US20030044403A1 - Anti-infective therapy - Google Patents

Anti-infective therapy Download PDF

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US20030044403A1
US20030044403A1 US10/005,675 US567501A US2003044403A1 US 20030044403 A1 US20030044403 A1 US 20030044403A1 US 567501 A US567501 A US 567501A US 2003044403 A1 US2003044403 A1 US 2003044403A1
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dnase
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Steven Shak
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Genentech Inc
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • C12N15/71—Expression systems using regulatory sequences derived from the trp-operon
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
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    • C12N2800/00—Nucleic acids vectors
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    • C12N2800/108—Plasmid DNA episomal vectors
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    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/42—Vector systems having a special element relevant for transcription being an intron or intervening sequence for splicing and/or stability of RNA
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    • C12N2840/00—Vectors comprising a special translation-regulating system
    • C12N2840/44—Vectors comprising a special translation-regulating system being a specific part of the splice mechanism, e.g. donor, acceptor

Definitions

  • This invention is a continuation-in-part of U.S. Ser. No. 07/289,958 filed Dec. 23, 1988.
  • This invention relates to new methods for making deoxyribonuclease (DNase), especially human DNase, and to nucleic acid encoding DNase.
  • DNase deoxyribonuclease
  • DNase is a phosphodiesterase capable of hydrolyzing polydeoxyribonucleic acid. It acts to extensively and non-specifically degrade DNA and in this regard is distinguished from the relatively limited and sequence-specific restriction endonucleases.
  • This invention is concerned principally with DNase I and II.
  • DNase I has a pH optimum near neutrality, an obligatory requirement for divalent cations, and produces 5′-phosphate nucleotides on hydrolysis of DNA.
  • DNase II exhibits an acid pH optimum, can be activated by divalent cations and produces 3′-phosphate nucleotides on hydrolysis of DNA. Multiple molecular forms of DNase I and II also are known.
  • DNase from various species has been purified to varying degree.
  • Bovine DNase A, B, C, and D was purified and completely sequenced as early as 1973 (Liao et al., J. Biol. Chem. 248:1489 [1973]; Salnikow et al., J. Biol. Chem. 248:1499 [1973]; Liao et al., J. Biol. Chem. 249:2354 [1973]).
  • Porcine and ovine DNase have been purified and fully sequenced (Paudel et al., J. Biol. Chem. 261:16006 [1986] and Paudel et al., J. Biol. Chem.
  • DNase finds a number of known utilities, and has been used for therapeutic purposes. Its principal therapeutic use has been to reduce the viscosity of pulmonary secretions in such diseases as pneumonia, thereby aiding in the clearing of respiratory airways. Obstruction of airways by secretions can cause respiratory distress, and in some cases, can lead to respiratory failure and death. Bovine pancreatic DNase has been sold under the tradename Dornavac (Merck), but this product was withdrawn from the market. Reports indicate that this product had some clinical efficacy. However, although some clinicians observed no significant side effects (Lieberman, JAMA 205:312 [1968]), others noted serious complications such as pulmonary irritation and anaphylaxis (Raskin, Am. Rev. Resp.
  • a further object is to enable the preparation of DNase having variant amino acid sequences or glycosylation not otherwise found in nature, as well as other derivatives of DNase, having improved properties including enhanced specific activity.
  • the objects of this invention have been accomplished by a method comprising providing nucleic acid encoding human DNase; transforming a host cell with the nucleic acid; culturing the host cell to allow DNase to accumulate in the culture; and recovering DNase from the culture.
  • a full length clone encoding human DNase has been identified and recovered, and moreover this DNA is readily expressed by recombinant host cells.
  • the mammalian DNase is full-length, mature human DNase, having the amino acid sequence of native human DNase, its naturally occurring alleles, or predetermined amino acid sequence or glycosylation variants thereof.
  • the nucleic acid encoding the DNase preferably encodes a preprotein which is processed and secreted from host cells, particularly mammalian cells.
  • FIG. 1 depicts the amino acid and DNA sequence of human DNase.
  • the native signal sequence is underlined, the potential initiation codons are circled, and the mature sequence is bracketed.
  • FIG. 2 shows a comparison between the amino acid sequence for mature human (hDNase) and bovine (bDNase) DNase. Asterisks denominate exact homology, periods designate conserved substitutions.
  • FIG. 3 shows the construction of the expression vectors pRK.DNase.3 and pSVe.DNase.
  • FIG. 4 shows the construction of the expression vector pSVI.DNase that contains the splice unit of the pRK5 vector without any modifications.
  • FIG. 5 shows the construction of the expression vectors pSVI12.DNase, pSVI3.DNase, pSVI5.DNase, and pSV16b.DNase containing the modifications in the splice unit and surrounding DNA.
  • FIG. 6 shows the complete nucleotide sequence of pSVI.DNase up to, but not including, the coding region of DNase.
  • FIG. 7 shows the complete nucleotide sequence of pSVI2.DNase up to, but not including, the coding region of DNase.
  • FIG. 8 shows the complete nucleotide sequence of pSVI3.DNase up to, but not including, the coding region of DNase.
  • FIG. 9 shows the complete nucleotide sequence of pSVI5.DNase up to, but not including, the coding region of DNase.
  • FIG. 10 shows the complete nucleotide sequence of pSVI6B.DNase up to, but not including, the coding region of DNase.
  • FIG. 11 shows a schematic representation of the splice unit nucleotide sequences involved in the preparation of the vectors of this example, i.e., SVI, SVI2, SVI3, SVI5, and SVI6B.
  • the boxes represent changes from the SVI sequence, the double underlining is a spurious ATG codon, the underlining shows spurious splice sites and added or changed branchpoint sequence (BPS) regions, the breaks in sequence represent deletions of the nucleotides for SVI3-SVI5, the “ . . . ” designation indicates sequence not shown, and the carets indicate the 5′ and 3′ cleavage sites within the splice donor and splice acceptor, respectively, of the splice unit.
  • BPS branchpoint sequence
  • Human DNase is defined as a polypeptide having the amino acid sequence of FIG. 1 together with amino acid sequence variants thereof which retain the qualitative enzymatic activity of DNase.
  • the variants are not immunogenic in humans.
  • Variants may possess greater enzymatic activity, enhanced resistance to inhibition (in particular by actin), improved solubility, or may be expressed at higher levels by host cells.
  • Amino acid sequence variants of DNase fall into one or more of three classes: Substitutional, insertional or deletional variants. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the DNase, by which DNA encoding the variant is obtained, and thereafter expressing the DNA in recombinant cell culture. However, variant DNase fragments having up to about 100-150 residues may be prepared conveniently by in vitro synthesis.
  • the amino acid sequence variants of human DNase are predetermined or are naturally occurring alleles.
  • bovine pancreatic DNase is found naturally as 4 molecular variants which possess the same enzymatic activity but differ in glycosylation pattern or substitution at the amino acid level.
  • human DNase is found naturally with an arginine or a glutamine residue at amino acid 222.
  • the variants typically exhibit the same qualitative biological activity as the naturally-occurring analogue.
  • sequences of naturally occurring bovine, porcine or ovine DNase are the sequences of naturally occurring bovine, porcine or ovine DNase.
  • the site for introducing an amino acid sequence variation is predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, saturation mutagenesis is introduced at the target codon or region and the DNase variants then screened for the optimal combination of desired activity.
  • Amino acid substitutions are typically introduced for single residues; insertions usually will-be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct. Obviously, the mutations that will be made in the DNA encoding the variant DNase must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure (EP 75,444A).
  • Substitutional variants are those in which at least one residue in the FIG. 1 sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Table 1 when it is desired to finely modulate the characteristics of DNase.
  • substitutions that are less conservative than those in Table 1, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain.
  • the substitutions which in general are expected to produce the greatest changes in DNase properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g.
