substrate
  • the substrate DNA may be selected from any natural source, e.g., genomic DNA, or a recombinant source such as a DNA fragment amplified by the polymerase chain reaction.
  • the substrate DNA may be prokaryotic or eukaryotic DNA.
  • the substrate DNA is mammalian DNA, and most preferredly, the substrate DNA is human DNA.
  • in vitro methylation of DNA may be used to direct or regulate the expression of said DNA in a biological system.
  • over-expression, under-expression or lack of expression of a particular native DNA sequence in a host cell or organism may be attributed to the fact that the DNA is under-methylated (hypomethylated) or not methylated.
  • in vitro methylation of a recombinant form of said DNA, and the subsequent introduction of the methylated, recombinant DNA into the cell or organism may effect an increase or decrease in the expression of the encoded polypeptide.
  • in vitro methylation pattern will be maintained after introduction into a biological system by the action of maintenance methyltransferase polypeptides in said system.
  • the biological system selected for the introduction of in vitro methylated DNA may be prokaryotic or eukaryotic.
  • the biological system is mammalian, and the most preferred embodiment is when the biological system is human.
  • the GenBank STS database was searched using Dnmt3a and Dnmt3b sequences as queries.
  • the search identified markers WI-6283 (GenBank Accession number G06200) and SHGC- 15969 (GenBank Accession number Gl 5302) as matching the cDNA sequence of Dnmt3a and Dnmt3b, respectively.
  • WI-6283 has been mapped to 2p23 between D2S171 and D2S174 (48-50 cM) on the radiation hybrid map by Whitehead Institute/MIT Center for Genome Research.
  • the corresponding mouse chromosome location is at 4.0 cM on chromosome 12.
  • SHGC- 15969 has been mapped to 20pl 1.2 between D20S184 and D20S106 (48-50 cM) by Stanford
  • mice chromosome locus Human Genome Center.
  • the corresponding mouse chromosome locus is at 84.0 cM on chromosome 2.
  • the differences in the cDNA or genomic sequence between affected and unaffected individuals can also be determined. If a mutation is observed in some or all of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease.
  • This invention also relates to the use of de novo DNA cytosine methyltransferase polynucleotides for use as diagnostic reagents. Detection of a mutated form of a de novo DNA cytosine methyltransferase gene associated with a dysfunction will provide a diagnostic tool that can add to or define a diagnosis of a disease or susceptibility to a disease which results from under-expression, over-expression or altered expression of the mutated de novo DNA cytosine methyltransferase. Individuals carrying mutations in one or more de novo DNA cytosine methyltransferase genes may be detected at the DNA level by a variety of techniques.
  • Nucleic acids for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material.
  • the genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR or other amplification techniques prior to analysis.
  • RNA or cDNA may also be used in similar fashion. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to labeled de novo DNA cytosine methyltransferase nucleotide sequences. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures.
  • DNA sequence differences may also be detected by alterations in electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing (see, e.g., Myers, etal, Science 230: 1242 (1985)). Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and S 1 protection or the chemical cleavage method (see Cotton, et al, Proc. Natl. Acad. Sci. USA 55:4397-4401 (1985)).
  • the diagnostic assays offer a process for diagnosing or determining a susceptibility to neoplastic disorders through detection of mutations in one or more de novo DNA cytosine methyltransferase genes by the methods described.
  • neoplastic disorders may be diagnosed by methods that determine an abnormally decreased or increased level of de novo DNA cytosine methyltransferase polypeptide or de novo DNA cytosine methyltransferase mRNA in a sample derived from a subject. Decreased or increased expression may be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides; for example, RT-PCR, RNase protection, Northern blotting and other hybridization methods may be utilized. Assay techniques that may be used to determine the level of a protein, such as an de novo DNA cytosine methyltransferase protein, in a sample derived from a host are well known to those of skill in the art. Such assay methods include radioimmunoassays. competitive-binding assays, Western blot analysis and ELISA assays.
  • methods for diagnosing or determining a susceptibility of an individual to neoplastic disorders, comprising (a) assaying the de novo DNA cytosine methyltransferase protein gene expression level in mammalian cells or body fluid; and (b) comparing said de novo DNA cytosine methyltransferase protein gene expression level with a standard de novo DNA cytosine methyltransferase protein gene expression level whereby an increase or decrease in said de novo DNA cytosine methyltransferase gene expression level over said standard is indicative of an increased or decreased susceptibility to a neoplastic disorder.
  • polypeptides of the invention or their fragments or analogs thereof, or cells expressing them may also be used as immunogens to produce antibodies immuno specific for the de novo DNA cytosine methyltransferase polypeptides.
  • immunospecific is meant that the antibodies have affinities for the polypeptides of the invention that are substantially greater in their affinities for related polypeptides such as the analogous proteins of the prior art.
  • Antibodies generated against the de novo DNA cytosine methyltransferase polypeptides can be obtained by administering the polypeptides or epitope- bearing fragments, analogs or cells to an animal, preferably a nonhuman, using routine protocols.
  • any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler, G. and Milstein, C, Nature
  • antibodies may be employed to isolate or to identify clones expressing the polypeptide or to purify the polypeptides by affinity chromatography.
  • Antibodies against de novo DNA cytosine methyltransferase polypeptides may also be employed to treat neoplastic disorders, among others.
  • the de novo DNA cytosine methyltransferase polypeptides of the present invention may be employed in a screening process for compounds which bind one of the proteins and which activate (agonists) or inhibit activation of (antagonists) one of the polypeptides of the present invention.
  • polypeptides of the invention may also be used to assess the binding of small molecule substrates and ligands in, for example, cells, cell-free preparations, chemical libraries, and natural product mixtures.
  • substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics (see Coligan, et al,
  • agonist is intended naturally occurring and synthetic compounds capable of enhancing a de novo DNA cytosine methyltransferase activity (e.g., increasing the rate of DNA methylation).
  • antagonist is intended naturally occurring and synthetic compounds capable of inhibiting a de novo DNA cytosine methyltransferase activity.
  • DNA methylation is an important, fundamental regulatory mechanism for gene expression, and, therefore, the methylated state of a particular DNA sequence may be associated with many pathologies. Accordingly, it is desirous to find both compounds and drugs which stimulate de novo DNA cytosine methyltransferase activity and which can inhibit the function of de novo DNA cytosine methyltransferase protein.
  • agonists are employed for therapeutic and prophylactic purposes including the treatment of ceratin types of neoplastic disorders.
  • de novo methylation of growth regulatory genes in somatic tissues is associated with tumorigenesis in humans (Laird, P. W. and Jaenisch, R. Ann. Rev. Genet. 50:441-464 (1996); Baylin, S. B. et al, Adv. Cancer. Res. 72:141-196 (1998); and Jones, P. A. and Gonzalgo, M. L. Proc. Natl. Acad. Sci. USA 94:2103-2105 (1997)).
  • Such screening procedures involve producing appropriate cells which express the polypeptide of the present invention.
  • Such cells include cells from mammals, yeast, Drosophila or E. coli.
  • Cells expressing the protein (or cell membrane containing the expressed protein) are then contacted with a test compound to observe binding, stimulation or inhibition of a functional response.
  • the screening procedure may be an in vitro procedure in which the activity of isolated DNMT3 protein is tested in the presence of a potential agonist or antagonist of DNMT3 de novo DNA cytosine methyltransferase activity.
  • in vitro assays are known to those skilled in the art, and by way of example are demonstrated in Example 4.
  • the assays may simply test binding of a candidate compound wherein adherence to the cells bearing the protein is detected by means of a label directly or indirectly associated with the candidate compound or in an assay involving competition with a labeled competitor. Further, these assays may test whether the candidate compound affects activity of the protein, using detection systems appropriate to the cells bearing the protein at their surfaces. Inhibitors of activation are generally assayed in the presence of a known agonist and the effect on activation by the agonist in the presence of the candidate compound is observed. Standard methods for conducting such screening assays are well understood in the art.
  • Examples of potential de novo DNA cytosine methyltransferase protein antagonists include antibodies or, in some cases, oligonucleotides or proteins which are closely related to the substrate of the de novo DNA cytosine methyltransferase protein, e.g., small molecules which bind to the protein so that the activity of the protein is prevented.
  • cystic fibrosis (Drumm, M.L. etal. , Cell (52:1227-1233 (1990); Gregory, R.l. etal, Nature 347:358-363 (1990); Rich, D.P. et al. Nature 347:358-363 (1990)); and Gaucher disease (Sorge, J. et al, Proc. Natl. Acad. Sci. (USA) 54:906-909 (1987); Fink, J.K. et al , Proc. Natl.
  • one or more isolated nucleic acid molecules of the invention are introduced into or administered to the animal.
  • Such isolated nucleic acid molecules may be incorporated into a vector or virion suitable for introducing the nucleic acid molecules into the cells or tissues of the animal to be treated, to form a transfection vector.
  • Techniques for the formation of vectors or virions comprising the de novo DNA cytosine methyltransferase-encoding nucleic acid molecules are well known in the art and are generally described in "Working Toward Human Gene Therapy," Chapter 28 in Recombinant DNA, 2nd Ed.,
  • Example vector systems utilized in the art include the following: retroviruses (Vile, R.G., supra.), adenoviruses (Brody, S.L. et al, Ann. N Y. Acad. Sci. 716: 90-101, (1994)), adenoviral/retroviral chimeras (Bilbao, G., et al, FASEB J. 11(8): 624-634, (1997)), adeno-associated viruses (Flotte, T.R. and Carter, B.J., Gene Ther. 2(6): 357-362, (1995)), herpes simplex virus (Latchman, D.S., Mol
  • Cell 85(1): 1-7, (1995) might be utilized for the introduction of de novo DNA cytosine methyltransferase polynucleotides into target cells; for example, receptor-mediated DNA delivery (Philips, S.C., Biologicals 23(1): 13- 16, (1995)) and lipidic vector systems (Lee, R.J. and Huang, L., Crit. Rev. Ther.
  • vectors comprising the isolated polynucleotides of the present invention are directly introduced into target cells or tissues of the affected animal, preferably by injection, inhalation, ingestion or introduction into a mucous membrane via solution; such an approach is generally referred to as "in vivo" gene therapy.
  • cells, tissues or organs may be removed from the affected animal and placed into culture according to methods that are well-known to one of ordinary skill in the art; the vectors comprising the de novo DNA cytosine methyltransferase polynucleotides may then be introduced into these cells or tissues by any of the methods described generally above for introducing isolated polynucleotides into a cell or tissue, and, after a sufficient amount of time to allow incorporation of the de novo DNA cytosine methyltransferase polynucleotides, the cells or tissues may then be re-inserted into the affected animal. Since the introduction of a de novo DNA cytosine methyltransferase gene is performed outside of the body of the affected animal, this approach is generally referred to as "ex vivo" gene therapy.
  • the isolated de novo DNA cytosine methyltransferase polynucleotides of the invention may alternatively be operatively linked to a regulatory DNA sequence, which may be a de novo DNA cytosine methyltransferase promoter or an enhancer, or a heterologous regulatory DN A sequence such as a promoter or enhancer derived from a different gene, cell or organism, to form a genetic construct as described above.
