# Patent

## Title
Detection of gleevec resistant mutations

## Abstract

The present invention relates to isolated polypeptides which comprise an amino acid sequence consisting of a mutated functional Abl kinase domain, said mutated functional kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof, to the use of such polypeptides to screen for compounds which inhibit the tyrosine kinase activity of such polypeptides, to nucleic acid molecules encoding such polypeptides, to recombinant vectors and host cells comprising such nucleic acid molecules and to the use of such nucleic acid molecules in the production of such polypeptides for use in screening for compounds which inhibit the tyrosine kinase activity of such polypeptides.

## Background
This application is a continuation of U.S. application Ser. No. 11/343,891 filed Jan. 31, 2006 pending, which is a continuation of U.S. Application Ser. No. 10/263,480 filed Oct. 3, 2002, now abandoned, which claims benefit of U.S. Provisional application No. 60,327,387, filed Oct. 5, 2001, incorporated by reference in their entirety.


FIELD OF THE INVENTION
This invention relates to isolated polypeptides which comprise an amino acid sequence consisting of a mutated functional Abl kinase domain, said mutated functional kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof, to the use of such polypeptides to screen for compounds which inhibit the tyrosine kinase activity of such polypeptides, to nucleic add molecules encoding such polypeptides, to recombinant vectors and host cells comprising such nucleic acid molecules and to the use of such nucleic acid molecules in the production of such polypeptides for use in screening for compounds which inhibit the tyrosine kinase activity of such polypeptides.
BACKGROUND OF THE INVENTION
Bcr-Abl, a constitutively activated tyrosine kinase resulting from the formation of the Philadelphia chromosome [Nowell P. C. and Hungerford D. A., Science 132, 1497 (1960)] by reciprocal translocation between the long arms of chromosomes 9 and 22 [Rowley J. D., Nature 243, 290-293 (1973)], has been established as the characteristic molecular abnormality present in virtually all cases of chronic myeloid leukemia (CML) and up to 20 percent of adult acute lymphoblastic leukemia (ALL) [Faderl S. et al., N Engl J Med 341, 164-172 (1999); Sawyers C. L., N Engl J Med 340, 1330-1340 (1999)]. Bcr-Abl is sufficient to cause CML in mice [Daley G. Q. et al., Science 247, 824-830 (1990)] and its transforming capacity is absolutely dependent on tyrosine kinase activity [Lugo T. G. et al., Science 247, 1079 (1990)]. The compound N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide (hereinafter also referred to as “STI571”; STI571 is described in EP-0 564 409 and, in the form of the methane sulfonate salt, in WO 99/03854), a competitive inhibitor at the ATP-binding site of Bcr-Abl, as well as of the receptor for platelet-derived growth factor, and c-kit tyrosine kinase [Lugo T. G. et al., Science 247, 1079 (1990)], has been shown to be capable of very rapidly reversing the clinical and hematological abnormalities of CML in chronic phase and in blast crisis as well as of Ph-chromosome-positive (Ph+) acute lymphoblastic leukemia (Ph+ ALL) [Druker B. J. et al., N Engl J Med 344, 1031-1037 (2001); Druker B. J. et al., N Engl J Med 344, 1038-1042 (2001)]. Whereas almost all chronic phase CML patients durably respond, remissions in CML blast crisis and Ph+ ALL are transient, and most patients relapse after several months, despite continued therapy with STI571 [Druker B. J. et al., N Engl J Med 344, 1038-1042 (2001)]. The mechanism of resistance to STI571 is subject of intense research.
I was now surprisingly found that mutations present in the kinase domain of the Bcr-Abl gene of patients suffering from CML or Ph+ ALL account for the biological resistance of these patients towards STI571 treatment in that said mutations lead to resistance of the Bcr-Abl tyrosine kinase towards inhibition by STI571.
These findings are extremely valuable in e.g. finding new compounds or combinations of compounds which are capable to overcome resistance towards treatment with STI571. Moreover, knowledge of such mutations is also very useful in the diagnosis of Ph+ leukemias in that it allows e.g. the detection of drug-resistant clones before clinical relapse of the patient.
Definitions:
Within the context of this disclosure the following expressions, terms and abbreviations have the meanings as defined below:

    
    
