Classifications

• • 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.)
  • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
  • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00

Definitions

• This invention is in the field of molecular biology and involves the identification of protein kinase B kinases, and their medical applications.
• PI phosphatidylinositol
• PI 3-kinase There are multiple forms of PI 3-kinase, and they are all able to phosphorylate the D-3 position of phosphatidylinositol (Ptdlns), phosphatidylinositol-4-phosphate (PtdIns-4-P) and phosphatidylinositol-4,5-bisphosphate (PtdIns-4,5-P2) to produce phosphatidylinositol-3-phosphate (PtdIns-3-P), phosphatidylinositol-3,4-bisphosphate (PtdIns-3,4- P2) and phosphatidylinositol-3,4,5-triphosphate (PtdIns-3,4,5-P3, or PIP3), respectively.
• Ptdlns phosphatidylinositol
• PtdIns-4-P phosphatidylinositol-4-phosphate
• PKB Protein kinase B
• PI 3-kinase the best known being Wortmannin or LY 294002
• overexpression of a dominant negative mutant of PI 3-kinase See, Burgering, B M. and Coffer, P.J. (1995) Nature, vol. 376, pages 599-602.
• PKB is a key enzyme in the PIP3 pathway, and is involved in regulating cell growth. It has been implicated in certain human cancers; for instance, it is known to be amplified in a percentage of ovarian carcinomas, breast carcinomas, and pancreatic carcinomas. See, Bellacosa, A. et al. (1995) Int. J. Cancer 64, pages 280-285, and Cheng, J. Q. et al. (1996) Proc. Natl. Acad. Sci. U.S.A. vol. 93, 3636-3641. The amplification of the enzyme affords tumor cells a mechanism to circumvent apoptosis. Thus, it will be appreciated that drugs that inhibit PKB activity will be beneficial for the treatment of diseases involving unwanted cell growth, including cancer. One way to achieve this end is to develop assays that identify such.
• a first object of the invention is a description of PKB kinases, methods and compositions for purifying and expressing the kinases, and cDNA sequences that encode them.
• a second object of the invention is a description of the activation of PKB kinases by Ptdlns (3,4,5)P 3. to effect the phosphorylation of PKB.
• a third object of the invention is a description of compositions and methods for identifying compounds that have prophylatic or therapeutic benefit for treating diseases involving unwanted cell growth, including cancer.
• the flow diagram summarizes the purification of PKB kinases A-D from sheep brain cytosol and records the quantity of protein carried through each step. The overall recovery of activity from the initial cytosol fractions was 15.5%.
• HPLC-SEC was performed with a Biosilect column (VT 11.6 mis, BioRad). 35-45 ul samples were loaded, the flow was 40 ul/min, 80 ul fractions were collected.
• the SEC buffer contained 0.15 M NaCl, 20 i M HEPES pH 7.4, 40C, 0.5 mM EGTA O.lmM EDTA, 1% betaine, 0.03% Tween 20, 0.01% azide, 2mM B- glycerophosphate, ImM DTT and pepstatin A, leupeptin, aprotinin and antipain, all at 2 ug/ml.
• the native sizes of the PKB kinases A-D were estimated to be 58, 58, 68 and 54 kD, respectively, and their SDS-denatured sizes to be 57, 57, 70 and 55 kD respectively (the position to which 220, 97, 69, 46 and 31 kD standard had migrated during SDS-PAGE are indicated).
• PKB kinase activity co-purifies with a [ 32 P]-PtdIns(3,4,5)P 3 binding protein.
• a partially purified preparation of PKB kinase was subjected to SEC and fractions were analyzed for PtdIns(3,4,5)P 3 -dependent PKB kinase activity (bottom panel), [ 32 P]-PtdIns(3,4,5)P 3 binding proteins (middle-panel, by probing a renatured Western blot with [ 32 P]-PtdIns(3,4,5)P 3 (18)) and (C) SDS-denatured proteins (upper panel, by silver staining an SDS-PAGE gel).
• [ 32 P]-PtdIns(3,4,5)P 3 binding was assayed by Western blotting proteins (samples only heated to 50°C with SDS sample buffer) onto Nitrocellulose.
• the filter was incubated in PBS containing, 1% NP40, 1 mM EGTA, 0.01% azide, for 12 hrs at 4°C.
• the filter was blocked for 30 mins (room temperature) in the above solution additionally containing 0.1% cholate, 50 ⁇ gml "1 phosphatidylserine and phosphatidylcholine, ImM MgCL and 1 mM DTT.
• [ 32 P]-PtdIns(3,4,5)P 3 (prepared from recombinant pl01/pl20-PI3K, PtdIns(4,5)P 2 and [ ⁇ PJ-ATP (See, L.R. Stephens et al, Cell 89, 105-114 (1997)) was sonicated into the block solution (lO ⁇ Ci in 10 mis) and applied to a blocked filter for 20 mins (room temperature) then washed away with fresh block solution (5x over 5 mins) and finally PBS containing 1% NP40. The filter was air dried and autoradiographed.
• the purified PKB kinases are PtdIns(3.4.5)P 3 -dependent and activate PKB. Assays were run in 2 stages. The first stage was run with mixed lipid vesicles either with or without D-D-S/A-PtdIns(3,4,5)P 3 (final concentration 5 ⁇ M) and in the presence or absence of PKB kinase A (6 nM), wild-type (EE)-PKB (2.5 ⁇ M) or T308A/S473A-(EE)-PKB) and [ ⁇ P]- ATP (50 ⁇ M).