  • leucyl isoleucyl, phenylalanyl, valyl or alanyl
  • a cysteine or proline is substituted for (or by) any other residue
  • a residue having an electropositive side chain e.g., lysyl, arginyl, or histidyl
  • an electronegative residue e.g., glutamyl or aspartyl
  • a residue having a bulky side chain e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.
  • sequence variation is introduced into residues 6-10, 41-43, 77-79, 110-112, 167-171, 250-253, 73, 93, 157, 149, 185, 187, 198, 17-20, 105-108 and 131-139.
  • the variants represent conservative substitutions. It will be understood that some variants may exhibit reduced or absent hydrolytic activity. These variants nonetheless are useful as standards in immunoassays for DNase so long as they retain at least one immune epitope of native human DNase.
  • Glycosylation variants are included within the scope of human DNase. Included are unglycosylated amino acid sequence variants, unglycosylated DNase having the native, unmodified amino acid sequence of DNase, and glycosylation variants. For example, substitutional or deletional mutagenesis is employed to eliminate the N-linked glycosylation sites of human DNase found at residues 18 and 106, e.g., the asparagine residue is deleted or substituted for by another basic residue such as lysine or histidine. Alternatively, flanking residues making up the glycosylation site are substituted or deleted, even though the asparagine residues remain unchanged, in order to prevent glycosylation by eliminating the glycosylation recognition site.
  • Unglycosylated DNase which has the amino acid sequence of native human DNase is produced in recombinant prokaryotic cell culture because prokaryotes are incapable of introducing glycosylation into polypeptides.
  • glycosylation variants may be generated by adding potential N-linked glycosylation sites through inserting (either by amino acid substitution or deletion) consensus sequences for N-linked glycosylation: Asn-X-Ser or Asn-X-Thr.
  • Glycosylation variants may be generated by both eliminating the N-linked glycosylation sites at residues 18 and 106 and by adding new ones.
  • Glycosylation variants i.e., glycosylation which is different from that of human pancreatic or urinary DNase, are produced by selecting appropriate host cells or by in vitro methods.
  • Yeast for example, introduce glycosylation which varies significantly from that of mammalian systems.
  • mammalian cells having a different species e.g. hamster, murine, insect, porcine, bovine or ovine
  • tissue origin e.g.
  • lung, liver, lymphoid, mesenchymal or epidermal than the source of the DNase are screened for the ability to introduce variant glycosylation as characterized for example by elevated levels of mannose or variant ratios of mannose, fucose, sialic acid, and other sugars typically found in mammalian glycoproteins.
  • mammalian or yeast cells which possess mutations with respect to glycosylation phenotype may be identified, selected for following mutation, or constructed and utilized to produce DNase.
  • In vitro processing of DNase typically is accomplished by enzymatic hydrolysis, e.g. neuramimidase or endoglycosydase H digestion.
  • Insertional amino acid sequence variants of DNases are those in which one or more amino acid residues are introduced into a predetermined site in the target DNase and which displace the preexisting residues. Most commonly, insertional variants are fusions of heterologous proteins or polypeptides to the amino or carboxyl terminus of DNase. DNase derivatives which are immunogenic in humans are not preferred, e.g. those which are made by fusing an immunogenic polypeptide to DNase by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding immunogenic fusions such as lacZ. For this reason, the typical insertional variants contemplated herein are the signal sequence variants described above.
  • Covalent modifications of the DNase molecule are included within the scope hereof. Such modifications are introduced by reacting targeted amino acid residues of the recovered protein with an organic derivatizing agent that is capable of reacting with selected side chains or terminal residues, or by harnessing mechanisms of post-translational modification that function in selected recombinant host cells. The resulting covalent derivatives are useful in programs directed at identifying residues important for biological activity, for immunoassays of DNase or for the preparation of anti-human DNase antibodies for immunoaffinity purification of recombinant DNase.
  • Cysteinyl residues most commonly are reacted with ⁇ -haloacetates (and corresponding amines), such as chloracetic acid or chloroacetamide to give carboxymethyl or carboxamidomethyl derivatives. Cysteinyl residues also are derivatized by reaction with bromotrifluoroacetone, ⁇ -bromo- ⁇ -(5-imidozoyl) propionic acid, chloroacetol phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyl disulfide, p-chloromercuribenzoate, 2-chloromercuri-4-nitrophenol or chloro-nitrobenzo-2-oxa-1,3-diazole.
  • Histidyl residues preferably are derivatized by reaction with diethylpyrocarbonate at pH 5.5 to 7.0 because this agent is relatively specific for the histidyl side chain.
  • Para-bromo-phenacyl bromide also is useful; the reaction should be performed in 0.1M sodium cacodylate at pH 6.0.
  • Lysinyl and amino terminal residues are reacted with succinic or other carboxylic acid anhydrides. Derivatization with these agents has the effect of reversing the charge of the lysinyl residues.
  • Other suitable reagents for derivatizing a amino-containing residues include imidoesters such as methyl picolinimidate; pyridoxal phosphate; pyridoxal; cloroborohydride; trinitrobenzenesulfonic acid; O-methylisourea; 2,4-pentanedione; and transaminase-catalyzed reaction with glyoxylate.
  • Arginyl residues are modified by reaction with one of several conventional reagents, among them phenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residues requires that the reaction be performed in alkaline conditions because of the high pKa of the guanidine functional group. Furthermore, these reagents may react with the groups of lysine as well as the arginine ⁇ -amino group.
  • Carboxyl side groups are selectively modified by reaction with carbodiimides (R′—N ⁇ C ⁇ N—R′) such as 1-cyclohexyl-3-(2-morpholinyl-(4)-ethyl) carbodiimide or 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)-carbodiimide.
  • carbodiimides R′—N ⁇ C ⁇ N—R′
  • carbodiimides Rosinyl or glutamyl
  • aspartyl and glutamyl residues are converted to asparaginyl and glutaminyl residues by reaction with ammonium ions, this being an alternative to mutating the nucleic acid to encode asparagine are glutamine.
  • Derivatization with bifunctional agents is useful for preparing intermolecular aggregates of the protein with immunogenic polypeptides as well as for cross-linking the protein to a water insoluble support matrix or surface for use in the assay or affinity purification of antibody.
  • a study of intrachain cross-links will provide direct information on conformational structure.
  • cross-linking agents include 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example esters with 4-azidosalicylic acid, homobifunctional imidoesters including disuccinimidyl esters such as 3,3′-dithiobis (succinimidyl-propionate), and bifunctional maleimides such as bis-N-maleimido-1,8-octane.
  • Derivatizing agents such as methyl-3-[(p-azido-phenyl)dithio] propioimidate yield photoactivatable intermediates which are capable of forming cross-links an the presence of light.
  • reactive water insoluble matrices such as cyanogen bromide activated carbohydrates and the reactive substrates described in U.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537 and 4,330,440 are employed for protein immobilization.
  • Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and aspartyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Either form of these residues falls within the scope of this invention.
  • Nonproteinaceous polymer ordinarily is a hydrophilic synthetic polymer, i.e., a polymer not otherwise found in nature.
  • hydrophilic polyvinyl polymers fall within the scope of this invention, e.g. polyvinylalcohol and polyvinylpyrrolidone.
  • polyalkylene ethers such as polyethylene glycol, polypropylene glycol, polyoxyethylene esters or methoxy polyethylene glycol
  • polyoxyalkylenes such as polyoxyethylene, polyoxypropylene, and block copolymers of polyoxyethylene and polyoxypropylene (Pluronics); polymethacrylates; carbomers; branched or unbranched polysaccharides which comprise the saccharide monomers D-mannose, D- and L-galactose, fucose, fructose, D-xylose, L-arabinose, D-glucuronic acid, sialic acid, D-galacturonic acid, D-mannuronic acid (e.g.