        In the expression “a mutated functional Abl kinase domain”, the part “mutated Abl kinase domain” refers to the native human Abl kinase domain containing mutations including amino acid exchanges, amino acid deletions and/or amino acid additions.
        In the expression “a mutated functional Abl kinase domain”, the term “functional” indicates that the respective kinase domain possesses tyrosine kinase activity. Preferably, the kinase activity of the mutated functional Abl kinase domain is in the range of that of the native human Abl kinase domain.
        In the expression “a mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by STI571 or a salt thereof”, the term “resistant” means that STI571 inhibits the respective mutated functional Abl kinase domain with an IC50 that is higher than that of the native human Abl kinase domain, i.e. higher than about 0.025 μM, preferably higher than about 0.15 μM, more preferably higher than about 0.25 μM, most preferably higher than about 5 μM.
        In the expression “amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof”, the part “or an essentially similar sequence thereof” refers to the amino acid sequence of the native human Abl kinase domain containing mutations, including amino acid exchanges, amino add deletions and/or amino acid additions, that are not essential for the functionality of the kinase and its resistance to inhibition by STI571 or a salt thereof within the meaning of the term “functional” and “resistant” as defined hereinabove.
        The expression “replaced by another amino acid” refers to the replacement of a certain natural amino acid by another natural amino acid.
        The names of the amino acids are either written out or the one letter or three letter codes are used. Mutations are referred to by accepted nomenclature, e.g. “Ala380Thr” or “380 Ala→Thr” both indicating that alanine at position 380 is replaced by threonine.
        SEQ ID NO:1 represents the cDNA coding for the native human Abl protein (human c-abl mRNA; GenBank Accession No.: X16416).
        SEQ ID NO:2 represents the amino acid sequence of the native human Abl protein (human c-Abl; SwissProt Acc. No.: P00519).
        Unless indicated otherwise, the number given for a certain amino acid refers to the numbering of the amino acids in SEQ ID NO:2. In an amino acid sequence that is essentially similar to the amino acid sequence of the native human Abl kinase domain within the meaning as defined above, the amino acids are numbered in accordance with the numbering of the amino acids in SEQ ID NO:2.
        The term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring).
        A “host cell”, refers to a prokaryotic or eukaryotic cell that contains heterologous DNA that has been introduced into the cell by any means, e.g., electroporation, calcium phosphate precipitation, microinjection, transformation, viral infection, and the like.
    
    




DESCRIPTION OF THE INVENTION
In practicing the present invention, many conventional techniques in molecular biology, microbiology, and recombinant DNA are used. These techniques are well known and are explained in, for example, Current Protocols in Molecular Biology, Volumes I, II, and III, 1997 (F. M. Ausubel ed.); Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; DNA Cloning: A Practical Approach, Volumes I and II, 1985 (D. N. Glover ed.); Oligonucleotide Synthesis, 1984 (M. L. Gait ed.); Nucleic Acid Hybridization, 1985, (Hames and Higgins); Transcription and Translation, 1984 (Hames and Higgins eds.); Animal Cell Culture, 1986 (R. I. Freshney ed.); Immobilized Cells and Enzymes, 1986 (IRL Press); Perbal, 1984, A Practical Guide to Molecular Cloning; the series, Methods in Enzymology (Academic Press, Inc.); Gene Transfer Vectors for Mammalian Cells, 1987 (J. H. Miller and M. P. Calos eds., Cold Spring Harbor Laboratory); and Methods in Enzymology Vol. 154 and Vol. 155 (Wu and Grossman, and Wu, eds., respectively).
In particular, the polypeptides of the present invention can be produced by recombinant DNA technology using techniques well-known in the art. Methods which are well known to those skilled in the art can be used to construct expression vectors containing the sequences encoding the polypeptides of the invention and appropriate transcriptional/translational control signals. A variety of host-expression vector systems can be utilized to express the polypeptides of the invention.

