HK1212397B - Method to determine responsiveness of cancer to epidermal growth factor receptor targeting treatments - Google Patents

Description

Method for determining responsiveness of cancer to epidermal growth factor receptor targeted therapy

The application is a divisional application of an invention patent application with the application date of 2005, 3 and 31 and the application number of 201210028631.5, and the invention name is the same as that of the invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims U.S. provisional application serial No. filed 3/31/2004 under 35U.S. C.119 (e): 60/558,218, U.S. provisional application serial No. 4/9 in 2004: 60/561,095, U.S. provisional application serial No. 4/27 in 2004: 60/565,753, U.S. provisional application serial No. 4/27 in 2004: 60/565,985, U.S. provisional application serial No. 5/25/2004: 60/574,035, U.S. provisional application serial No. 6/7 in 2004: 60/577,916 and U.S. provisional application serial No. filed on 29/7/2004: 60/592,287, the contents of which are hereby incorporated by reference in their entirety.

Government support

The present invention is supported by National Institutes of Health (NIH) accreditation numbers RO 1CA 092824, P50CA 090578, PO195281, and 1K12CA87723-01, the U.S. government having certain rights therein.

Technical field and background

Epithelial cell cancers, e.g., prostate cancer, breast cancer, colon cancer, lung cancer, pancreatic cancer, ovarian cancer, spleen cancer, testicular cancer, thymus cancer, and the like, are diseases characterized by abnormal, accelerated growth of epithelial cells. This accelerated growth initially initiates tumor formation. Finally, metastasis to different organ sites can also occur. Although some progress has been made in the diagnosis and treatment of various cancers, these diseases still result in significant mortality.

Lung cancer is the leading cause of cancer death in industrialized countries. Cancers that start in the lung are classified into two major types, non-small cell lung cancer and small cell lung cancer, depending on how the cells appear under the microscope. Non-small cell lung cancers (squamous cell carcinoma, adenocarcinoma, and large cell carcinoma) generally spread to other organs more slowly than small cell lung cancer. Approximately 75% of lung cancer cases are classified as non-small cell lung cancer (e.g., adenocarcinoma), while the other 25% are small cell lung cancers. Non-small cell lung cancer (NSCLC) is the leading cause of cancer death in the united states, japan and western europe. Chemotherapy offers the most modest benefit in survival for patients with progressive disease, but at the cost of significant toxicity, underscoring the need for therapeutic agents that specifically target the critical genetic impairment of lipoguided tumor growth (Schiller JH et al, N Engl J Med, 346: 92-98, 2002).

Epidermal Growth Factor Receptor (EGFR) is a 170 kilodalton (kDa) membrane-bound protein that is expressed on the surface of epithelial cells. EGFR is a member of the growth factor receptor family of protein tyrosine kinases, a class of cell cycle regulatory molecules (W.J. Gullick et al, 1986, Cancer Res., 46: 285-292). EGFR is activated when its ligand (EGF or TGF-. alpha.) binds to the extracellular domain, resulting in autophosphorylation of the tyrosine kinase domain within the receptor cells (S.Cohen et al, 1980, J.biol.chem., 255: 4834-4842; A.B.Schreiber et al, 1983, J.biol.chem., 258: 846-853).

EGFR is a protein product of the growth-promoting oncogene, erbB or erbB1, but this gene is a member of a family, the erbB family of proto-oncogenes, which is believed to play an important role in the development and progression of many human cancers. In particular, increased EGFR expression has been observed in breast, bladder, lung, head, neck and stomach cancers as well as glioblastomas. The ERBB family of oncogenes encodes four, structurally related transmembrane receptors, namely EGFR, HER-2/neu (erbB2), HER-3(erbB3) and HER-4(erbB 4). Clinically, ERBB Oncogene amplification and/or receptor overexpression in tumors has been reported to be associated with disease recurrence and poor patient prognosis, as well as with responsiveness in therapy (L.Harris et al, 1999, int.J.biol.markers, 14: 8-15; and J.Mendelsohn and J.Baselga, 2000, Oncogene, 19: 6550-.

EGFR consists of three major domains, the extracellular domain (ECD), which is glycosylated and contains a ligand-binding pocket and two cysteine-rich regions; a short transmembrane domain, and an intracellular domain with intrinsic tyrosine kinase activity. The transmembrane region connects the ligand binding domain to the intracellular domain. Amino acid and DNA sequence analysis, as well as studies of The unglycosylated form of EGFR, have shown that The protein backbone of EGFR has a mass of 132kDa, with 1186 amino acid residues (A.L.Ullrich et al, 1984, Nature, 307: 418 425; J.Downward et al, 1984, Nature, 307: 521-.

Binding of EGF or TGF- α to EGFR activates signal transduction pathways and leads to cell proliferation. Dimerization, conformational changes and internalization of EGFR serve to transmit cellular signaling leading to cell growth regulation (G.Carpenter and S.Cohen, 1979, Ann.Rev.biochem., 48: 193-216). Genetic changes that affect growth factor receptor function, or cause overexpression of the receptor and/or ligand, result in cell proliferation. In addition, EGFR has been determined to play a role in cell differentiation, increased cell motility, protein secretion, neovascularization, invasion, metastasis and cancer cell tolerance to chemotherapeutic agents and radiation. (M. -J.Oh et al, 2000, Clin.cancer Res., 6: 4760-.

A variety of inhibitors of EGFR have been identified, including a variety that have been clinically tested for the treatment of various cancers. A recent summary, see de Bono, j.s. and Rowinsky, E.K. (2002), "The ErbB receiver Family: ATherapeutic Target For Cancer ", Trends in Molecular Medicine, 8, S19-26.

A promising group of targets for therapeutic intervention in the treatment of cancer includes members of the HER-kinase axis. They are frequently upregulated in solid epithelial tumors, e.g., prostate, lung, and breast tumors, and are also upregulated in glioblastoma. Epidermal Growth Factor Receptor (EGFR) is a member of the HER-kinase axis and has been the target of choice for the development of several different cancer therapies. EGFR tyrosine kinase inhibitors (EGFR-TKIs) are one of these therapies, as reversible phosphorylation of tyrosine residues is essential for EGFR pathway activation. In other words, EGFR-TKIs suppress cell surface receptors responsible for promoting and/or maintaining cellular signaling pathways that induce tumor chest growth and division. In particular, these inhibitors are believed to interfere with the EGFR kinase domain, designated HER-1. More promising EGFR-TKIs are three series of compounds: quinazolines, pyridopyrimidines and pyrrolopyrimidines.

Two more advanced compounds in clinical development include Gefitinib (compound ZD1839 developed by AstraZeneca UK ltd.; trade name IRESSA; hereinafter "IRESSA") and Erlotinib (compound OSI-774 developed by Genentech, inc. and OSI Pharmaceuticals, inc.; trade name TARCEVA; hereinafter "TARCEVA"); both produce encouraging clinical results. Conventional cancer treatments with IRESSA and TARCEVA all involve oral administration of no more than 500mg of the respective compound per day. In month 5 of 2003, IRESSA became the first of these products to enter the us market when it was approved for the treatment of advanced non-small cell lung cancer patients.

IRESSA is an orally active quinazoline that acts by directly inhibiting tyrosine kinase phosphorylation on the EGFR molecule. It competes for Adenosine Triphosphate (ATP) binding sites, resulting in inhibition of HER-kinase axis. The exact mechanism of the IRESSA response is not completely understood, however, studies suggest that the presence of EGFR is a prerequisite for its action.

A significant limitation in the use of these compounds is that their receptors may develop tolerance to their therapeutic effect after they begin to respond to treatment, or they may not respond at all to EGFR-TKIs to any measurable extent. In fact, only 10-15% of patients with advanced non-small cell lung cancer respond to EGFR kinase inhibitors. Thus, a better understanding of the molecular mechanisms underlying sensitivity to IRESSA and TARCEVA would be of great benefit in targeted therapy for those individuals most likely to benefit from such therapy.

There is a clear need in the art for satisfactory treatment of cancer, particularly epithelial cancers such as lung, ovarian, breast, brain, colon and prostate cancers, that incorporate the benefits of TKI treatment and overcome the anergy exhibited by patients. Such treatment can have dramatic effects on the health of an individual, particularly the elderly where cancer is particularly common.

Disclosure of Invention

Tyrosine Kinase Inhibitor (TKI) therapy such as gefitinibIs not effective in most individuals affected by the above-mentioned cancers. The present inventors have surprisingly found that the presence of somatic mutations in the EGFR kinase domain substantially increases the sensitivity of EGFR to TKIs such as IRESSA, TARCEVA. For example, less than 30% of patients with such cancers are susceptible to treatment by current TKIs, while more than 50%, more preferably 60, 70, 80, 90% of patients with mutations in the EGFR kinase domain are susceptible. In addition, these mutations confer increased kinase activity on EGFR. Thus, patients with these mutations will likely respond to current Tyrosine Kinase Inhibitor (TKI) therapies, e.g., gefitinib.

Accordingly, the present invention provides a novel method for determining the likelihood of effectiveness of Epidermal Growth Factor Receptor (EGFR) targeted therapies in human patients affected by cancer. The method comprises detecting the presence or absence of at least one nucleic acid variation in the kinase domain of the erbB1 gene in said patient relative to the wild-type erbB1 gene. The presence of at least one variation indicates that an EGFR-targeted treatment is likely to be effective. Preferably, the nucleotide variation increases the kinase activity of EGFR. The patient may then be treated with an EGFR-targeted therapy. In one embodiment of the invention, the EGFR targeted therapy is a tyrosine kinase inhibitor. In a preferred embodiment, the tyrosine kinase inhibitor is an anilinoquinazoline. The anilinoquinazoline may be a synthetic anilinoquinazoline. Preferably, the synthetic anilinoquinazoline is gefitinib or erlotinib. In another embodiment, the EGFR-targeting treatment is an irreversible EGFR inhibitor comprising 4-dimethylamino-but-2-enoic acid [4- (3-chloro-4-fluoro-phenylamino) -3-cyano-7-ethoxy-quinolin-6-yl ] -amide ("EKB-569", sometimes referred to as "EKI-569", see, e.g., WO/2005/018677 and Torrance et al, Nature Medicine, vol.6, No.9, Sept.2000, p.1024) and/or HKI-272 or HKI-357 (Wyeth; see Greenberger et al, Proc.111th NCI EORTC-AACR Symposium on New drug in Cancer Therapy, Clinical Cancer Res.Vol.6Supple 2004, Nov.2000, ISSN 1078-0432; Racebin et al, Cancer Res 64: 58. Holbor 3965, Relbu.3944, et al (Tolb, mcd chem.2005, 48, 1107-; and Tejpar et al, J.Clin.Oncol.ASCO Annual Meeting Proc.Vol.22, No. 14S: 3579(2004)).

In one embodiment of the invention, the EGFR is obtained from a biological sample of a patient having or at risk of developing cancer. Variations in the kinase domain of the EGFR (or erbB1 gene) affect the conformational structure of the ATP binding pocket. Preferably, the variation in the EGFR kinase domain is an in-frame deletion or a substitution in exon 18, 19, 20 or 21.

In one embodiment, the in-frame deletion is in exon 19 of egfr (erbb). Preferably the in-frame deletion in exon 19 consists of at least the amino acids leucine, arginine, glutamic acid and alanine at codons 747, 748, 749, and 750 at the deletion. In one embodiment, the in-frame deletion comprises nucleotides 2235-2249 and deletions 746-750 (sequences glutamic acid, leucine, arginine, glutamic acid, and alanine), as shown in Table 2, Table S2, FIG. 2B, FIG. 4A, FIG. 5, FIG. 6C, and FIG. 8C. In another embodiment, the in-frame deletion comprises nucleotide 2236-. Alternatively, the in-frame deletion comprises nucleotide 2240-. Alternatively, the in-frame deletion comprises the deletion of nucleotide 2239-2247 with a guanine substitution at the cysteine at nucleotide 2248, as shown in Table S3A and FIG. 8D, or the deletion of nucleotide 2238-2255 with an adenine substitution at nucleotide 2237, as shown in Table S3A and FIG. 8F, or the deletion of nucleotide 2254-2277, as shown in Table S2(SEQ ID NO: 437). Alternatively, the deletion comprises nucleotides 2239-2250delTTAAGAGAAGCA (SEQ ID NO: 554); 2251A > C, or 2240-.

In another embodiment, the substitution is in exon 2 of EGFR. The substitution in exon 2 comprises at least one amino acid. In one embodiment, the substitution in exon 2 comprises a guanine-thymine substitution at nucleotide 2573, see fig. 4A and 5. Such substitutions result in amino acid substitutions in which the wild-type leucine is replaced with arginine at amino acid 858, see fig. 5, table 2, table S2, table S3A, fig. 2D, fig. 6A, fig. 8B, and SEQ ID NO: 512. alternatively, the substitution in exon 2 comprises an adenine to thymine substitution at nucleotide 2582, see fig. 4A and 5. This substitution resulted in an amino acid substitution in which the wild type leucine was replaced by glutamine at amino acid 861, as shown in FIG. 5(SEQ ID NOS 740 &720, in order of occurrence, respectively), Table 2(SEQ ID NOS 730 &720, 739, in order of occurrence, respectively), FIG. 2E, Table 3B (SEQ ID NOS 554&720 & 729, in order of occurrence, respectively), and SEQ ID NO: 512.

the substitution may also be in exon 18 of EGFR. In one embodiment, the substitution in exon 18 is a thymine to guanine substitution at nucleotide 2155, see fig. 4A and 5. This substitution results in an amino acid substitution in which the wild-type glycine is substituted with cysteine at codon 719, see fig. 5, SEQ ID NO: 512. in another embodiment, the substitution in exon 18 is a guanine to adenine substitution at nucleotide 2155 resulting in an amino acid substitution wherein wild type glycine is substituted with serine at codon 719, as shown in table S2, fig. 6B, fig. 8A, fig. 5 and seq id NO: 512.

in another embodiment, the substitution is an insertion of guanine, and thymine (GGT) (23162317ins GGT) after nucleotide 2316 and before nucleotide 2317 as shown in figure 5. This can also be described as the insertion of valine (V) at amino acid 772 (P772_ H733 insV). Additional mutations are shown in table S3B and include, for example, an insertion of CAACCCGG after nucleotide 2309 and before nucleotide 2310 as shown in figure 5 and an insertion of GCGTGGACA after nucleotide 2311 and before nucleotide 2312 as shown in figure 5. The substitution may also be in exon 20 and in one embodiment is a substitution of AA for GG at nucleotides 2334 and 2335, see table S3B.

In summary, in preferred embodiments, the nucleic acid variation of the erbB1 gene is a thymine to guanine or adenine to guanine substitution at nucleotide 2155 as shown in FIG. 5, a deletion at nucleotides 2235 and 2249, 2240 and 2251, 2240 and 2257, 2236 and 2250, 2254 and 2277, or 2236 and 2244 as shown in FIG. 5, an insertion of the nucleotides guanine, and thymine (GGT) after nucleotide 2316 and before nucleotide 2317 as shown in FIG. 5, and a guanine to thymine or an adenine to thymine substitution at nucleotide 2573 as shown in FIG. 5.

Detection of the presence or absence of at least one nucleic acid variation can be determined by amplification of a nucleic acid fragment encoding the receptor. The fragment to be amplified is 1000 nucleotides long, preferably 500 nucleotides long, most preferably 100 nucleotides long or less. The fragment to be amplified may include a variety of variations.

In another embodiment, detection of the presence or absence of at least one nucleic acid variation provides contacting an EGFR nucleic acid comprising a site of variation with at least one nucleic acid probe. The probes preferably hybridize under selective hybridization conditions to a nucleic acid sequence that includes a site of variation and that includes complementary nucleotides at the site of variation. Hybridization can be detected using a detectable label.

In yet another embodiment, the detection of the presence or absence of at least one nucleic acid variation comprises sequencing at least one nucleic acid sequence and comparing the sequence obtained to a known erbB1 nucleic acid sequence. Alternatively, the presence or absence of at least one nucleic acid variation comprises a mass spectrometric determination of at least one nucleic acid sequence.

In a preferred embodiment, the detection of the presence or absence of at least one nucleic acid variation comprises performing a Polymerase Chain Reaction (PCR). Amplifying the erbB1 nucleic acid sequence comprising the putative variation and determining the nucleotide sequence of the amplified nucleic acid. Determining the nucleotide sequence of the amplified nucleic acid comprises sequencing at least one nucleic acid fragment. Alternatively, the amplification products can be analyzed by using any method capable of separating the amplification products according to their sizes, including automated and manual gel electrophoresis, and the like.

Alternatively, the detection of the presence or absence of at least one nucleic acid variation comprises determining the haplotype of a plurality of variations in a gene.

In another embodiment, the presence or absence of EGFR mutations can be detected by analysis of the erbB1 gene product (protein) t. In this embodiment, probes that specifically bind to variant EGFR are used. In a preferred embodiment, the probe is an antibody that preferentially binds to variant EGFR. The presence of variant EGFR predicts the possibility of EGFR targeted therapy being effective. Alternatively, the probe may be an antibody fragment, a chimeric antibody, a humanized antibody or an aptamer.

The invention further provides a probe that specifically binds to a nucleotide sequence comprising at least one nucleic acid variation in the EGFR gene (erbB1) under selective binding conditions. In one embodiment, the variation is a mutation in the kinase domain of erbB1 that confers a structural change to the ATP-binding pocket.

Probes of the invention may comprise a nucleotide sequence of about 500 nucleotide bases, preferably about 100 nucleotide bases, and most preferably about 50 nucleotide bases or about 25 nucleotide bases or less in length. The probe may be composed of DNA, RNA, or Peptide Nucleic Acid (PNA). In addition, the probe may comprise a detectable label, such as, for example, a fluorescent or enzymatic label.

The present invention additionally provides a novel method of determining the likelihood that an Epidermal Growth Factor Receptor (EGFR) targeted therapy will be effective in a patient affected by cancer. The method comprises determining the kinase activity of EGFR in a biological sample from the patient. The increase in kinase activity after stimulation with EGFR ligands compared to normal controls indicates that EGFR-targeted therapy is likely to be effective.

The invention further provides a novel method of treating a patient having or at risk of developing cancer. The method comprises determining whether the kinase domain of EGFR of the patient comprises at least one nucleic acid variation. Preferably, the EGFR is located at the site of a tumor or cancer and the nucleic acid variation is somatic. The presence of such a variation indicates that EGFR-targeted therapy will be effective. Administering a tyrosine kinase inhibitor to the patient if the variation is present.

As above, the tyrosine kinase inhibitor administered to the identified patient may be an anilinoquinazoline or an irreversible tyrosine kinase inhibitor, such as, for example, EKB-569, HKI-272 and/or HKI-357 (Wyeth). Preferably, the anilinoquinazoline is a synthetic anilinoquinazoline and most preferably the synthetic anilinoquinazoline is gefitinib and erlotinib.

Cancers to be treated by the methods of the invention include, for example, but are not limited to, gastrointestinal cancer, prostate cancer, ovarian cancer, breast cancer, head and neck cancer, lung cancer, non-small cell lung cancer, nervous system cancer, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genitourinary system cancer, and bladder cancer. In a preferred embodiment, the cancer is non-small cell lung cancer.

Kits for carrying out the PCR methods of the invention are also included. The kit comprises at least one pair of degenerate primers designed to anneal to a border nucleic acid region of a gene encoding the ATP-binding pocket of the EGFR kinase domain. In addition, the kit comprises the products and reagents necessary to carry out the PCR amplification, as well as instructions.