  • polymannuronic acid or alginic acid
  • D-glucosamine D-galactosamine
  • D-glucose and neuraminic acid including homopolysaccharides and heteropolysaccharides such as lactose, amylopectin, starch, hydroxyethyl starch, amylose, dextran sulfate, dextran, dextrins, glycogen, or the polysaccharide subunit of acid mucopolysaccharides, e.g. hyaluronic acid; polymers of sugar alcohols such as polysorbitol and polymannitol; and heparin or heparon.
  • the site of substitution may be located at other than a native N or O-linked glycosylation site wherein an additional or substitute N or O-linked site has been introduced into the molecule.
  • Mixtures of such polymers are employed, or the polymer may be homogeneous.
  • the polymer prior to crosslinking need not be, but preferably is, water soluble, but the final conjugate must be water soluble.
  • the polymer should not be highly immunogenic in the conjugate form, nor should it possess viscosity that is incompatible with intravenous infusion or injection if it is intended to be administered by such routes.
  • the polymer contains only a single group which is reactive. This helps to avoid cross-linking of protein molecules. However, it is within the scope herein to optimize reaction conditions to reduce cross-linking, or to purify the reaction products through gel filtration or chromatographic sieves to recover substantially homogeneous derivatives.
  • the molecular weight of the polymer ranges about from 100 to 500,000, and preferably is about from 1,000 to 20,000.
  • the molecular weight chosen will depend upon the nature of the polymer and the degree of substitution. In general, the greater the hydrophilicity of the polymer and the greater the degree of substitution, the lower the molecular weight that can be employed. Optimal molecular weights will be determined by routine experimentation.
  • the polymer generally is covalently linked to the polypeptide herein through a multifunctional crosslinking agent which reacts with the polymer and one or more amino acid or sugar residues of the protein.
  • a multifunctional crosslinking agent which reacts with the polymer and one or more amino acid or sugar residues of the protein.
  • directly crosslink the polymer by reacting a derivatized polymer with the protein, or vice versa.
  • the covalent crosslinking site on the polypeptide includes the N-terminal amino group and epsilon amino groups found on lysine residues, as well as other amino, imino, carboxyl, sulfhydryl, hydroxyl or other hydrophilic groups.
  • the polymer may be covalently bonded directly to the protein without the use of a multifunctional (ordinarily bifunctional) crosslinking agent.
  • crosslinking agents examples include 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example esters with 4-azidosalicylic acid, homobifunctional imidoesters including disuccinimidyl esters such as 3,3′-dithiobis (succinimidyl-propionate), and bifunctional maleimides such as bis-N-maleimido-1,8-octane.
  • Derivatizing agents such as methyl-3-[(p-azido-phenyl)dithio] propioimidate yield photoactivatable intermediates which are capable of forming cross-links in the presence of light.
  • reactive water soluble matrices such as cyanogen bromide activated carbohydrates and the systems described in U.S. Pat. Nos. 3,959,080; 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537; 4,055,635 and 4,330,440 are suitably modified for cross-linking.
  • Covalent bonding to amino groups is accomplished by known chemistries based upon cyanuric chloride, carbonyl diimidazole, aldehyde reactive groups (PEG alkoxide plus diethyl acetal of bromoacetaldehyde; PEG plus DMSO and acetic anhydride, or PEG chloride plus the phenoxide of 4-hydroxybenzaldehyde, succinimidyl active esters, activated dithiocarbonate PEG, 2,4,5-trichlorophenylchloroformate or p-nitrophenylchloroformate activated PEG.
  • Carboxyl groups are derivatized by coupling PEG-amine using carbodiimide.
  • Polymers are conjugated to oligosaccharide groups by oxidation using chemicals, e.g. metaperiodate, or enzymes, e.g. glucose or galactose oxidase, (either of which produces the aldehyde derivative of the carbohydrate), followed by reaction with hydrazide or amino-derivatized polymers, in the same fashion as is described by Heitzmann et al., P.N.A.S., 71:3537-3541 (1974) or Bayer et al., Methods in Enzymology, 62:310 (1979), for the labeling of oligosaccharides with biotin or avidin.
  • chemicals e.g. metaperiodate
  • enzymes e.g. glucose or galactose oxidase, (either of which produces the aldehyde derivative of the carbohydrate)
  • hydrazide or amino-derivatized polymers in the same fashion as is described by Heitzmann e
  • oligosaccharides are particularly advantageous because, in general, there are fewer substitutions than amino acid sites for derivatization, and the oligosaccharide products thus will be more homogeneous.
  • the oligosaccharide substituents also are optionally modified by enzyme digestion to remove sugars, e.g. by neuramimidase digestion, prior to polymer derivatization.
  • the polymer will bear a group which is directly reactive with an amino acid side chain, or the N- or C-terminus of the polypeptide herein, or which is reactive with the multifunctional cross-linking agent.
  • polymers bearing such reactive groups are known for the preparation of immobilized proteins.
  • chemistries here one should employ a water soluble polymer otherwise derivatized in the same fashion as insoluble polymers heretofore employed for protein immobilization. Cyanogen bromide activation is a particularly useful procedure to employ in crosslinking polysaccharides.
  • Water soluble in reference to the polymer conjugate means that the conjugate is soluble in physiological fluids such as blood in an amount which is sufficient to achieve a therapeutically effective concentration.
  • Water soluble in reference to the starting polymer means that the polymer or its reactive intermediate used for conjugation is sufficiently water soluble to participate in a derivatization reaction.
  • the degree of substitution with polymer will vary depending upon the number of reactive sites on the protein, whether all or a fragment of protein is used, whether the protein is a fusion with a heterologous protein, the molecular weight, hydrophilicity and other characteristics of the polymer, and the particular protein derivatization sites chosen.
  • the conjugate contains about from 1 to 10 polymer molecules, while any heterologous sequence may be substituted with an essentially unlimited number of polymer molecules so long as the desired activity is not significantly adversely affected.
  • the optimal degree of crosslinking is easily determined by an experimental matrix in which the time, temperature and other reaction conditions are varied to change the degree of substitution, after which the ability of the conjugates to function in the desired fashion is determined.
  • the polymer e.g. PEG
  • PEG polymer
  • Cyanuric chloride chemistry leads to many side reactions, including protein cross-linking. In addition, it may be particularly likely to lead to inactivation of proteins containing sulfhydryl groups.
  • Carbonyl diimidazole chemistry (Beauchamp et al., “Anal. Biochem.” 131:25-33 [1983]) requires high pH (>8.5), which can inactivate proteins.
  • conjugates of this invention are separated from unreacted starting materials by gel filtration. Heterologous species of the conjugates are purified from one another in the same fashion.
  • the polymer also may be water insoluble, as a hydrophilic gel or a shaped article. Particularly useful are polymers comprised by surgical tubing such as catheters or drainage conduits.
  • DNA encoding human DNase is synthesized by in vitro methods or is obtained readily from human pancreatic cDNA libraries. Since FIG. 1 gives the entire DNA sequence for human DNase, one needs only to conduct hybridization screening with labelled DNA encoding human DNase or fragments thereof (usually, greater than about 50 bp) in order to detect clones in the cDNA libraries which contain homologous sequences, followed by analyzing the clones by restriction enzyme analysis and nucleic acid sequencing to identify full-length clones. If full length clones are not present in the library, then appropriate fragments may be recovered from the various clones and ligated at restriction sites common to the fragments to assemble a full-length clone. DNA encoding DNase from other animal species is obtained by probing libraries from such species with the human sequence, or by synthesizing the genes in vitro (for bovine, porcine or ovine DNase).
  • nucleic acid probes which are capable of hybridizing under high stringency conditions to the cDNA of human DNase or to the genomic gene for human DNase (including introns and 5′ or 3′ flanking regions extending to the adjacent genes or about 5,000 bp, whichever is greater).