    (1) The invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain that is resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (2) The invention further relates in particular to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (3) The invention especially relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid selected from Leu248, Glu255, Lys271, Glu286, Met290, Thr315, Tyr320, Asn322, Glu373, His375 and Ala380 is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (4) A preferred embodiment of the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid selected from Leu248, Glu255, Lys271, Glu286, Met290, Tyr320, Asn322, Glu373, His375 and Ala380 is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (5) Another preferred embodiment of the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid selected from Leu248, Lys271, Glu286, Met290, Tyr320, Asn322, Glu373, His375 and Ala380 is replaced by another amino acid, said mutated functional. Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (6) Another especially preferred embodiment of the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid-sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid selected from Glu255, Thr315 and Ala380 is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (7) Another very preferred embodiment of the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which at least one amino acid selected from Glu255 and Ala380 is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (8) Most preferably the invention relates to an isolated polypeptide-according to any one of the preceding paragraphs (2)-(7), wherein in the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof a single amino acid is replaced by another amino acid.
    (9) The invention relates very especially preferred to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof in which Glu255 is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (10) Most especially preferred the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof that contains at least one amino acid mutation selected from Glu255Val, Glu255Lys, Thr315Val, Thr315Leu, Thr315Met, Thr315Gln, Thr315Phe and Ala380Thr, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (11) In a further very preferred embodiment the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof that contains at least one amino acid mutation selected from Glu255Val, Thr315Val, Thr315Leu, Thr315Met, Thr315Gln, Thr315Phe and Ala380Thr, said mutated functional Abl kinase-domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)benzamide or a salt thereof.
    (12) In another especially preferred embodiment the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino add sequence of the native human Abl kinase domain or an essentially similar sequence thereof that contains at least one amino add mutation selected from Thr315Leu, Thr315Met, Thr315Gln and Thr315Phe, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (13) Most preferably the invention relates to an isolated polypeptide according to any one of the preceding paragraphs (10)-(12), wherein the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof contains a single amino acid mutation.
    (14) Preferred above all the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain or an essentially similar sequence thereof that contains the amino acid mutation Glu255Val, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
    (15) In a preferred embodiment the invention relates to an isolated polypeptide according to any one of the preceding paragraphs (2)-(14), wherein the amino acid sequence of the native human Abl kinase domain consists of amino acids 229-500 of SEQ ID NO:2.
    (16) In another preferred embodiment the invention relates to an isolated polypeptide according to any one of the preceding paragraphs (2)-(15), said isolated polypeptide being a Bcr-Abl tyrosine kinase.
    (17) In yet another preferred embodiment the invention relates to the use of an isolated polypeptide of any one of the preceding paragraphs (2) to (16) to screen for compounds which inhibit the tyrosine kinase activity of said polypeptide.
    (18) The invention also relates to an isolated nucleic acid molecule comprising a nucleotide sequence that encodes a polypeptide according to any one of the preceding paragraphs (2)-(16).
    (19) The invention further relates to the use of a nucleic acid molecule of the preceding paragraph (18) in the production of a polypeptide of any one of the preceding paragraphs (2) to (16) for use in screening for compounds which inhibit the tyrosine kinase activity of said polypeptide.
    (20) The invention also relates to a recombinant vector comprising a nucleic acid molecule according to the preceding paragraph (18).
    (21) The invention further relates especially to a recombinant vector according to the preceding paragraph (20), which is a recombinant expression vector.
    (22) The invention also relates to a host cell comprising a recombinant vector according to the preceding paragraph (20) or (21).