• Assays contained; a constant concentration of mixed lipid vesicles containing the indicated concentrations of inositol phospholipids, (EE)-PKB (2.5 ⁇ M), PKB kinase A (5 nM) and [ ⁇ 32 P]-ATP (1 ⁇ M, total volume 12 ⁇ l).
• the lipid vesicles were prepared by: sonicating dry lipid films into 0.2 M sucose; 20 mM KCl; 20 mM HEPES, pH 7.4 30°C; 0.01% azide (to give 200 ⁇ M phosphatidylcholine, 150 ⁇ M phosphatidylserine, 20 ⁇ M phosphatidylethanolamine, 10 ⁇ M spingomylin plus the indicated concentrations of inositol lipids final in the assay.
• the assays were to estimate associated of the kinases with the lipid vesicles then after 4 mins at 30°C the assays were centrifuged (airfuge (Beckman) maximum speed for 30 mins). Aliquots of the supernatents were removed for assays or immunoblotting. The pellets were rinsed rapidly with assay buffer, recentrifuged and dissolved in SDS-sample buffer. Phosphorylation of PKB(s) were quantitated as described above.
• PKB kinase A (5 nM) was mixed with sucrose-loaded lipid vesicles (or their vehicle alone) containing various concentrations of inositol phospholipids as shown in Figure 2B. After 4 mins and 30°C the vesicles were pelted by centrifugation and aliquots of the supernatents were assayed of PKB kinase activity in the presence of 5 ⁇ M D-D-S/A-PtdIns(3,4,5)P 3 .
• FIG. 3 Primary structure of a PKB kinase A minimum potential ORF defined by cDNAs isolated from our human U937 cell library is shown. The four peptide sequences derived from sheep brain PKB kinase A are shown in bold above the sequence. The are of homology to other protein kinase catalytic domains is boxed in a solid line; the area of holology to other PH-domains is boxed in a dashed line.
• (EE)-II refers to the complete ORF and (EE)-I refers to the 'kinase-compromised' splice variant) were transiently expressed in cos-7 cells. Proteins were purified via their (EE)-tags (myc antibodies were used as controls) and aliquots were Western blotted. PVDF filters, probed with an ⁇ (EE) monoclonal antibody (detection by ECL; right hand upper panel) were then stained with Coomassie blue (left hand upper panel; data shown are for (EE)-II only; similar results were obtained with (EE)-I).
• Figure 5 shows a cDNA (Seq I. D. No. 1) and encoded amino acid sequence of a PKB kinase.
• PKB or protein kinase B
• PKB is used herein to mean an approximately 60 kD kinase with homology to protein kinase c and protein kinase a, as described by Coffer, P. J. and Woodgett, J. R. (1991) Eur. J. Biochem. vol. 201, pages 475-481, and Jones, P. F. et al., (1991) Proc. Natl. Acad. Sci. USA vol. 88, 4171-4175. See also, WO 97/22360, and Stokoe, D., et al (1997) Science, vol. 277, pages 567-570.
• the definition includes isoforms of the enzyme of which four are presently known.
• PKB is also termed c-Akt or Rac-Pk.
• the formal name of the 'biological stereoisomer isomer' of phosphatidylinositol(3,4,5)- trisphosphate is (for a specific fatty acid combination); (1-stearoyl, 2-arachidonyl) snphosphatidyl D-myo-inositol (3,4,5)-trisphosphate.
• D-L-S/A-PtdIns(3,4,5)P 3 is (2-arachidonyl, 3-stearoyl) sn-phosphatidyl D-myoinositol(3,4,5)-trisphosphate. Dipalmitoyl derivatives are abbreviated to D-D-P/P-PtdIns(3,4,5)P 3 .
• the enantiomer of D-D-S/A-PtdIns(3,4,5)P 3 is L-L-S/A- PtdIns(3,4,5)P 3 .
• naturally-occurring refers to the fact that an object can be found in nature.
• a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally-occurring.
• polynucleotide as referred to herein means a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
• the term includes single and double stranded forms of DNA.
• oligonucleotide includes naturally occurring, and modified nucleotides linked together by naturally occurring, and non-naturally occurring oligonucleotide linkages.
• Oligonucleotides are a polynucleotide subset with 200 bases or fewer in length. Preferably oligonucleotides are 10 to 60 bases in length and most preferably 12, 13, 14, 15, 16, 17, 18, 19, or 20 to 40 bases in length. Oligonucleotides are usually single stranded, e.g. for probes; although oligonucleotides may be double stranded, e.g. for use in the construction of a gene mutant.
• Oligonucleotides of the invention can be either sense or antisense oligonucleotides.
• naturally occurring nucleotides referred to herein includes deoxyribonucleotides and ribonucleotides.
• modified nucleotides referred to herein includes nucleotides with modified or substituted sugar groups and the like.
• oligonucleotide linkages referred to herein includes oligonucleotides linkages such as phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phoshoraniladate, phosphoroamidate, and the like.
• An oligonucleotide can include a label for detection, if desired.
• sequence homology describes the proportion of base matches between two nucleic acid sequences or the proportion amino acid matches between two amino acid sequences.
• sequence homology is expressed as a percentage, e.g., 50%, the percentage denotes the proportion of matches over the length of sequence from a PKB kinase that is compared to some other sequence. Gaps (in either of the two sequences) are permitted to maximize matching; gap lengths of 15 bases or less are usually used, 6 bases or less are preferred with 2 bases or less more preferred.