  • Identification of the genomic DNA for DNase is a straight-forward matter of probing a human genomic library with the cDNA or its fragments which have been labelled with a detectable group, e.g. radiophosphorus, and recovering clone(s) containing the gene. The complete gene is pieced together by “walking” if necessary.
  • the probes do not encode bovine, ovine or porcine DNase, and they range about from 10 to 100 bp in length.
  • prokaryotes are used for cloning of DNA sequences in constructing the vectors useful in the invention.
  • E. coli K12 strain 294 ATCC No. 31446
  • Other microbial strains which may be used include E. coli B and E. coli X1776 (ATCC No. 31537). These examples are illustrative rather than limiting.
  • in vitro methods of cloning e.g., PCR, are suitable.
  • DNase is expressed directly in recombinant cell culture as an N-terminal methionyl analogue, or as a fusion with a polypeptide heterologous to human DNase, preferably a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the DNase.
  • a polypeptide heterologous to human DNase preferably a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the DNase.
  • the native DNase signal is employed with hosts that recognize the human signal.
  • the host signal peptidase is capable of cleaving a fusion of the leader polypeptide fused at its C-terminus to the desired mature DNase.
  • the signal is substituted by a prokaryotic signal selected for example from the group of the alkaline phosphatase, penicillinase, lpp or heat stable enterotoxin II leaders.
  • a prokaryotic signal selected for example from the group of the alkaline phosphatase, penicillinase, lpp or heat stable enterotoxin II leaders.
  • yeast secretion the human DNase signal may be substituted by the yeast invertase, alpha factor or acid phosphatase leaders.
  • the native signal is satisfactory, although other mammalian secretory protein signals are suitable, as are viral secretory leaders, for example the herpes simplex gD signal.
  • DNase is expressed in any host cell, but preferably is synthesized in mammalian hosts. However, host cells from prokaryotes, fungi, yeast, pichia, insects and the like are also are used for expression. Exemplary prokaryotes are the strains suitable for cloning as well as E. coli W3110 (F ⁇ , ⁇ ⁇ prototrophic, ATTC No. 27325), other enterobacteriaceae such as Serratia marcescans , bacilli and various pseudomonads. Preferably the host cell should secrete minimal amounts of proteolytic enzymes.
  • Expression hosts typically are transformed with DNA encoding human DNase which has been ligated into an expression vector. Such vectors ordinarily carry a replication site (although this is not necessary where chromosomal integration will occur). It is presently preferred to utilize an expression vector as described in Example 4 below, where the vector contains a splice-donor-intron-splice-acceptor sequence or unit.
  • Expression vectors also include marker sequences which are capable of providing phenotypic selection in transformed cells.
  • E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species (Bolivar, et al., Gene 2: 95 [1977]).
  • pBR322 contains genes for ampicillin and tetracycline resistance and thus provides easy means for identifying transformed cells, whether for purposes of cloning or expression.
  • Expression vectors also optimally will contain sequences which are useful for the control of transcription and translation, e.g., promoters and Shine-Dalgarno sequences (for prokaryotes) or promoters and enhancers (for mammalian cells).
  • the promoters may be, but need not be, inducible; surprisingly, even powerful constitutive promoters such as the CMV promoter for mammalian hosts have been found to produce DNase without host cell toxicity. While it is conceivable that expression vectors need not contain any expression control, replicative sequences or selection genes, their absence may hamper the identification of DNase transformants and the achievement of high level DNase expression.
  • Promoters suitable for use with prokaryotic hosts illustratively include the ⁇ -lactamase and lactose promoter systems (Chang et al., “Nature”, 275: 615 [1978]; and Goeddel et al., “Nature” 281: 544 [1979]), alkaline phosphatase, the tryptophan (trp) promoter system (Goeddel “Nucleic Acids Res.” 8: 4057 [1980] and EPO Appln. Publ. No. 36,776) and hybrid promoters such as the tac promoter (H. de Boer et al., “Proc. Natl. Acad. Sci.
  • Saccharomyces cerevisiae is the most commonly used eukaryotic microorganism, although a number of other strains are commonly available. Strains of Saccharomyces cerevisiae having the identifying characteristics of strain AB107-30(4)-VN#2 (ATCC Accession No. 20937), particularly its resistance to 4M orthovanadate, is particularly suitable for DNase expression (see U.S. Ser. No. 07/343,863, filed Apr. 26, 1989, specifically incorporated by reference).
  • VN#2 strain it is desirable to stably transform the cells with a high-copy-number plasmid derived from a yeast 2-micron plasmid, id.
  • the plasmid YRp7 is a satisfactory expression vector in yeast (Stinchcomb, et al., Nature 282: 39 [1979]; Kingsman et al., Gene 7: 141 [1979]; Tschemper et al. , Gene 10: 157 [1980]).
  • This plasmid already contains the trp1 gene which provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example ATCC no.
  • Suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase (Hitzeman et al., “J. Biol. Chem.” 255: 2073 [1980]) or other glycolytic enzymes (Hess et al., “J. Adv.
  • enolase such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphogluco
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in R. Hitzeman et al., European Patent Publication No. 73,657A.
  • Expression control sequences are known for eukaryotes. Virtually all eukaryotic genes have an AT-rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a CXCAAT region where X may be any nucleotide. At the 3′ end of most eukaryotic genes is an AATAAA sequence which may be the signal for addition of the poly A tail to the 3′ end of the coding sequence. All of these sequences may be inserted into mammalian expression vectors.
  • Suitable promoters for controlling transcription from vectors in mammalian host cells are readily obtained from various sources, for example, the genomes of viruses such as polyoma virus, SV40, adenovirus, MMV (steroid inducible), retroviruses (e.g. the LTR of HIV), hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. the beta actin promoter.
  • the early and late promoters of SV40 are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication. Fiers et al., Nature, 273: 113 (1978).
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment. Greenaway, P. J. et al., Gene 18: 355-360 (1982).
  • Enhancers are cis-acting elements of DNA, usually about from 10-300 bp, that act on a promoter to increase its transcription. Enhancers are relatively orientation and position independent having been found 5′ (Laimins, L. et al., PNAS 78: 993 [1981]) and 3′ (Lusky, M. L., et al., Mol. Cell Bio. 3: 1108 [1983]) to the transcription unit, within an intron (Banerji, J. L.
  • enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • Expression vectors used in eukaryotic host cells will also contain sequences necessary for the termination of transcription which may affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding DNase. The 3′ untranslated regions also include transcription termination sites.
  • Expression vectors may contain a selection gene, also termed a selectable marker.
  • selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase (TK) or neomycin.
  • DHFR dihydrofolate reductase
  • TK thymidine kinase
  • neomycin neomycin
  • These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media.
  • An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which are successfully transformed with a heterologous gene express a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs neomycin (Southern et al. , J. Molec. Appl. Genet. 1: 327 (1982)), mycophenolic acid (Mulligan et al. , Science 209: 1422 (1980)) or hygromycin (Sugden et al., Mol. Cell. Biol. 5: 410-413 (1985)). The three examples given above employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively.
  • Suitable eukaryotic host cells for expressing human DNase include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham, F. L. et al ., J. Gen Virol. 36: 59 [1977]); baby hamster kidney cells (BHK, ATCC CCL 10); chinese hamster ovary-cells-DHFR (CHO, Urlaub and Chasin, PNAS (USA) 77: 4216, [1980]); mouse sertoli cells (TM4, Mather, J. P., Biol. Reprod.
  • monkey kidney cells (CV1 ATCC CCL 70); african green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); and, TR1 cells (Mather, J. P. et al., Annals N.Y. Acad. Sci. 383: 44-68 [1982]).
  • Plasmids containing the desired coding and control sequences employ standard ligation techniques. Isolated plasmids or DNA fragments are cleaved, tailored, and religated in the form desired to form the plasmids required.