Preferably the invention relates to an isolated polypeptide which comprises a mutated functional Abl kinase domain comprising the amino acid sequence of the native human Abl kinase domain in which at least one amino acid is replaced by another amino acid, said mutated functional Abl kinase domain being resistant to inhibition of its tyrosine kinase activity by N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-4-(4-methyl-piperazin-1-ylmethyl)-benzamide or a salt thereof.
Most preferred are the mutations described herein, which are present in patients who suffer from Philadelphia chromosome-positive leukemia and are resistant against treatment with STI571.
A preferred salt of STI571 is the methane sulfonate salt described in WO 99/03854.
Screening for compounds which inhibit the tyrosine kinase activity of the polypeptides of the invention may be done for example by using an isolated polypeptide of the invention in any in vitro tyrosine kinase phosphorylation assay known in the art and determining the potential of a compound to inhibit the tyrosine kinase activity of a polypeptide of the invention in such an assay.
High-throughput screening assays known in the art may be used to screen large compound libraries for compounds which inhibit the tyrosine kinase activity of the polypeptides of the invention.
Besides the random screening of large compound libraries, the polypeptides of the present invention may also be used in the following screening approach: The 3-dimensional structure of a polypeptide of the invention is determined by e.g. X-ray crystallography. The atomic coordinates of a polypeptide of the invention are then used to design a potential inhibitor. Said potential inhibitor is then synthesized and tested for its ability to inhibit the tyrosine kinase activity of the polypeptide of the invention in any in vitro tyrosine kinase phosphorylation assay.
EXAMPLES
The following Examples serve to illustrate the invention without limiting its scope.
Example 1
Methods:
Plasmids and Site Directed Mutagenesis:
The hybrid cDNA coding for HckAblSH1 was cloned by amplifying the respective DNA fragments from pUCΔNdeI/XbaIHck [Warmuth M. et al., J. Biol. Chem. 272, 33260-70 (1997)] and pcDNA3bcr-abl. These fragments were ligated blunt end to yield pUCΔNdeI/XbaIhckablSH1. Because of its relatively small size when compared to Bcr-Abl or c-Abl, this construct, hckAblSH1, allowed to introduce point mutations into the kinase domain of Abl by a one step cloning procedure. Point mutations were introduced into hckablSH1 using the QuickChange site directed mutagenesis protocol from Stratagene (La Jolla, Calif.). In order to introduce point mutations into Bcr-Abl, a KpnI/Eco47III-subfragment of Bcr-Abl containing the sequence coding for Bcr-Abl's kinase domain was cloned into pUCΔNdeI/XbaI engineered by site directed mutagenesis to contain an Eco47III site in the polylinker. After introduction of point mutations, this fragment was first recloned into pcDNA3abl. Thereafter, the 5′ part of abl up to the KpnI site was substituted by Bcr coding sequences using a KpnI-fragment from pcDNA3bcr-abl. All mutations were confirmed by sequencing. For expression in Cos7 and 32D cells cDNAs were cloned into pApuro.
Cell Lines:
Parental 32D cells as well as 32D cells expressing Bcr-Abl and mutants thereof (32Dp210) were grown in Iscove's modified dulbeccos media (IMDM) supplemented with 10% FBS. COS7 cells were cultured in Dulbecco's modified eagle medium (DMEM) containing 4.5 g/l glucose) and supplemented with 10% FBS. All media and FBS were purchased from Gibco Life Technologies, Inc, Karlsruhe, Germany.
Transfection of Cells:
Cos7 cells were transfected using Effecten® transfection reagent as to the guidelines of the manufacturer (Quiagen, Hilden, Germany). 32D cells were transfected by electroporation. Puromycin was used for selection at a concentration of 1 μg/ml.
Cell Lysis:
Cos7 cells were lysed as described recently [Warmuth M. et al., J. Biol. Chem. 272, 33260-70 (1997)]. For lysis, exponentially growing 32D cells were harvested and washed twice in cold PBS. For experiments evaluating the activity profile of STI571, cells were incubated with the indicated concentrations of inhibitor or with DMSO at a density of 5×106 cells/ml for 1.5-2 h. 107 cells were lysed in 100 μl of lysis buffer containing 1% NP-40, 20 mM Tris (pH 8.0), 50 mM NaCl, and 10 mM EDTA, 1 mM phenylmethylsulfonylfluorid, 10 μg/ml aprotinin, 10 μg/ml leupeptin, and 2 mM sodium orthovanadate. After resuspension in lysis buffer, cells were incubated for 25 min on ice. Finally, unsoluble material was removed by centrifugation at 15,000 g. Clarified lysates were checked for protein concentrations using a BioRad protein assay.
Immunoprecipitation:
For immunoprecipitation 150 μl of standardized 32D cell lysate was diluted by addition of 450 μl of incubation buffer containing 20 mM Tris (pH 8.0), 50 mM NaCl, and 10 mM EDTA, 1 mM phenylmethylsulfonylfluorid, 10 μg/ml aprotinin, 10 μg/ml leupeptin, and 2 mM sodium orthovanadate and incubated with 5 μg of the indicated antibodies for 2 hours on a overhead rotor at 4° C. Sepharose A beads (Pharmacia Biotech Inc., Freiburg, Germany) were prepared by washing twice in IP buffer [0.1% NP-40, 20 mM Tris (pH 8.0), 50 mM NaCl, and 10 mM EDTA, 1 mM phenylmethylsulfonylfluorid, 10 μg/ml aprotinin, 10 μg/ml leupeptin, and 2 mM sodium orthovanadate] and added to each sample for 2 additional hours. Finally, the immunoprecipitates were washed three times in IP buffer, subsequently boiled in 2× sample buffer and prepared for SDS-PAGE.
Gel Electrophoresis and Immunoblotting:
Gel electrophoresis and immunoblotting were performed as described [Danhauser-Riedl S. et al., Cancer Res. 56, 3589-96 (1996); Warmuth M. et al., J. Biol. Chem. 272, 33260-70 (1997)] with some minor modifications. Proteins were routinely blotted on nitrocellulose membranes (Schleicher & Schuell, Dassel, Germany). Membranes were blocked in 5% milk powder for 1 h. Primary and secondary antibodies were diluted-1:500 to 1:5000 in TBS containing 1% milk powder. Proteins were detected using the ECL or ECL Plus detection system as recommended by the manufacturer (Amersham, Braunschweig, Germany).
Detection of Apoptosis by Flow Cytometry:
For assessing apoptosis induced by the various kinase inhibitors, cells were incubated with the indicated concentrations of STI571 at a density of 5×104 per ml. Apoptosis was routinely assessed by measuring the binding of FITC-conjugated Annexin V to the membranes of apoptosing cells. About 5×104 cells were taken at the indicated time points and washed once in PBS. Thereafter, cells were resuspended in 195 μl of Annexin V binding buffer and 5 μl of Annexin V-FITC (Bender MedSystems Diagnostics, Vienna, Austria) were added. Cells were mixed and incubated at room temperature for 10-20 min. Afterwards, cells were pelleted again, washed once and resuspended in 190 μl of Annexin V binding buffer. 10 μl of a 20 μg/ml propidium iodide stock solution were added and the ratio of Annexin V-positive to negative cells was determined by FACS-analysis using a Coulter EPICS XL 4-color cytometer.
Results:
Mutations to either Valine (V), Leucine (L), Isoleucine (I), Methionine (M), Glutamine (Q) or Phenylalanine (F) at position 315 and to either Serine (S), Cysteine (C) or Threonine (T) at position 380 were generated in a hybrid kinase, HckAblSH1, consisting of the SH2 and SH3 domain of Hck and the SH1/kinase domain of Abl. When expressed in Cos7 cells, these hybrid kinases and all mutants at position 315 and 380 showed a high spontaneous kinase activity, proving that these positions are not critical for ATP binding (Table 1). In marked contrast, when tested for inhibition by STI571, no inhibition was seen with up to 10 μM of compound for the mutants T315L, T315I, T315M, T315Q and T315F (Table 1), whereas HckAblSH1 wild-type (wt) could be inhibited with similar kinetics by STI571 as were found for Bcr-Abl (IC50 cellular tyrosine phosphorylation (IC50CTP) approx. 0.5 μM). The mutants T315V and A380T retained some partial sensitivity but IC50CTP values were still higher than 10 μM. In contrast, the mutants A380S and A380C displayed sensitivity to STI571, which was comparable to HckAblSH1 wt (see Table 1 for summary).