• the sequence homology between the target nucleic acid and the oligonucleotide sequence is generally not less than 17 target base matches out of 20 possible oligonucleotide base pair matches (85%); preferably not less than 9 matches out of 10 possible base pair matches (90%), and most preferably not less than 19 matches out of 20 possible base pair matches (95%).
• Two amino acid sequences are homologous if there is a partial or complete identity between their sequences. For example, 85% homology means that 85% of the amino acids are identical when the two sequences are aligned for maximum matching. Gaps (in either of the two sequences being matched) are allowed in maximizing matching; gap lengths of 5 or less are preferred with 2 or less being more preferred. Alternatively and preferably, two protein sequences (or polypeptide sequences derived from them of at least 30 amino acids in length) are homologous, as this term is used herein, if they have an alignment score of at more than 5 (in standard deviation units) using the program ALIGN with the mutation data matrix and a gap penalty of 6 or greater.
• substantially pure means an object species is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition), and preferably a substantially purified fraction is a composition wherein the object species comprises at least about 50 percent (on a molar basis) of all macromolecular species present. Generally, a substantially pure composition will comprise more than about 80 percent of all macromolecular species present in the composition, more preferably more than about 85%, 90%, 95%, and 99%. Most preferably, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
• DNA regions are operably linked when they are functionally related to each other.
• a promoter is operably linked to a coding sequence if it controls the transcription of the sequence
• a ribosome binding site is operably linked to a coding sequence if it is positioned so as to permit translation.
• operably linked means contiguous and, in the case of leader sequences, contiguous and in reading frame.
• Suitable host cells include prokaryotes, yeast cells, or higher eukaryotic cells.
• Prokaryotes include gram negative or gram positive organisms, for example Esche chia coli (E. coli) or Bacilli.
• Higher eukaryotic cells include established cell lines (i.e. cos cells) of mammalian origin as described below.
• Exemplary host cells are DH5a , E. coli W3110 (ATCC 27,325), E coli B, E. coli X1776 (ATCC 31,537) and E. coli 294 (ATCC 31,446).
• Pseudomonas species, Bacillus species, and Serratia marcesans are also suitable.
• Autographa californica nuclear polyhidrosis virus may be used as a vector to express foreign genes.
• AcNPV Autographa californica nuclear polyhidrosis virus
• Sf9 insect cells are infected with a baculovirus vectors expressing a PKB kinase construct with either a 6x histidine tag , myc, or an EE-tag (i.e. Glu-Glu-tag).
• E refers to the amino acid glutamine.
• microbial vectors A broad variety of suitable microbial vectors are available. Generally, a microbial vector will contain an origin of replication recognized by the intended host, a promoter which will function in the host and a phenotypic selection gene such as a gene encoding proteins conferring antibiotic resistance or supplying an autotrophic requirement. Similar constructs will be manufactured for other hosts. E. coli is typically transformed using pBR322. See Bolivar et al, Gene 2, 95 (1977). pBR322 contains genes for ampicillin and tetracycline resistance and thus provides easy means for identifying transformed cells. Expression vectors should contain a promoter which is recognized by the host organism. This generally means a promoter obtained from the intended host.
• Promoters most commonly used in recombinant microbial expression vectors include the beta-lactamase (penicillinase) and lactose promoter systems (Chang et al., Nature 275, 615 (1978); and Goeddel et al., Nucleic Acids Res. 8, 4057 (1980) and EPO Application Publication Number 36,776) and the tac promoter (H. De Boer et al, Proc. Natl. Acad. Sci. USA 80, 21 (1983)).
• PKB Kinases can be identified using several different techniques, including methods for detecting protein-protein interactions. At some point in the verification of PKB kinase activity it is expected that its activation by PIP3 will be determined. See, Stokoe, D., et al (1997) Science. vol. 277, pages 567-570.
• an amino acid sequence of an intracellular PKB Kinase which interacts with PKB can be ascertained using techniques well known to those of skill in the art, such as the Edman degradation technique.
• Edman degradation technique See, e.g.. Creighton, 1983, "Proteins: Structures and Molecular Principles", W.H. Freeman & Co., N.Y., pp.34-49.
• the amino acid sequence obtained may be used as a guide for the generation of oligonucleotide mixtures that can be used to screen for gene sequences encoding such intracellular proteins. Screening may be accomplished, for example, by standard hybridization or PCR techniques. Techniques for the generation of oligonucleotide mixtures and the screening are well-known. (See, e.g.. Ausubel, supra., and PR Protocols: A Guide to Methods and Applications, 1990. Innis, M. et al., eds. Academic Press, Inc., New York).
• methods may be employed which result in the simultaneous identification of genes which encode the intracellular proteins interacting with PKB Kinase.
• These methods include, for example, probing expression libraries in a manner similar to the well known technique of antibody probing of ⁇ gtl 1 libraries, using labeled protein, or fusion protein, e.g.. fused to a marker (e.g.. and enzyme, fluor, luminescent protein, or dye), or an Ig-Fc domain.
• a marker e.g. and enzyme, fluor, luminescent protein, or dye
• One method which detects protein interactions in vivo, and which does not rely on the kinase activity of PKB Kinase is the two-hybrid system, and is described in detail for illustration only and not by way of limitation. This system has been described ( U. S. Patent No.