  • This genetic construct may then be inserted into a vector, which is then used in a gene therapy protocol.
  • the need for transcriptionally targeted and regulatable vectors providing cell-type specific and inducible promoters is well recognized in the art
  • the construct/vector may be introduced into the animal by an in vivo gene therapy approach, e.g., by direct injection into the target tissue, or into the cells or tissues of the affected animal in an ex vivo approach.
  • the genetic construct of the invention may be introduced into the cells or tissues of the animal, either in vivo or ex vivo, in a molecular conjugate with a virus (e.g., an adenovirus or an adeno-associated virus) or viral components (e.g., viral capsid proteins; see WO 93/07283).
  • a virus e.g., an adenovirus or an adeno-associated virus
  • viral components e.g., viral capsid proteins; see WO 93/07283
  • transfected host cells which may be homologous or heterologous, may be encapsulated within a semi-permeable barrier device and implanted into the affected animal, allowing passage of de novo DNA cytosine methyltransferase polypeptides into the tissues and circulation of the animal but preventing contact between the animal's immune system and the transfected cells (see WO 93/09222).
  • Antisense oligonucleotides are short synthetic DNA or RNA nucleotide molecules formulated to be complementary to a specific gene or RNA message.
  • RNA as a target Through the binding of these oligomers to a target DNA or mRNA sequence, transcription or translation of the gene can be selectively blocked and the disease process generated by that gene can be halted (see, for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press (1989)).
  • the cytoplasmic location of mRNA provides a target considered to be readily accessible to antisense oligodeoxynucleotides entering the cell; hence much of the work in the field has focused on RNA as a target.
  • the use of antisense oligodeoxynucleotides provides a useful tool for exploring regulation of gene expression in vitro and in tissue culture (Rothenberg, et al. , J.
  • Antisense therapy is the administration of exogenous oligonucleotides which bind to a target polynucleotide located within the cells.
  • antisense oligonucleotides may be administered systemically for anticancer therapy (Smith, International Application Publication No. WO 90/09180).
  • antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack
  • S-oligos are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom.
  • the S-oligos of the present invention may be prepared by treatment of the corresponding O-oligos with 3H- 1 ,2-benzodithiol-3-one- 1 , 1 -dioxide which is a sulfur transfer reagent. See Iyer et a , J. Org. Chem. 55:4693-4698 (1990); and Iyer et al, J. Am. Chem. Soc. 772:1253-1254 (1990), the disclosures of which are fully incorporated by reference herein.
  • sequence analysis of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3 or the SEQ ID NO:4 cDNA clone shows that sequence that is nonhomologous to known DNA methyltransferase sequences may be identified (see Figures 1 and 4).
  • the antisense oligonucleotides of the present invention may be RNA or DNA that is complementary to and stably hybridize with such sequences that are specific for a de novo DNA cytosine methyltransferase gene of the invention.
  • Use of an oligonucleotide complementary to such regions allows for selective hybridization to a de novo DNA cytosine methyltransferase mRNA and not to an mRNA encoding a maintenance methyltransferase protein.
  • the antisense oligonucleotides of the present invention are a 15 to 30-mer fragment of the antisense DNA molecule coding for unique sequences of the de novo DNA cytosine methyltransferase cDNAs.
  • Preferred antisense oligonucleotides bind to the 5 '-end of the de novo DNA cytosine methyltransferase mRNAs.
  • Such antisense oligonucleotides may be used to down regulate or inhibit expression of the gene.
  • Other criteria that are known in the art may be used to select the antisense oligonucleotides, varying the length or the annealing position in the targeted sequence.
  • compositions comprising an effective amount of at least one of the antisense oligonucleotides of the invention in combination with a pharmaceutically acceptable carrier.
  • a single antisense oligonucleotide is utilized.
  • two antisense oligonucleotides are utilized which are complementary to adjacent regions of the genome.
  • Administration of two antisense oligonucleotides that are complementary to adjacent regions of the genome or corresponding mRNA may allow for more efficient inhibition of genomic transcription or mRNA translation, resulting in more effective inhibition of protein or mRNA production.
  • the antisense oligonucleotide is coadministered with an agent which enhances the uptake of the antisense molecule by the cells.
  • the antisense oligonucleotide may be combined with a lipophilic cationic compound which may be in the form of liposomes.
  • liposomes to introduce nucleotides into cells is taught, for example, in U.S. Patent Nos. 4,897,355 and 4,394,448, the disclosures of which are incorporated by reference in their entirety (see also U.S. Patent Nos. 4,235,871, 4,231,877, 4,224,179, 4,753,788, 4,673,567,4,247,41 1, and 4,814,270 for general methods of preparing liposomes comprising biological materials).
  • the antisense oligonucleotide may be combined with a lipophilic carrier such as any one of a number of sterols including cholesterol, cholate and deoxycholic acid.
  • a preferred sterol is cholesterol.
  • the antisense oligonucleotide may be conjugated to a peptide that is ingested by cells. Examples of useful peptides include peptide hormones, antigens or antibodies, and peptide toxins. By choosing a peptide that is selectively taken up by the targeted tissue or cells, specific delivery of the antisense agent may be effected.
  • the antisense oligonucleotide may be covalently bound via the 5 'OH group by formation of an activated aminoalkyl derivative.
  • the peptide of choice may then be covalently attached to the activated antisense oligonucleotide via an amino and sulfhydryl reactive hetero bifunctional reagent.
  • the latter is bound to a cysteine residue present in the peptide.
  • the peptidyl antisense agent Upon exposure of cells to the antisense oligonucleotide bound to the peptide, the peptidyl antisense agent is endocytosed and the antisense oligonucleotide binds to the target mRNA to inhibit translation (Haralambid et al, WO 8903849 and Lebleu et al., E? 0263740).