In a preferred embodiment, the primer pair comprised in the kit is selected from the group consisting of SEQ ID NO: 505, SEQ ID NO: 506, SEQ ID NO: 507, and SEQ ID NO: 508. the primers listed in tables 6 and 7in the examples are also preferred.

In yet another embodiment, the invention discloses a method of selecting a compound that inhibits the catalytic kinase activity of a variant Epidermal Growth Factor Receptor (EGFR). As a first step, variant EGFR is contacted with a potential compound. The resulting kinase activity of the variant EGFR is then detected and compounds are selected that inhibit the kinase activity of the variant EGFR. In one embodiment, the variant EGFR is contained in a cell.

The methods can also be used to select compounds that have a variant EGFR kinase activity with secondary mutations in the kinase domain that confer tolerance to TKIs, such as gefitinib or erlotinib.

In one embodiment, the variant EGFR is labeled. In another embodiment, EGFR is bound to a solid support. In a preferred embodiment, the solid support is a protein chip.

In yet another embodiment of the present invention, a pharmaceutical composition for inhibiting the catalytic kinase activity of a variant Epidermal Growth Factor Receptor (EGFR) is disclosed. The compound that inhibits the catalytic kinase activity of the variant EGFR is selected from the group consisting of antibodies, antibody fragments, small molecules, peptides, proteins, antisense nucleic acids, ribozymes, PNAs, sirnas, oligonucleotide aptamers, and peptide aptamers.

Also disclosed is a method of treating a patient suffering from an EGFR-mediated disease. According to the method, a pharmaceutical composition that inhibits the catalytic kinase activity of a variant Epidermal Growth Factor Receptor (EGFR) is administered to a patient.

In one embodiment, the EGFR-mediated disease is cancer. In a preferred embodiment, the cancer is of epithelial origin. For example, the cancer is gastrointestinal cancer, prostate cancer, ovarian cancer, breast cancer, head and neck cancer, lung cancer, non-small cell lung cancer, cancer of the nervous system, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, cancer of the genito-urinary system, and bladder cancer. In a preferred embodiment, the cancer is non-small cell lung cancer.

In another embodiment, a method of predicting secondary mutations (or selection mutations) obtained in the kinase domain of the erbB1 gene is disclosed. Cells expressing a variant form of erbB1 were contacted with an effective, but sub-lethal dose of a tyrosine kinase inhibitor. Cells were selected for growth retardation against tyrosine kinase inhibitors and were analysed for erbB1 nucleic acid for the presence of other mutations in the erbB1 kinase domain. In one embodiment, the cell is in vitro. In another embodiment, the cell is obtained from a transgenic animal. In one embodiment, the transgenic animal is a mouse. In this mouse model, the cells to be studied are obtained from tumor biopsies. Cells selected by the invention that contain a secondary mutation in the erbB1 kinase domain may be used in the above methods to select compounds that inhibit the kinase activity of a variant EGFR that has a secondary mutation in the kinase domain.

In another embodiment where secondary mutations are predicted to be obtained in the kinase domain of the erbB1 gene, cells expressing a variant form of the erbB1 gene are first contacted with an effective amount of a mutagen. Such mutagens are, for example, Ethyl Methanesulfonate (EMS), N-ethyl-N-nitrosourea (ENU), N-methyl-N-nitrosourea (MNU), phosphonobutyric hydrochloride (Pre), methyl methanesulfonate (MeMS), chlorambucil (Chl), melphalan, porcapazine hydrochloride, cyclophosphamide (Cp), diethyl sulfate (Et)₂SO₄) Acrylamide monomer (AA), Triethylenemelamine (TEM), mechlorethamine, vincristine, dimethylnitrosamine, N-methyl-N' -nitro-nitrosoguanidine (MNNG), 7, 12 dimethylbenzene (a) anthracene (DMBA), ethylene oxide, hexamethylphosphoramide, bisufan, or ethyl methyl tauroformate (EtMs). The cells are then contacted with an effective, but sub-lethal dose of a tyrosine kinase inhibitor. Cells were selected for growth retardation against tyrosine kinase inhibitors and were analysed for erbB1 nucleic acid for the presence of other mutations in the erbB1 kinase domain.

Drawings

FIGS. 1A-1B show representative graphical representations of Gefitinib responses in refractory non-small cell lung cancer (NSCLC). A chest CT scan of case 6 (table 1) showed (fig. 1A) large mass in the right lung before treatment with Gefitinib (fig. 1B) a significant improvement occurred six weeks after initiation of Gefitinib treatment.

Figure 2 shows EGFR mutations in Gefitinib-reactive tumors.

FIGS. 2A-2C show the nucleotide sequence of the EGFR gene in tumor samples with heterozygous in-frame deletions (doublets) in the kinase domain (SEQ ID NOS643-644 and 690-699, respectively). Tracking in both sense and antisense orientations showed a two-person breakpoint that demonstrated deletion; wild-type nucleotide sequences are shown in uppercase letters, while mutant sequences are shown in lowercase letters. The 5' breakpoint of the delL747-T751insS mutation is preceded by a T-C substitution, which does not alter the encoded amino acid.

FIGS. 2D and 2E show heterozygous missense mutations (arrows) resulting in amino acid substitutions in the tyrosine kinase domain (SEQ ID NOS 701& 703). The doublets represent two nucleotides at the site of the heterozygous mutation. For comparison, the corresponding wild-type sequences are also shown (SEQ ID NOS 700& 702).

Figure 2F is a scheme of binding of dimeric EGFR molecules by EGF ligands. Highlighting the extracellular domain (containing two receptor ligands [ L)]-a domain and a furin-like domain), a transmembrane region, and a cytoplasmic domain (comprising a catalytic kinase domain). Tyrosine indicating autophosphorylation sites Using receptor activation markers¹⁰⁶⁸(Y-1068), and downstream effectors activated by EGFR autophosphorylation (STAT3, MAP kinase (MAPK), and AKT). The localization of tumor-associated mutations, all in the tyrosine kinase domain, is shown.

Figure 3 demonstrates enhanced EGF-dependent activation of mutant EGFR and increased sensitivity of mutant EGFR to Gefitinib.

FIG. 3A shows the ligand-induced activation time course of the delL747-P753insS and L858R mutants after addition of EGF to serum-starved cells compared to wild-type EGFR. EGFR autophosphorylation was used as a marker for receptor activation using phosphorylated tyrosines that specifically recognize EGFR as compared to the total level of EGFR expressed in Cos-7 cells (control; right panel)¹⁰⁶⁸Western blot of antibody for residues (left panel). Autophosphorylation of EGFR was measured at intervals of EGF addition (10 ng/ml).

FIG. 3B is a graphical representation of EGF induction of phosphorylation of wild type and mutant receptors (see panel A). Quantification of autoradiograms from three independent experiments using NIH image software; the intensity of EGFR phosphorylation was normalized to overall protein expression and shown as percent activation of the receptor with standard deviation.

Figure 3C shows dose-dependent inhibition of EGFR activation by Gefitinib. Demonstration of tyrosine of EGFR by Western blot analysis of Cos-7 cells expressing wild-type or mutant receptors¹⁰⁶⁸And stimulated with 100ng/ml EGF for 30 min. Cells were either left untreated (U) or pretreated with increasing concentrations of Gefitinib for 3hrs as indicated (left panel). The total amount of EGFR protein expressed is shown as a control (right panel).

Figure 3D shows quantification of the results from two experiments described for plate 3C (NIH image software). Phosphorylated EGFR concentration was normalized to protein expression level and expressed as percent activation of the receptor.

FIG. 4 shows clustering of mutations at key sites within the ATP-binding pocket of EGFR.

FIG. 4A shows the position of overlapping in-frame deletions in exon 19 and missense mutations in exon 21 of the EGFR gene in various NSCLC cases (SEQ ID NOS 495-504 (DNA)). For each exon, a partial nucleotide sequence is shown, with deletions marked by dashed lines and highlighted and missense mutations underlined; the wild-type EGFR nucleotide and amino acid sequence is shown (SEQ ID NOS 493&494(DNA) &509-510 (amino acids)).

Figure 4B shows the spatial structure of EGFR ATP cleft flanked by amino (N) and carboxyl (C) protrusions of the kinase domain (equivalent from PDB1M14 and demonstrated using Cn3D software). Inhibitor Gefitinib, shown to occupy ATP cleft. The location of two missense mutations is shown, within the activating loop of the kinase; all three in-frame deletions are present in another loop, flanking the ATP cleft.

Figure 4C shows a close-up of the EGFR kinase domain showing the amino acid residues associated with binding ATP or inhibitor.

Specifically, 4-anilinoquinazoline compounds such as gefitinib, are catalyzed by occupying the ATP binding site inhibition, where they form hydrogen bonds with methionine 793(M793) and cysteine 775(C775) residues, while their aniline rings are adjacent to methionine 766(M766), lysine (K745), and leucine 788(L788) residues. In-frame deletions within the loop targeted by the mutation are predicted to alter the position of these amino acids relative to the inhibitor. The mutated residue is shown to be within the activation loop of the tyrosine kinase.

Figure 5 shows the nucleotide and amino acid sequence of the erbB1 gene. The amino acids are described as single letters known to those skilled in the art. Nucleotide variations in the kinase domain are highlighted by patient number, see table 2. Nucleotides 1 to 3633 are included as shown in FIG. 5. SEQ ID NO: 512 includes amino acids 1 through 1210.

FIGS. 6A-6C: sequence alignment of selected regions within the EGFR and B-Raf kinase domains. Delineation of EGFR mutations in human NSCLC. Mutations in iEGFR (gb: X00588;) NSCLC tumors are highlighted in gray. The B-Raf (gb: M95712) mutations in various tumor types (5) are highlighted in black. Asterisks indicate conserved residues between residues EGFR and B-Raf. FIG. 6A depicts the L858R mutation in the activation loop (SEQ ID NOS 477-479). FIG. 6B depicts the G719S mutation in the P loop (SEQ ID NOS 480-482). FIG. 6C depicts a deletion mutation in exon 19 of EGFR (SEQ ID NOS 483-489).

FIG. 7: missense mutations G719S and L858R in the three-dimensional structure of the EGFR kinase domain and the location of the Del-1 deletion. The activation ring is shown in yellow and the P-ring is shown in blue and indicates the C-terminal protrusion and the N-terminal protrusion. Residues targeted by mutations or deletions are highlighted in red. The Del-1 mutation targets the residue ELREA of codon 746-750. Mutations are localized in highly conserved regions within kinases and are found in the p-loop and activation loop, which surround ATP and are also regions where gefitinib and erlotinib are predicted to bind.

Fig. 8A-8f representative chromatograms of EGFR DNA from normal tissue and from tumor tissue. The location of the identified mutations is as follows. FIG. 8A depicts the exon 18 kinase domain P loop (SEQ ID NOS 704-705). FIG. 8B depicts the exon 21 kinase domain A-loop (SEQ ID NOS 706-707). FIG. 8C depicts the exon 19 kinase domain Del-1(SEQ ID NOS 708-710). FIG. 8D depicts the exon 19 kinase domain Del-3(SEQ ID NOS 711-713). FIG. 8E depicts the exon 19 kinase domain Del-4(SEQ ID NOS 714-716). FIG. 8F depicts the exon 19 kinase domain Del-5(SEQ ID NOS 717-719).

FIG. 9: sequence alignment of EGFR and BCR-ABL polypeptides and the location of residues conferring a drug tolerance phenotype. The EGFR polypeptide (SEQ ID NO: 492) encoded by the nucleotide disclosed in GenBank accession No. NM005228 and the BCR-ABL polypeptide (SEQ ID NO: 491) encoded by the nucleotide sequence disclosed in GenBank accession No. M14752 are aligned and the conserved residues are shaded. BCR-ABL mutations conferring tolerance to the tyrosine kinase inhibitor imatinib (STI571, Gleic/Gleevec) are indicated by asterisks.

Figure 10 shows the decision making procedure for EGFR testing for patients with metastatic NSCLC.

FIG. 11 is a diagram of EGFR exons 18-24 (not to scale). Arrows depict the location of identified mutations. Asterisks indicate the number of patients with mutations at each position. The single cross plot depicts the overlap of exon 19 deletions, as well as the number of patients with each deletion (nucleotide 2233. sup. 2277 and residue 745. sup. 749 of SEQ ID NO: 512, as shown in FIG. 5). Note that these results do not include all EGFR mutations at present.

Detailed Description

The present invention provides a novel method for determining the likelihood that an Epidermal Growth Factor Receptor (EGFR) targeted therapy will be effective in human patients affected by cancer. The method comprises detecting the presence or absence of at least one nucleic acid variation in the kinase domain of the erbB1 gene in said patient. The presence of at least one variation indicates that an EGFR-targeted treatment is likely to be effective. Preferably, the nucleotide variation increases the kinase activity of EGFR. The patient may then be treated with an EGFR-targeted therapy. In one embodiment of the invention, the EGFR targeted therapy is a tyrosine kinase inhibitor. In a preferred embodiment, the tyrosine kinase inhibitor is an anilinoquinazoline. The anilinoquinazoline may be a synthetic anilinoquinazoline. Preferably, the synthetic anilinoquinazoline is gefitinib or erlotinib.

Defining:

the terms "ErbB 1", "epidermal growth factor receptor", and "EGFR" are used interchangeably herein and refer to the compounds as described, for example, in Carpenter et al ann.rev.biochem.56: 881 (1987) including variants thereof (e.g., deletion mutant EGFR as described in Humphrey et al PNAS (USA) 87: 4207 (1990)). ErbB1 refers to a gene encoding an EGFR protein product.

The term "nucleotide variation that increases kinase activity" as used herein refers to a variation (i.e., a mutation) in the nucleotide sequence of a gene that results in increased kinase activity. The increased kinase activity is a direct result of a variation in the nucleic acid and the protein encoded by the gene is associated.

The term "drug" or "compound" as used herein refers to a chemical entity or biological product, or a combination of chemical entities or biological products, that is administered to an individual for the treatment or prevention or control of a disease or condition. Preferably, but not necessarily, the chemical entity or biological product is a low molecular weight compound, but may also be a larger compound, such as an oligomer of nucleic acids, amino acids, or carbohydrates, including but not limited to proteins, oligonucleotides, ribozymes, dnases, glycoproteins, siRNAs, lipoproteins, aptamers, and modifications and combinations thereof.

The term "genotype" in the context of the present invention refers to a particular allelic form of a gene, which may be defined by the presence of a particular nucleotide at a particular site in a nucleic acid sequence.

The term "variant form of a gene", "form of a gene", or "allele" refers to a particular form of a gene in a population that differs from other forms of the same gene in at least one, and often more than one, sequence of the gene sequence. Sequences at these sites of variation that differ between different alleles of a gene are referred to as "gene sequence variations" or "variants". Other equivalent terms known in the art include mutations and polymorphisms, although mutations are often used to refer to alleles associated with deleterious phenotypes. In a preferred aspect of the invention, the variation is selected from the variations listed in the variation tables herein.

In the context of the present invention, the term "probe" refers to a molecule capable of detectably distinguishing structurally different target molecules. Depending on the type of probe and the type of target molecule used, detection can be achieved in a number of different ways. Thus, for example, the detection may be a difference in the level of activity of the gene target molecule, but detection based on specific binding is preferred. Examples of such specific binding include antibody binding and nucleic acid probe hybridization. Thus, for example, probes may include enzyme substrates, antibodies and antibody fragments, preferably nucleic acid hybridization probes.

As used herein, the terms "effective" and "effectiveness" include pharmaceutical effectiveness and physiological safety. Pharmaceutically effective refers to the ability of a treatment to result in a desired biological effect in a patient. Physiological safety refers to the level of toxicity, or other deleterious physiological effects (often referred to as side effects) at the cellular, tissue and/or biological level that result from administration of a treatment. "less effective" means that the treatment results in a therapeutically significant lower level of pharmaceutical effectiveness and/or a therapeutically higher level of deleterious physiological effects.

The term "primer", as used herein, refers to an oligonucleotide that: that is, such an oligonucleotide can serve as a point of initiation of polynucleotide synthesis along a complementary strand when placed under conditions that catalyze the synthesis of a primer extension product that is complementary to the polynucleotide. These conditions include the presence of four different nucleotide triphosphates or nucleoside analogues and one or more agents for polymerization, such as DNA polymerase and/or reverse transcriptase, in an appropriate buffer ("buffer" includes as a cofactor or ingredient that affects pH, ionic strength, etc.), and at an appropriate temperature. The primer must be long enough to prime the synthesis of extension products in the presence of reagents for the polymerase. Typical primers contain a sequence that is substantially complementary to the target sequence that is at least about 5 nucleotides in length, but somewhat longer primers are preferred. The primers will typically contain about 15-26 nucleotides, but longer primers may also be used.

The primers always contain a sequence which is substantially complementary to the target sequence, i.e.the specific sequence to be amplified to which the primer can anneal. The primer may optionally comprise other sequences in addition to the sequence complementary to the target sequence. The term "promoter sequence" defines a single strand of a nucleic acid sequence specifically recognized by an RNA polymerase that binds to the recognized sequence and initiates the transcription process that produces an RNA transcript. In principle, any promoter sequence can be used, as long as there are known polymerases available for the promoter that are capable of recognizing the starting sequence. Known useful promoters are those recognized by certain phage polymerases, such as bacteriophage T3, T7, or SP 6.

A "microarray" is a linear or two-dimensional array of preferably discrete regions, each region having a defined area, formed on the surface of a solid support. From the surface of a single solid supportThe total number of target polynucleotides to be detected determines the density of discrete regions on the microarray, preferably at least about 50/cm²More preferably at least about 100/cm²And even more preferably at least about 500/cm²And more preferably at least about 1,000/cm². As used herein, a DNA microarray is an array of oligonucleotide primers disposed on a chip or other surface for amplifying or cloning a target polynucleotide. Since the position of each specific primer set in the array is known, their properties can be determined based on the binding of the target polynucleotide to a specific position in the microarray.

The term "label" refers to a composition that is capable of producing a detectable signal indicative of the presence of a target polynucleotide in an assay sample. Suitable labels include radioisotopes, nucleotide chromophores, enzymes, substrates, fluorescent molecules, chemiluminescent moieties, magnetic particles, bioluminescent moieties and the like. Thus, a label is any composition that can be detected by spectroscopic, photochemical, biochemical, immunochemical, electronic, optical or chemical means.

The terms: "support" refers to conventional supports such as beads, particles, rods, fibers, filters, membranes, and silane or silicate supports such as glass slides.

The term "amplification" broadly refers to the generation of amplification products that may include, for example, other target molecules, or target-like molecules or molecules complementary to target molecules resulting from the presence of target molecules in a sample. In the case where the target is a nucleic acid, the amplification product may be enzymatically produced using a DNA or RNA polymerase or a transcriptase.

As used herein, "biological sample" refers to a sample of tissue or fluid isolated from an individual, including, but not limited to, for example, blood, plasma, serum, tumor biopsy tissue, urine, stool, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, external secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, cells (including but not limited to blood cells), tumors, organs, and also includes samples of in vitro cell culture components. In preferred embodiments, the sample is from an excision, bronchial biopsy, or core needle biopsy of a primary or metastatic tumor, or a cell mass from pleural effusion. Thereafter, the sample was aspirated using a fine needle. The sample may be paraffin embedded or frozen tissue.

The term "antibody" means an immunoglobulin that is capable of binding an antigen. An antibody as used herein is meant to include antibody fragments, such as F (ab ') 2, Fab', Fab, which are capable of binding to the antigen or antigen fragment of interest. Preferably, the antibody binds to an antigen that inhibits the activity of a variant form of EGFR.