  • the ligation mixtures are used to transform E. coli K12 strain 294 (ATCC 31446) and successful transformants selected by ampicillin or tetracycline resistance where appropriate. Plasmids from the transformants are prepared, analyzed by restriction and/or sequenced by the method of Messing et al., Nucleic Acids Res. 9: 309 (1981) or by the method of Maxam et al., Methods in Enzymology 65: 499 (1980).
  • Host cells are transformed with the expression vectors of this invention and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants or amplifying the DNase gene.
  • the culture conditions such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
  • Transformation means introducing DNA into an organism so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integration.
  • the method used herein for transformation of the host cells is the method of Graham, F. and van der Eb, A., Virology 52: 456-457 (1973).
  • other methods for introducing DNA into cells such as by nuclear injection or by protoplast fusion may also be used.
  • the preferred method of transfection is calcium treatment using calcium chloride as described by Cohen, F. N. et al., Proc. Natl. Acad. Sci. (USA), 69: 2110 (1972).
  • Transfection refers to the introduction of DNA into a host cell whether or not any coding sequences are ultimately expressed. Numerous methods of transfection are known to the ordinarily skilled artisan, for example, CaPO 4 and electroporation. Transformation of the host cell is the indicia of successful transfection.
  • DNase is recovered and purified from recombinant cell cultures by methods used heretofore with human, bovine, ovine, or porcine DNase, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography (e.g. using DNA or nucleotides on a solid support), hydroxyapatite chromatography and lectin chromatography. Moreover, reverse-phase HPLC and chromatography using anti-DNase antibodies are useful for the purification of DNase. As noted previously, (Price et al. , J. Biol. Chem.
  • DNase may be purified in the presence of a protease inhibitor such as PMSF.
  • Human DNase is placed into therapeutic formulations together with required cofactors, and optionally is administered in the same fashion as has been the case for animal DNase such as bovine pancreatic DNase.
  • the formulation of DNase may be liquid, and is preferably an isotonic salt solution such as 150 mM sodium chloride, containing 1.0 mM calcium at pH 7.
  • the concentration of sodium chloride may range from 75-250 mM.
  • the concentration of calcium may range from 0.01-5 mM, and other divalent cations which stabilize DNase may be included or substituted for calcium.
  • the pH may range from 5.5-9.0, and buffers compatible with the included divalent cation may also be utilized.
  • the formulation may be lyophilized powder, also containing calcium.
  • nebulizers for liquid formulations, including jet nebulizers and ultrasonic nebulizers are useful for administration.
  • Liquid formulations may be directly nebulized and lyophilized power nebulized after reconstitution.
  • DNase may be aerosolized using a fluorocarbon formulation and a metered dose inhaler, or inhaled as a lyophilized and milled powder.
  • the liquid formulation of DNase may be directly instilled in the nasotracheal or endotracheal tubes in intubated patients.
  • the purified DNase is employed for enzymatic alteration of the visco-elasticity or the stickiness of mucous.
  • Human DNase is particularly useful for the treatment of patients with pulmonary disease who have abnormal, viscous or inspissated purulent secretions in conditions such as acute or chronic bronchopulmonary disease (infectious pneumonia, bronchitis or tracheobronchitis, bronchiectasis, cystic fibrosis, asthma, TB or fungal infections), atelectasis due to tracheal or bronchial impaction, and complications of tracheostomy.
  • a solution or finely divided dry preparation of human DNase is instilled in conventional fashion into the bronchi, e.g.
  • DNase Human DNase is also useful for adjunctive treatment for improved management of abscesses or severe closed-space infections in conditions such as empyema, meningitis, abscess, peritonitis, sinusitis, otitis, periodontitis, pericarditis, pancreatitis, cholelithiasis, endocarditis and septic arthritis, as well as in topical treatments in a variety of inflammatory and infected lesions such as infected lesions of the skin and/or mucosal membranes, surgical wounds, ulcerative lesions and burns.
  • DNase finds utility in maintaining the flow in medical conduits communicating with a body cavity, including surgical drainage tubes, urinary catheters, peritoneal dialysis ports, and intratracheal oxygen catheters. DNase may improve the efficacy of antibiotics in infections (e.g., gentamicin activity is markedly reduced by reversible binding to intact DNA). It also may be useful as an oral supplement in cases of pancreatic insufficiency. DNase will be useful in degrading DNA contaminants in pharmaceutical preparations: the preparation is contacted with DNase under conditions for degrading the contaminant DNA to oligonucleotide and thereafter removing the oligonucleotide and DNase from the preparation. Use of DNase immobilized on a water insoluble support is convenient in this utility.
  • DNase may be useful in treating non-infected conditions in which there is an accumulation of cellular debris, including cellular DNA.
  • DNase would be useful after systemic administration in the treatment of pyelonephritis and tubulo-interstitial kidney disease (e.g., with blocked tubules secondary to cellular debris), including drug-induced nephropathy or acute tubular necrosis.
  • DNase may also be administered along with other pharmacologic agents used to treat the conditions listed above, such as antibiotics, bronchodilators, anti-inflammatory agents, and mucolytics (e.g. n-acetyl-cysteine). It may also be useful to administer DNase along with other therapeutic human proteins such as growth hormone, protease inhibitors, gamma-interferon, enkephalinase, lung surfactant, and colony stimulating factors.
  • pharmacologic agents used to treat the conditions listed above, such as antibiotics, bronchodilators, anti-inflammatory agents, and mucolytics (e.g. n-acetyl-cysteine). It may also be useful to administer DNase along with other therapeutic human proteins such as growth hormone, protease inhibitors, gamma-interferon, enkephalinase, lung surfactant, and colony stimulating factors.
  • Plasmids are designated by a lower case p preceded and/or followed by capital letters and/or numbers.
  • the starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures.
  • equivalent plasmids to those described are known in the art and will be apparent to the ordinarily skilled artisan.
  • “Digestion” of DNA refers to catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA.
  • the various restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements were used as would be known to the ordinarily skilled artisan.
  • For analytical purposes typically 1 ⁇ g of plasmid or DNA fragment is used with about 2 units of enzyme in about 20 ⁇ l of buffer solution.
  • For the purpose of isolating DNA fragments for plasmid construction typically 5 to 50 ⁇ g of DNA are digested with 20 to 250 units of enzyme in a larger volume. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37° C. are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion the reaction is electrophoresed directly on a polyacrylamide gel to isolate the desired fragment.
  • Dephosphorylation refers to the removal of the terminal 5′ phosphates by treatment with bacterial alkaline phosphatase (BAP). This procedure prevents the two restriction cleaved ends of a DNA fragment from “circularizing” or forming a closed loop that would impede insertion of another DNA fragment at the restriction site. Procedures and reagents for dephosphorylation are conventional. Maniatis, T. et al. , Molecular Cloning pp. 133-134 (1982). Reactions using BAP are carried out in 50 mM Tris at 68° C. to suppress the activity of any exonucleases which may be present in the enzyme preparations. Reactions were run for 1 hour. Following the reaction the DNA fragment is gel purified.
  • BAP bacterial alkaline phosphatase
  • “Oligonucleotides” refers to either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5′ phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide will ligate to a fragment that has not been dephosphorylated.
  • Ligase refers to the process of forming phosphodiester bonds between two double stranded nucleic acid fragments (Maniatis, T. et al., Id., p. 146). Unless otherwise provided, ligation may be accomplished using known buffers and conditions with 10 units of T4 DNA ligase (“ligase”) per 0.5 ⁇ g of approximately equimolar amounts of the DNA fragments to be ligated.
  • ligase T4 DNA ligase
  • “Filling” or “blunting” refers to the procedures by which the single stranded end in the cohesive terminus of a restriction enzyme-cleaved nucleic acid is converted to a double strand. This eliminates the cohesive terminus and forms a blunt end. This process is a versatile tool for converting a restriction cut end that may be cohesive with the ends created by only one or a few other restriction enzymes into a terminus compatible with any blunt-cutting restriction endonuclease or other filled cohesive terminus.