TABLE 1







Influence of mutations of T315 and A380 of HckAblSH1


on kinase activity and inhibiton by STI571










kinase activity
Inhibition by STI571















T315V
+++
IC50 > 10



T315L
+++
CR



T315I
+++
CR



T315M
++++
CR



T315Q
++
CR



T315F
++
CR



A380C
+++
NS



A380S
+++
NS



A380T
+
IC50 > 10










All data based on inhibition of cellular tyrosine phosphorylation of transiently transfected Cos7 cells determined by Western blot analysis using the monoclonal α-phosphotyrosine antibody PY99. IC50 values were determined using scion image software. Complete remission (CR) was defined as no detectable reduction of cellular tyrosine phosphorylation by 10 μM STI571. NS (normal sensitivity)=inhibition with similar kinetics as HckAblSH1 wt.
Our data identify positions 315 and 380 as critical gatekeepers for the binding pocket of STI571, which contribute to define the sensitivity of individual protein kinases towards STI571. For example, the STI571-insensitive receptor tyrosine kinase Flt-3, which has high homology to the c-Kit and the PDGF-R kinases, has a phenylalanine at the position homologous to T315, which would, based on our data, not be in accordance with STI571 binding. In a similar way, the resistance of most other kinases tested with STI571 could be explained.
In order to investigate whether and to what degree some of the above described point mutations of the gatekeeper position T315 are able to induce biological resistance towards STI571 we introduced into full length Bcr-Abl the mutations T315V, T315L, T315I, T315M, T315Q and T315F. When expressed in Cos7 cells all mutants displayed kinase activity close to or similar to wild-type Bcr-Abl (Bcr-ABLwt). If tested for inhibition by STI571, identical results were obtained as described for the corresponding mutations in HckAblSH1 (Table 2). Similar to Scr-Ablwt, expression of these mutants in 32D, an IL-3-dependent, hematopoietic cell line of murine origin, gave rise to cell lines growing IL-3 independently. Exposure of 32DBcr-Ablwt cells to 1 or 10 μM STI571 lead to a rapid stop of proliferation and induction of apoptotic cell death in more than 90% of cells. On the contrary, if T315 mutant Bcr-Abl kinases, for example T315I, were expressed the block in proliferation and the induction of apoptosis caused by 1 μM STI571 were completely abolished (Table 2) and the effects of STI571 seen at 10 μM were reduced to levels found in control experiments using parental 32D cells grown in the presence of IL-3. Phosphotyrosine blots of samples of cells expressing either wt or mutant Bcr-Abl proteins confirmed that mutations at position 315 completely abolished the effect of STI571 on Abl auto- and substrate phosphorylation, with the exception of T315V which was still to some degree inhibited by STI571 but displayed a similar biological phenotype as the other mutants (Table 2). This suggests that the reminder biological activity of STI571 at 10 μM was rather due to cytotoxicity than to a reminder sensitivity of the mutants or cross-reaction of STI571 with another tyrosine kinase. In summary, all mutations lifted the IC50 for inhibition of proliferation (IC50IOP) from 0.09 to approximately 7.5 μM and for inhibition of survival (IC50IOS) from 0.5 to more than 10 μM (Table 2). Taken together, these data show that mutations of “molecular gatekeeper” positions as described above are able to confer complete biological resistance towards STI571 in a cell culture model.