• plasmids are constructed that encode two hybrid proteins: one plasmid consists of nucleotides encoding the DNA-binding domain of a transcription activator protein fused to a PKB nucleotide sequence encoding PKB, or peptide or fusion protein, and the other plasmid consists of nucleotides encoding the transcription activator protein's activation domain fused to a cDNA encoding an unknown protein which has been recombined into this plasmid as a part of the cDNA library.
• the DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g.. HBS or lacZ) whose regulatory region contain the transcription activator's binding site.
• a reporter gene e.g.. HBS or lacZ
• Either hybrid protein alone cannot activate transcription of the reporter gene; the DNA-binding domain hybrid cannot because it does not provide activation function, and the activation domain hybrid cannot because it cannot localize to the activator's binding sites. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product.
• the two-hybrid system or related methodology may be used to screen activation domain libraries for proteins that interact with the "bait" gene product.
• PKB or a peptide, or fusion protein derived therefrom may be used as the bait gene product.
• Total genomic or cDNA sequences are fused to the DNA encoding an activation domain.
• This library and a plasmid encoding a hybrid of a bait PKB gene product fused to the DNA-binding domain are cotransformed into a yeast reporter strain, and the resulting tranformants are screened for those that express the reporter gene. These colonies are purified and the library plasmids responsible for reporter gene expression are isolated. DNA sequencing is then used to identify the proteins encoded by the library plasmids.
• a cDNA library of the cell line from which proteins that interact with bait cell cycle target gene product are to be detected can be made using methods routinely practiced in the art. According to the particular system described herein, for example, the cDNA fragments can be inserted into a vector such that they are translationally fused to the transcriptional activation domain of GAL4.
• This library can be co-transfected along with the bait cell cycle target gene- GAL4 fusion plasmid into a yeast strain which contains a lacZ gene driven by a promoter which contains GAL4 activation sequence.
• a cDNA encoded protein, fused to GAL4 transcriptional activation domain, that interacts with bait cycle target gene product will reconstitute an active GAL4 protein and thereby drive expression of the HIS3 gene.
• Colonies which express HIS3 can be detected by their growth on petri dishes containing semi-solid agar based media lacking histidine. The cDNA can then be purified from these strains, and used to produce and isolate the bait cycle target gene-interacting protein using techniques routinely practiced in the art.
• a PKB kinase encoding nucleic acid according to the present invention can be obtained from a variety of different sources. It can be obtained from DNA or RNA, such as polyadenylated mRNA, e.g., isolated from tissues, cells, or whole organism.
• the nucleic acid can be obtained directly from DNA or RNA, or from a cDNA library.
• the nucleic acid can be obtained from a cell at a particular stage of development, having a desired genotype, phenotype (e.g., an oncogenically transformed cell or a cancerous cell), etc.
• a nucleic acid comprising a nucleotide sequence coding for a polypeptide according to the present invention can include only coding sequence of PKB kinase; coding sequence of PKB kinase and additional coding sequence (e.g., sequences coding for leader, secretory, targeting, enzymatic, fluorescent or other diagnostic peptides), coding sequence of PKB kinase and non- coding sequences, e.g., untranslated sequences at either a 5' or 3' end, or dispersed in the coding sequence, e.g., introns.
• a nucleic acid comprising a nucleotide sequence coding without interruption for a PKB kinase polypeptide means that the nucleotide sequence contains an amino acid coding sequence for a PKB kinase polypeptide, with no non-coding nucleotides interrupting or intervening in the coding sequence, e.g., absent intron(s).
• Such a nucleotide sequence can also be described as contiguous.
• a nucleic acid according to the present invention also can comprise an expression control sequence operably linked to a nucleic acid as described above.
• expression control sequence means a nucleic acid sequence which regulates expression of a polypeptide coded for by a nucleic acid to which it is operably linked. Expression can be regulated at the level of the mRNA or polypeptide.
• the expression control sequence includes mRNA-related elements and protein-related elements. Such elements include promoters, enhancers (viral or cellular), ribosome binding sequences, transcriptional terminators, etc.
• An expression control sequence is operably linked to a nucleotide coding sequence when the expression control sequence is positioned in such a manner to effect or achieve expression of the coding sequence. For example, when a promoter is operably linked 5' to a coding sequence, expression of the coding sequence is driven by the promoter.
• Expression control sequences can be heterologous or endogenous to the normal gene.
• a nucleic acid in accordance with the present invention can be selected on the basis of nucleic acid hybridization.
• the ability of two single-stranded nucleic acid preparations to hybridize together is a measure of their nucleotide sequence complementarity, e.g., base-pairing between nucleotides, such as A-T, G-C, etc.
• the invention thus also relates to nucleic acids which hybridize to a nucleic acid comprising a nucleotide sequence as set forth in Fig. 5 (SEQ ID NO: 1).
• a nucleotide sequence hybridizing to the latter sequence will have a complementary nucleic acid strand, or act as a template for one in the presence of a polymerase (i.e., an appropriate nucleic acid synthesizing enzyme).
• the present invention includes both strands of nucleic acid, e.g., a sense strand and an anti-sense strand.
• Hybridization conditions can be chosen to select nucleic acids which have a desired amount of nucleotide complementarity with the nucleotide sequence set forth in Fig. 5 (SEQ ID NO: 1).
• a nucleic acid capable of hybridizing to such sequence preferably, possesses 50%, more preferably, 70% complementarity, between the sequences.
• the present invention particularly relates to DNA sequences which hybridize to the nucleotide sequence set forth in Fig. 5 (SEQ ID NO: 1) under stringent conditions.