  • blunting is accomplished by incubating 2-15 ⁇ g of the target DNA in 10 mM MgCl 2 , 1 mM dithiothreitol, 50 mM NaCl, 10 mM Tris (pH 7.5) buffer at about 37° C. in the presence of 8 units of the Klenow fragment of DNA polymerase 1 and 250 ⁇ M of each of the four deoxynucleoside triphosphates.
  • the incubation generally is terminated after 30 min. phenol and chloroform extraction and ethanol precipitation.
  • a human pancreatic cDNA library was constructed in ⁇ gt10 using polyadenylated mRNA prepared from freshly obtained and liquid N 2 frozen human pancreas (Lauffer et al., Nature 318:334 [1985]). Using oligo dT primers and EcoRI-SalI-XhoI-SstII adapters, a cDNA library of 0.9 ⁇ 10 6 independent isolates of greater than 600 bp was obtained.
  • Probe 1 5′GTG-CTG-GAC-ACC-TAC-CAG-TAT-GAT-GAT-GGC-TGT-GAG-TCC-TGT-GGC-AAT-GAC 3′ (51 mer corresponding to the amino sequence Val-Leu-Asp-Thr-Tyr-Gln-Tyr-Asp-Asp-Gly-Cys-Glu-Ser-Cys-Gly-Asn-Asp)
  • Probe 2 5′TAT-GAC-GTC-TAC-CTG-GAC-GTG-CAG-CAG-AAG-TGG-CAT-CTG-AAT-GAT-GTG-ATG-CTG-ATG-GGC-GAC-TTC-AAC-GC 3′ (71 mer corresponding to the amino acid sequence Tyr-Asp-Val-Tyr-Leu-Asp-Val-Gln-Gln-Lys-Trp-His-Leu-Asn-Asp-Val-Met-Leu-Met-Gly-Asp-Phe-Asn)
  • the two probes were end-labeled with T4 polynucleotide kinase and [ 32 P]adenosine triphosphate (Maniatis et al., Molecular Cloning, [Cold Spring Harbor Laboratory, 1982]), and used separately to screen the human pancreatic cDNA library under low stringency hybridization conditions: 20% formamide, 5 ⁇ SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 ⁇ Denhardt's solution, sonicated salmon sperm DNA (50 ⁇ g/ml), 0.1% SDS, and 10% dextran sulfate at 42° C.
  • Probe 4 N-terminal probe: 5′ CTG-AAG-ATC-GCA-GCC-TTC-AAC-ATC-CAG-ACA-TTT-GGG-GAG-ACC (42 mer)
  • Probe 5 (putative intron probe): 5′TCC-GCA-TGT-CCC-AGG-GCC-ACA-GGC-AGC-GTT-TCC-TGG-TAG-GAC (42 mer)
  • the probes were labeled with 32 P and used to rescreen 1.3 ⁇ 10 6 clones from the human pancreatic cDNA library at high stringency: 50% formamide, 5 ⁇ SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 ⁇ Denhardt's, sonicated salmon sperm DNA (50 g/ml), 0.1% SDS, and 10% dextran sulfate at 42° C. Washes were carried out at 42° C. in 0.2 ⁇ SSC and 0.1% SDS. Four clones hybridized with probe 4 (N-terminal probe) and not with probe 5 (putative intron probe).
  • clone 18-1 which contained an insert of approximately 1.1 kB by PAGE, was subcloned into M13 and sequenced. The full nucleotide sequence of clone 18-1 and the deduced amino acid sequence is shown in FIG. 1.
  • Clone 18-1 is composed of 1039 bp and has a long open reading frame without the intron found in clone 6.
  • two possible initiation codons (ATG) are present (positions 160-162 and 169-171). Either may be used.
  • the former ATG with a purine at position -3 more closely conforms to the Kozak rule (Kozak, Cell 44:283 [1986]).
  • CTG at position 226-228 are nucleotides encoding a short, relatively hydrophobic amino acid sequence (19-22 amino acids in length) which is a likely secretion signal sequence.
  • Radiolabeled 32 P-DNA was prepared using an M13 single-stranded template, a 17mer sequencing primer, 32 P-dCTP, non-radioactive dATP, dTTP, and dGTP, and Klenow. Briefly, 1.5 ⁇ MgCl2 (35 mM), 1.5 ⁇ 10 ⁇ restriction buffer (70 mM Tris-HCl, pH 7.6; 35 mM dithiothreitol; 1 mM EDTA), and 6 ⁇ H 2 O were mixed with 1 ⁇ template (approximately 1 ⁇ g) and 1.5 ⁇ Palmer (0.5 ⁇ M) and heated to 55° C. for 7 min.
  • Nucleotide mix was prepared by taking 40 ⁇ 32 P-dCTP (sp. act.3000 Ci/mmol; 400 ⁇ Ci) plus 1 ⁇ each of 2 mM stocks of non-radioactive dATP, dTTP, and dGTP to dryness and then reconstituting the nucleotides in 7 ⁇ 1 ⁇ restriction buffer. The nucleotide mix and 1 ⁇ Klenow were added to the template-primer mixture and the reaction was incubated at 37° C. After 15 min, 2 ⁇ of a non-radioactive deoxynucleotides were added and the incubation was continued for an additional 15 min. Radiolabeled DNA was then separated from free nucleotides by centrifugation through Sephadex G-50 (Maniatis et al., [1982]).
  • DNase activity is measured by incubating samples with 100,000 cpm 32 P-DNA plus 80 ⁇ g/ml non-radioactive salmon sperm DNA in DNase buffer (10 mM Tris-HCl pH 7, 4 mM MgCl2, 4 mM CaCl 2 ) for 45 min at 37° C. The reaction is terminated by the addition of one-half volume of non-radioactive DNA (2 mg/ml) and one volume of ice-cold 20% trichloroacetic acid. After 10 min at 4° C., the mixture is centrifuged at 12,000 g ⁇ 10 min, and an aliquot of the supernatant is counted. The presence of acid-soluble counts in the supernatant reflects DNase activity. Each day a standard curve is generated by testing 0.1-200 ng of bovine DNase I (Sigma D-5025).
  • Agar plate DNase assay Smith, Hankock, and Rhoden (Applied Microbiology, 18:991 [1969]) described a test agar containing methyl green and DNA for determining DNase activity of microorganisms. This assay was modified in order to develop a rapid semi-quantitative assay for soluble DNase activity in order to screen cell supernatants to monitor expression and to screen column fractions to monitor purification.
  • bacto agar 7.5 g
  • 500 ml of buffer 25 mM Tris pH 7.5, 5 mM MgCl2, 5 mM CaCl 2 , 0.1% sodium azide).
  • these reagents are also used in an aqueous format (e.g. in 96-well plates) to rapidly, sensitively, and specifically quantitate DNase activity.
  • SDS-polyacrylamide gel electrophoresis and xymography SDS-polyacrylamide gel electrophoresis and xymography was performed by a modification of the procedure of Rosenthal and Lacks (Anal. Biochem. 80:76 [1977]). Briefly, the buffer system of Laemmli was used to prepare 12% polyacrylamide gels. Salmon sperm DNA (10 ⁇ g/ml) and EDTA (2 mM) were added to both the stacking and the resolving gels prior to polymerization. Proteins were suspended in sample buffer, heated at 100° C. for 3 min, prior to application to the gels. Electrophoresis was conducted at room temperature at constant current.
  • the gel was rinsed with water and incubated in 250 ml of 40 mM Tris-HCl, pH 7.5, 2 mM MgCL 2 , 0.02% azide. After 1 hr, fresh buffer was added and the gel was soaked for 12 hr at 24° C. To reveal DNase activity, the gel was put into fresh buffer containing 2 mM CaCl 2 and 1 ⁇ g/ml ethidium bromide, and then examined under short-wave UV light at intervals from 5 min to 24 hr. To stop the reaction EDTA is added (final concentration 15 mM), and the xymogram is photographed. The gel can then be stained for protein by Coomassie blue.