TABLE 2







Biochemical and biological characterization of mutations


of T315 in Bcr-Abl to amino acids with longer side chains














IC50 (μM) cellular
Induction of
IC50 (μM)
IC50 (μM)



kinase
tyrosine phosphorylation
factor-independent
apoptosis
proliferation













mutant
activity
Cos7
32D
growth in 32D
32D
32D
















(32D)




>10
7.5


wt
+++
0.25
0.25
yes
0.5
0.09


T315V
+++
>10
>10
yes
>10
7.5


T315L
++++
c.r.
c.r.
yes
>10
7.5


T315I
+++
c.r.
c.r.
yes
>10
7.5


T315M
++++
c.r.
c.r.
yes
>10
7.5


T315Q
+++
c.r.
c.r.
yes
>10
7.5


T315F
+++
c.r.
c.r.
yes
>10
7.5





c.r: complete remission (no detectable reduction of cellular tyrosine phosphrylation by 10 μM STI571)






Example 2
STI571 inhibits the Abl tyrosine kinase with an IC50 of 0.025 μM for purified Bcr-Abl and c-Abl but not the fms or the Src family kinases. The mechanism of inhibition is through competitive inhibition of ATP binding. To better understand the mechanism of specificity of the tyrosine kinase inhibitor the Abl kinase was compared to a model of the Lck kinase domain. This model predicts the following sites are critical for STI571 association: L248, Y320, N322, E373, H375 and A380. Each of these residues were changed to the corresponding residue in Src or fms and IC50 values for STI571 with each mutant were determined. L248A and H375L yielded kinase inactive mutants, Y320K, N322S, E373N and A380G had IC50 values identical to wild type Abl. A380T, however, demonstrated an IC50 of 0.34 μM suggesting that STI571 bound less efficiently when a larger residue replaced the alanine. Recent crystallization of the Abl kinase domain with a related inhibitor shows that the configuration of the activation loop of the Abl kinase domain differs significantly from that of the Src family kinases. This structure identifies K271, E286, M290, T315, M318 and D381 as critical contacts of STI571. All of these residues are conserved between Src and Abl. The last two of these bind STI571 via their peptide backbone, thus mutants in these residues cannot be created. The remainder of the residues were mutated to residues lacking the potential for hydrogen bonding and IC50 values were determined. K271R, E286L and M290A were kinase inactive. T315V had an IC50 value of 0.35 μM, which is consistent with the crystal structure of the Abl kinase domain which predicts that the side chain of T315 forms a critical hydrogen bond with STI571.
Example 3
A group of 32 patients who are either refractory to treatment with STI571 or who relapsed whilst being treated were investigated. The median duration of therapy was 95 days; prior to STI571 treatment, two patients were in chronic phase, nine in accelerated phase, 20 in myeloid and, and one in lymphoid blast crisis of the disease. Reverse transcriptase-polymerase chain reaction (RT-PCR) products specific for the Bcr-Abl tyrosine kinase domain were sequenced (Heminested RT-PCR was performed to amplify the sequence specifically coding for the Bcr-Abl tyrosine kinase: 1st step B2B ACAGAATTCCGCTGACCATCAATAAG and A7-AGACGTCGGACTTGATGGAGAACT; 2nd step FA4+ AAGCGCAACAAGCCCACTGTCTAT and A7-).
An acquired A→T point mutation at position 58802 (GeneBank accession number U07563, locus HSABLGR3)—which results in a Glu255Val substitution—was detected in one patient. Restriction analysis of cDNA and genomic DNA (RT-PCR and genomic PCR were performed using primers A4+ TCACCACGCTCCATTATCCA, A4-CTTCCACACGCTCTCGTACA; Mnl I restriction digest of PCR products; removal of an Mnl I restriction site as the result of the point mutation A58802T) was used to confirm the presence of the mutation and to track it during the course of treatment. Only wild-type Abl sequence was present before the STI571 therapy. The patient was treated with STI571 in late chronic phase, went into complete hematologic remission, but progressed to blast crisis after five months. Reactivation of Bcr-Abl was confirmed by CrkI immunoblotting [K. Senechal, Mol. Cell. Biol. 18, 5082 (1998)]. The relative proportion of phosphorylated CrkI (reflecting active Bcr-Abl) was 49% before STI571 therapy, 24% at day 27, 28% at day 83, and 77% at the time of clinical resistance at day 166. The biological significance of the Glu255Val change is determined by an Abl autophosphorylation assay. STI571 inhibits wild-type Abl with an IC50 of 0.025 μM. The mutation leads to a virtual insensitivity to STI571, with an IC50 of >5 μM.
Example 4