• stringent conditions means any conditions in which hybridization will occur where there is at least about 95%, preferably 97%, nucleotide complementarity between the nucleic acids.
• Such conditions include, e.g., hybridization for Northern: 5X SSPE, 10X Denhardts solution, 100 ⁇ g/ml freshly denatured and sheared salmon sperm DNA, 50% formamide, 2% SDS at 42°C; hybridization for cloning from cDNA library: IX
• a nucleic acid or polypeptide can comprise one or more differences in the nucleotide or amino acid sequence set forth in Fig. 5 (SEQ ID NO: 1). Changes or modifications to the nucleotide and/or amino acid sequence can be accomplished by any method available, including directed or random mutagenesis.
• a nucleic acid coding for a PKB kinase according to the invention can comprise nucleotides which occur in a naturally-occurring PKB kinase gene e.g., naturally-occurring polymo ⁇ hisms, normal or mutant alleles (nucleotide or amino acid), mutations which are discovered in a natural population of mammals, such as humans, monkeys, pigs, mice, rats, or rabbits.
• naturally-occurring it is meant that the nucleic acid is obtained from a natural source, e.g., animal tissue and cells, body fluids, tissue culture cells, forensic samples.
• Naturally- occurring mutations to PKB kinase can include deletions (e.g., a truncated amino- or carboxy- terminus), substitutions, or additions of nucleotide sequence. These genes can be detected and isolated by nucleic acid hybridization according to methods which one skilled in the art would know. It is recognized that, in analogy to other oncogenes, naturally-occurring variants of PKB kinase include deletions, substitutions, and additions which produce pathological conditions in the host cell and organism.
• a nucleotide sequence coding for a PKB kinase polypeptide of the invention can contain codons found in a naturally-occurring gene, transcript, or cDNA, for example, e.g., as set forth in Fig. 5 (SEQ ID NO: 1), or it can contain degenerate codons coding for the same amino acid sequences.
• Another aspect of the present invention is a nucleotide sequence which is unique to PKB kinase.
• a unique sequence to PKB kinase it is meant a defined order of nucleotides which occurs in PKB kinase, e.g., in the nucleotide sequence of Fig. 5 (SEQ ID NO: 1), but rarely or infrequently in other nucleic acids, especially not in an animal nucleic acid, preferably mammal, such as human, rat, mouse, etc. Both sense and antisense nucleotide sequences are included.
• a unique nucleic acid according to the present invention can be determined routinely.
• a nucleic acid comprising a unique sequence of PKB kinase can be used as a hybridization probe to identify the presence of PKB kinase in a sample comprising a mixture of nucleic acids, e.g., on a Northern blot.
• Hybridization can be performed under stringent conditions to select nucleic acids having at least 95% identity (i.e., complementarity) to the probe, but less stringent conditions can also be used.
• a unique PKB kinase nucleotide sequence can also be fused in-frame, at either its 5' or 3' end, to various nucleotide sequences as mentioned throughout the patent, including coding sequences for other parts of PKB kinase, enzymes, GFP, etc, expression control sequences, etc.
• Hybridization can be performed under different conditions, depending on the desired selectivity, e.g., as described in Sambrook et al., Molecular Cloning, 1989.
• an oligonucleotide can be hybridized to a target nucleic acid under conditions in which the oligonucleotide only hybridizes to PKB kinase, e.g., where the oligonucleotide is 100% complementary to the target.
• Different conditions can be used if it is desired to select target nucleic acids which have less than 100% nucleotide complementarity, at least about, e.g., 99%, 97%, 95%, 90%, 70%, 67%.
• an oligonucleotide according to the present invention can be used diagnostically.
• a patient having symptoms of a cancer or other condition associated with the PKB kinase signaling pathway can be diagnosed with the disease by using an oligonucleotide according to the present invention, in polymerase chain reaction followed by DNA sequencing to identify whether the sequence is normal.
• the present invention relates to a method of diagnosing a cancer comprising contacting a sample comprising a target nucleic acid with an oligonucleotide under conditions effective to permit hybridization between the target and oligonucleotide; detecting hybridization, wherein the oligonucleotide comprises a sequence of PKB kinase, preferably a unique sequence of PKB kinase; and determining the nucleotide sequence of the target nucleic acid to which the oligonucleotide is hybridized.
• the sequence can be determined according to various methods, including isolating the target nucleic acid, or a cDNA thereof, and determining its sequence according to a desired method.
• a variety of methods can be employed for the diagnostic and prognostic evaluation of cell growth disorders, including cancer, and for the identification of subjects having a predisposition to such disorders.
• Such methods may, for example, utilize reagents such as the PKB kinase nucleotide sequences, and PKB kinase antibodies, as described above.
• reagents such as the PKB kinase nucleotide sequences, and PKB kinase antibodies, as described above.
• such reagents may be used, for example, for: (1) the detection of the presence of PKB kinase gene mutations, or the detection of either over- or under-expression of PKB kinase mRNA relative to the non cell growth disorder state; (2) the detection of either an over- or an under-abundance of PKB kinase gene product relative to the non-cell growth disorder state; and (3) the detection of perturbations or abnormalities in the signal transduction pathway mediated by PKB kinase.
• the methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one specific PKB kinase nucleotide sequence or PKB kinase antibody reagent described herein, which may be conveniently used, e.g.. in clinical settings, to diagnose patients exhibiting cell activation disorder abnormalities.
• any nucleated cell can be used as a starting source for genomic nucleic acid.