  • the antisense oligonucleotides and the pharmaceutical compositions of the present invention may be administered by any means that achieve their intended purpose.
  • administration may be by parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, or transdermal routes.
  • the dosage administered will be dependent upon the age, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired.
  • Compositions within the scope of this invention include all compositions wherein the antisense oligonucleotide is contained in an amount effective to achieve the desired effect, for example, inhibition of proliferation and/or stimulation of differentiation of the subject cancer cells. While individual needs vary, determination of optimal ranges of effective amounts of each component is with the skill of the art.
  • antisense oligonucleotides can be prepared which are designed to interfere with transcription of the gene by binding transcribed regions of duplex DNA (including introns, exons, or both) and forming triple helices (e.g., see Froehler et al, WO 91/06626 or Toole, WO 92/10590).
  • Preferred oligonucleotides for triple helix formation are oligonucleotides which have inverted polarities for at least two regions of the oligonucleotide (Id.).
  • Such oligonucleotides comprise tandem sequences of opposite polarity such as 3 '— 5 '- L-5' — 3 ', or 5' — 3'-L-3' — 5', wherein L represents a 0-10 base oligonucleotide linkage between oligonucleotides.
  • L represents a 0-10 base oligonucleotide linkage between oligonucleotides.
  • the inverted polarity form stabilizes single- stranded oligonucleotides to exonuclease degradation (Froehler et al, supra).
  • triple helix-forming oligonucleotides can be formulated in pharmaceutical preparations for a variety of modes of administration, including systemic or localized administration, as described above.
  • the antisense oligonucleotides of the present invention may be prepared according to any of the methods that are well known to those of ordinary skill in the art, as described above.
  • Ribozymes provide an alternative method to inhibit mRNA function. Ribozymes may be RNA enzymes, self-splicing RNAs, and self-cleaving RNAs (Cech et al, Journal of Biological Chemistry 267:17479-17482 (1992)). It is possible to construct de novo ribozymes which have an endonuclease activity directed in trans to a certain target sequence. Since these ribozymes can act on various sequences, ribozymes can be designed for virtually any RNA substrate. Thus, ribozymes are very flexible tools for inhibiting the expression of specific genes and provide an alternative to antisense constructs.
  • the ribozyme contains three structural domains: 1) a highly conserved region of nucleotides which flank the cleavage site in the 5 ' direction; 2) the highly conserved sequences contained in naturally occurring cleavage domains of ribozymes, forming a base-paired stem; and 3) the regions which flank the cleavage site on both sides and ensure the exact arrangement of the ribozyme in relation to the cleavage site and the cohesion of the substrate and enzyme.
  • RNA enzymes constructed according to this model have already proved suitable in vitro for the specific cleaving of RNA sequences (Haseloff et al, supra).
  • hairpin ribozymes may be used in which the active site is derived from the minus strand of the satellite RNA of tobacco ring spot virus (Hampel et al, Biochemistry 25:4929-4933 (1989)). Recently, a hairpin ribozyme was designed which cleaves human immunodeficiency virus type 1 RNA (Ojwang et ⁇ /., Proc. Natl. Acad. Sci. USA 59:10802-10806 (1992)). Other self-cleaving RNA activities are associated with hepatitis delta virus (Kuo et al,
  • ribozyme molecules of the present invention is designed based upon the chloramphenicol acetyltransferase ribozyme or hai ⁇ in ribozymes, described above.
  • ribozyme molecules are designed as described by Eckstein et al. (International Publication No. WO 92/07065) who disclose catalytically active ribozyme constructions which have increased stability against chemical and enzymatic degradation, and thus are useful as therapeutic agents.
  • an external guide sequence can be constructed for directing the endogenous ribozyme, RNase P, to intracellular mRNA, which is subsequently cleaved by the cellular ribozyme (Altman et al, U.S. Patent No. 5,168,053).
  • the EGS comprises a ten to fifteen nucleotide sequence complementary to an mRNA and a 3'-NCCA nucleotide sequence, wherein N is preferably a purine (Id.).
  • EGS molecules After EGS molecules are delivered to cells, as described below, the molecules bind to the targeted mRNA species by forming base pairs between the mRNA and the complementary EGS sequences, thus promoting cleavage of mRNA by RNase P at the nucleotide at the 5 'side of the base-paired region (Id.).
  • compositions comprising an effective amount of at least one ribozyme or EGS of the invention in combination with a pharmaceutically acceptable carrier.
  • the ribozyme or EGS is coadministered with an agent which enhances the uptake of the ribozyme or EGS molecule by the cells.
  • the ribozyme or EGS may be combined with a lipophilic cationic compound which may be in the form of liposomes, as described above.
  • the ribozyme or EGS may be combined with a lipophilic carrier such as any one of a number of sterols including cholesterol, cholate and deoxycholic acid.
  • a preferred sterol is cholesterol.
  • the ribozyme or EGS, and the pharmaceutical compositions of the present invention may be administered by any means that achieve their intended pu ⁇ ose.
  • administration may be by parenteral, subcutaneous, intravenous, intramuscular, intra-peritoneal, or transdermal routes.
  • the dosage administered will be dependent upon the age, health, and weight of the recipient. kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired.
  • compositions within the scope of this invention include all compositions wherein the ribozyme or EGS is contained in an amount which is effective to achieve inhibition of proliferation and/or stimulate differentiation of the subject cancer cells, or alleviate AD. While individual needs vary, determination of optimal ranges of effective amounts of each component is with the skill of the art.
  • the therapeutic molecules may be administered as part of a pharmaceutical preparation containing suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the antisense oligonucleotide, ribozyme, or EGS into preparations which can be used pharmaceutically.