The Bcr-Abl kinase domain from cells obtained from 12 CML and Ph+ acute leukemia patients who relapsed while receiving STI571 was sequenced. A functional point-mutation in the kinase domain in one case was identified. This was a G→A change that results in a Glu→Lys substitution at position 255 of Abl.
Example 5
Patients and Sample Preparation:
Thirty bone marrow samples from 21 patients with Ph+ ALL who were enrolled into consecutive “Phase II study to determine the safety and anti-leukemic effect of STI571 in adult patients with Ph+ acute leukemias” were analyzed. According to the study protocol, these patients had relapsed ALL or were refractory after at least 2 cycles of standard chemotherapy. From all of the patients, samples were obtained before beginning STI571 treatment: 13 of these samples were from individuals who later were classified as good responders to STI571 (Nos. 1-13, sensitive, S) including 12 patients with hematological complete remission (CR) and one patient with partial remission (PR) but complete peripheral hematological recovery (No. 1). Eight samples were collected from individuals who later were found not to respond to STI571 (Nos. 14-21, primarily resistant, R) including 6 patients without any hematological response, one with cytoreduction in the bone marrow but persistent peripheral leukemic cells (No. 20) and another with PR but incomplete peripheral hematological recovery (No. 16). Matched bone marrow samples from 9 patients (Nos. 1-5 and Nos. 14-17) were also obtained while they were on treatment with STI571. Mononuclear cells were separated by density gradient centrifugation through Ficoll-Hypaque (Biochrom, Berlin, Germany). Total RNA was extracted using the acid guanidium/phenol/chloroform method with minor modifications. [Puissant C. and Houdebine L. M., Biotechniques 8, 148-149 (1990)]. Only samples with leukemic blast cell infiltration of more than 80% were included into the analysis.
Reverse Transcription Polymerase Chain Reaction and Sequencing Analysis:
One microgram of total RNA was used for reverse transcription (RT) by Superscript II RT (Life Technologies, Grand Island, N.Y.) according to standard protocols, Primers specific for the ATP binding site of ABL including the ‘loop’ were designed using gene bank information GI6382056: ATP-F 5′-GCG CAA CAA GCC CAC TGT CT-3′; ATP-R 5′-GCA CTC CCT CAG GTA GTC CA-3′ and LOOP-F 5′-TGG ACT ACC TGA GGG AGT GC-3′; LOOP-R 5′-CGG TAG TCC TTC TCT AGC AGC-3′. Oligonucleotides were synthesized by Life Technologies. Polymerase chain reaction (PCR) was performed as described previously [Hofmann W. K. et al., Leuk. Res. 25, 333-338 (2001)] using an annealing temperature of 58° C. PCR-products were separated on a 2% agarose gel containing 0.3 mg/ml ethidium bromide and purified using the QIAquick purification system (Qiagen, Valencia, Calif.) according to the manufacturers protocol. The purified DNA was directly sequenced in both directions (sense and antisense) by the ABI PRISM dye terminator cycle sequencing reaction (Perkin-Elmer, Foster, Calif.).
Results:
Analysis of the sequence of the ATP binding site revealed a single point mutation at nucleotide 1127 (GI6382056) changing a G to an A resulting in a substitution at codon 255 of Lys (mutant) for a Glu (wild-type). This mutation was found in 6 samples from patients after they were treated with STI571 (Nos. 1, 2, 4, 5, 15, 16) but mutations were not found in any other sample including the matched samples from the patients before beginning treatment with STI571 (Table 3). The change was verified by sequencing from both the sense and antisense directions. In addition, one sample (No: 17) from a patient with an aberrant CALL had a single point mutation at nucleotide 1308 changing a C to T resulting in a substitution at codon 315 of isoleucine (mutant) for a threonine (wild-type). This sample was unusual because the cells also expressed CD33, a cell surface protein expressed on myeloid cells.
Our data strongly suggest that E255K developed during treatment with STI571. Our analysis of matched samples found, that none of the samples from untreated patients (including sensitive patients and those with primary resistance) had this mutation. In contrast, six of 9 samples (67%) from these patients undergoing treatment with STI571 had this substitution at E255. The overall frequency of mutations in the ATP binding site was 7 of 9 (78%) in our paired bone marrow samples from patients undergoing therapy with STI571.