  • Plasmid pRK.DNase.7 was constructed from clone 18-1, described above, as follows:
  • the plasmid pRK5 was digested with EcoRI, dephosphorylated, and fragment 1 comprising the bulk of the plasmid was isolated.
  • pRK5 is described in Suva et al., Science 237:896 (1987); U.S. Ser. No. 97,472, filed Sep. 11, 1987; and EP Publ. 307,247, published Mar. 15, 1989, where the pCIS2.8c28D starting plasmid is described in EP 278,776 published Aug. 17, 1988 based on U.S. Ser. Nos. 07/071,674 and 06/907,297.
  • the A DNase clone 18-1 was digested with EcoRI and the insert (fragment 2) was isolated.
  • Fragment 1 and fragment 2 were ligated and the ligation mixture transformed into E. coli strain 294.
  • the transformed culture was plated on ampicillin media plates and resistant colonies selected. Plasmid DNA was prepared from transformants and checked by restriction analysis for the presence of the correct fragment.
  • pRK.DNase.7 was transfected into human embryonic kidney-293 cells for transient and stable expression.
  • human DNase I 60 mm plates of confluent HEK-293 cells (50%) were transfected as previously described (Eaton et al. 1986) by the calcium phosphate method (Wigler et al., 1979).
  • HEK-293 cells were similarly transfected simultaneously with pRK.DNase.7 and a plasmid expressing the neomycin resistance gene pRSV neo (Gorman et al., 1985).
  • pSVeDNAseDHFR3 a plasmid suitable for recombinant synthesis of human DNase I in CHO cells was constructed as follows:
  • Plasmid pRK.DNase.7 was digested with EcoRI and SphI and the largest fragment containing the 5′ portion of the DNase coding region was isolated (fragment 3). Plasmid pRK.DNase.7 was digested with SalI, blunted with Klenow, digested with SphI, and the intermediate size fragment containing the 3′ portion of the DNase coding region was isolated (fragment 4). pRK5 was cut with SmaI and EcoRI and the fragment comprising the bulk of the plasmid was isolated (fragment 5). Fragments 3, 4 and 5 were ligated and the mixture was transformed into E. coli strain 294. The transformed culture was plated on ampicillin media plates and resistant colonies selected. Plasmid DNA was prepared from transformants and checked by restriction analysis for the presence of the correct fragment. The resulting plasmid is referred to as pRKDNaseInt.
  • Plasmid pE342HBV.E400D22 (Crowley et al., “Mol. Cell Biol.” 3:44 [1983]) was digested with EcoRI and PvuI and the smallest fragment containing the SV40 early promoter and part of the ⁇ -lactamase gene was isolated (fragment 5). Plasmid pE342HBV.E400D22 was also digested with BamHI and PvuI and the fragment comprising the bulk of the plasmid containing the balance of the ⁇ -lactamase gene as well as the SV40 early promoter and the DHFR gene was isolated (fragment 6).
  • Plasmid pRKDNaseInt was digested with EcoRI and BamHI and the DNase coding fragment was isolated (fragment 7). Fragments 5, 6, and 7 were ligated and the mixture was transformed into E. coli strain 294. The transformed culture was plated on ampicillin media plates and resistant colonies selected. Plasmid DNA was prepared from transformants and checked by restriction analysis for the presence of the correct fragment. The resulting plasmid is referred to as pSVeDNaseDHFR3.
  • a plasmid was constructed suitable for recombinant synthesis of DNase in E. coli as a secreted protein. This plasmid is called pDNA11 and was constructed as follows.
  • Plasmid pTF.III (U.S. Ser. No. 07/152,698) was digested with NsiI and SalI and the largest fragment comprising the bulk of the plasmid was isolated (fragment 8). Plasmid pRKDNase7 was digested with SalI and BstXI and the 798 bp fragment comprising most of the coding region was isolated (fragment 9). Two synthetic oligonucleotides were synthesized:
  • DLink 1 5′TTG-AAG-ATC-GCA-GCC-TTC-AAC-ATC-CAG-ACA-T (31mer)
  • DLink 3 5′CTG-GAT-GTT-GAA-GGV-TGC-GAT-CTT-CAA-TGC-A (31mer)
  • Fragments 8 and 9 and synthetic oligonucleotides DLink 1 and DLink 3 were ligated and the mixture was transformed into E. coli strain 294. The transformed culture was plated on ampicillin media plates and resistant colonies selected. Plasmid DNA was prepared from transformants and checked by restriction analysis for the presence of the correct fragment and preservation of the NsiI and BstXI restriction sites. Several plasmids were sequenced to confirm incorporation of correct synthetic DNA. 294 cells transformed with pDNA11 expressed >500 mg/L of two new major proteins as revealed by SDS-PAGE—a major band at approximately 32 kD and a minor band at approximately 30 kD.
  • Human DNase expressed in E. coli is active. 294 cells transformed with pDNA11 grown on agar plates supplemented with calcium, magnesium, and low phosphate revealed secretion of active DNase, as evidenced the presence of a clear zone surrounding the transformed cells, and not control cells. In addition, transformed cells solubilized with SDS and beta-mercaptoethanol were run into SDS-PAGE gels and xymography was performed. DNase activity was associated with the band of properly processed human DNase, but not with unprocessed human DNase.
  • a plasmid was constructed for recombinant expression of human DNase I as an intracellular protein in E. coli .
  • the plasmid is called pDNA2, and was constructed as follows.
  • Plasmid pHGH207/307 was prepared from pHGH207 (U.S. Pat. No. 4,663,283) by removing the EcoRI site upstream from the trp promoter (EcoRI digested, blunted and religated).
  • Plasmid pHGH207/307 was digested with XbaI and SalI and the largest fragment comprising the bulk of the plasmid was isolated (fragment 10).
  • Plasmid pRK.DNase.7 was digested with SalI and BstXI and the 798 bp fragment comprising most of the coding region was isolated (fragment 9).
  • Two synthetic oligonucleotides were synthesized:
  • DLink 4 5′CTAGAATTATG-TTA-AAA-ATT-GCA-GCA-TTT-AAT-ATT-CAA-ACA-T (42mer)
  • DLink 5 5′TTG-AAT-ATT-AAA-TGC-TGC-AAT-TTT-TAACATAATT (34mer)
  • Fragments 9 and 10 and synthetic oligonucleotides DLink 4 and DLink 5 were ligated and the mixture was transformed into E. coli strain 294. The transformed culture was plated on ampicillin media plates and resistant colonies selected. Plasmid DNA was prepared from transformants and checked by restriction analysis for the presence of the correct fragment and preservation of the XbaI and BstXI restriction sites. Several plasmids were sequenced to confirm incorporation of correct synthetic DNA.
  • the CMV transcription regulatory sequences and the splice unit of pRK.DNase.3 were replaced by the SV40 transcription regulatory sequences and different splice donor-intron-splice acceptor units as described below.
  • a corresponding vector lacking the splice unit was also created (pSve.DNase).
  • Vector pRK.DNase.3 (FIG. 3) was constructed as follows: pRK5 was digested with SmaI and SalI, which cut exclusively in the polylinker region between the 5′ and 3′ control sequences, and the large fragment was isolated.
  • the pRK5 vector contains a splice donor-intron-splice acceptor region upstream of a coding region and downstream of a promoter, where the intron region consists of a cytomegalovirus (CMV) immediate early splice donor and intron sequences, a bacteriophage SP6 promoter insert, and immunoglobulin (Ig) heavy chain variable region (V H ) intron and splice acceptor sequences.