  • Suitable formulations for parenteral administration include aqueous solutions of the antisense oligonucleotides, ribozymes, EGS in water-soluble form, for example, water-soluble salts.
  • suspensions of the active compounds as appropriate oily injection suspensions may be administered.
  • Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, ethyl oleate or triglycerides.
  • Aqueous injection suspensions may contain substances which increase the viscosity of the suspension include, for example, sodium carboxymethyl cellulose, sorbitol, and/or dextran.
  • the suspension may also contain stabilizers.
  • antisense RNA molecules, ribozymes, and EGS can be coded by DNA constructs which are administered in the form of virions, which are preferably incapable of replicating in vivo (see, for example, Taylor, WO 92/06693).
  • DNA constructs may be administered using he ⁇ es-based viruses (Gage et al, U.S. Patent No. 5,082,670).
  • antisense RNA sequences, ribozymes, and EGS can be coded by RNA constructs which are administered in the form of virions, such as retroviruses.
  • retroviral vectors is well known in the art (see, for example, Brown et al, "Retroviral Vectors," in DNA Cloning: A Practical Approach, Volume 3,
  • Specificity for gene expression may be conferred by using appropriate cell-specific regulatory sequences, such as cell-specific enhancers and promoters.
  • Such regulatory elements are known in the art, and their use enables therapies designed to target specific tissues, such as liver, lung, prostate, kidney, pancreas, etc., or cell populations, such as lymphocytes, neurons, mesenchymal, epithelial, muscle, etc.
  • gene therapeutic applications may be employed to provide expression of the polypeptides of the invention.
  • Example 1 Cloning and Sequence Analysis of the Mouse Dnmt3a and Dnmt3b and the Human DNMT3A and DNMT3B Genes and Polypeptides
  • RT/PCR-based screening using oligonucleotide primers corresponding to the conserved motifs of the known cytosine DNA methyltransferases failed to detect any novel methyltransferase gene from Dnmtl null ES cells (data not shown).
  • the second approach was atblastn search of the dbEST database using full length bacterial cytosine methyltransferase sequences as queries.
  • a search of the dbEST database was performed with the tblastn program (Altschul, S. F. et al, J. Mol. Biol. 275:403-410 (1990)) using bacterial cytosine methyltransferases as queries.
  • Candidate EST sequences were used one by one as queries to search the non-redundant protein sequence database in GenBank with the blastx program. This process would eliminate EST clones corresponding to known genes (including known DNA methyltransferases) and those which show a higher similarity to other sequences than to DNA methyltransferases.
  • Two EST clones (GenBank numbers W7611 1 andN88352) were found after the initial search.
  • Two more EST sequences were later found after a blastn search of dbEST with the EST sequence of W76111 as a query.
  • Two of the EST clones (W761 1 1 and T66356) were deposited by the I.M.A.G.E. Consortium (Lawrence Livermore National Laboratory, Livermore, CA) and obtained from American Type Culture Collection (Manassas, VA). Sequencing of these two cDNA clones revealed that they were partial cDNA clones with large open reading frames corresponding to two related genes. The translated amino acid sequences revealed the presence of the highly conserved motifs characteristic of DNA cytosine methyltransferases. The EST sequences were then used as probes for screening mouse E7.5 embryo and ES cell cDNA libraries and a human heart cDNA library (Clontech, CA).
  • Dnmt2 DNA methyltransferase gene
  • Dnmt3a and Dnmt3b The full length Dnmt3a and Dnmt3b genes encode 908 and 859 amino acid polypeptides, termed Dnmt3a and Dnmt3bl, respectively. Nucleotide and amino acid sequences of each are presented in Figures 1 A, IB, 2 A, and 2B.
  • the Dnmt3b gene also produces through alternative splicing at least two shorter iso forms of 840 and 777 amino acid residues, termed Dnmt3b2 and Dnmt3b3, respectively, (Fig. 4).
  • fetal heart and fetal testis cDNA libraries were screened using EST clones as probes. Sequencing analysis of several overlapping DNMT3A cDNA clones indicates that the DNMT3A gene encodes a polypeptide of 912 amino acid residues.
  • DNMT3B cDNA clones were not detected in the fetal heart library, but several DNMT3B cDNA clones were obtained after screening the fetal testis library.
  • PCR screening of large cDNA clones from 24 human tissues was also performed using the Human Rapid- ScreenTM cDNA Library Panels (OriGene Technologies, MD). The largest cDNA clone contained a 4.2 kb insert from a small intestine cDNA library. Sequencing analysis of overlapping cDNA clones indicated that the deduced full length
  • DMNT3B consists of 853 amino acid residues. Since in-frame stop codons are found upstream of the ATG of both DNMT3 A and DNMT3B, it is concluded that these cDNA clones encode full-length DNMT3A and DNMT3B proteins.
  • DNMT3A and DNMT3B cDNAs encode 912 and 853 amino acid polypeptides, termed DNMT3A and DNMT3B1, respectively.
  • DNMT3B2 comprises amino acid residues 1 to 355 and 376 to 853 of SEQ ID NO:4; and DNMT3B3 comprises amino acid residues 1 to 355 and 376 to 743 and 807 to 853 of SEQ ID NO:4.
  • Zmt-3 zebrafish gene
  • the GenBank STS database was used to map chromosome localization by using DNMT3A and DNMT3B sequences as queries.
  • the results identified markers WI-6283 (GenBank Accession number G06200) and SHGC-15969 (GenBank Accession number G15302), which matched the cDNA sequence of DNMT3A and DNMT3B, respectively.