• any cell type or tissue in which the PKB kinase is expressed may be utilized.
• Mutations within the PKB kinase gene(s) can be detected by utilizing a number of techniques.
• Nucleic acid from any nucleated cell can be used as the starting point for such assay techniques, and may be isolated according to standard nucleic acid preparation procedures which are well known to those of skill in the art.
• DNA may be used in hybridization or amplification assays of biological samples to detect abnormalities involving gene structure, including point mutations, insertions, deletions and chromosomal rearrangements.
• Such assays may include, but are not limited to, Southern analyses, single stranded conformational polymo ⁇ hism analyses (SSCP), and PCR analyses.
• SSCP single stranded conformational polymo ⁇ hism analyses
• Such diagnostic methods for the detection of PKB kinase specific mutations can involve for example, contacting and incubating nucleic acids including recombinant DNA molecules, cloned genes or degenerate variants thereof, obtained from a sample, e.g.. derived from a patient sample or other appropriate cellular source, with one or more labeled nucleic acid reagents including recombinant DNA molecules, cloned genes or degenerate variants thereof, as described above, under conditions favorable for the specific annealing of these reagents to their complementary sequences within the PKB kinase.
• the lengths of these nucleic acid reagents are at least 15 to 30 nucleotides.
• nucleic acid from the cell type or tissue of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads.
• a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads.
• PKB kinase nucleic acid reagents Detection of the remaining, annealed, labeled PKB kinase nucleic acid reagents is accomplished using standard techniques well known to those in the art.
• the PKB kinase gene sequences to which the nucleic acid reagents have annealed can be compared to the annealing pattern expected from a normal gene sequence in order to determine whether a gene mutation is present.
• Alternative diagnostic methods for the detection of PKB kinase gene specific nucleic acid molecules, in patient samples or other appropriate cell sources may involve their amplification, e.g.. by PCR (the experimental embodiment set forth in Mullis, K.B., 1987, U.S. Patent No. 4,683,202), followed by the detection of the amplified molecules using techniques well known to those of skill in the art.
• the resulting amplified sequences can be compared to those which would be expected if the nucleic acid being amplified contained only normal copies of the PKB kinase gene in order to determine whether a gene mutation exists.
• Antibodies directed against wild type or mutant PKB kinase gene products or conserved variants or peptide fragments thereof, which are discussed, above, may also be used as cell growth disorder diagnostics and prognostics, as described herein. Such diagnostic methods, may be used to detect abnormalities in the level of PKB kinase gene expression, or abnormalities in the structure and/or temporal, tissue, cellular, or subcellular location of the PKB kinase, and may be performed in vivo or in vitro, such as, for example, on biopsy tissue.
• the tissue or cell type to be analyzed will generally include those which are known, or suspected, to contain cells express the PKB kinase gene, such as, for example, neutrophil cells which have infiltrated an inflamed tissue.
• the protein isolation methods employed herein may, for example, be such as those described in Harlow and Lane (Harlow, E. and Lane, D., 1988, “Antibodies: A Laboratory Manual", Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York), which is inco ⁇ orated herein by reference in its entirety.
• the isolated cells can be derived from cell culture or from a patient.
• the analysis of cells taken from culture may be a necessary step in the assessment of cells that could be used as part of a cell-based gene therapy technique or, alternatively, to test the effect of compounds on the expression of the PKB kinase gene.
• antibodies, or fragments of antibodies, such as those described above are useful in the present invention to quantitatively or qualitatively detect the presence of PKB kinase gene products or conserved variants or peptide fragments thereof. This can be accomplished, for example, by immunofluorescence techniques employing a fluorescently labeled antibody (see below) coupled with light microscopic, flow cytometric, or fluorimetric detection.
• the antibodies (or fragments thereof) or fusion or conjugated proteins useful in the present invention may, additionally, be employed histologically, as in immunofluorescence, immunoelectron microscopy or non-immuno assays, for in situ detection of PKB kinase gene products or conserved variants or peptide fragments thereof.
• In situ detection may be accomplished by removing a histological specimen from a patient, and applying thereto a labeled antibody or fusion protein of the present invention.
• the antibody (or fragment) or fusion protein is preferably applied by overlaying the labeled antibody (or fragment) onto a biological sample.
• Immunoassays and non-immunoassays for PKB kinase gene products or conserved variants or peptide fragments thereof will typically comprise incubating a sample, such as a biological fluid, a tissue extract, freshly harvested cells, or lysates of cells which have been incubated in cell culture, in the presence of a detectably labeled antibody capable of identifying PKB kinase gene products or conserved variants or peptide fragments thereof, and detecting the bound antibody by any of a number of techniques well-known in the art.
• the biological sample may be brought in contact with and immobilized onto a solid phase support or carrier such as nitrocellulose, or other solid support which is capable of immobilizing cells, cell particles or soluble proteins.
• a solid phase support or carrier such as nitrocellulose, or other solid support which is capable of immobilizing cells, cell particles or soluble proteins.
• the support may then be washed with suitable buffers followed by treatment with the detectably labeled PKB kinase antibody or fusion protein.
• the solid phase support may then be washed with the buffer a second time to remove unbound antibody or fusion protein.
• the amount of bound label on solid support may then be detected by conventional means.
• Solid phase support or carrier is intended to encompass any support capable of binding an antigen or an antibody.
• Well-known supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite.
• the nature of the carrier can be either soluble to some extent or insoluble for the pu ⁇ oses of the present invention.
• the support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody.
• the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod.