The term "humanized antibody" is used herein to describe a fully antibody molecule, i.e., consisting of two complete light chains and two complete heavy chains, and consisting of antibody fragments only, e.g., Fab', f (ab)2, and Fv, in which the CDRs are derived from a non-human source and the remaining part of the Ig molecule, or parts thereof, is derived from a human antibody, preferably from a nucleic acid sequence encoding a human antibody.

The terms "human antibody" and "humanized antibody" are used herein to describe an antibody in which all portions of the antibody molecule are derived from a nucleic acid sequence encoding a human antibody. These human antibodies are suitable for use in antibody therapy, as these antibodies will elicit a small or no immune response in human patients.

The term "chimeric antibody" is used herein to describe antibody molecules as well as antibody fragments, as described above in the definition of the term "humanized antibody". The term "chimeric antibody" expresses a humanized antibody. A chimeric antibody has at least a portion of a heavy or light chain amino acid sequence from a first mammalian species and another portion of a heavy or light chain amino acid sequence from a second, different mammalian species.

Preferably, the variable region is derived from a non-human mammalian species and the constant region is derived from a human species. Specifically, the chimeric antibody is preferably produced from a non-human mammal 9 nucleotide sequence encoding a variable region and a human nucleotide sequence encoding an antibody constant region.

Table 2 is a partial listing of DNA sequence variations in the kinase domain of erbB1 that are relevant to the methods described in the present invention. These changes were identified by the inventors in studies of biological samples from patients with NSCLC who responded to gefitinib, as well as patients who were not exposed to gefitinib.

Nucleic acid molecules can be isolated from a particular biological sample using any technique known in the art, the particular isolation method chosen being appropriate for the particular biological sample. For example, freeze-thaw and alkaline lysis methods can be used to obtain nucleic acid molecules from the solid material; thermal and alkaline lysis methods can be used to obtain nucleic acid molecules from urine; proteinase K extraction, in turn, can be used to obtain nucleic acids from blood (Rolff, A et al PCR: Clinical Diagnostics and Research, Springer (1994).

Detection method

The presence or absence of a particular variation or variations in the kinase domain of the erbb gene in a patient having or at risk of developing cancer may be determined in a variety of ways. These tests are typically performed using DNA or RNA samples collected from biological samples, such as biopsies, urine, stool, saliva, blood, cells, tissue scrapings, breast aspirates, or other cellular material, and can be performed by a variety of methods, including, but not limited to, PCR, hybridization to allele-specific probes, enzymatic mutation detection, chemical shear mismatch, mass spectrometry, or DNA sequencing, including mini-sequencing. In particular embodiments, hybridization to allele-specific probes can be performed in two formats: (1) allele-specific oligonucleotides are bound to solid phases (glass, silicon, nylon membranes) and labeled samples in solution, as in many DNA chip applications, or (2) sample (often cloned DNA or PCR amplified DNA) and labeled oligonucleotides (which may be allele-specific or short to allow sequencing by hybridization) are bound in solution. Diagnostic tests may include a set of variations, often on a solid support, that enable the simultaneous determination of more than one variation.

In another aspect, a haplotype test is necessary to determine the presence of at least one nucleic acid variation in the erbB1 gene that increases kinase activity. Methods for determining haplotypes are known to those skilled in the art, for example, in WO 00/04194.

Preferably, determining the presence or absence of at least one nucleic acid variation that increases kinase activity comprises determining the sequence of the variation site by Polymerase Chain Reaction (PCR). Alternatively, determining the presence or absence of a nucleic acid variation that increases kinase activity may comprise strand end DNA sequencing or mini-sequencing, oligonucleotide hybridization or mass spectrometry.

The methods of the invention can be used to predict the likelihood that an EGFR-targeted treatment will be effective (or ineffective) in a patient having or at risk of developing cancer. Preferably, the cancer comprises cancer of epithelial tissue origin, including, but not limited to, gastrointestinal cancer, prostate cancer, ovarian cancer, breast cancer, head and neck cancer, lung cancer, non-small cell lung cancer, nervous system cancer, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genitourinary system cancer, and bladder cancer. In a preferred embodiment, the cancer is non-small cell lung cancer.

The present invention relates generally to the identification of variations in the kinase domain of the erbB1 gene that are an indication that EGFR-targeted therapy is effective in patients having or at risk of developing cancer. Furthermore, the identification of specific variations in the kinase domain of EGFR can, in effect, be used as a diagnostic or prophylactic test. For example, the presence of at least one variation in the kinase domain of the erbB1 gene indicates that the patient will likely benefit from treatment with an EGFR-targeting compound, such as, for example, a tyrosine kinase inhibitor.

Methods for diagnostic testing are well known in the art and are disclosed in patent application WO 00/04194, which is incorporated herein by reference. In an exemplary method, the diagnostic test comprises amplifying DNA or RNA (typically after converting RNA into eDNA) fragments spanning one or more variations in the kinase domain of the erbB1 gene sequence. Such amplified fragments are then sequenced and/or subjected to polyacrylamide gel electrophoresis to identify nucleic acid variations in the amplified fragments.

PCR

In one embodiment, the invention provides a method of screening for variation in the kinase domain of the erbB1 gene by PCR, or, alternatively, in Ligation Chain Reaction (LCR) (see, e.g., Landegran, et al, 1988, Science 241: 1077-. The method comprises the following steps: degenerate primers are designed for amplification of a target sequence, the primers corresponding to one or more conserved regions of a gene, an amplification reaction is performed with the primers using DNA or eDNA obtained from a test biological sample as a template, and PCR products are analyzed. Comparison of the PCR products of the test biological sample with the control sample indicates variation in the test biological sample. The change can be a deletion or presence of a nucleic acid variation in the test biological sample.

Alternative amplification methods include: self-sustained sequence replication (see, Guatelli, et al, 1990.Proc. Natl. Acad. Sci. USA 87: 1874-; qb replicase (see, Lizardi, et al, 1988.Biotechnology 6: 1197), or any other nucleic acid amplification method, and the amplified molecules are then detected using techniques well known to those skilled in the art. These detection schemes are particularly useful for the detection of nucleic acid molecules if these molecules are present in very low numbers.

Useful primers according to the invention are designed using the amino acid sequence of a protein or the nucleic acid sequence of the kinase domain of erbB1 gene as a guide, for example the sequences shown in SEQ ID NO: 493, SEQ ID NO: 494, SEQ ID NO: 509, and SEQ ID NO: 510. primers are designed in the homologous regions of the gene, where at least two homologous regions are separated by a difference in variable sequence, which is variable in length or nucleic acid sequence.

For example, identical or highly homologous, preferably having at least 80% -85%, more preferably at least 90-99% homologous amino acid sequences of at least about 6, preferably at least 8-10, linked amino acids. Most preferably, the amino acid sequences are 100% identical. Forward and reverse primers were designed based on codon degeneracy and the retention of various amino acids at given positions between known gene family members. The degree of homology referred to herein is based on amino acid sequence analysis using standard sequence comparison software, such as protein-BLAST (http:// www.ncbi.nlm.nih.gov/BLAST /) using the default settings.

The usage of degenerate codons and their standard symbols are given in table 3 below:

preferably any 6-fold degenerate codons such as L, R and S are avoided as they will introduce more than 6-fold degeneracy. TTR and CTN are traded off to YTN (8-fold degeneracy) for L, CGN and AGR are traded off to MGN (8-fold degeneracy) for R, and finally S, TCN and AGY can be traded off to WSN (16-fold degeneracy). Inall three cases on 6 of the se will match the target sequence. To avoid this loss of specificity, it is preferred to avoid these regions, or to make two populations, each population having alternative degenerate codons, e.g., S in one set comprising TCN and AGY in the other set.

Utilizing a variety of existing computer programs, including, but not limited to Oligo Analyzer 3.0; OligoCalculator; NetPrimer; a Methprimer; primer 3; WebPrimer; PrimerFinder; primer 9; oligo 2002; pride or GenomePride; oligos; and Codehop allows the design of primers. Details about these procedures can be found, for example, in www.molbiol.Net.

The primers can be labeled using labels known to those skilled in the art. These labels include, but are not limited to, radioactive, fluorescent, dye, and enzymatic labels.

Analysis of the amplification products can be performed by any method capable of separating the amplification products according to their sizes, including automated and manual gel electrophoresis, mass spectrometry, and the like.

Alternatively, the amplification products can be isolated using sequence differences, using SSCP, DGGE, TGGE, chemical cleavage or restriction fragment polymorphisms and hybridization to, for example, a nucleic acid array.

Methods for nucleic acid isolation, amplification and analysis are routine to those skilled in the art and examples of protocols can be found, for example, in Molecular Cloning: a Laboratory Manual (3-Volume Set) Ed. Joseph Sambrook, David W.Russel, and Joe Sambrook, Cold Spring Harbor Laboratory; 3rd edition (January15, 2001), ISBN: 0879695773. particularly useful protocol sources for PCR amplification are PCR (Basics: From Background to Bench) by M.J.McPherson, S.G.Mller, R.Beynon, C.Howe, Springer Verlag; 1st edition (October 15, 2000), ISBN: 0387916008.

preferably, exons 19 and 21 of human EGFR are amplified by Polymerase Chain Reaction (PCR) using the following primers: exon 19 sense primer, 5'-GCAATATCAGCCTTAGGTGCGGCTC-3' (SEQ ID NO: 505); exon 19 antisense primer, 5'-CATAGAA AGTGAACATTTAGGATGTG-3' (SEQ ID NO: 506); exon 21 sense primer, 5'-CTAACGTTCG CCAGCCATAAGTCC-3' (SEQ ID NO: 507); and exon 21 antisense primer, 5'-GCTGCGAGCTCACCCAG AATGTCTGG-3' (SEQ ID NO: 508).

In an alternative embodiment, mutations in the EGFR gene from the sample cells can be identified by changes in the restriction enzyme cleavage pattern. For example, sample and control DNA are separated, amplified (optionally), digested with one or more restriction enzymes, and fragment length sizes determined by gel electrophoresis and compared. The difference in fragment length size between the sample and control DNA indicates a mutation in the sample DNA. In addition, the use of sequence-specific ribozymes (see, e.g., U.S. Pat. No.5,493,531) can be used to assess the presence of specific mutations by the formation or deletion of ribozyme cleavage sites.

Other methods of detecting mutations in the EGFR gene include methods that utilize a protective nicking agent to detect mismatched bases in RNA/RNA or RNA/DNA hybrid duplexes. See, e.g., Myers, et al, 1985.Science 230: 1242. generally, the art "mismatch splicing" technique begins by providing a hybrid duplex formed by hybridizing (labeling) RNA or DNA comprising wild-type EGFR sequences with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplex is treated with an agent that cleaves a single-stranded region of the duplex, such as the region that exists due to base mismatches between the control and sample strands. For example, an RNA/DNA duplex can be treated with RNase and a DNA/DNA hybrid treated with S1 ribozyme to enzymatically digest mismatched regions. In other embodiments, both DNA/DNA or RNA/DNA duplexes may be treated with hydroxylamine or osmium tetroxide or with piperidine to digest mismatched regions. After digestion of mismatch I, the resulting material was subsequently size fractionated on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton, et al, 1988.proc.Natl.Acad.Sci.USA 85: 4397; saleeba, et al, 1992, Methods Enzymol.217: 286-295. In one embodiment, the control DNA or RNA may be labeled for detection.

In yet another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA in a defined system that detects and maps the final spectrum of point mutations in EGFR cDNAs obtained from cellular samples (so-called "DNA mismatch repair" enzymes). For example, the mutY enzyme of E.coli (E.coli) cleaves A on G/A mismatches and the thymine DNA glycosylase from Hela cells cleaves T on G/T mismatches. See, e.g., Hsu, et al, 1994. carcinogenetics 15: 1657-1662. According to an exemplary embodiment, EGFR-based sequences, e.g., DEL-1 to DEL-5, G719S, G857V, L883S or L858R EGFR sequences, will be hybridized to cDNA or other DNA products from test cells. The double helix is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected by electrophoresis or the like. See, for example, U.S. Pat. No.5,459,039.

In other embodiments, the change in electrophoretic mobility will be used to identify mutations in the EGFR gene. For example, single-stranded conformational polymorphism (SSCP) can be used to detect differences in electrophoretic mobility between mutant and wild-type nucleic acids. See, for example, Orita, et al, 1989. proc.natl.acad.sci.usa: 86: 2766; cotton, 1993, mut.res.285: 125-144; hayashi, 1992, genet.anal.tech.appl.9: 73-79. The single stranded DNA fragments of the sample and the control EGFR nucleic acid will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies depending on the sequence, and the resulting change in electrophoretic mobility makes it possible to detect even a single base change. The DNA fragments may be labeled or detected with a labeling probe. The sensitivity of the assay can be increased by using RNA (rather than DNA), where the secondary structure is more sensitive to changes in sequence. In one embodiment, the subject methods utilize hybrid duplex analysis to separate double-stranded hybrid duplex molecules based on changes in electrophoretic mobility. See, e.g., Keen, et al, 1991.Trends Genet.7: 5.

in yet another embodiment, the migration of a mutant or wild-type fragment in a polyacrylamide gel containing a gradient denaturant is determined using Denaturing Gradient Gel Electrophoresis (DGGE). See, e.g., Myers, et al, 1985.Nature 313: 495. when DGGE is used as an analytical method, the DNA will be modified to ensure that it is not completely denatured, for example by PCR adding a GC clamp of approximately 40bp of highly soluble GC-rich DNA. In another embodiment, a temperature gradient is used instead of a denaturation gradient to identify differences in the mobility of control and sample DNA. See, e.g., Rosenbaum and Reissner, 1987. biophysis. chem.265: 12753.

examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers can be prepared in which a known mutation is centered and subsequently hybridized to the target DNA under conditions that allow hybridization only if a perfect match is found. See, e.g., Saiki, et al, 1986.Nature 324: 163; saiki, et al, 1989.Proc.Natl.Acad.Sci.USA 86: 6230. when oligonucleotides are attached to the hybridization membrane and hybridized to the labeled target DNA, these allele-specific oligonucleotides are hybridized to the PCR amplified target DNA or to a variety of different mutations.

Alternatively, allele-specific amplification techniques that rely on selective PCR amplification may be used in connection with the present invention. Oligonucleotides used as specific amplification primers can carry the mutation of interest either in the center of the molecule (so that amplification is dependent on differential hybridization; see, e.g., Gibbs, et al, 1989.Nucl. acids Res.17: 2437-2448) or at the outermost 3' end of a primer that, under appropriate conditions, can prevent mismatches or reduce polymerase extension (see, e.g., Prossner, 1993. Tibtech.11: 238). It is also desirable to introduce new restriction sites in the mutated region to create a cleavage-based assay. See, for example, Gasparini, et al, 1992, mol. cell Probes 6: 1. it is contemplated that amplification may also be performed using Taq ligase for amplification in certain embodiments. See, for example, Barany, 1991.proc.natl.acad.sci.usa 88: 189. in these cases, ligation will only occur if there is a perfect match at the 3 'end of the 5' sequence, enabling detection of the presence of a known mutation at a specific site by observing the presence or absence of amplification.

Solid support and probe

In an alternative embodiment, detecting the presence or absence of at least one nucleic acid variation comprises contacting a nucleic acid sequence identified above corresponding to the desired region of the erbB1 gene with a probe. The probes are capable of discriminating between the presence of a particular form or variation or variations of a gene, for example, by differential binding or hybridization. Thus, exemplary probes include nucleic acid hybridization probes, peptide nucleic acid probes, nucleotide-containing probes that further comprise at least one nucleotide analog, and antibodies, such as monoclonal antibodies, and other probes discussed herein. Those skilled in the art are familiar with the preparation of specific probes. One skilled in the art will recognize that a variety of variables can be adjusted to optimize the differentiation between two variant forms of a gene, including changes in salt concentration, temperature, pH, and the addition of various compounds that affect the differential affinity of GC for AT base pairs, such as tetramethylammonium chloride (see Current Protocols in Molecular Biology by f.m. ausubel, r.brent, r.e.kingston, d.d.moore, j.g.seidman, k.struhlarxd v.b.chanda (Editors), john wiley & Sons.).

Thus, in a preferred embodiment, detecting the presence or absence of at least one variation comprises contacting a nucleic acid sequence comprising at least one variation site in a plurality of instances with a probe, preferably a nucleic acid probe, wherein the probe hybridizes preferentially to a form of the nucleic acid sequence comprising a complementary base at the variation site as compared to a form of the nucleic acid sequence having a non-complementary base at the variation site, wherein the hybridization is performed under selective hybridization conditions. Such nucleic acid hybridization probes may span two or more sites of variation. Unless otherwise specified, a nucleic acid probe may include one or more nucleic acid analogs, probes, or other substitutions or moieties, so long as base-pairing functionality is retained.

Probes can be designed to bind to, for example, SEQ ID NO: 495, SEQ ID NO: 497, or SEQ ID NO: 499 on at least three consecutive nucleotides on either side of the deletion region. When hybridized under appropriate conditions, such probes will bind to variant forms of EGFR, but will not bind to wild-type EGFR.

Such hybridization probes are well known in the art (see, e.g., Sambrook et al, eds., (host registration), Molecular Cloning: A Laboratory Manual, (third registration, 2001), Vol.1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). Stringent hybridization conditions will generally include a salt concentration of less than about 1M, more typically less than about 500mM and preferably less than about 200 mM. Hybridization temperatures can be as low as 5 ℃, but are generally greater than 22 ℃, more generally greater than about,preferably greater than about 37 deg.c. Longer fragments may require higher hybridization temperatures for specific hybridization. Other factors may affect the stringency of hybridization, including base composition and length of the complementary strand, presence of organic solvents and degree of base mismatches; the combination of parameters used is more important than the absolute measurement of any one of the individual parameters. Other hybridization conditions that may be controlled include buffer type and concentration, solution pH, presence and concentration of blocking agents (e.g., repeat sequences, Cotl DNA, blocking protein solutions) to reduce background binding, detergent type and concentration, molecules that increase the relative concentration of polynucleotides such as polymers, metal ions and their concentrations, chelators and their concentrations, and other conditions known or discovered in the art. The optimal melting temperature for a given probe for a perfectly complementary sequence can be predicted using a formula, but the true melting concentration of the probe under a set of hybridization conditions must be determined empirically. In addition, the probe must be tested against its exact complement to determine the exact melting temperature for a given set of conditions, as in Sambrook et al, "Molecular Cloning," 3^ndedition, Cold Spring Harbor Laboratory Press, 2001. The use of a support associated with nucleotides allows for systematic variation of the hybridization temperature for a given hybridization solution until a temperature range is identified that allows for detection of binding at a desired stringency level, either at a high stringency level where only the target polynucleotide hybridizes to a high complement, or at a lower level where other target polynucleotides with complementary regions to the probe detectably hybridize above a background level provided by non-specific binding to non-complementary target polynucleotides or to the support. When hybridization is performed on a support from potential target polynucleotides under a given set of conditions, the support is then washed under increased stringency conditions (typically lower salt concentrations and/or increased temperatures, but other conditions may vary) until background binding is reduced to a point where a significant positive signal is visible. This can be monitored progressively using a Geiger counter in which the probe is radiolabeled, using a fluorescence imager, or by other means of detecting probe binding. At this pointDuring these procedures the support is not allowed to dry or the probes can be reversibly bound even to background sites. When the probe produces a favorable background or false positive, a blocking agent is employed, or a different region of the probe or a different probe is used until the positive signal can be distinguished from the background. Once conditions are found to provide a satisfactory signal above background, the target polynucleotides that provide a positive signal are isolated and further characterized. The isolated polynucleotide may be sequenced; if necessary, full-length clones are obtained by techniques known in the art; and the polynucleotides may be expressed using suitable vectors and hosts to determine whether the identified polynucleotide encodes a protein having similar activity to the protein from which the probe polynucleotide was derived. The probe may be 10-50 nucleotides. However, larger probes, e.g., 50-500 nucleotides or larger, can also be used.