  • WI-6283 has been mapped to 2p23 between D2S171 and D2S174 (48-50 cM) on the radiation hybrid map by Whitehead Institute/MIT Center for Genome Research. The corresponding mouse chromosome location is at 4.0 cM on chromosome 12.
  • SHGC-15969 has been mapped to 20pl 1.2 between D20S184 and D20S106 (48-50 cM) by Stanford Human Genome Center.
  • the corresponding mouse chromosome locus is at 84.0 cM on chromosome 2.
  • DNMT3A cDNA did not match any related genornic sequences in the database
  • a DNMT3B genomic YAC clone from GenBank (AL035071) was identified when DNMT3B cDNA sequences were used as queries.
  • the DNMT3B cDNA and the genomic DNA GenBank (AL035071) clone were used to map all exons using BESTFIT of the GCG program. As shown in Figure 4C, there are total 23 exons, spanning some 48 kb genomic DNA. The putative first exon is located within a CpG island where the promoter is probably located as predicted by the GENSCAN program (Whitehead/MIT Center for
  • DNMT3B gene structure may facilitate analysis of DNMT3B mutations in certain cancers with characteristic hypomethylation of genomic: DNA (Narayan, A., et al. ,
  • Figure 3A presents an alignment of mouse Dnmt3a and Dnmt3b polypeptide sequences that was accomplished using the GCG program.
  • the vertical lines indicate amino acid identity, while the dots and the colons indicate similarities. Dots in amino acid sequences indicate gaps introduced to maximize alignment. The conserved Cys-rich region is shaded.
  • the full length mouse Dnmt3a and Dnmt3b genes encode 908 and 859 amino acid polypeptides.
  • Dnmt3b2 (76%> identity in the catalytic domain).
  • Dnmt3b3b3b3 also produces at least two shorter isoforms of 840 and 777 amino acid residues, termed Dnmt3b2 and Dnmt3b3, respectively, through alternative splicing (Fig. 4).
  • Figure 3B presents a GCG program alignment using the of the protein sequences of human DNMT3 A and DNMT3B 1. Vertical lines represent identical amino acid residues, whereas dots represent conserved changes. Dots in amino acid sequences indicate gaps introduced to maximize alignment.
  • FIG 4A presents a schematic diagram of the overall protein structures for mouse DnmtX, mouse Dnmt2, a putative methyltransferase, and the family of Dnmt3a and Dnmt3b(l-3) methyltransferases.
  • DnmtX, Dnmt3a and Dnmt3bs all have a putative N-terminal regulatory domain.
  • the filled bars represent the five conserved methyltransferase motifs (I, IV, VI, IX, and X).
  • the shaded boxes in Dnmt3a and Dnmt3bs represent the Cys-rich region that shows no sequence homology to the Cys-rich, Zn 2+ -binding region of DnmtX polypeptide. Sites of alternative splicing at amino acid residues 362-383 and 749- 813 in Dnmt3bs are indicated.
  • FIG. 4B presents a similar schematic of the human DNMT3 proteins and zebrafish Znmt3 protein. The homology between differences between these DNMT3 proteins is indicated by the percentage of sequence identity when compared to DNMT3A.
  • FIG. 4D presents the size of the exons and introns as well as sequences (uppercase for exons and lowercase for introns) at exon/intron boundaries.
  • sequence analysis of the catalytic domain indicates that this new family of DNA methyltransferases contains conserved amino acid residues in each of the five highly conserved motifs, but significant differences are discernible when compared to the known consensus sequences.
  • Figure 5A presents an alignment by ClustalW 1.7 of the amino acid sequences of the five highly conserved motifs in eukaryotic methyltransferase genes. Amino acid residues which are conserved in five or more genes are highlighted. The Dnmt3 family methyltransferases are most closely related to a bacterial DNA methyltransferase (M. Spr.).
  • the cysteine-rich region located upstream of the catalytic domain was found to be conserved among all of the DNMT3 proteins (Fig. 5B). This Cysteine-rich region, however, is unrelated to the Cysteine-rich (or Zn 2" " -binding) region of DNMTl (Bestor, T.H., et al., J. Mo. Biol. 205:971-983 (1998); Bestor, T.H., EMBO J. 77:2611-2617 (1992)).
  • Cysteine-rich domain of DNMT3 proteins shares homology with a similar domain found in the X- linked ATRX gene of the SNF2/SWI family (Picketts, D.J., et al, Hum. Mol. Genet. 5: 1899-1907 (1996)), raising the interesting possibility that this domain may mediate protein-protein or protein-DNA interactions.
  • the evolutionary relatedness of cytosine-5 methyltransferases as shown by a non-rooted phylogenic tree is presented in Figure 5C. Amino acid sequences from motif I to motif VI of bacterial and eukaryotic cytosine-5 methyltransferases were used for sequence alignment, and the alignment data was analyzed by ClustalW 1.7 under conditions excluding positions with gaps.
  • Example 2 Baculovirus-mediated Expression ofDnmt3a andDnmt3b
  • Dnmt3a Dnmt3a, Dnmt3bl , Dnmt3b2, and Dnmtl were overexpressed in insect cells using the baculovirus-mediated expression system (Clontech, CA).
  • the Xma I/Eco Rl fragment of Dnmt3a cDNA was first cloned into the Nco I/Eco Rl sites of pET2 Id with the addition of an Xma I/Nco I adapter (SX165: 5'-
  • pSXl 34 was obtained by cloning the EcoR I/Xba I fragment of pSX 132His into the EcoR I/Xba I sites of pBacPAK9.
  • Sf21 host cells were grown in the SF-900 II SFM medium with 10% of the certified FBS (both from GIBCO, MD) and infected with the recombinant viruses 12-24 hours after the cells were split when they reached 90-95% affluence. After 3 days, the infected insect cells were harvested and frozen in the liquid nitrogen for future use.