  • CMV cytomegalovirus
  • Ig immunoglobulin heavy chain variable region
  • Vector pRK.DNase.7 was cleaved with BsmI, the 3′ protruding ends were trimmed back with T4 DNA polymerase, and the material was redigested with SalI to release the entire human DNase I coding sequence as a 921-nt fragment. After gel isolation, this fragment was ligated to the pRK5 large fragment using standard ligation methodology (Maniatis et al. , 1982, supra) to create vector pRK.DNase.3.
  • pRK.DNase.3 contains CMV transcription regulatory elements, and a splice unit located between the transcription and translation initiation sites (“Intron” in FIG. 3). In this vector, the splice unit of the pRK5 vector is present without any modifications.
  • Vector pSVe.DNase was constructed as follows (FIG. 3): The regulatory sequences preceding the DNAse coding region in vector pRK.DNase.3 were separated from the remainder of the vector by digestion with SstI and ClaI; DNA prepared from dam+bacterial host cells was used to prevent cleavage of the second ClaI site in the vector, located towards the 3′ end of the SV40 early polyadenylation region. The largest fragment lacking the 5′ control region was gel isolated.
  • DHFR expression vector pE348DHFRUC served as a source of the SV40 transcription regulatory sequences.
  • the vector pE348DHFRUC (Vannice and Levinson, J. Virology, 62:1305-1313, 1988, where it is designated pE, FIG. 1) contains the SV40 enhancer and early promoter region upstream of the HindIII site, including the SV40 early sites of transcription initiation (position 5171 in the virus), preceding cDNA encoding murine dihydrofolate reductase (DHFR), which is followed by the 584-bp Hepatitis B virus (HBV) polyA signal in plasmid pMLl from the GamHI to the BGlII sites of HBV.
  • HBV Hepatitis B virus
  • This plasmid contains a polylinker immediately upstream of the SV40 sequences.
  • the SV40 transcription regulatory sequences were released by digestion with SstI and ClaI, and the resulting 5′ protruding ends were filled in using Klenow poll in the presence of all four deoxyribonucleotides (dNTPs: dATP, dGTP, dCTP, TTP).
  • dNTPs deoxyribonucleotides
  • XbaI the SV40 transcription regulatory sequences (enhancer and early promoter, including the SV40 early sites of transcription initiation), present on the smaller XbaI-ClaI fragment (360 nucleotides) were gel isolated.
  • Vector pSVI.DNase (FIG. 4) was prepared after insertion of the DNase coding sequence into an intermediate plasmid, pRK5.5Ve. This intermediate was created by replacing the pRK5 CMV transcription regulatory elements, located between SpeI and SacII restriction sites, with the small XbaI-HindIII fragment from pE348DHFRUC that contains the SV40 early promoter and enhancer. The 3′ protruding ends generated by SacII digestion of pRK5 were chewed back with T4 DNA polymerase, and the 5′ protruding ends resulting from HindIII digestion of pE348DHFRUC were filled in using T4 polymerase in the presence of all four dNTPs.
  • the DNase coding sequence was isolated from vector pRK.DNase.3 by cleavage with EcoRI and HindIII, and inserted into the large fragment of pRK5.Sve that had been isolated after digestion with the same two enzymes.
  • Vector pSVI.DNase contains the SV40 transcription regulatory elements (enhancer and early promoter, including the SV40 early sites of transcription initiation) and mRNA cap sites, followed by the splice-donor-intron-splice acceptor unit of the pRK5 vector without any modifications, the cDNA encoding DNase, the SV40 early polyadenylation (“polyA”) region, and the SV40 origin of replication (“ori”) regions from SV40.
  • polyA SV40 early polyadenylation
  • ori SV40 origin of replication
  • Vectors pSVI2.DNase, pSVI3.DNase, pSVI5.DNase, and pSVI6B.DNase were constructed (FIG. 5) by recombining two fragments in each case. The first was the large pRK.DNase.3 fragment resulting from digestion with EcoRI, treatment with T4 DNA polymerase in the presence of dNTPs, and subsequent cleavage with SstI; the second was in each case the small fragment containing the SV40 5′ regulatory sequences and a modified splice unit.
  • FIG. 11 shows a schematic representation of the splice unit nucleotide sequences involved in the preparation of the vectors of this example, i.e., SVI, SVI2, SVI3, SVI5, and SVI6B.
  • the boxes represent changes from the SVI sequence, the double underlining is a spurious ATG codon, the underlining shows spurious splice sites and added or changed branchpoint sequence (BPS) regions, the breaks in sequence represent deletions of the nucleotides for SVI3-SVI5, the designation indicates sequence not shown, and the carets indicate the 5′ and 3′ cleavage sites within the splice donor and splice acceptor, respectively, of the the splice unit.
  • BPS branchpoint sequence
  • FIGS. 7 - 10 show the complete nucleotide sequences of PSVI2.DNase, pSVI3.DNase, pSVI5.DNase, and pSVI6B.DNase, respectively, up to but not including the coding region of DNase.
  • the splice unit sequences of FIG. 11 are incorporated in FIGS. 7 - 10 .
  • Transient expression directed by the different DNase vectors was analyzed after transfection into CHO dhfr ⁇ cells.
  • Cells were transfected by a modification of the DEAE-dextran procedure and levels of DNase accumulated in the cell media 36 to 48 hours after transfection. Approximately 4 ⁇ 10 5 cells were plated per well in six-well 35 mm culture dishes. The following day, the volume of 2 ⁇ g DNase expression vector was adjusted to 15 ⁇ l by the addition of TBS (137 mM NaCl, 5 mM KCl, 1.4 mM Na 2 PO 4 , 24.7 mM TrisHCl, 1.35 mM CaCl 2 , 1.05 mM MgCl 2 , pH 7.5).
  • TBS 137 mM NaCl, 5 mM KCl, 1.4 mM Na 2 PO 4 , 24.7 mM TrisHCl, 1.35 mM CaCl 2 , 1.05 mM MgCl 2 , pH 7.5).
  • This plasmid may be prepared by replacing the ras promoter of rasP.hGH described in Cohen and Levinson, Nature, 334: 119-124 (1988) with the RSV promoter.
  • the amount of hGH synthesized in each case served as a standard to allow for a more precise comparison of the DNase levels obtained in the different transfections.
  • DNase levels in the media were measured by a standard ELISA using serum from rabbits injected either with human DNase or bovine DNase and adjuvant ( Practice and Theory of Enzyme Immunoassays, P.Tijssen, Chapter 5, “Production of antibodies”, pg. 43-78 (Elsevier, Amsterdam 1985)).
  • hGH levels were determined using a commercially available assay kit (IRMA, immunoradiometric assay) purchased from Hybritech, Inc., La Jolla, Calif.

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US20050009056A1 (en) 2005-01-13
EP0449968A1 (en) 1991-10-09
EP0853121B1 (en) 2007-03-28
DE68928934D1 (de) 1999-04-01
AU630658B2 (en) 1992-11-05
ATE176924T1 (de) 1999-03-15
AU4826590A (en) 1990-08-01
EP0449968B1 (en) 1999-02-24
CA2006473A1 (en) 1990-06-23
BG62870B2 (bg) 2000-09-29
JP3162372B2 (ja) 2001-04-25
ES2130120T3 (es) 1999-07-01
CA2006473C (en) 2002-02-05
HU211232A9 (en) 1995-11-28
US20080026426A1 (en) 2008-01-31
DE68929551D1 (de) 2007-05-10
EP0853121A3 (en) 1998-08-05
ATE358176T1 (de) 2007-04-15
US7297526B2 (en) 2007-11-20
WO1990007572A1 (en) 1990-07-12
JPH04502406A (ja) 1992-05-07
DE68929551T2 (de) 2008-03-06
EP0853121A2 (en) 1998-07-15
JP2001157580A (ja) 2001-06-12
DE68928934T2 (de) 1999-08-05

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