Solid support

The solid support of the present invention can be any solid material and structure suitable for supporting nucleotide hybridization and synthesis. Preferably, the solid support comprises at least one relatively rigid surface to which the oligonucleotide primers can be immobilized. The solid support may be comprised of materials such as glass, synthetic polymers, plastics, rigid non-porous nylon or ceramic. Other suitable solid support materials are known to those skilled in the art and are readily available. The size of the solid support may be any standard microarray size useful for DNA microarray technology, and may be adapted to the particular instrument used to carry out the reaction of the invention. Methods and materials for derivatizing solid supports for immobilizing oligonucleotides are known to those skilled in the art and are described, for example, in U.S. Pat. No.5,919,523, the disclosure of which is incorporated herein by reference.

The solid support may be present in or be part of a container containing a liquid. For example, the solid support can be placed in a chamber with edges that create a seal along the edges of the solid support to accommodate Polymerase Chain Reaction (PCR) that occurs on the support. In a specific embodiment, the chamber has walls on each side of a rectangular support to ensure that the PCR mixture is preserved on the support, also making the entire surface available for providing primers.

Any available means may be used to attach, immobilize, provide and/or apply the oligonucleotides or oligonucleotide primers of the invention to the surface of the solid support in order to locate, immobilize, provide and/or apply the oligonucleotides at specific locations on the solid support. For example, oligonucleotide primers can be applied to specific locations on a chip or solid support using photolithography (Affymetrix, Santa Clara, Calif.), as in U.S. Pat. Nos. 5,919,523, 5,837,832, 5,831,070, and 5,770,722, which are incorporated herein by reference. Oligonucleotide primers can be applied to solid supports as described in Brown and Shalon, U.S. Pat. No.5,807,522 (1998). In addition, primers can be applied to the solid support using robotic systems, such as those manufactured by Genetic Microsystems (Woburn, Mass.), GeneMachines (San Carlos, Calif.), or Cartesian Technologies (Irvine, Calif.).

In one aspect of the invention, solid phase amplification of a target polynucleotide from a biological sample is performed wherein a plurality of sets of oligonucleotide primers are immobilized on a solid support. In a preferred embodiment, the primers in one set comprise at least a first set of primers having the same sequence, which are complementary to the designated sequence of the target polynucleotide, capable of hybridizing to the target polynucleotide under suitable conditions, and suitable as initial primers for nucleic acid synthesis (i.e., chain extension or extension). The primers selected to cover specific regions of the reference sequence are immobilized as a set at discrete locations on a solid support. Preferably, the distance between sets is greater than the resolution of the method used to detect the amplification products. In a preferred embodiment, the immobilized primers form a microarray or chip, which can be processed and detected in an automated manner. The immobilized primers are used to perform solid phase amplification of a target polynucleotide under conditions suitable for a nucleic acid amplification method. In this way, the presence or absence of a number of potential variations in the kinase domain of the erbB1 gene can be determined in one assay.

In measuring whether a biological source has at least one variation in the kinase domain of the erbB1 gene that increases kinase activity, a population of target polynucleotides isolated from healthy individuals can be used as controls. Alternatively, a target polynucleotide isolated from a healthy tissue of the same individual may be used as the above control.

In situ PCR reactions on microarrays can be substantially as described, for example, in Embretson et al, Nature 362: 359-362 (1993); gosden et al, BioTechniques 15 (1): 78-80 (1993); henifond et al, nuc. acid res.21 (14): 3159 3166 (1993); long et al, Histochemistry 99: 151, 162 (1993); nuoovo et al, PCRmethods and Applications 2 (4): 305-312 (1993); patterson et al, Science 260: 976-979 (1993).

Alternatively, variations in the kinase domain of the erbB1 gene can be determined by solid phase techniques without performing PCR on a support. A plurality of oligonucleotide probes, each containing a different variation in the kinase domain of erbB1, may be bound to the solid support in duplicate, triplicate or quadruplicate. The presence or absence of variation in a test biological sample can be detected by selective hybridization techniques known in the art and described above.

Mass spectrometric analysis

In another embodiment, the presence or absence of a nucleic acid variation that increases kinase activity in the kinase domain of the erbB1 gene is determined using mass spectrometry. Amplification may be necessary in order to obtain the appropriate amount of nucleic acid molecules for mass spectrometry. Examples of suitable amplification methods that can be used in the present invention include: cloning (Sambrook et al, Molecular Cloning: A Laboratory Manual (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989), Polymerase Chain Reaction (PCR) (C.R.Newton and A.Graham, PCR, BIOS Publishers, (1994)), Ligase Chain Reaction (LCR) (Wiedmann M et al, (1994) application of PCR methods (PCR methods appl.), Vol.3, pp.57-64; F.Barany, Proc.Natl.Acad.Sci.USA, 1991, Vol.189-93), Strand Displacement Amplification (SDA) (G.Terranr Walker et al, Nucleic acids research) (Nucleic acids sRs. Acerand. Sci.USA), Vol.22-77) and modification methods such as ASA (Biotechnology) 11/11 Bioaugmentation Technology (Biotechnology) 1993).

To facilitate mass spectrometry, nucleic acid molecules containing the sequence to be detected can be immobilized on a solid support. Examples of suitable solid supports include beads (e.g., silica gel, controlled pore glass, magnetic beads, Sephadex/Sepharose, cellulose), platform surfaces or patches (e.g., glass fiber filters, glass surfaces, metal surfaces (steel, gold, silver, aluminum, copper, and silicon), capillaries, plastics (e.g., polyethylene, polypropylene, polyamide, polydiethylene oxide membranes, or microtiter plates)); or a peg or comb made of a similar material that includes the ball or platform surface, or a ball placed in a depression in the platform surface such as a pad (e.g., a silicon pad).

Immobilization can be accomplished using hybridization methods, for example, based on hybridization between a capture nucleic acid sequence that has been immobilized to a solid support and a complementary nucleic acid sequence that is also contained in the nucleic acid molecule containing the nucleic acid sequence to be detected. So that hybridization between complementary nucleic acid molecules is not hindered by the support, the capture nucleic acid molecule may comprise a spacer of at least 5 nucleotides in length between the solid support and the capture nucleic acid sequence. The dimer formed under the influence of the laser pulse can be cleaved and desorption can be excited. The solid support bound base sequence may be provided by natural oligoribonucleotides or oligodeoxyribonucleotides and analogs thereof (e.g., sulfhydryl-modified phosphodiester or phosphotriester backbones) or using oligonucleotide mimics such as PNA analogs (see, e.g., Nielsen et al, Science, 254, 1497(1991)), which reduce the susceptibility of the base sequence to enzymatic degradation, thereby increasing the overall stability of the solid support bound capture base sequence.

Prior to mass spectrometry, it may be useful to "modify" the nucleic acid molecule, for example to reduce the laser energy required for vaporization and/or to minimize fragmentation. The modification is preferably applied to the immobilized target detection site. One example of a modification is a modification of the phosphodiester backbone in a nucleic acid molecule (e.g., cation exchange), which can be used to eliminate peak broadening phenomena due to heterogeneity of the bound cations per nucleotide unit. Contacting a nucleic acid molecule with an alkylating agent such as alkyl iodide, iodoacetamide, β -iodoethanol or 2, 3-oxirane-1-propanol, the monothiophosphodiester bond of the nucleic acid molecule can be converted to a phosphotriester bond. Likewise, phosphodiester bonds can be converted to uncharged derivatives using trialkylsilyl chlorides. Further modifications include the incorporation of nucleotides which reduce the sensitivity to depurination (fragmentation in MS), such as N7-or N9-deazapurine nucleotides or RNA elements, or the use of oligonucleotide triesters or the incorporation of alkylated phosphorothioate functions or the incorporation of oligonucleotide mimetics such as PNA.

For some applications it may be useful to simultaneously detect more than one (mutated) site on a specific captured nucleic acid fragment (at one spot on the array) or to perform parallel detection using an array arrangement of oligonucleotides or oligonucleotide mimics on different solid supports. "multiplexing" can be achieved by several different methods. For example, several mutations in a target sequence can be detected simultaneously by using corresponding detection (probe) molecules (e.g., oligonucleotides or oligonucleotide mimetics). However, the difference in molecular weight between the detector nucleotides D1, D2 and D3 must be sufficiently large to allow simultaneous detection (multiplex detection). Such differences can be obtained by introducing the mass-modifying functional groups M1-M3 into the sequence itself (composition or length) or into the detector oligonucleotide.

Preferred mass spectrometric detection means for use in the present invention are Matrix Assisted Laser Desorption Ionization (MALDI), Electrospray (ES), Ion Cyclotron Resonance (ICR) and Fourier transform. Methods for performing mass spectrometry are known to those skilled in the art and are described in Methods of Enzymology, vol.193: "MassSpectrometry" (J.A. McCloskey, editor), 1990, Academic Press, New York.

Sequencing

In other preferred embodiments, determining the presence or absence of at least one nucleic acid variation that increases kinase activity comprises sequencing at least one and the nucleic acid sequences. The sequencing comprises sequencing one or more parts of the kinase domain of erbB1 that includes at least one site of variation, and possibly a plurality of such sites. Preferably, the moiety is 500 nucleotides or less in length, more preferably 100 nucleotides or less, most preferably 45 nucleotides or less in length. Such sequencing can be performed by a variety of methods recognized by those skilled in the art, including dideoxy termination methods (e.g., using dye-labeled dideoxynucleotides), and using mass spectrometry.

Immunoassay

In one embodiment, determining the presence or absence of at least one nucleic acid variation that increases kinase activity comprises determining the activation state of a downstream target of EGFR.

The inventors of the present invention compared the phosphorylation states of major downstream targets of EGFR. For example, EGF-induced activation of Erk1 and Erk2 by Ras, Akt by PLC γ/PI3K, and STAT3 and STAT5 by JAK2 have been examined. Erk1 and Erk2 by Ras, Akt by PLC γ/PI3K, and STAT3 and STAT5 by JAK2 are the basic downstream pathways mediating the oncogenic effects of EGFR (r.n. jorissen et al, exp. cell res.284, 31 (2003)).

The inventors of the present invention showed that EGF-induced Erk activation is indistinguishable between expression of wild-type EGFR and either of two activating EGFR mutants.

In contrast, phosphorylation of Akt and STAT5 was substantially increased in cells expressing either of the two mutant EGFR. . Phosphorylation of STAT3 was similarly observed in cells expressing mutant EGFRs. Thus, selective EGF-induced autophosphorylation of the C-terminal tyrosine residue in EGFR mutants is closely associated with selective activation of downstream signaling pathways.

In one embodiment of the invention, the presence of EGFR mutations can be determined using immunological techniques well known in the art, for example, antibody techniques such as immunohistochemistry, immunocytochemistry, FACS scanning, immunoblotting, radioimmunoassay, western blotting, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA), derivatization techniques using antibodies directed against downstream targets of EGFR activation. Examples of such targets include, for example, phosphorylated STAT3, phosphorylated STAT5, and phosphorylated Akt. Activation status of STAT3, STAT5, and Akt can be determined using phospho-specific antibodies. Activation of STAT3, STAT5, and Akt can be used as a diagnostic indicator of activating EGFR mutations.

In one embodiment of the invention, the presence of activated (phosphorylated) STAT5, STAT3, or Akt indicates that EGFR targeted therapy may be effective.

The present invention provides a method of screening for variations in the kinase domain of the erbB1 gene in a test sample by immunohistochemical or immunocytochemical methods.

For example, immunohistochemistry ("IHC") and immunocytochemistry ("ICC") techniques may be utilized. IHC is the application of immunochemistry to tissue sections, while ICC is the application of immunochemistry to cells or tissue markers after they have been subjected to a specific cytological preparation such as, for example, a liquid-based preparation. Immunochemistry is a family of applications based on the use of specific antibodies, wherein the use of antibodies specifically targets molecules inside or on the surface of cells. Antibodies typically comprise a label that undergoes a biochemical reaction upon encountering a target molecule, thereby undergoing a color change. In some cases, signal amplification may be incorporated into specific protocols in which a secondary antibody comprising a labeled stain is used after application of a specific primary antibody.

Immunohistochemical assays are known to those skilled in the art (see, e.g., Jalkanen, et al, J.cell. biol.101: 976-305 (1985); Jalkanen, et al, J.cell. biol.105: 3087-3096 (1987).

Polyclonal or monoclonal Antibodies, which are commercially available from a variety of commercial suppliers, may be produced using well known methods, for example, as described in Harlow et al, Antibodies: a Laboratory Manual, 2nd Ed; cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1988). In general, examples of antibodies useful in the invention include anti-phospho-STAT 3, anti-phospho-STAT 5, and anti-phospho-Akt antibodies. These antibodies can be purchased, for example, from Upstate Biotechnology (Lake Placid, NY), New England Biolabs (Beverly, MA), NeoMarkers (Fremont, Calif.).

Generally, for immunohistochemistry, tissue sections are obtained from a patient and fixed by a suitable fixative, such as ethanol, acetone, and paraformaldehyde, with which the antibody reacts. Routine methods for immunohistochemistry are described in Harlow and Lane (eds) (1988), in "Antibodies A Laboratory Manual", Cold Spring harborPress, Cold Spring Harbor, New York; ausbel et al (eds) (1987) is described in Current protocols in Molecular Biology, John Wiley and Sons (New York, N.Y.). Biological samples suitable for these detection assays include, but are not limited to, cells, biopsies, whole blood, plasma, serum, sputum, cerebrospinal fluid, breast aspirates, pleural effusion, urine, and the like.

For direct labeling techniques, labeled antibodies are used. For indirect labeling techniques, the sample is further reacted with a labeled substance.

Alternatively, immunocytochemistry may be utilized. Typically, cells are obtained from a patient and fixed by a suitable fixative, such as ethanol, acetone, and paraformaldehyde, with which the antibody reacts. Methods for immunocytological staining of human samples are known to those skilled in the art and are described, for example, in Brauer et al, 2001(FASEB J, 15, 2689-2701), Smith-Swintosky et al, 1997.

The immunological methods of the invention are advantageous because they require only small amounts of biological material. These methods can be performed at the cellular level and thus require a minimum of one cell. Preferably, several cells are obtained from a patient having or at risk of developing cancer and assayed according to the methods of the invention.

Other diagnostic methods

The reagent for detecting the mutant EGFR protein is an antibody, preferably an antibody having a detectable label, capable of binding to the mutant EGFR protein. The antibody may be polyclonal, or more preferably, monoclonal. Intact antibodies, or fragments thereof (e.g., F) may be used_abOr F: (_ab)₂). With respect to probes or antibodies, the term "labeled" is intended to include direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reaction with another directly labeled reagent. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and labeling of the DNA probe with biotin so that it can be detected with fluorescently labeled streptavidin. The term "biological sample" is intended to include tissues, cells, and biological fluids isolated from a subject, as well as tissues, cells, and fluids present in a subject. That is, the detection method of the present invention can be used to detect mutant EGFR mRNA, protein, or genomic DNA in biological samples in vitro as well as in vivo. For example, in vitro techniques for detecting mutant EGFR mRNA include northern blot hybridization and in situ hybridization. In vitro techniques for detecting mutant EGFR proteins include enzyme-linked immunosorbent assays (ELISAs), western blots, immunoprecipitations, and immunofluorescence. In vitro techniques for detecting mutant EGFR genomic DNA include introducing into a subject a labeled anti-mutant EGFR protein antibody. For example, the antibody may be labeled with a radiolabel, the presence and location of which in a subject may be detected by labelled imaging techniques.

In one embodiment, the biological sample comprises protein molecules from a test subject. Alternatively, the biological sample may comprise mRNA molecules from a test subject or genomic DNA molecules from a test subject.

In another embodiment, the method further comprises obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting mutant EGFR mRNA, protein, or genomic DNA, thereby detecting the presence of mutant EGFR mRNA, protein, or genomic DNA in the biological sample, and comparing the presence of mutant EGFR mRNA, protein, or genomic DNA in the control sample to the presence of mutant EGFR mRNA, protein, or genomic DNA in the test sample.

In various embodiments, the diagnostic assay is directed to mutant EGFR activity. In a specific embodiment, the mutant EGFR activity is tyrosine kinase activity. One such diagnostic assay is the detection of EGFR-mediated phosphorylation of at least one EGFR substrate. The level of EGFR activity can be determined, for example, for various mutant EGFR polypeptides, various tissues comprising mutant EGFR, biopsies from cancer tissues suspected of having at least one mutant EGFR, and the like. Optionally, a comparison of the level of EGFR activity in these various cells, tissues or extracts thereof can be made. In one embodiment, high levels of EGFR activity levels in cancer tissues can diagnose cancers that may be susceptible to treatment with one or more tyrosine kinase inhibitors. In related embodiments, an inhibitor of the level of EGFR activity can be assayed between treated and untreated biopsy tissue samples, cell lines, transgenic animals, or extracts of any of these, in order to determine the effect of a given treatment on mutant EGFR activity as compared to untreated controls.

Method of treating a patient

In one embodiment, the invention provides a method of selecting a treatment for a patient having or at risk of developing cancer by determining the presence or absence of at least one nucleic acid variation in the kinase domain of the erbB1 gene that increases kinase activity. In another embodiment, the variation is a plurality of variations, wherein a plurality may include variations from one, two, three, or more loci.

In certain embodiments, the presence of at least one variation is an indication that the treatment will be effective or beneficial (or more likely to be beneficial) in the patient. It is stated that such treatment would be an effective approach, i.e. the potential for beneficial therapeutic effects is greater in individuals who do not have the appropriate presence of the particular nucleic acid variation that increases kinase activity in the kinase domain of the erbB1 gene.

The treatment will comprise administration of a tyrosine kinase inhibitor. The treatment may include treating tissue, including, but not limited to, tyrosine kinase inhibitors in combination with other tyrosine kinase inhibitors, chemotherapy, radiation therapy, and the like.

Thus, in connection with the administration of tyrosine kinase inhibitors, drugs that are "effective against" cancer have been shown to result in a clinically appropriate manner of administration that results in a beneficial effect for at least a statistically significant portion of patients, such as an improvement in the condition, cure, reduction in disease burden, reduction in tumor mass or cell number, prolongation of life, improvement in quality of life, or other effects that are generally considered positive by physicians familiar with the treatment of a particular type of disease or condition.

In a preferred embodiment, the compound is a phenylaminoquinazoline or a synthetic phenylaminoquinazoline. European patent publication No. 0566226 discloses phenylaminoquinazolines having anti-Epidermal Growth Factor (EGF) receptor tyrosine kinase activity. It is also known from European patent publication Nos. 0520722 and 0566226 that certain 4-anilinoquinazoline derivatives may be used as inhibitors of receptor tyrosine kinases. The very tight structure-activity relationships shown by these compounds suggest a well-defined binding pattern in which the quinazoline ring is bound in the adenine pocket and the anilino ring is bound in the adjacent distinct lipophilic pocket. Three 4-anilinoquinazoline analogs (two reversible and one irreversible inhibitors) have been clinically evaluated as anticancer drugs. Denny, Farmaco January-February 2001; 56(1-2): 51-6. Alternatively, the compound is EKB-569, an inhibitor of EGF receptor kinase (Torrance et al, Nature Medicine, vol.6, No.9, Sept.2000, p.1024). In a most preferred embodiment, the compound is gefitinibOr erlotinib

Cancer cell-targeting therapeutics comprising at least one mutant EGFR described herein can be administered alone or in combination with any other suitable anti-cancer therapeutic and/or therapeutic known to those of skill in the art. In one embodiment, treatment of a pathology such as cancer is provided, comprising administering to a subject in need thereof a therapeutically effective amount of a compound that inhibits EGFR kinase activity, such as gefitinib, erlotinib, or the like, alone or in combination with at least one other anti-cancer agent or therapy. Inhibition of activated protein kinases by using targeted small molecule drugs or antibody-based strategies has become an effective approach to cancer therapy. See, e.g., g.d. demmetri et al, n.engl.j.med.347, 472 (2002); druker et al, N.Engl.J.Med.344, 1038 (2001); d.j.slamon et al, n.engl.j.med.344, 783 (2001).