• the surface may be flat such as a sheet, test strip, etc.
• Preferred supports include polystyrene beads. Those skilled in the art will know many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation.
• the binding activity of a given lot of PKB kinase antibody or fusion protein may be determined according to well known methods. Those skilled in the art will be able to determine operative and optimal assay conditions for each determination by employing routine experimentation.
• one of the ways in which the antibody can be detectably labeled is by linking the same to an enzyme and use in an enzyme immunoassay (EIA) (Voller, "The Enzyme Linked Immunosorbent Assay (ELISA)", 1978, Diagnostic Horizons 2:1-7, Microbiological Associates Quarterly Publication, Walkersville, MD); Voller et al., 1978, J. Clin. Pathol. 31:507-520; Butler, 1981, Meth. Enzymol.
• EIA enzyme immunoassay
• the enzyme which is bound to the antibody will react with an appropriate substrate, preferably a chromogenic substrate, in such a manner as to produce a chemical moiety which can be detected, for example, by spectrophotometric, fluorimetric or by visual means.
• Enzymes which can be used to detectably label the antibody include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5 -steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase.
• the detection can be accomplished by colorimetric methods which employ a chromogenic substrate for the enzyme. Detection may also be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards.
• Detection may also be accomplished using any of a variety of other immunoassays.
• a radioimmunoassay RIA
• the radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography.
• fluorescent labeling compounds fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin and fluorescamine.
• the antibody can also be detectably labeled using fluorescence emitting metals such as ⁇ c 7
• DTP A diethylenetriaminepentacetic acid
• EDTA ethylenediaminetetraacetic acid
• the antibody also can be detectably labeled by coupling it to a chemiluminescent compound.
• the presence of the chemiluminescent-tagged antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction.
• chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester.
• Bioluminescence is a type of chemiluminescence found in biological systems in, which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds forpu ⁇ oses of labeling are luciferin, luciferase and aequorin. PHARMACEUTICAL PREPARATIONS
• the compounds that are determined to affect PKB kinase gene expression or PKB kinase activity, or the interaction of PKB kinase with any of its binding partners including but not limited to PIP3 or PKB, can be administered to a patient at therapeutically effective doses to treat or ameliorate hematopoietic cell growth disorders, including cancer.
• a therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration of symptoms of such disorders.
• Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g.. for determining the LD ⁇ Q
• the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD ⁇ Q/ED ⁇ Q.
• Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
• the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
• the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED ⁇ Q with little or no toxicity.
• the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
• the therapeutically effective dose can be estimated initially from cell culture assays.
• a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC ⁇ Q (i.e.. the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
• IC ⁇ Q i.e. the concentration of the test compound which achieves a half-maximal inhibition of symptoms
• levels in plasma may be measured, for example, by high performance liquid chromatography.
• compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.
• the compounds and their physiologically acceptable salts and solvates may be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration.
• the pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g.. pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g.. lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g.. magnesium stearate, talc or silica); disintegrants (e.g... potato starch or sodium starch glycolate); or wetting agents (e.g.. sodium lauryl sulphate).
• binding agents e.g.... pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose
• fillers e.g... lactose, microcrystalline cellulose or calcium hydrogen phosphate
• lubricants e.g.. magnesium stearate, talc or silica
• disintegrants e.g.
• Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use.
• Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g.. sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g.. lecithin or acacia); non-aqueous vehicles (e.g.. almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g.. methyl or propyl-p- hydroxybenzoates or sorbic acid).
• the preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.
• Preparations for oral administration may be suitably formulated to give controlled release of the active compound.
• the compounds may be formulated for parenteral administration by injection, e.g.. by bolus injection or continuous infusion.
• Formulations for injection may be presented in unit dosage form, e.g.. in ampoules or in multi-dose containers, with an added preservative.
• the assay used to purify PKB kinase activities contained l ⁇ l of column fraction which was mixed with 5 ⁇ l of a mixture (put together 5 mins before use and stored on ice) of: 1) 3 ⁇ l of [ ⁇ PJ-ATP 5 ⁇ Ci; (1 ⁇ M final concentration in assay); 2) l ⁇ l of assay buffer (0.1 M KCl, 5 mM MgCl 2 , 1 mM EGTA, 30 mM HEPES, pH 7.4, 30°C; final concentrations in a 6 ⁇ l assay); 3) 0.5 ⁇ l of (EE)-PKB (final concentration 2.5 ⁇ M; the stock was in PBS containing ImM DTT, 1 mM EGTA and then mixed 1: 1 (v/v) with glycerol; the kinase was purified from SF9 cells infected with clonal, recombinant bacullo-virus, the protein purified via its (EE)-tag and the eluting peptid
• the assays were run for 12 mins at 30°C, stopped by the addition of 400 ⁇ l of ice- cold 1% triton XI 00, 0.3 M NaCl, 10 mM EDTA, 1 mM sodium pyrophosphate, 10 mM ⁇ - glycerophosphate, 50 mM sodium flouride, 1 mM EGTA, 0.01% azide, 25 mM HEPES pH 7.4, 4°C and then 30 ⁇ l of ⁇ (EE) beads (4 ⁇ l of packed beads per assay; protein G-sepharose covalently crosslinked to a saturating quantity of ⁇ (EE) monoclonal antibody).