  • ES cells were routinely cultured on a feeder layer of mouse embryonic fibroblasts in DMEM medium containing LIF (500 units/ml) and were differentiated as embryoid bodies in suspension culture as described (Lei, H., et al, Development 722:3195-3205 (1996)). Ten days after seeding, embryoid bodies were harvested for RNA preparation. Total RNA was prepared from ES cells, ovary and testis tissue using the
  • GTC-CsCl centrifugation method fractionated on a formaldehyde denaturing 1 % agarose gel by electrophoresis and transferred to a nylon membrane.
  • PolyA+ RNA blots (2 ⁇ g per lane) of mouse and human tissues were obtained from Clontech, CA. All blots were hybridized to random-primed cDNA probes in hybridization solution containing 50% formamide at 42 °C and washed with 0.2 X
  • Fig. 6A presents mouse polyA+ RNA blots of adult tissues (left) and embryos (right) probed with full length Dnmt3a, Dnmt3b and a control ⁇ -actin cDNA probe. Each lane contains 2 ⁇ g of poly A+ RNA.
  • Ht Heart; Br, Brain; Sp, Spleen; Lu, Lung; Li, Liver; Mu, Skeletal Muscle; Ki, Kidney; Te, Testis; and embryos at gestation days 7 (E7), 1 1 (El 1), 15 (E15). and 17 (E17).
  • Fig. 6B is a mouse total RNA blot (10 ⁇ g per lane) of ES cell and adult organ RNA samples and Fig.
  • 6C shows a mouse total RNA blot (20 ⁇ g per lane) of undifferentiated (Undiff.) and differentiated (Diff) ES cells RNA hybridized to Dnmt3a, Dnmt3b or ⁇ -actin probes.
  • Dnmt3b transcript is detected in embryo and adult organ RNAs, with relatively high levels in testes and E 11.5 embryo samples (Fig.6A). Interestingly, both genes are expressed at much higher levels in ES cells than in adult tissues (Fig. 6B), and their expression decreased dramatically upon differentiation of ES cells in culture (Fig. 6C). In addition, Dnmt3a and Dnmt3b expression levels are unaltered in Dnmtl -deficient ES cells (Fig. 6C), suggesting that regulation of Dnmt3a and Dnmt3b expression is independent of Dnmtl.
  • RNA expression analysis of human DNMT3 genes polyA+ RNA blots were hybridized using DNMT3 A and DNMT3B cDNA fragments as probes. Results indicate that DNMT3 A RNA was expressed ubiquitously and was readily detected in most tissues examined at levels slightly lower than DNMT1 RNA (Fig.X). Three major DNMT3A transcripts, approximately 4.0, 4.4, and 9.5 kb, were detected. The relative expression level of the transcripts appeared to vary from tissue to tissue. Transcripts of similar sizes were also detected in mouse tissues.
  • DNMT3 RNA expression was analyzed in several tumor cell lines by Northern blot hybridization. Results demonstrated that DNMT3 A was expressed at higher levels in most tumor cell lines examined. ( Figure 10). As in the normal tissues, three different size transcripts were also detected in tumor cells. The ratio of these transcripts appeared to be variable in different tumor cell lines. DNMT3B expression was dramatically elevated in most tumor cell lines examined though it was expressed at very low levels in normal adult tissues ( Figure 10). The expression levels of both DNMT3A and DNMT3B appear to be comparable and proportional to that of DNMTL The murine Dnmt3a and Dnmt3b genes are highly expressed in undifferentiated ES cells, consistent with their potential role in de novo methylation during early embryonic development.
  • both genes are highly expressed in early embryos. Differences in their expression patterns in adult tissues in both human and mice suggest that each gene may have a distinct function in somatic tissues and may methylate different genes or genomic sequences.
  • the elevated expression of DNMT3 genes in human tumor cell lines suggests that the DNMT3 enzyme may be responsible for de novo methylation of CpG islands in tumor suppressor genes during tumor formation.
  • polypeptides of the invention were expressed and purified from recombinant host cells for use in in vitro assays.
  • Infected insect Sf21 cells and NIH3T3 cells were homogenized by ultrasonication in lysis solution (20 mM Tris-HCl, pH7.4, 10 mM EDTA, 500 mM NaCl, 10% glycerol, ImM DTT, ImM PMSF, 1 ug/ml leupeptin, 10 ug/ml
  • TPCK 10 ug/ml TLCK
  • DNA substrates used in the assays include: poly (dl-dC), poly (dG-dC) (Pharmacia Biotech), lambda phage DNA (Sigma), pBluescriptllSK (Stratagene, CA), pMu3 plasmid, which contains tandem repeats of 535bp Rsal-Rsal fragment of MMLV LTR region in pUC9, and oligonucleotides.
  • the oligonucleotide sequences utilized include: #1 , 5'-AGACMGGTGCCAGMGCAGCTGAGCMGGATC-3', #2, 5'-GATCMGGCTCAGCTGMGCTGGCACMGGTCT-3',
  • Oligonucleotides were synthesized and purified by polyacrylamide gel electrophoresis (PAGE). To make double strand oligonucleotides, equimolar amounts of the two complimentary oligonucleotides were heated at 94°C for 10 min., mixed, incubated at 78°C for 1 hr and cooled down slowly at room temperature. The annealing products were quantified for the yield of double- stranded oligonucleotides (dsDNA) by PAGE and methylene blue staining.
  • dsDNA double- stranded oligonucleotides
  • dsDNA of #1 and #2 were used as 'fully' methylated substrates, dsDNA of #1 and #4 as the hemi -methylated substrates, and dsDNA of #3 and #4 as unmethylated substrates.