In one embodiment, the anti-cancer agent is at least one chemotherapeutic agent. In related embodiments, the anti-cancer agent is at least one radiotherapeutic agent. In variant embodiments, the anti-Cancer therapy is an anti-angiogenic therapy (e.g., endostatin, angiostatin, TNP-470, Caplostatin (Stachi-Fainaro et al, Cancer Cell 7(3), 251 (2005)).

The therapeutic agents may be the same or different and may be, for example, a therapeutic radionuclide, a drug, a hormone antagonist, a receptor antagonist, an enzyme or a proenzyme activated by another agent, an autocrine factor, a cytokine or any suitable anti-cancer agent known to those of skill in the art. In one embodiment, the anti-cancer agent is Avastin, a VEGF antibody that has proven successful in anti-angiogenic therapy against solid cancers and hematologic malignancies. See, for example, Ribatti et al 2003J hepatother Stem Cell Res.12(1), 11-22. Toxins may also be used in the methods of the invention. Other therapeutic agents that may be used in the present invention include anti-T-DNA, anti-RNA, radiolabeled oligonucleotides, such as antisense oligonucleotides, anti-proteins and anti-chromatin cytotoxic or antimicrobial agents. Other therapeutic agents are known to those skilled in the art and the use of these other therapeutic agents in accordance with the present invention is specifically claimed.

The antineoplastic agent may be one of a variety of chemotherapeutic agents, such as alkylating agents, antimetabolites, hormonal agents, antibiotics, antibodies, anticancer biologics, gleevec, colchicine, vinca alkaloids, L-asparaginase, procarbazine, hydroxyurea, mitotane, nitrosoureas, or carbamoylimidazole. Suitable agents are those that promote tubulin depolarization or inhibit tumor cell proliferation. Chemotherapeutic agents included within the scope of the present invention include, but are not limited to, the anti-cancer agents listed in Orange Book of applied Drug Products With Therapeutic efficacy Evaluations, compiled by Food and Drug Administration and the U.S. department of Health and human services. Non-limiting examples of chemotherapeutic agents include, for example, carboplatin and paclitaxel. Therapeutic agents that target EGFR kinase activity may also be administered with radiation therapy. Other anti-cancer therapeutic agents known in the art are included within the scope of the present invention.

The therapeutic agent may be a chemotherapeutic agent. Chemotherapeutic agents are known in the art and include at least a taxane, a nitrogen mustard, an aziridine derivative, an alkyl sulfonate, a nitrosourea, a triazene (triazenes), a folic acid analog, a pyrimidine analog, a purine analog, a vinca alkaloid, an antibiotic, an enzyme, a platinum coordination complex, a surrogate urea, a derivative of methylhydrazine, an inhibitor of the adrenal cortex, or an antagonist. More specifically, the chemotherapeutic agent may be one or more agents selected from the non-limiting group of steroids progesterone, estrogens, antiestrogens, and androgens. Still more specifically, the chemotherapeutic agent may be azalipine, bleomycin, bryostatin-1, busulfan, carmustine, chlorambucil, carboplatin, cisplatin, CPT-11, cyclophosphamide, cytarabine, dacarbazine, actinomycin, daunorubicin, dexamethasone, diethylstilbestrol, doxorubicin, ethinyl estradiol, etoposide, fluorouracil, fluoxymesterone, gemcitabine, hydroxyprogesterone hexanoate, hydroxyurea, asparaginase, leucovorin, lomustine, nitrogen mustard, medroprogesterone acetate, megestrol, melphalan, 6-mercaptopurine, methotrexate, mithramycin, mitomycin, mitotane, paclitaxel, phenyl butyrate, prednisone, procarbazine, semustine, tamoxifen, taxane, taxol, propionic acid, a sedative, 2-aminopurine-6-thiol, thiotepa, uracil mustard, vinblastine, or vincristine. The use of any combination of chemotherapeutic agents is also claimed. Administration of the chemotherapeutic agent may be prior to, during or after administration of the therapeutic agent targeting EGFR activity.

Other suitable therapeutic agents are selected from radioisotopes, boraddend, immunomodulators, toxins, photosensitizers or dyes, cancer chemotherapeutic drugs, antiviral drugs, antifungal drugs, antibacterial drugs, antiprotozoal drugs and chemosensitizers (see, U.S. Pat. nos. 4,925,648 and 4932,412). Suitable chemotherapeutic agents are described in REMINGTON 'S PHARMACEUTICAL SCIENCES, 19th Ed. (Mack Publishing Co.1995), and in Goodman and Gilman' S the pharmacological Basis of Therapeutics (Goodman et al, eds. Macmillan Publishing Co., New-York, 1980and 2001 editions). Other suitable chemotherapeutic agents, such as experimental drugs, are known to those skilled in the art. Further suitable therapeutic radioisotopes are selected from the group consisting of alpha-radiation sources, beta-radiation sources, gamma-radiation sources, Auger's electron radiation sources, neutron capture agents that emit alpha particles and radioisotopes attenuated by electron capture. Preferably, the radioisotope is selected from 225Ac, 198Au, 32P, 125I131I, 90Y, 186Re, 188Re, 67Cu, 177Lu, 213Bi, 10B, and 211 At.

When more than one therapeutic agent is used, they may be the same or different. For example, the therapeutic agent may comprise a different radionuclide, or a drug and a radionuclide. In preferred embodiments, the treatment targeting EGFR activity inhibits mutant EGFR kinase activity.

In another embodiment, different isotopes are used as the first and second therapeutic agents, the different isotopes being effective at different distances as a result of their respective energy emissions. These agents can be used to achieve more effective tumor treatment and can be used in patients presenting with multiple tumors of different sizes, as in normal clinical situations.

Few isotopes are available for the treatment of very small tumor deposits and single cells. In these cases, the drug or toxin may be a more useful therapeutic agent. Thus, in a preferred embodiment of the invention, isotopes may be used in combination with non-isotopic species such as drugs, toxins and neutron capture agents. Many drugs and toxins are known, which have cytotoxic effects on cells, and can be used in connection with the present invention. They are found in the drug and toxin profiles, such as merck index, Goodman and Gilman, and others, and in the references cited above.

Drugs that interfere with intracellular protein synthesis may also be used in the methods of the invention; such agents are known to those skilled in the art and include puromycin, cycloheximide, and rnase.

The therapeutic methods of the present invention may be used for cancer therapy. It is well known that radioisotopes, drugs and toxins may be conjugated to antibodies or antibody fragments produced by or associated with cancer cells that specifically bind to a label, and these antibody conjugates may be used to target radioisotopes, drugs or toxins to the tumor site to increase their therapeutic efficacy and minimize side effects. Examples of such agents and methods are described in Wawrzynczaka-nd Thorpe (introduction to the Cellular and Molecular Biology of Cancer, L.M.Franks and dN.M.Teich, eds., Chapter 18, PP.378-410, Oxford University Press.Oxford, 1986), Inimmunoconjugates: an overview is given in Antibody Conjugates in radioimagining and Therapy of Cancer (C.W.Vogel, ed., 3-300, Oxford University Press, N.Y., 1987), in Dillman, R.O. (CRCCritical Reviews in pharmacology/Hematology 1: 357, CRC Press, Inc., 1984), in Pastan et al (Cell 47: 641, 1986), in Vitetta et al (Science 238: 1099-. Examples of applications of immunoconjugates for cancer and other forms of therapy are disclosed in U.S. Pat. nos. 4,331,647, 4,348,376, 4,361,544, 4,468,457, 4,444,744, 4,460,459, 4,460,5614,624,846, 4,818,709, 4,046,722, 4,671,958, 4,046,784, 5,332,567, 5,443,953, 5,541,297, 5,601,825, 5,635,603, 5,637,288, 5,677,427, 5,686,578, 5,698,178, 5,789,554, 5,922,302, 6,187,287, and 6,319,500, among others.

In addition, the treatment methods of the present invention may be used in combination with other compounds or techniques used to prevent, alleviate or reverse the side effects of certain cytotoxic agents. Examples of such combinations include, for example, IL-1 administered with an antibody for rapid clearance, as described in, for example, U.S. patent No. 4,624,846. Such administration may be performed 3 to 72 hours after administration of the primary therapeutic agent targeting EGFR activity combined with an anti-cancer agent (e.g., with a radioisotope, drug or toxin as the cytotoxic component). This can be used to enhance clearance of the conjugate, drug or toxin from the environment and reduce or reverse bone marrow and other hematopoietic tissue toxicity induced by the therapeutic agent.

In another aspect of the invention, cancer treatment may include combining more than one tomocidal agent, e.g., a drug and a radioisotope, or a radioisotope and a Boron-10 agent for neutron activation therapy, or a drug and a biological response modifier, or a fusion molecule conjugate and a biological response modifier. Cytokines can be incorporated into such treatment regimens to maximize the efficacy of each of their components.

Similarly, anti-leukemia and anti-lymphoma antibodies conjugated to beta or alpha emitting source radioisotopes may induce bone marrow and other hematopoietic side effects when these agents are not directed only to tumor cells. This is particularly found when the tumor cells are in circulation and in blood-forming organs. Preferably, at least one hematopoietic cytokine (e.g., a growth factor, such as colony stimulating factors, e.g., G-CSF and GM-CSF) is administered simultaneously and/or subsequently to reduce or ameliorate hematopoietic tissue side effects while enhancing anti-cancer effects.

It is well known in the art that various methods of radionuclide Therapy can be used to treat cancer and other pathological conditions, as described, for example, in Harbert, "nucleic Medicine Therapy", New York, Thieme medical publishers, 1087, pp.1-340. Clinicians familiar with these procedures will be able to readily adapt the cytokine adjunctive therapy described herein to these procedures to alleviate any of their hematopoietic tissue side effects. Similarly, for example, cytotoxic drug therapy may be used to administer therapeutic agents that target EGFR activity to treat cancer or other cell proliferative diseases. This treatment is guided by similar theory as radioisotope therapy with isotopes or radiolabeled antibodies. The ordinarily skilled clinician will be able to apply other anti-cancer therapies before, during and/or after the primary anti-cancer treatment.

Reagent kit

The present invention therefore provides a predictive, diagnostic, and prognostic kit comprising degenerate primers to amplify a target nucleic acid in the kinase domain of the erbB1 gene and instructions including an amplification protocol and analysis of the results. Alternatively, the kit further comprises a buffer, an enzyme, and a cuvette to perform amplification or analysis of the amplification product. The kit may also be part of a screening, diagnostic or prognostic kit comprising further means such as a DNA microarray. Preferably the kit further provides one or more control templates, such as nucleic acid isolated from a tissue sample, and/or a series of samples representing different variations in the kinase domain of the erbB1 gene.

In one embodiment the kit provides two or more primer pairs, each pair being capable of amplifying a different region of the erbB1 gene (one potential site of variation for each region), thereby providing a kit for analysing the expression of several genetic variations in a biological sample in one reaction or in several parallel reactions.

The primers in the kit may be labeled, e.g., fluorescently labeled, to facilitate detection of the amplification products and subsequent analysis of nucleic acid variations.

In one embodiment, more than one variation may be detected in a single assay. The kit of parts will therefore consist of primers capable of amplifying different fragments of the kinase domain of the erbB1 gene. The primers may be differentially labelled, for example with different fluorescent labels, to distinguish between variations.

The primers contained in the kit may include the following primers: exon 19 sense primer, 5' -GCAATATCAGCCTTAGSTGCGGCTC-3S (SEQ ID NO: 505); exon 19 antisense primer, 5'-CATAGAAAGTGAACATTTAGGATGTG-3' (SEQ ID NO: 506); exon 21 sense primer, 5'-CTAACGTTCGCCAGCCATAAGTCC-3' (SEQ ID NO: 507) and exon 21 antisense primer, 5'-GCTGCGAGCTCACCCAGAATGTCTGG-3' (SEQ ID NO: 508).

In a preferred embodiment, the primer is selected from SEQ ID NOS 646-673 (see tables 5 and 6). These primers have SEQ ID NO 645 at the 5 'end of the forward primer and SEQ ID NO 674 at the 5' end of the reverse primer.

Immunoassay kit

In other embodiments, the invention provides immunoassay kits for detecting the level of activation of downstream EGFR targets (i.e., STAT3, STAT5, and Akt). These kits will generally comprise one or more antibodies immunospecific for phosphorylated forms of STAT3, STAT5, or Akt.

In the present invention, a kit is provided comprising an antibody capable of immunospecifically binding to a phosphorylated protein in a mammalian cell selected from the group consisting of phosphorylated Akt, STAT3, and STAT5 proteins, and instructions for using the antibody to detect activation of the Akt, STAT3, or STAT5 pathway in the mammalian cell. In a preferred method, the kit comprises different antibodies, each capable of immunospecifically binding to a phosphorylated protein in a mammalian cell selected from the group consisting of phosphorylated Akt, STAT3, and STAT5 proteins.

The kit generally comprises, a) a pharmaceutically acceptable carrier; b) antibodies against phosphorylated STAT3, STAT5, or Akt in a suitable container device; and c) an immunodetection reagent. Antibodies (monoclonal or polyclonal) are commercially available and can also be prepared by methods known to those skilled in the art, for example, in Current Protocols in immunology, John Wiley & Sons, Edited by: john e.coligan, Ada m.kruisbeam, davidh.margulies, Ethan m.shevach, Warren Strober, 2001.

In certain embodiments, the antigen or antibody may be bound to a solid support, such as a column matrix or a well of a microtiter plate. The immunodetection reagents of the kit may take any of a variety of forms, including those detectable labels associated with, or linked to, a given antibody or antigen itself.

Suitable assay labels are known in the art and include enzyme labels, such as glucose oxidase; radioisotopes, e.g. iodine (A)¹³¹I，¹²⁵I，¹²¹I，¹²¹I) Carbon (C)¹⁴C) Sulfur (S) (S)³⁵S), tritium (³H) Indium (I)^115mIn，^113mIn，¹¹²In，¹¹¹In), and technetium (⁹⁹Tc，^99mTc), thallium (²⁰¹Ti), gallium (⁶⁸Ga，⁶⁷Ga), palladium (A)¹⁰³Pd), molybdenum (C)⁹⁹Mo), xenon (¹³³Xe), fluorine (¹⁸F)，¹⁵³Sm，¹⁷⁷Lu，¹⁵⁹Gd，¹⁴⁹Pm，¹⁴⁰La，¹⁷⁵Yb，¹⁶⁶Ho，⁹⁰Y，⁴⁷Sc，¹⁸⁶Re，¹⁸⁸Re，¹⁴²Pr，¹⁰⁵Rh，⁹⁷Ru; luminescent labels such as luminol; and fluorescent labels such as fluorescein and rhodamine, and biotin.

Other immunodetection reagents suitable for use in the present kit include two component reagents comprising a secondary antibody having binding affinity for a primary antibody or antigen, and a tertiary antibody having binding affinity for the secondary antibody, wherein the tertiary antibody is linked to a detectable label.

Many exemplary markers are known in the art and all of these markers can be used in connection with the present invention. Radiolabels, nuclear magnetic resonance isotopes, fluorescent labels and enzyme labels capable of generating coloured products upon contact with a suitable substrate are suitable examples.

The kit may comprise the antibody-label conjugate in fully conjugated form, or in intermediate form, or as a separate moiety to be conjugated to the user of the kit.

The kit may further comprise an appropriate aliquot of labeled or unlabeled antigen composition, which may be used to prepare a labeled curve for a detection assay or used as a positive control.

The kits of the invention, regardless of type, will generally comprise one or more containers into which the biological reagents are placed and, preferably, appropriate aliquots are made. The components of the kit may be packaged in liquid media or in lyophilized form.

The immunoassay kit of the present invention may additionally comprise one or more of a number of other cancer marker antibodies or antigens, if so desired. These kits are thus able to provide a panel of cancer markers that can be better used to test multiple patients. For example, these other markers may include other tumor markers such as PSA, SeLe (X), HCG, and asp53, cyclin D1, psi 6, tyrosinase, MAGE, BAGE, PAGE, MUC18, CEA, p27, [ bgr ] HCG or other markers known to those skilled in the art.

The container means for the reagents will generally comprise at least one vial, test tube, flask, bottle, or even syringe or other container means into which the antibody or antigen may be placed, preferably suitably aliquoted. Where a second or third binding ligand or other component is provided, the kit will also generally comprise a second, third or other additional container into which such ligand or component may be placed.

The kits of the invention will also typically include a device containing the antibody, antigen or any other reagent container sealed for commercial sale. These containers may include injection or blow-molded plastic containers that hold the desired vials.

The methods of the invention also include identifying compounds that interfere with the kinase activity of the variant forms of EGFR. The variant EGFR comprises at least one variant in its kinase domain. These compounds may, for example, be tyrosine kinase inhibitors. Methods for identifying compounds that interfere with receptor kinase activity are generally known to those of skill in the art and are further described, for example, in Dhanabal et al, Cancer res.59: 189-197 (1999); xin et al, j.biol.chem.274: 9116-9121 (1999); sheu et al, Anticancer Res.18: 4435-4441; ausprunk et al, Dev.biol.38: 237- > 248 (1974); gimbrone et al, J.Natl.cancer Inst.52: 413-427; nicosia et al, In vitro 18: 538, 549, which is incorporated herein by reference. In general, compounds are identified using the methods disclosed herein that interfere with the increased kinase activity characteristic of at least one variation in the kinase domain of the erbB1 gene.

Solid support

In another embodiment, the invention provides a kit for performing the method of the invention. In one embodiment, a kit for detecting variations in the kinase domain of the erbB1 gene on a solid support is described. The kit may include, for example, materials and reagents for detecting multiple variations in a single assay. The kit may include, for example, a solid support, oligonucleotide primers for a particular set of target polynucleotides, polymerase chain reaction reagents and components, e.g., enzymes for DNA synthesis, labeling substances, and other buffers and reagents for washing. The kit may further comprise instructions for using the kit to amplify a specific target on a solid support. Where the kit comprises a prepared solid support, which is designed and constructed as described above, with a set of primers already immobilized on the solid support, e.g., to amplify a particular set of target polynucleotides. The kit also includes reagents necessary for performing PCR on a solid support, for example, using an in situ-type or solid phase-type PCR method when the support is capable of PCR amplification using an in situ-type PCR machine. PCR reagents included in the kit include typical PCR buffers, thermostable polymerases (e.g., Taq DNA polymerase), nucleotides (e.g., dNTPs), and other components and labeling molecules (e.g., direct or indirect labeling as described above). Kits can be assembled to support the performance of PCR amplification methods using immobilized primers alone, or in combination with solution phase primers.

Alternatively, the kit may comprise a solid support having attached oligonucleotides specific for any EGFR variation, further defined in fig. 4A-4C and fig. 7 and 8. The test biological sample may be applied to a solid support under selective hybridization conditions for determining the presence or absence of a variation in the kinase domain of the erbB1 gene.