• the SEC buffer contained 0.15 M NaCl, 20 mM HEPES pH 7.4 4°C, 0.5 mM EGTA 0.1 mM EDTA, 1% betaine, 0.03% Tween 20, 0.01% azide, 2mM ⁇ - glycerophosphate, ImM DTT and pepstatin A, leupeptin, aprotinin and antipain (all 2 ⁇ gml "1 ).
• Fig. 1 shows that phosphatidylinositol(3,4,5)-trisphosphate [ 32 P]-PtdIns(3,4,5)P 3 binding protein(s) co-purify with the PKB kinase activity and that ultimately four distinct forms of PKB kinase can be resolved from larger scale versions of similar partially-purified preparations. All four activities phosphorylate and activate (as judged by mylein basic protein (MBP) phosphorylation) PKB in the presence of the biological stereoisomers of PtdIns(3,4,5)P 3 or PtdIns(3,4)P 2 (e.g.
• MBP mylein basic protein
• the purified kinases were, like the partially purified activity, (a) inactive against PKB in the presence of the enantiomers of these lipids or PtdIns(4,5)P 2 ; (b) active at lower concentrations of stearoylarachidonyl than dipalmitoyl versions of these lipids and (c) equally effectively activated by D-D-S/A-PtdIns(3,4,5)P 3 and its diastereoisomer only differing in the arrangement of the chiral centre in the glycerol backbone (i.e.
• the lipid vesicles were prepared by: sonicating dry lipid films into 0.2 M sucose; 20 mM KCl; 20 mM HEPES, pH 7.4 30°C; 0.01% azide (to give 200 ⁇ M phosphatidylcholine, 150 ⁇ M phosphatidylserine, 20 ⁇ M phosphatidylethanolamine, 10 ⁇ M spingomylin plus the indicated concentrations of inositol lipids final in the assay.
• the assays were to estimate associated of the kinases with the lipid vesicles then after 4 mins at 30°C the assays were centrifuged (airfuge (Beckman) maximum speed for 30 mins). Aliquots of the supernatents were removed for assays or immunoblotting. The pellets were rinsed rapidly with assay buffer, recentrifuged and dissolved in SDS-sample buffer. Phosphorylation of PKB(s) was quantitated as described herein.
• PKB kinases(s) can bind [ 32 P]-PtdIns(3,4,5)P 3 and that phosphorylation of a water-soluble, 30-mer peptide, based on the sequence of PKB around Thr308, was dramatically inhibited by PtdIns(3,4,5)P 3 or PtdIns(3,4)P 2 (not shown).
• a preparation of PKB kinase A was Western blotted onto nitrocellulose and trypsinised in situ. The liberated peptides were subjected to analysis by N-terminal sequencing and mass spectrometry. See, L.R. Stephens et al, Cell 89, 105-114 (1997). Four peptides were defined and used to search the data bases; a family of human EST sequences were identified (TIGR: THC 193570).
• a version was also constructed using a cDNA missing the nucleotides coding for residues 188-213 (this was made using IMAGE clones 510982 and 526583: referred to in the text as the 'kinase-compromised splice varient'). All constructs were verified by sequencing. These proteins were expressed in, and purified from cos-7 cells (See, L.R. Stephens et al, Cell 89, 105-114 (1997), see, Fig. 4.). The protein with the intact protein kinase domain phosphorylated PKB in a PtdIns(3,4,5)P 3 -sensitive manner indicating that this activity resided in the ORF defined in Fig. 3.
• proteins were purified via their (EE)-tags (myc antibodies were used as controls) and aliquots were Western blotted.
• PVDF filters probed with an ⁇ (EE) monoclonal antibody (detection by ECL; right hand upper panel) were then stained with Coomassie blue (left hand upper panel; data shown are for (EE)-II only; similar results were obtained with (EE)-I).
• Aliquots were assayed for PKB kinase activity in the presence of lipid vesicles either with or without D-D- S/A-PtdIns(3,4,5)P 3 and [ ⁇ 32 P]-ATP (300 nM; 3 ⁇ M and 1 ⁇ M final concentrations, respectively).
• a photograph of an autoradiogram is shown displaying [ 32 P] in PKB.
• PKB is a key enzyme in the PIP3 pathway, and is involved in regulating cell growth. It has been implicated in certain human cancers; for instance, it is known to be amplified in a percentage of ovarian carcinomas, breast carcinomas, and pancreatic carcinomas. See, Bellacosa, A. et al. (1995) Int. J. Cancer 64, pages 280-285, and Cheng, J. Q. et al. (1996) Proc. Natl. Acad. Sci. U.S.A. vol. 93, 3636-3641. The amplification of the enzyme affords tumor cells a mechanism to circumvent apoptosis. Thus, it will be appreciated that drugs that inhibit PKB activity will be beneficial for the treatment of diseases involving unwanted cell growth, including cancer. One way to achieve this end is to develop assays that measure the effect of compounds on PKB kinase activity.
• the identification of PKB kinase inhibitors can be achieved by assaying for compounds that inhibit PIP3 activation of PKB kinase activity. This would be done by measuring PKB phosphorylation in the presence and absence of a compound.
• the assay can be carried out as described above, or by Stokoe, D., et al (1997) Science, vol. 277, pages 567-570.
• terminally EE-tagged forms of the 55 kd PKB kinase would be incubated with PIP3, an ATP regenerating system, preferrably consisting of 5 mM MgC12, 2 mM ATP, 10 mM creatine phosphate, creatine kinase (50 ug/ml), 1% NP-40, and PKB, or another suitable substrate.
• PKB can be immunoprecipitated and the amount of phosphorlyation determined.

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