  • An MMLV full length cDNA was methylated for 1-5 times by incubation with protein extract from control Sf21 cells or Sf21 cells infected with baculoviruses expressing DnmtX, Dnmt3a or Dnmt3b polypeptides.
  • the Hpa HIMsp I target sequence, CCGG is resistant to the Hpa II restriction enzyme, but sensitive to Msp I digestion when the internal C is methylated, and the restriction site becomes resistant to Msp I digestion when the external C is methylated (Jentsch, S. et al. , Nucleic Acids Res. 9:2753-2759 (1981)).
  • Dnmt3a and Dnmt3b polypeptides could methylate multiple Hpa II sites in the 3' LTR regions of the MMLV DNA, as indicated by the presence of Hpa Il-resistant fragments, though less efficiently than DnmtX polypeptide (Fig.7b).
  • the viral DNA was completely digested by Msp I. This result indicates that both Dnmt3a and Dnmt3b polypeptides methylate predominantly the internal cytosine residues, therefore, CpGs.
  • the same region of the proviral DNA was efficiently methylated in Dnmtl null ES cells infected by the MMLV virus (Lei, H. et al, Development 722:3195-3205 (1996)).
  • Fig. 7A shows 3 H-methyl inco ⁇ oration into different DNA substrates (poly (dl-dC), poly (dG-dC) (squares), lambda phage DNA (circles), pBluescriptllSK (triangles), and pMu3 (diamonds)) when incubated with protein extracts of Sf21 cells expressing Dnmtl, Dnmt3a, or Dnmt3bl .
  • Fig. 7B shows Southern blot analysis of the in vitro methylation of untreated pMMLV DNA
  • DnmtX protein appears to function primarily as a maintenance methyltransferase because of its strong preference for hemimethylated DNA and direct association with newly replicated DNA (Leonhardt, H. et al, Cell 77:865- 873 ( 1992)).
  • Dnmt3a and Dnmt3b polypeptides show any preference for hemimethylated DNA over unmethylated DNA, a comparison was done to examine the methylation rate of unmethylated versus hemimethylated oligonucleotides.

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Abstract

La présente invention concerne, d'une part des polynucléotides ainsi que des polypeptides à cytosine méthyltransférase d'ADN adventif, et d'autre part des procédés de production de ces polypeptides. L'invention concerne également des procédés permettant d'utiliser dans des dosages de diagnostic ces polynucléotides et polypeptides à cytosine méthyltransférase d'ADN adventif, et ce, dans le cadre d'applications à méthylation in vitro de l'ADN et d'applications thérapeutiques telles que le traitement de troubles néoplasiques.
PCT/US1999/014373 1998-06-25 1999-06-25 Genes a cytosine methyltransferase d'adn adventif, polypeptides et leur utilisation Ceased WO1999067397A1 (fr)

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CA002331781A CA2331781C (fr) 1998-06-25 1999-06-25 Genes a cytosine methyltransferase d'adn adventif, polypeptides et leur utilisation
US10/623,813 US7368551B2 (en) 1998-06-25 2003-07-22 De novo DNA cytosine methyltransferase genes, polypeptides and uses thereof
US11/980,427 US20080131901A1 (en) 1998-06-25 2007-10-31 De novo DNA cytosine methyltransferase genes, polypeptides and uses thereof

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EP1384787A1 (fr) * 2002-07-25 2004-01-28 Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts Procédé de criblage pour l'identification et la charactérisation d'inhibiteurs d'ADN méthyltransférase
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US8043835B1 (en) 1996-03-26 2011-10-25 Oncomedx, Inc. Methods for detecting and monitoring cancer using extracellular RNA
US8163524B2 (en) 1998-09-22 2012-04-24 Oncomedx, Inc. Comparative analysis of extracellular RNA species
US8440396B2 (en) 1997-03-14 2013-05-14 Oncomedx, Inc. Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer

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Cited By (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7767423B2 (en) 1996-03-26 2010-08-03 OncoMEDx, Inc Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer
US7785842B2 (en) 1996-03-26 2010-08-31 Oncomedx, Inc. Comparative analysis of extracellular RNA species
US7972817B2 (en) 1996-03-26 2011-07-05 Oncomedx, Inc. Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer
US8030031B2 (en) 1996-03-26 2011-10-04 Oncomedx, Inc. Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer
US8043835B1 (en) 1996-03-26 2011-10-25 Oncomedx, Inc. Methods for detecting and monitoring cancer using extracellular RNA
US8809020B2 (en) 1996-03-26 2014-08-19 Oncomedx, Inc. Method enabling the use of extracellular ribonucleic acid (RNA) extracted from plasma or serum to detect, monitor or evaluate cancer or premalignant conditions
US8440396B2 (en) 1997-03-14 2013-05-14 Oncomedx, Inc. Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer
US7709233B2 (en) 1998-09-22 2010-05-04 Oncomedx, Inc. Method enabling use of extracellular RNA extracted from plasma or serum to detect, monitor or evaluate cancer
US8163524B2 (en) 1998-09-22 2012-04-24 Oncomedx, Inc. Comparative analysis of extracellular RNA species
WO2001027249A1 (fr) * 1999-10-15 2001-04-19 Fit Biotech Oyj Plc Nouveau gene codant une adn methyltransferase dnmt3l
EP1384787A1 (fr) * 2002-07-25 2004-01-28 Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts Procédé de criblage pour l'identification et la charactérisation d'inhibiteurs d'ADN méthyltransférase
US7405287B2 (en) * 2004-08-03 2008-07-29 Board Of Regents, The University Of Texas System Method of treating a cancer

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