The methods of the invention also include compounds that interfere with the kinase activity of the EGFR variant. The variant EGFR comprises at least one variation in its kinase domain. However, in alternative embodiments, the variant EGFR comprises a secondary mutation that confers tolerance to the first TKI, e.g., gefitinib or erlotinib. These compounds may be, for example, tyrosine kinase inhibitors. Methods for identifying compounds that interfere with receptor kinase activity are generally known to those of skill in the art and are further described, for example, in Dhanabal et al, Cancer res.59: 189-197 (1999); xin et al, j.biol.chem.274: 9116-9121 (1999); sheu et al, Anticancer Res.18: 4435-4441; ausprunk et al, Dev.biol.38: 237- > 248 (1974); gimbrone et al, J.Natl.cancer Inst.52: 413-427; nicosia et al, In vitro 18: 538, 549, which is incorporated herein by reference. In general, compounds are identified using the methods disclosed herein that interfere with the increased kinase activity characteristic of at least one variation in the kinase domain of the erbB1 gene. These known variations are described in figures 4,7, 8 and table 2.

Once identified, these compounds are administered to patients in need of EGFR targeted therapy, e.g., patients having or at risk of developing cancer.

The route of administration may be intravenous (i.v.), intramuscular (I.M.), subcutaneous (s.c.), intradermal (i.d.), intraperitoneal (I.P.), intravaginal (I.T.), intrapleural, intrauterine, rectal, vaginal, topical, intratumoral, and the like. The compounds of the invention are administered by injection or by gradual infusion or delivered by peristaltic means.

Administration may be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, bile salts and fusidic acid derivatives. In addition, detergents may be used to facilitate permeation. Transmucosal administration can be accomplished, for example, by nasal spray, or by the use of suppositories. For oral administration, the compounds of the present invention are formulated into conventional oral forms such as capsules, tablets and tonics.

For topical administration, the pharmaceutical composition (inhibitor of kinase activity) is formulated as an ointment, plaster, gel or cream, as is generally known in the art.

The therapeutic compositions of the present invention are routinely administered intravenously, for example, by injection of a unit dose. The term "unit dose" when used in relation to the therapeutic compositions of the present invention refers to physically discrete units suitable as unitary dosages for subjects, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., a carrier, or vehicle.

The compositions are administered in a manner compatible with the dosage form and in a therapeutically effective amount. The amount and time to be administered will depend on the subject to be treated, the ability of the subject to systemically utilize the active ingredient, and the degree of therapeutic effect desired. The precise amount of active ingredient to be administered depends on the judgment of the physician and is unique to each individual.

Tyrosine kinase inhibitors useful in the methods of the invention are described herein. Any dosage form or drug delivery system containing the active ingredient may be used, which is suitable for the intended use, as is generally known to those skilled in the art. Suitable pharmaceutically acceptable carriers for oral, rectal or parenteral (including inhalation, subcutaneous, intraperitoneal, intramuscular and intravenous) administration are known to those skilled in the art. The carrier must be pharmaceutically acceptable and not deleterious to the recipient thereof in the sense of being compatible with the other ingredients of the dosage form.

As used herein, the terms "pharmaceutically acceptable", "physiologically tolerable" and grammatical variations thereof, as they refer to compositions, carriers, diluents and reagents, are used interchangeably and represent that the substance is capable of being administered to a mammal without producing adverse physiological effects.

Dosage forms suitable for parenteral administration conveniently comprise a sterile aqueous preparation of the active compound which is preferably isotonic with the blood of the recipient. Thus, these dosage forms may conveniently comprise 5% glucose in distilled water, distilled water or physiological saline. Useful dosage forms also include concentrated solutions or solids containing the compounds, which upon dilution with a suitable solution, give solutions suitable for parenteral administration as above.

For enteral administration, the compounds may be incorporated into inert carriers in discrete units such as capsules, sachets, tablets or lozenges, each containing a predetermined amount of the active compound; such as powders or granules; or as a suspension or solution in an aqueous or non-aqueous liquid, such as a syrup, elixir, emulsion or drink. Suitable carriers may be starches or sugars and include lubricants, fragrances, binders and other materials of the same nature.

Tablets may be prepared by compression or molding, optionally with one or more additional ingredients. Compressed tablets may be prepared by compressing, in a suitable machine, the active compound in a free-flowing form such as a powder or granules, optionally together with one or more additional ingredients such as a binder, lubricant, inert diluent, surface active agent or dispersing agent. Compressed tablets may be prepared by moulding the active compound in a suitable machine, containing any suitable carrier.

Syrups or suspensions may be prepared by adding the active compound to a concentrated aqueous solution of a sugar, for example sucrose, to which any additional ingredients may also be added. These additional ingredients may include flavoring agents, agents that retard the crystallization of sugar, or agents that increase the solubility of any other ingredient, such as a polyol, e.g., glycerin or sorbitol.

Formulations for rectal administration may be presented as suppositories with conventional carriers, for example, cocoa butter or Witepsol S55 (trade name Dynamite Nobel Chemical, Germany) may be used as suppository carriers.

Dosage forms for oral administration may give enhancers. Absorption enhancers which can be orally administered include surfactants such as sodium lauryl sulfate, palmitoyl carnitine, polyethylene glycol monododecyl ether, phosphatidylcholine, cyclodextrin and derivatives thereof; bile salts such as sodium deoxycholate, sodium taurocholate, sodium glycocholate, and sodium fusidate; chelating agents include EDTA, citric acid and salicylates; and fatty acids (e.g., oleic acid, lauric acid, acylcarnitines, monoglycerides, and diglycerides). Other oral absorption enhancers include benzalkonium chloride, benzethonium chloride, CHAPS (3- (3-cholamidopropyl) -dimethylammonium-1-propanesulfonate), Big-CHAPS (N, N-bis (3-D-glucamidopropyl) -cholamide), chlorobutanol, octoxynol-9, benzyl alcohol, phenol, cresol, and alkyl alcohols. One particularly preferred oral absorption enhancer for the present invention is sodium lauryl sulfate.

Alternatively, the compounds may be administered in the form of liposomes and microspheres (or microparticles). Methods of preparing liposomes and microspheres for administration to a patient are well known to those skilled in the art, and U.S. Pat. No. 4,789,734, the contents of which are hereby incorporated by reference, describes methods of encapsulating biological material in liposomes. Basically, the material is dissolved in an aqueous solution, if necessary with the addition of surfactants and the addition of suitable phospholipids and lipids, and if necessary with the addition of dialyzed or sonicated material. For reviews of known methods, see G.Gregoriadis, Chapter fourteenth, "Liposomes", drugs in Biology and Medicine, pp.287-341(Academic Press, 1979).

Microspheres formed of polymers or proteins are well known to those skilled in the art and may be designed to pass through the gastrointestinal tract directly into the bloodstream. In addition, the compounds may be incorporated into microspheres, combinations of microspheres, which are slowly released over a period of time ranging from days to months. See, for example, U.S. patents 4,906,474, 4,925,673, 3,625,214 and Jein, TIPS 19: 155, 157(1998), the contents of which are incorporated herein by reference.

In one embodiment, the tyrosine kinase inhibitors of the present invention may be formulated as liposomes or microspheres of a suitable size to enter the capillary layer after intravenous administration. When the liposomes or microspheres are applied to the capillary layer surrounding the ischemic tissue, the agent can be administered locally to the site where they are most effective. Suitable liposomes for targeting ischemic tissue are generally less than about 200 nanometers and are also generally monolayer vehicles, as, for example, in U.S. patent No.5,593,688 entitled "lipogel targeting of ischemic tissue" to Baldeschweiler, the contents of which are hereby incorporated by reference.

Preferred microparticles are formed from biodegradable polymers such as polyglycolide, polylactide and copolymers thereof. One skilled in the art can readily determine the appropriate carrier system based on various factors, including the desired drug release rate and the desired dosage.

In one embodiment, the dosage form is administered directly intravascularly via a catheter. The administration may, for example, occur through a hole in the catheter. In those embodiments where the active compound has a relatively long half-life (1 day to one week or more), the dosage form may be included in a biodegradable polymeric hydrogel, such as those disclosed in U.S. Pat. No.5,410,016 to Hubbell et al. These polymeric hydrogels can be delivered into tissue lumens and the active compounds can be released over time as polymer degradants. If desired, the polymeric hydrogel may have microparticles or liposomes that include the active compound dispersed therein, which provides another mechanism for the controlled release of the active compound.

The dosage forms may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. All methods include associating the active compound with a carrier that constitutes one or more accessory ingredients. In general, the dosage forms are prepared by uniformly and intimately bringing into association the active compound with liquid carriers or finely divided solid carriers and then, if necessary, shaping the product into the desired unit dosage form.

The dosage form may further comprise one or more optional adjuvants used in the art of pharmaceutical agent formulation, such as diluents, buffers, flavoring agents, binders, surfactants, thickeners, lubricants, suspending agents, preservatives (including antioxidants), and the like.

The compounds of the invention may be given for administration to the respiratory tract as an odorant or aerosol or nebulizer solution, or as a finely divided powder for spraying, alone or in combination with an inert carrier such as lactose. The active compound in this case suitably has a diameter of less than 50 microns, preferably less than 10 microns, more preferably between 2 and 5 microns.

A mildly acidic pH is generally preferred for nasal administration. Preferably the compositions of the present invention have a pH of from about 3 to 5, more preferably from about 3.5 to about 3.9, and most preferably 3.7. The pH is adjusted by adding a suitable acid such as hydrochloric acid.

The preparation of pharmaceutical compositions comprising an active ingredient dissolved or dispersed therein is well known in the art and need not be defined on a dosage form basis. These compositions are generally prepared as injectable solutions as liquid solutions or suspensions, although solid forms suitable for solution or suspension may also be prepared prior to use. The preparation may also be emulsified.

The active ingredient may be admixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient and in amounts suitable for use in the methods of treatment described herein. Suitable excipients are, for example, water, physiological saline, dextrose, glycerol, ethanol, and the like, and combinations thereof. In addition, if desired, the compositions may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents and the like which enhance the effectiveness of the active ingredient.

The kinase inhibitors of the present invention may include pharmaceutically acceptable salts of the components therein. Pharmaceutically acceptable salts include acid addition salts formed with inorganic acids (formed with the three free amino groups of the polypeptide), such as, for example, hydrochloric or phosphoric acids, or organic acids such as acetic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or iron, and organic bases such as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine and the like.

Physiologically tolerable vectors are well known in the art. Examples of liquid carriers are sterile aqueous solutions which contain no other substances than the active ingredient and water, or which contain buffers such as sodium phosphate at physiological pH, physiological saline or both, e.g. phosphate buffered saline. In addition, the aqueous carrier may contain one or more buffer salts, as well as salts such as sodium and potassium chloride, glucose, polyethylene glycol, and other solutes.

The liquid composition may also comprise a liquid phase, in addition to water. Examples of such other liquid phases are glycerol, vegetable oils such as cottonseed oil, and water-oil emulsions.

Predicting mutations

In another embodiment, the invention discloses a method of predicting a variation in the erbB1 gene following treatment with a tyrosine kinase inhibitor. It is generally known that the response to treatment with tyrosine kinase inhibitors is generally followed by resistance to the compound or other similar compounds. This resistance is thought to occur by acquiring a drug target, e.g., a mutation in EGFR. Predicting (and selecting) these mutations allows for better treatment options and fewer relapses.

In one embodiment of the invention DNA encoding the EGFR kinase domain is isolated and sequenced from cancer patients who respond to gefitinib (or similar EGFR targeting therapy) but subsequently relapse. Recurrence in these patients is expected to involve secondary mutations within the EGFR kinase domain. Compounds that target these newly defined mutations and inhibit their kinase activity are then identified using the methods disclosed herein. These compounds can be used alone, or in combination with other known EGFR-targeted therapies, to treat cancer patients with primary and secondary (as above) mutations in the EGFR kinase domain.

In one embodiment, the prediction of a variation in the kinase (catalytic) domain of EGFR (erbB1 gene) is performed in vivo. In this method, cells, such as fibroblasts, are stably transfected with cDNAs containing kinase domain mutations that have been identified in human cancer cell lines. For example, a polypeptide having a sequence such as SEQ ID NO: 495, or transfected with any number of kinase domain-mutated EGFRs, identified or not identified, said kinase domain-mutated EGFRs of SEQ ID NO: 495 is further depicted in fig. 4A. Transfection of kinase domain mutated EGFRs into cells will result in abnormal cell proliferation in culture. Methods of stable transfection are known to those skilled in the art and are further defined in current protocols in Molecular Biology by f.m.ausubel, r.brent, r.e.kingston, d.d.moore, j.g.seidman, k.struhl and v.b.chanda (Editors), John Wiley & sons, 2004, which is incorporated herein by reference. The cells are then administered an effective, yet sub-lethal dose of the drug, preferably a tyrosine kinase inhibitor predicted to inhibit cell proliferation. In a preferred embodiment, the drug is a phenylaminoquinazoline, a synthetic phenylaminoquinazoline, gefitinib or erlotinib. Cells were serially passaged in the presence of drug and surviving subclones were selected. Cells that survived many generations (i.e., against the compound) were selected and analyzed for variation in the crbB1 gene. It is therefore possible to predict the occurrence of secondary mutations after repeated in vivo treatment with tyrosine kinase inhibitors.

Alternatively, cells are transfected with anti-gefitinib mutant cDNA from human NSCLC cell lines, e.g., NCI-1650 and NCI-1975. Each cell line has a heterozygous mutation in the kinase domain of EGFR and is therefore predicted to be sensitive to gefitinib. The EGFR mutation in NCI-1650 consists of an in-frame deletion of 15 nucleotides at position 2235-2249(delLE746-A750) within exon 19, while NCI-1975 has a missense mutation within exon 21 that replaces T with G at nucleotide 2573 (L858R). As shown herein, the L858R mutation in NCI-H1975 is activating and confers increased sensitivity to gefitinib in vitro. Other cancer cell lines with EGFR kinase domain mutations can be used. The cancer cell lines may include lung cancer as well as other cancers found to have these mutations.

Cells may be treated with a mutagen to increase the frequency with which the cells acquire secondary mutations. Mutagens can induce mutations at different frequencies depending on the dosage regimen, the mode of delivery, the developmental stage of the organism or cell at the time of mutagen administration, all of which parameters are disclosed in the prior art for different mutagens or mutagenesis techniques. The above-mentionedThe mutagen may be an alkylating agent such as Ethyl Methanesulfonate (EMS), N-ethyl-N-nitrosourea (ENU) or N-methyl-N-nitrosourea (MNU). Alternatively, the mutagen may be, for example, carbaxine hydrochloride (Prc), methyl methanesulfonate (MeMS), chlorambucil (Chl), melphalan, porarbazine hydrochloride, cyclophosphamide (Cp), diethyl sulfate (Et)₂SO₄) Acrylamide monomer (AA), Triethylenemelamin (TEM), mechlorethamine, vincristine, dimethylnitrosamine, N-methyl-N' -nitro-nitrosoguanidine (MNNG), 7, 12 Dimethylbenzanthracene (DMBA), oxaproylene, hexamethylphosphoramide, bisufan, and ethyl methanesulfate (EtMs). Methods of treating cells with mutagens are described, for example, in U.S. Pat. No.6,015,670, which is incorporated herein by reference. After mutagenesis, cells (i.e., transfected with mutated EGFR or derived from human cancer cell lines) can be cultured in medium supplemented with gefitinib to select for growth of resistant clones. Subculture of individual clones next, for example, after specific PCR-mediated amplification of genomic DNA corresponding to the EGFR kinase domain, nucleotide sequence determination of the EGFR gene is carried out.

In another embodiment, cells (with EGFR mutation) are serially passaged for several weeks or months in the presence of increasing concentrations of gefitinib (or similar tyrosine kinase inhibitor) to select for spontaneous acquisition of mutations within the EGFR gene that confer resistance to gefitinib. Selected cells, which continue to proliferate at fairly high concentrations of gefitinib, can be isolated as colonies and mutations will be identified as described above. These variations can thus be predicted to occur after repeated treatment with tyrosine kinase inhibitors in vivo. See, for example, Scappini et al, Cancer, April 1, 2004, Vol.100, pg.1459, incorporated herein by reference.

In yet another embodiment, the variant form of EGFR may be amplified in a DNA repair deficient bacterial strain prior to its introduction into a stably selected cell line. Replication of these bacteria will increase the frequency of mutagenesis. Alternatively, "error-causing" PCR can be used to increase the mutation frequency of EGFR DNA cloned in vitro using standard methods known to those skilled in the art.

In another embodiment, the prediction of a variation in the kinase domain of the erbB1 gene is performed in vivo. For example, a cancer model is generated by transfecting a variant of the erbB1 gene, which increases kinase activity, into an animal, i.e., a mouse. The animal is then treated with an effective amount of a compound, preferably an anilinoquinazoline, a synthetic anilinoquinazoline, gefitinib or erlotinib. After repeated exposure to the compound, the cancer is initially inhibited. As in humans treated with these compounds, tumor cells in animals acquire mutations that render them resistant to such treatment. The method of the invention allows the isolation and characterisation of the erbB1 gene in these resistant tumours. Compounds that specifically target these newly identified variations may be useful in treating patients suspected of carrying such a mutated erbB1 gene. These patients include, for example, patients who initially respond to therapy with a tyrosine kinase inhibitor, but who subsequently do not respond to the same or similar compound.

Methods of generating animal models are known to those of skill in the art and are further described in, for example, Ohashi et al, Cell, 65: 305-317 (1991); adams et al, Nature, 325: 223-228 (1987); and Roman et al, Cell, 61: 383-396(1990), which is incorporated herein by reference. For fertilized oocytes, the preferred method of introducing the transgene is by microinjection. See, for example, Leder et al, U.S. patent nos. 4,736,866 and 5,175,383, which are incorporated herein by reference, while for Embryonic Stem (ES) cells, the preferred method is electroporation. However, other methods may be used, including viral delivery systems such as retroviral infection, or liposome fusion. Isolation and characterization of nucleic acids is described above and in the examples.

Using the methods of the invention, patients (diagnostic or prognostic) can be screened for variations in the erbB1 gene identified above that increase kinase activity. The presence or absence of such mutations can then be used as a criterion to determine the sensitivity of an individual to treatment with an EGFR-targeting compound, such as, for example, a tyrosine kinase inhibitor.

Compounds can be selected that specifically target these newly defined variations, whether identified in vivo or in vitro, using techniques known in the art and discussed herein. Candidate drug screening assays can be used to identify biologically active candidate agents that inhibit the activity of the EGFR variant. Of particular interest are screening assays for agents that have low toxicity to human cells. A number of assays may be utilized for this purpose, including in vitro labeled protein-protein binding assays, electrophoretic mobility shift assays, enzyme activity assays, protein binding immunoassays, and the like. Purified mutant EGFR proteins can also be used to determine three-dimensional crystal structures, which can be used to model intermolecular interactions, transporter functions, and the like. These compounds may be, for example, tyrosine kinase inhibitors, antibodies, aptamers, siRNAs, and vectors that inhibit EGFR kinase activity.

In another embodiment, the compounds useful in the present invention are antibodies that interfere with kinase signaling through variant EGFR, including monoclonal, chimeric humanized, and recombinant antibodies and fragments thereof, characterized by their ability to inhibit the kinase activity of EGFR and which have low toxicity.