TABLE 3







Matched bone marrow samples: Development of mutations


in the region coding for the ATP binding site of ABL


during treatment of Ph+ ALL with STI571.













ABS status

ABS status




prior to treatment
Response
after treatment


No.
Diagnosis
with STI571
to STI571
with STI571














1
Ph+ cALL
Wild type
PR
E255K


2
Ph+ cALL
Wild type
CR
E255K


3
Ph+ cALL
Wild type
CR
Wild type


4
Ph+ cALL
Wild type
CR
E255K


5
Ph+ cALL
Wild type
CR
E255K


14
Ph+ cALL
Wild type
no
Wild type


15
Ph+ cALL
Wild type
no
E255K


16
Ph+ pre
Wild type
PR
E255K



B-ALL


17
Ph+ cALL,
Wild type
no
T315I



CD33+





ABS, ATP binding site; PR, partial remission; CR, complete remission; Ph+ cALL, Philadelphia chromosome positive, common ALL (CD10+).

## Claims

1. A method of detecting a mutant Abl kinase domain polypeptide in a subject, comprising
determining the sequence of a nucleic acid encoding an Abl kinase domain polypeptide in a sample from the subject; and
comparing the amino acid sequence encoded by the nucleic acid with the amino acid sequence set forth as SEQ ID NO: 2,
wherein a difference in the amino acid sequence of the Abl kinase domain polypeptide from the sample from SEQ ID NO: 2 indicates the presence of mutant Abl kinase domain polypeptide in the subject.

2. The method of claim 1 wherein the difference in the amino acid sequence is an amino acid substitution at position 315.

3. The method of claim 1 wherein the difference in the amino acid sequence is an amino acid substitution at position 255.

4. The method of claim 1, wherein determining the nucleic acid sequence comprises reverse transcriptase polymerase chain reaction.

5. The method of claim 1, wherein determining the nucleic acid sequence comprises DNA sequencing.

6. The method of claim 1, wherein the method comprises detection of an A to T point mutation that results in a glutamic acid to valine substitution or a G to A point mutation that results in the substitution of lysine for glutamic acid at position 255.

7. The method of claim 2, wherein the method comprises detection of a C to T point mutation that results in a substitution of isoleucine for threonine at position 315.

8. The method of claim 1, wherein the subject has a tumor.

9. The method of claim 8, wherein the tumor is a leukemia.

10. The method of claim 9, wherein the leukemia is myelogenous leukaemia.

11. The method of claim 2 wherein the subject has a tumor, and wherein the presence of an amino acid substitution at amino acid position 315 indicates that the tumor is resistant to kinase inhibition by STI-571.

12. The method of claim 7, wherein the subject has a tumor, and wherein the detection of an C to T point mutation that results in a substitution of isoleucine for threonine at position 315 of SEQ ID NO:2 indicates that the tumor is resistant to kinase inhibition by STI-571.

13. The method of claim 3, wherein the subject has a tumor, and wherein the presence of an amino acid substitution at amino acid position 255 indicates that the tumor is resistant to kinase inhibition by STI-571.

14. The method of claim 6, wherein the subject has a tumor, and wherein the detection of an A to T point mutation that results in a glutamic acid to valine substitution or a G to A point mutation that results in the substitution of lysine for glutamic acid at position 255 of SEQ ID NO:2 indicates that the tumor is resistant to kinase inhibition by STI-571.