The suppression antibodies are readily generated in animals such as rabbits or mice by immunization with EGFR having at least one nucleic acid mutation in its kinase domain. Immunized mice are particularly useful for providing a source of B cells that produce hybridomas that are in turn cultured to produce large quantities of anti-EGFR monoclonal antibodies. Chimeric antibodies are immunoglobulin molecules characterized by two or more fragments or portions from different animal species. Typically, the variable region of a chimeric antibody is derived from a non-human mammalian antibody, such as a murine monoclonal antibody, while the immunoglobulin constant region is derived from a human immunoglobulin molecule. Preferably, both regions and combinations thereof have low immunogenicity as determined routinely. Humanized antibodies are immunoglobulin molecules generated by genetic engineering techniques in which a murine constant region is replaced by a human counterpart, while retaining the murine antigen binding region. The resulting mouse-human chimeric antibody should have reduced immunogenicity and enhanced pharmacokinetics in humans. Preferred examples of high affinity monoclonal antibodies and chimeric derivatives thereof that can be used in the method of the invention are described in european patent application EP186,833; PCT patent applications WO 92/16553; and U.S. patent No.6,090,923.

The newly identified compounds, either existing or as described above, may be used to treat patients carrying primary or secondary EGFR mutations.

In a preferred embodiment, the compounds are tyrosine kinase activity inhibitors of EGFR having at least one variation in its kinase domain, particularly small molecule inhibitors having a selective effect on "mutated" EGFRs as compared to other tyrosine kinases. Inhibitors of EGFR include, but are not limited to, tyrosine kinase inhibitors such as quinazolines, e.g., PID153035, 4- (3-chloroaniline) quinazoline, or CP-358, 774, pyridopyrimidines, pyrimidopyrimidines, pyrazolopyrimidines, e.g., CGP 59326, CGP 60261 and CGP 62706, and pyrazolopyrimidines, 4- (phenylamino) -7H-pyrrolo [2, 3-d ] pyrimidine (Traxler et al, (1996) J.Med Chem 39: 2285-; nitrothiophene moieties containing tyrphostins (Brunton et al (1996) Anti Cancer Drug Design 11: 265-295); protein kinase inhibitor ZD-1839 (AstraZeneca); CP-358774(Pfizer, Inc.); PD-0183805(Warner-Lambert), EKB-569(Torrance et al, Nature Medicine, Vol.6, No.9, Sept.2000, p.1024), HKI-272 and HKI-357 (Wyeth); or as described in International patent application W099/09016(American cyanamid); w098/43960(American Cyanamid); w097/38983(Warener Labert); w099/06378 (WarnerLambert); w099/06396(Warner Lambert); w096/30347(Pfizer, Inc.); w096/33978 (Zeneca); w096/33977 (Zeneca); andW096/33980) Zeneca; all incorporated herein by reference.

In another embodiment, an antisense strategy can be used to interfere with the kinase activity of variant EGFR. Such methods may, for example, utilize antisense nucleic acids or nucleic acids that inhibit translation of a specific mRNA by masking the mRNA with the antisense nucleic acid or cleaving it with a ribozyme. For a general discussion of Antisense technology, see, e.g., Antisense DNA and RNA, (Coldspring Harbor Laboratory, D.Melton, ed., 1988).

Reversible transient inhibition of transcription of variant EGFR genes may be useful. This inhibition may be achieved by using siRNAs. RNA interference (RNAi) technology prevents gene expression by using small RNA molecules such as small interfering RNAs (siRNAs). This technology in turn makes use of the fact that RNAi is a natural biological mechanism for silencing genes in most cells of many living organisms, from plants to insects to mammals (McManus et al, Nature Reviews Genetics, 2002, 3(10) p.737). RNAi prevents a gene from producing a functional protein by ensuring that the intermediate molecule, the messenger RNA of the gene, is destroyed. siRNAs can be used in naked molecular form as well as incorporated into vectors, as described below. Aptamer-specific inhibition of variant EGFR gene transcription can be further exploited, see, e.g., U.S. patent 6,699,843. Aptamers useful in the present invention can be identified using the SELEX method. The SELEX process has been described, for example, in U.S. Pat. nos. 5,707,796, 5,763,177, 6,011,577, 5,580,737, 5,567,588, and 5,660,985.

An "antisense nucleic acid" or "antisense oligonucleotide" is a single-stranded nucleic acid molecule that, upon hybridization under cytoplasmic conditions to complementary bases in an RNA or DNA molecule, inhibits the action of the latter. If the RNA is a messenger RNA transcript, the antisense nucleic acid is a complementary nucleic acid that interferes with the transcript or mRNA. As used herein, "antisense" broadly includes RNA-RNA interactions, RNA-DNA interactions, ribozymes, RNAi, aptamers, and RNAse H-mediated blockade.

Ribozymes are RNA molecules that have the ability to specifically cleave other single-stranded RNA molecules in a manner somewhat analogous to DNA restriction endonucleases. Ribozymes have been discovered from the observation that certain mRNAs have the ability to cleave their own introns. By modifying these nucleotide sequences, researchers have been able to engineer molecules that recognize a specific nucleotide sequence in an RNA molecule and cleave it (Cech, 1989, Science 245(4915) p.276). Because they are sequence specific, only mRNAs with specific sequences are inactivated.

Antisense nucleic acid molecules can be encoded by recombinant genes for expression in cells (e.g., U.S. Pat. No.5,814,500; U.S. Pat. No.5,811,234), or they can be prepared synthetically (e.g., U.S. Pat. No.5,780,607).

The invention further provides methods of treating cancer patients. In particular, patients having at least one nucleic acid variation in the kinase domain of EGFR. The method of treatment comprises administering to the patient a composition comprising an siRNA within an appropriate time window. The siRNAs can be chemically synthesized, produced using in vitro transcription, and the like. Furthermore, the siRNA molecules can be tailored to individual patients in such a way as to correspond precisely to the mutations identified in their tumors. Since siRNAs are able to distinguish nucleotide sequences differing by only one nucleotide, it is possible to design siRNAs that uniquely target mutant forms of the EGFR gene, which are associated with single nucleotide substitutions or small deletions of several nucleotides-both identified as described herein. SiRNAs have been identified in Brummelkamp et al, Science 296; 550-; 435-438, 2002, Elbashir S.M. et al (2001) Nature, 411: 494-498, McCaffrey et al (2002), Nature, 418: 38-39; xia h. et al (2002), nat. biotech.20: 1006 + 1010, Novina et al (2002), nat. Med.8: 681, 686, and U.S. application No. 20030198627.

An important advantage of this therapeutic strategy over the use of drugs that inhibit mutant and normal receptors, such as gefitinib, is that sirnas are directed against mutant EGFR and do not inhibit wild-type EGFR. This is significant because it is generally believed that the "side effects" of gefitinib treatment, including diarrhea and dermatitis, are the result of EGFR inhibition in normal tissues where EGFR function is required.

Delivery of siRNA to tumors can potentially be achieved by any of several existing delivery "vehicles". These include viral vectors such as adenovirus, lentivirus, herpes simplex virus, vaccinia virus, and retrovirus, as well as chemically mediated gene delivery systems (e.g., liposomes), or mechanical DNA delivery systems (DNA guns). The length of the oligonucleotide to be expressed for such siRNA-mediated inhibition of gene expression is between 18 and 28 nucleotides.

In another embodiment, the compound is an antisense molecule specific for a human sequence encoding EGFR with at least one variation in its kinase domain. The therapeutic agent administered may be an antisense oligonucleotide, particularly a synthetic oligonucleotide; nucleic acid constructs having chemical modifications made from natural nucleic acids, or expressing these antisense molecules as RNA. The antisense sequence is complementary to mRNA targeting the EGFR gene and inhibits expression of the targeted gene product (see, e.g., Nyce et al (1997) Nature 385: 720). Antisense molecules inhibit gene expression by reducing the amount of mRNA available for translation, by rnase H or steric hindrance. One or a combination of antisense molecules can be administered, where the combination can comprise a plurality of different sequences from the target gene, or sequences complementary to several different genes.

Preferred target genes are EGFR having at least one nucleic acid variation in its kinase domain. The gene sequences are incorporated herein, as, for example, in fig. 5. In general, the antisense sequences will be of the same species origin as the animal host.

Antisense molecules can be produced by expression of all or part of a target gene sequence in a suitable vector introduced and expressed in a targeted host cell. The transcription initiation will be directed such that the antisense strand is produced as an RNA molecule.

The antisense RNA hybridizes to the endogenous sense strand mRNA, thereby repressing expression of the target gene. A native transcriptional initiation region, or an exogenous transcriptional initiation region, may be used. Promoters may be introduced by in vitro recombinant methods, or as a result of sequence homology integration into the chromosome. Many strong promoters active in muscle cells are known in the art, including the O-actin promoter, SV40 early and late promoters, the human cytornegalovirus promoter, retroviral LTRs, and the like. Transcription vectors typically have convenient restriction sites located near the promoter sequence to provide for insertion of the nucleic acid sequence. The transcription cassette can be prepared to include a transcription initiation region, a target gene or a fragment thereof, and a transcription termination region. The transcription cassette can be introduced into a variety of vectors, such as plasmids; retroviruses, such as lentiviruses; an adenovirus; and the like, wherein the vector is capable of being transiently or stably maintained in the cell, typically for a period of at least about one day, more typically for a period of at least about several days.

Aptamers are also useful. Aptamers are a new promising class of therapeutic oligonucleotides or peptides and are selected in vitro to bind specifically to a given target, such as for example a ligand receptor, with high affinity. Their binding properties may be a reflection of the ability of the oligonucleotides to form a three-dimensional structure held together by intra-molecular core base pairing. Aptamers are synthetic DNA, RNA or peptide sequences, which may be normal and modified (e.g. Peptide Nucleic Acid (PNA) thiol-phosphorylated DNA, etc.), which interact with target proteins, ligands (lipids, sugars, metabolites, etc.). In another embodiment, RNA aptamers specific for variant EGFR can be introduced or expressed in cells as therapeutic agents.

Peptide Nucleic Acids (PNAs) are compounds that are similar in some respects to oligonucleotides and analogs thereof, and thus can mimic DNA and RNA. In PNA, the deoxyribose backbone of the oligonucleotide has been replaced by a pseudopeptide backbone (Nielsen et al 1991Science 254, 1457-1500). Each subunit, or monomer, has a naturally occurring or non-naturally occurring nucleobase attached to such a scaffold. One such backbone is composed of N- (2-aminoethyl) glycine linked by amide linkages. PNAs hybridize to complementary nucleic acids by Watson and Crick base pairing and helix formation. The pseudopeptide backbone provides good hybridization properties (Egholm et al Nature (1993)365, 566-568), resistance to enzymatic degradation (Demidov et al biochem. Pharmacol. (1994)48, 1310-1313) and acceptance of various chemical modifications (Nielsen and Haaima chemical society Reviews (1997) 73-78). PNAs specific for variant EGFR may be introduced or expressed in cells as therapeutic agents. PNAs have been described, for example, in U.S. application No. 20040063906.

Patients to be treated with a compound targeting a variant EGFR include, for example, patients diagnosed with a primary or secondary mutation in their EGFR, patients who initially respond to treatment with a tyrosine kinase inhibitor, but subsequently do not respond to the same or similar compound. Alternatively, compounds targeting secondary EGFR mutations can be combined to target primary EGFR mutated compounds, e.g., gefitinib, to cancer patients as a combination therapy. By combining compounds targeting primary and secondary EGFR mutations, the likelihood of resistance will be reduced.

Other mutations of EGFR that confer resistance to currently known anti-cancer therapeutics, including but not limited to the EGFR tyrosine kinase inhibitors gefitinib, erlotinib, and the like, are within the scope of the present invention. Resistant EGFR mutations are predicted to have mutations similar to those identified in the kinase domain of proteins comprising the relevant tyrosine kinase domain. Papers that introduce mutations in similar proteins include those known in the art for BCR-ABL. See, e.g., Bradford et al, blood.2003Jul 1; 102(1): 276-83, Epub 2003Mar 06; hachhaus et al, Leukemia.2002Nov; 16(11): 2190-6; and Al-Ali et Al, Hematol J.2004; 5(1): 55-60.

Mutant EGFR that are resistant to known EGFR tyrosine kinase inhibitors include any one or more EGFR polypeptides, or nucleotides encoding same, having a non-wild-type residue at one or more positions similar to the c-ab1(BCR-ABL) residue that defines the imatinib resistant phenotype. Residues that confer drug resistance when mutated in EGFR specifically include those from the kinase domain, including but not limited to, for example, P-loops and activation loops, where the mutated residues in the EGFR polypeptide are similar to c-able residues. The expected resistant EGFR mutations have non-wild type residues at amino acid positions similar to at least the following positions: met 244, Leu 248, Gly 250, Gln 252, Tyr 253, Glu255, Asp 276, Thr 315, Phe317, Met 351, Glu 355, Phe 359, His 396, Ser 417, and Phe 486 of BCR-ABL, see, e.g., table S3C and fig. 9. These BCL-ABL residues correspond to residues Lys 714, Leu 718, Ser720, Ala 722, Phe 723, Thr 725, Ala 750, Thr 790, Leu 792, Met 825, Glu 829, Leu 833, His 870, Thr 892, Phe 961 in EGFR, respectively. See, for example, table S3C, fig. 9.

Prognostic test

The method of the invention is used as a prognostic indicator of cancer progression. Alternatively, the method is used to detect cancer that is already present but has not yet been diagnosed or is at an undetectable stage. Patients at risk of developing cancer are screened for the presence of a nucleic acid variation in the erbB1 gene that increases kinase activity using the methods of the invention. The presence of a variation in the kinase domain of the erbB1 gene is indicative of the presence or imminent occurrence of cancer. Thus, the presence of variation in the kinase domain of the erbB1 gene suggests that patients will benefit from EGFR-targeted therapy. As described herein, EGFR targeted therapy is preferably treatment with tyrosine kinase inhibitors.

In a preferred embodiment of the invention, the patient is screened for the presence or absence of a nucleic acid variation in the kinase domain of the erbB1 gene by obtaining a biological sample. The sample may be any sample from a patient, including from tissue such as the tongue, mouth, cheek, trachea, bronchi, and lungs, or from a liquid such as sputum or lung aspirates. Methods for obtaining such biological samples are well known to those skilled in the art.

Thus, the present invention provides a method for identifying a disease or disorder associated with aberrant mutant EGFR expression or activity, wherein a test sample is obtained from a subject and a mutant EGFR protein or nucleic acid (e.g., mRNA, gene DNA) is detected, wherein the presence of the mutant EGFR protein or nucleic acid is diagnostic of a patient having or at risk of developing a disease or disorder associated with aberrant mutant EGFR expression or activity. As used herein, the term "test sample" refers to a biological sample obtained from a subject of interest. For example, the test sample may be a biological fluid (e.g., serum), a cell sample, or a tissue, particularly a biopsy tissue sample.

In addition, the prognostic assays described herein can be used to determine whether a subject is capable of administering an agent (e.g., an activator, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant mutant EGFR expression or activity. For example, the methods can be used to determine whether a subject is capable of effective treatment of a disorder with an agent. Thus, the present invention provides methods for determining whether a subject is capable of effectively treating a disorder associated with aberrant mutant EGFR expression or activity with an agent, wherein a test sample is obtained and the mutant EGFR protein or nucleic acid is detected (e.g., wherein the presence of the mutant EGFR protein or nucleic acid is diagnostic of a subject capable of being administered an agent to treat a disorder associated with mutant EGFR expression or activity).

Examples

Example 1

Nucleotide sequence analysis of tumor samples

Tumor samples from initial diagnosis or surgical procedures were collected from patients with NSCLC, who were subsequently treated with Gefitinib under IRB-approved protocols. Frozen tumor samples, as well as matched normal tissue, were obtained from four cases and paraffin-embedded material was used for the remaining samples. In addition, 25 unselected primary NSCLC cases (15 bronchoalveolar carcinomas, 7 adenocarcinomas, and 3 large-cell lung carcinomas), as well as matched normal tissues, were obtained from the Massachusetts General Hospital tumor bank. To perform mutation analysis of the entire EGFR coding sequence, DNA was extracted from the sample, followed by amplification of all 28 exons, sequencing of the uncloneable PCR fragments, and electropherograms in both sense and antisense orientations for the presence of heterozygous mutations. All sequence variants were confirmed by multiple independent PCR amplifications.

Primer sequences and amplification conditions are provided in the appendix. EGFR mutations in exons 19 and 21 were also sought in primary tumors of breast (15 cases), colon (20 cases), kidney (16 cases), and brain (4 cases), as well as in a group of 78 cancer-derived cell lines (listed below) that exhibited different histologies. .

Functional analysis of mutant EGFR constructs

The L858R and delL747-P753insS mutations were introduced into the full-length EGFR coding sequence and inserted into the cytomegalovirus-derived expression construct (pause, Upstate) using site-directed mutagenesis. Cos-7 cells (Lipofectamine2000, Invitrogen) were transfected with 1. mu.g of expression construct, 18hrs later at 5X 10⁴Cells/well (12-well plate, Costar) were re-seeded in DMEM-deficient fetal calf serum. After 16hrs of serum starvation, cells were stimulated with 10ng/ml EGF (SIGMA). To demonstrate the inhibitory effect of Gefitinib, the drug was added to the medium 3hrs before EGF (30 min stimulated with 100ng/ml EGF) was added. Cell lysates were prepared in 100 μ L Laemmli lysis buffer, followed by protein analysis on 10% SDS-PAGE, transfer to PVDF membrane, and western blot analysis using enhanced chemiluminescence reagents (Amersham). Autophosphorylation of EGFR was measured using an antibody against phosphotyrosine Y-1068, and comparable protein expression was shown using an anti-EGFR antibody (action concentration 1: 1000; Cell Signaling Technology).

Mutation analysis

The 28 exons containing the EGFR gene were amplified using the polymerase chain reaction using DNA isolated from primary tumor tissue or tumor-derived cell lines. The primer pairs used were: the expression of the exon 1in the gene sequence,

CAGATTTGGCTCGACCTGGACATAG (sense) (SEQ ID NO: 513) and

CAGCTGATCTCAAGGAAACAGG (antisense) (SEQ ID NO: 514); the expression of the exon 2,

GTATTATCAGTCAC TAAAGCTCAC (sense) (SEQ ID NO: 515) and

CACACTTCAAGTGGAATTCTGC (SEQ ID NO: 516); exon 3, CTCGTG

TGCATTAGGGTTCAACTGG (sense) (SEQ ID NO: 517) and

CCTTCTCCGAGGTGGAATTGAGTGAC (antisense) (SEQ ID NO: 518); the presence of the exon 4 in the gene sequence,

GCTAATTGCGGGACTCTTGTTCGCAC (sense) (SEQ ID NO: 519) and

TACATGC TTTTCTAGTGGTCAG (antisense) (SEQ ID NO: 520); (ii) an exon 5 of a protein,

GGTCTCAAGTGATTCTACAAACCAG (sense) (SEQ ID NO: 521) and

CCTTCACCTACTGGTTCACATCTG (antisense) (SEQ ID NO: 522); (ii) an exon 6 which is,

CATGGTTTGACTTAGTTTGAATGTGG (sense) (SEQ ID NO: 523) and

GGATACTAAAGATACTTTGTCAC CAGG (antisense) (SEQ ID NO: 524); exon 7, GAACACTAGGCTGCAAAGACAGTAAC (sense) (SEQ ID NO: 525) and

CCAAGCAAGGCAAACACATCCACC (antisense) (SEQ ID NO: 526); the presence of the exon 8 in the gene sequence,

GGAGGATGGAGCC TTTCCATCAC (sense) (SEQ ID NO: 527) and

GAAGAGGAAGATGTGTTCCTTTGG (antisense) (SEQ ID NO: 528); the presence of exons 9 and 10, respectively,

GAATGAAGGATGATGTGGCAGTGG (sense) (SEQ ID NO: 529) and

CAAAACATCAGCC ATTAACGG (antisense) (SEQ ID NO: 530); the presence of the exon 11 in the gene sequence,

CCACTTACTGTTCATATAATACAGAG (sense) (SEQ ID NO: 531) and

CATGTGAGATAGCATTTGGGAATGC (antisense) (SEQ ID NO: 532); the presence of the exon 12 in the nucleic acid sequence,

CATGACCT ACCATCATTGGAAAGCAG (sense) (SEQ ID NO: 533) and

GTAATTTCACAGTTAGGAATC (sense) (SEQ ID NO: 534); exon 13, GTCACCCAAGGTCATGGAGCACAGG (sense) (SEQ ID NO: 535) and

CAGAATGC CTGTAAAGCTATAAC (antisense) (SEQ ID NO: 536); exon 14, GTCCTGGAGTCCCAACTCCTTGAC (sense) (SEQ ID NO: 537) and

GGAAGTGGCTCTGA TGGCCGTCCTG (antisense) (SEQ ID NO: 538); the presence of the exon 15 in the gene sequence,

CCACTCACACACACTAAATATTTTAAG (sense) (SEQ ID NO: 539) and

GACCAAAACACCTTAAGTAA CTGACTC (antisense) (SEQ ID NO: 540); the presence of the exon 16 in the gene sequence,

CCAA TCCAACATCCAGACACATAG (sense) (SEQ ID NO: 541) and

CCAGAGCCATAGAAACTTGATCAG (antisense) (SEQ ID NO: 542); (ii) an exon 17 of the polypeptide sequence,

GTATGGACTATGGC ACTTCAATTGCATGG (sense) (SEQ ID NO: 543) and

CCAGAGAACATGGCAACCAGCACAGGAC (antisense) (SEQ ID NO: 544); the presence of the exon(s) 18,

CAAATGAGCTGGCAAGTGCCGTGTC (sense) (SEQ ID NO: 545) and

GAGTTT CCCAAACACTCAGTGAAAC (antisense) (SEQ ID NO: 546) or

CAAGTGCCGTGTCCTGGCACCCAAGC (sense) (SEQ ID NO: 675) and

CCAAACACTCAGTGAAACAAAGAG (antisense) (SEQ ID NO: 676); the presence of the exon 19 in the gene sequence,

GCAATATCAGCC TTAGG TGCGGCTC (sense) (SEQ ID NO: 547) and

CATAGAAAGTGAACATTTAGGATGTG (antisense) (SEQ ID NO: 548); the presence of the exon 20 in the gene sequence,

CCATGAGTACGTATTTTGAAACTC (sense) (SEQ ID NO: 549) and

CATATCC CCATGGC AAACTCTTGC (antisense) (SEQ ID NO: 550); the presence of the exon 21 in the gene sequence,

CTAACGTTCGCCAGCCATAAGTCC (sense) (SEQ ID NO: 551) and

GCTGCGAGCTCACCCAGAATGTCTGG (antisense) (SEQ ID NO: 552); the presence of the exon(s) 22,

GACGGG TCCTGGGGTGATCTGGCTC (sense) (SEQ ID NO: 553) and

CTCAGTACAATAGATAGACAGCAATG (antisense) (SEQ ID NO: 684); the presence of the exon 23 in the DNA sequence,

CAGGACTACAGAAATGTAGGTTTC (sense) (SEQ ID NO: 555) and

GTGCCTG CCTTAAGTAATGTGATGAC (antisense) (SEQ ID NO: 556); the presence of the exon 24 in the DNA sequence,

GACTGG AAGTGTCGCA TCACCAATG (sense) (SEQ ID NO: 557) and

GGTTTAATAATGCGATCTGGGACAC (antisense) (SEQ ID NO: 558); the presence of the exon 25 in the gene sequence,

GCAGCTATAATTTAGAGAACCAAGG (sense) (SEQ ID NO: 559) and

GGTT AAAATTGACTTC ATTTCCATG (antisense) (SEQ ID NO: 560); exon 26, CCTAGTTGCTCTAAA ACTAACG (sense) (SEQ ID NO: 561) and

CTGTGAGGCGTGACAGCCGTGCAG (antisense) (SEQ ID NO: 562); the presence of the exon 27 in the gene sequence,

CAACCTACTAATCAG AACCAGCATC (sense) (SEQ ID NO: 563) and

CCTTCACTGTGTCTGC AAATCTGC (antisense) (SEQ ID NO: 564); the presence of the exon 28 in the gene sequence,

CCTGTCATAAGTCTCCTTGTTGAG (sense) (SEQ ID NO: 565) and

CAGTCTGTGGGTCTAAG AGCTAATG (antisense) (SEQ ID NO: 566).

Annealing temperatures were 58 ℃ (exons 1, 3, 4, 7-10, 12-25, 27, and 28), 56 ℃ (exons 2,5, 6, and 26), or 52 ℃ (exon 11).

Nested PCR amplification of DNA extracted from preserved tumor tissues was performed as follows. Initial PCR was performed on exons 2,5, 6,7, 11, 12, 14, 16, 18, 19, 20, 21, 23, 24, 25, 26, and 27 using primers and the conditions described above. Subsequently, 2. mu.l of this reaction was amplified in a second PCR using the following inner primer pair: exon 2

CAGGAATGGGTGAGTCTCTGTGTG (sense) (SEQ ID NO: 567) and

GTGGAATTCTGCCCAGGCCTTTC (antisense) (SEQ ID NO: 568); (ii) an exon 5 of a protein,

GATTCTACAAACCA GCCAGCCAAAC (sense) (SEQ ID NO: 569) and

CCTACTGGTTCACATCTGACCCTG (antisense) (SEQ ID NO: 570); (ii) an exon 6 which is,

GTTTGAATGTGGTTTCGTTGGAAG (sense) (SEQ ID NO: 571) and

CTTTGTCACCAGG CAGAGG GCAATATC (antisense) (SEQ ID NO: 572); (ii) an exon 7 of a protein,

GACAGTAACTTGGGCTTTCTGAC (sense) (SEQ ID NO: 573) and

CATCCACCCAAAGACTCTCCAAG (antisense) (SEQ ID NO: 574); the presence of the exon 11 in the gene sequence,

CTGTTCATA TAATAC AGAGTCCCTG (sense) (SEQ ID NO: 575) and GAGAGATGCAGGAGCTCTGTGC (antisense) (SEQ ID NO: 576); exon l2, GCAGTTTGTAGTCAATCAAAGGTGG (sense) (SEQ ID NO: 577) and

GTAATTTAAATGGGAAT AGCCC (antisense) (SEQ ID NO: 578); exons l4, CAACTCCTTGACCATTACCTCAAG (sense) (SEQ ID NO: 579) and GATGGCCGTCCTGCCCACACAGG (antisense) (SEQ ID NO: 580); the presence of the exon 16 in the gene sequence,

GAGTAGTTTAGCA TATATTGC (sense) (SEQ ID NO: 581) and GACAGTCAGAAATGCAGGAAAGC (antisense) (SEQ ID NO: 582); the exon (l 8) was used,

CAAGTGCCGTGTCCTGGCACCCAAGC (sense) (SEQ ID NO: 583) and

CCAAACACTCA GTGAAACAAAGAG (antisense) (SEQ ID NO: 584) or GCACCCAAGCCCATGCCGTGGCTGC (sense) (SEQ ID NO: 677) and

GAAACAAAGAGTAAAGTAGATGATGG (antisense) (SEQ ID NO: 678); the presence of the exon 19 in the gene sequence,

CCTTAGGTGCGGCTCCACAGC (sense) (SEQ ID NO: 585) and CATTTAGGATGTGGAGATGAGC (antisense) (SEQ ID NO: 586); the presence of the exon 20 in the gene sequence,

GAAACTCAAG ATCGCATTCATGC (sense) (SEQ ID NO: 587) and

GCAAACTCTTGCTATCCCAGGAG (antisense) (SEQ ID NO: 588); the presence of the exon 21 in the gene sequence,

CAGCCATAAGTCCTCGACGTGG (sense) (SEQ ID NO: 589) and CATCCTCCCCTGCATGTGTTAAAC (antisense) (SEQ ID NO: 590); the presence of the exon 23 in the DNA sequence,

GTAGGTTTCTAAACATCAAGAAAC (sense) (SEQ ID NO: 591) and

GTGATGACATTTCTCCAGGGATGC (antisense) (SEQ ID NO: 592); the presence of the exon 24 in the DNA sequence,

CATCACCA ATGCCTTCTTTAAGC (sense) (SEQ ID NO: 593) and

GCTGGAGGGTTTAATAATGCGATC (antisense) (SEQ ID NO: 594); the presence of the exon 25 in the gene sequence,

GCAAACACACAGGCACCTGCTGGC (sense) (SEQ ID NO: 595) and

CATTTC CATGTGAGTTTCACTAGATGG (antisense) (SEQ ID NO: 596); the presence of the exon 26 in the DNA fragment,

CACCTTCACAATATACCCTCCATG (sense) (SEQ ID NO: 679) and

GACAGCCGTGCAGGGAAAAACC (antisense) (SEQ ID NO: 680); the presence of the exon 27 in the gene sequence,

GAACCAGCATCTCAAGGAGATCTC (sense) (SEQ ID NO: 681) and

GAGCACCTGGCTTGGACACTGGAG (antisense) (SEQ ID NO: 682).

Nested PCR amplification of the remaining exons consisted of initial PCR using the following primers. The expression of the exon 1in the gene sequence,

GACCGGACGACAGGCCACCTCGTC (sense) (SEQ ID NO: 597) and

GAAGAACGAAACGTCCCGTTCCTCC (antisense) (SEQ ID NO: 598); (ii) an exon 3 of a protein,

GTTGAGCACT CGTGTGCATTAGG (sense) (SEQ ID NO: 599) and

CTCAGTGCACGTGTACTGGGTA (antisense) (SEQ ID NO: 600); the presence of the exon 4 in the gene sequence,

GTTCACTGGGCTAATTGCGGGACTCTTGTTCGCAC (sense) (SEQ ID NO: 601) and

GGTA AATACATGCTTTTCTAGTGGTCAG (antisense) (SEQ ID NO: 602); the presence of the exon 8 in the gene sequence,

GGAGGATGGA GCCTTTCCATCAC (sense) (SEQ ID NO: 603) and

GAAGAGGAAGATGTGTTCCTTTGG (antisense) (SEQ ID NO: 604); the presence of the exon 9 in the gene sequence,

GAATGAAGGATGATGTGGCAGTGG (sense) (SEQ ID NO: 605) and

GTATGTGTGAAGGAG TCACTGAAAC (antisense) (SEQ ID NO: 606); the presence of the exon 10 in the gene sequence,

GGTGAGTCACAGGTTCAGTTGC (sense) (SEQ ID NO: 607) and CAAAACATCAGCCATTAACGG (antisense) (SEQ ID NO: 608); the presence of the exon 13 in the gene sequence,

GTAGCCAGCATGTC TGTGTCAC (sense) (SEQ ID NO: 609) and CAGAATGCCTGTAAAGCTATAAC (antisense) (SEQ ID NO: 610); the presence of the exon 15 in the gene sequence,

CATTTGGCTTTCCCCACTCACAC (sense) (SEQ ID NO: 611) and

GACCAAAACACCTTAA GTAACTGACTC (antisense) (SEQ ID NO: 612); (ii) an exon 17 of the polypeptide sequence,

GAAGCTACATAGTGTCTCACTTTCC (sense) (SEQ ID NO: 613) and

CACAACTGCTAATGGCCCGTTCTCG (antisense) (SEQ ID NO: 614); the presence of the exon(s) 22,

GAGCAGCCCTGAACTCCGTCAGACTG (sense) (SEQ ID NO: 683) and

CTCAGTACAATAGATAGACAGCAATG (antisense) (SEQ ID NO: 684); exon 28a

GCTCC TGCTCCCTGTCATAAGTC (sense) (SEQ ID NO: 615) and

GAAGTCCTGCTGGTAGTCAGGGTTG (antisense) (SEQ ID NO: 616); the exon(s) 28b is (are),

CTGCAGTGGGCAACCCCGAGTATC (sense) (SEQ ID NO: 617) and

CAGTC TGTGGGTCTAAGAGCTAATG (antisense) (SEQ ID NO: 618).

A second PCR amplification was performed using the following primer pairs: the expression of the exon 1in the gene sequence,

GACAGGCCACCTCGTCGGCGTC (sense) (SEQ ID NO: 619) and

CAGCTGATCTCAAGGAAACAGG (antisense) (SEQ ID NO: 620); (ii) an exon 3 of a protein,

CTCGTG TGCATTA GGGTTCAACTGG (sense) (SEQ ID NO: 621) and

CCTTCTCCGAGGTGGAATTGAGTGAC (antisense) (SEQ ID NO: 622); the presence of the exon 4 in the gene sequence,

GCTAATTGCGGGACTCTTGTTCGCAC (sense) (SEQ ID NO: 623) and

TACATGCTTT TCTAGTGGTCAG (antisense) (SEQ ID NO: 624); the presence of the exon 8 in the gene sequence,

CCTTTCCATCACCCCTCAAGAGG (sense) (SEQ ID NO: 625) and

GATGTGTTCCTTTGGAGGTGGCATG (antisense) (SEQ ID NO: 626); the presence of the exon 9 in the gene sequence,

GATGTGG CAGTGGCGGTTCCGGTG (sense) (SEQ ID NO: 627) and

GGAGTCACTGAAACAAACAACAGG (antisense) (SEQ ID NO: 628); the presence of the exon 10 in the gene sequence,

GGTTCAGTTGCTTGTATAAAG (sense) (SEQ ID NO: 629) and CCATTAACGGT AAAATTTCAGAAG (antisense) (SEQ ID NO: 630); the presence of the exon 13 in the gene sequence,

CCAAGGTCATGGAGCACAGG (sense) (SEQ ID NO: 631) and CTGTAAAGCTATAACAACAACCTGG (antisense) (SEQ ID NO: 632); the presence of the exon 15 in the gene sequence,

CCACTCACA CACACTAAATATTTTAAG (sense) (SEQ ID NO: 633) and

GTAACTGACTCAAATACAAACCAC (antisense) (SEQ ID NO: 634); (ii) an exon 17 of the polypeptide sequence,

GAAGCTACATAGTGTCTCACTTTCC (sense) (SEQ ID NO: 635) and

CACAA CTGCTAATGGCCCGTTCTCG (antisense) (SEQ ID NO: 636); the presence of the exon(s) 22,

GACGGGTCCTGGGGTGATCTGGCTC (sense) (SEQ ID NO: 685) and CTCAGTACAATAGATAGACAGCAATG (antisense) (SEQ ID NO: 686); exons 28a, CCTGTCATAAGTCTCCTTGTTGAG (sense) (SEQ ID NO: 637) and

GGTAGTCAGGGTTGTCCAGG (antisense) (SEQ ID NO: 638); the exon(s) 28b is (are),

CGAGTATCTCAACACTGTCCAGC (sense) (SEQ ID NO: 639) and

CTAAGAGCTAATGCGGGC ATGGCTG (antisense) (SEQ ID NO: 640).

The annealing temperature for exon 1 amplification was 54 ℃. The annealing temperatures for both the initial and second amplifications were 58 ℃ (exons 3, 4, 7-10, 12-17, 19-25, 27, and 28), 56C (exons 2,5, 6, and 26), or 52C (exons 11 and 18).

PCR amplicons were purified prior to sequencing using exonuclease I (United States Biochemical, Cleveland, OH), and shrimp alkaline phosphatase (United States Biochemical, Cleveland, OH). The purified DNA was diluted and cycle sequenced using the ABI BigDye Terminator kit v1.1(ABI, Foster City, CA) according to the manufacturer's instructions. The sequencing reactions were electrophoresed on an ABI3100 genetic analyzer. Electropherograms were analyzed in both sense and antisense orientations using the sequence navigator software in combination with Factura to label heterozygous locations. All sequence variants were confirmed in multiple independent PCR amplification and sequencing reactions.

Cancer-derived cell lines:

a group of 14 lung cancer-derived cell lines were analyzed for EGFR mutations. These are derived from the tumors NSCLC (N ═ 5), small cell lung cancer (N ═ 6), adenocarcinoma (N ═ 1), bronchial carcinoma (N ═ 1), and unknown histology (N ═ 1). Specific cell lines are: NCI-H460, NCI-522, HOP-92, NCIH841, NCIH734, NCIH2228, NCIH596, NCIH727, NCIH446, NCIH1781, NCIH209, NCIH510, NCIH82, NCIH 865. In addition, 64 cancer-derived cell lines were screened for mutations in exons 19 and 21. These represent the following organization: breast cancer (BT549, BT483, UACC893, HS467T, HS578T, MCF7, MCF7-ADR, MDA-MB-15, MDA-MB-175, MDA-MB-231, MDA-MB-415, MDA-MB-436, MDA-MB-453, MDA-MB-468, T47D), ovarian cancer (ES-2, IGROV-1, MDAH2774, OV1063, OVCAR3, OVCAR4, OVCAR5, SKOV3, SW626), CNS cancer (SF-295, SNB-19, U-251, CCF-STTG1, SW-1088, SW-1783, T98G, M059K, A172, SK-N-DZ, SK-N-MC), leukemia (CCLT-CEM, K562, MOMI 8226, SR 145, prostate cancer (PC-HT 29-HT-15, HCHT-116, PCHT-1, PCHT-15, SW-620), renal cancer (786-O, ACHN, CAKI-1, SN-12C, UO-31), melanoma (LOX-IMVI, M14, SKMEL2, UACC-62), osteosarcoma (SAOS-2), and head and neck cancer (011, O13, 019, 028, 022, 029, 012). The head and neck cancer cell lines were obtained from dr.

Genomic DNA was isolated from snap-frozen tumor samples. Tumor samples were first ground to a fine powder using a pre-cooled and sterilized mortar and pestle. Tumor tissue was immediately transferred to a DNA extraction solution consisting of 100mM sodium chloride, 10mM Tris pH 7.5, 25mM EDTA (disodium ethylenediaminetetraacetate) pH8.0, and 0.5% (w/v) sodium dodecylsulfate, and 100. mu.g/ml freshly prepared proteinase K and incubated at 37 ℃ overnight or at 50 ℃ for 3 hours. The DNA was then extracted using standard phenol-chloroform, ethanol precipitated, washed with 70fi ethanol, air dried and resuspended in TE buffer. The DNA concentration was determined using a spectrophotometer. Exons 19 and 21 of human EGFR were amplified by polymerase chain reaction using the following primer pairs: exon 19 sense primer, 5'-GCAATATCAGCCTTAGGTGCGGCTC-3' (SEQ ID NO: 505); exon 19 antisense primer, 5'-CATAGAAAGTGAACATTTAGGATGTG-3' (SEQ ID NO: 506); exon 21 sense primer, 5'-CTAACGTTCGCCAGCCATAAGTCC-3' (SEQ ID NO: 507) exon 21 antisense primer, 5'-GCTGCGAGCTCACCCAGAATGTCTGG-3' (SEQ ID NO: 508). For each sample, 1.25 units of expanded Long Template enzyme complex (TaqMan polymerase DNA) was amplified in a final reaction volume consisting of 1X expanded Long Template buffer 1(Roche, Mannhein Germany), 50 μ M sequencing grade dATP (Amersham Biosciences, Cleveland OH), 50 μ M sequencing grade dCTP (Amersham Biosciences, Cleveland OH), 50 μ M sequencing grade dGTP (Amersham Biosciences, Cleveland OH), 50 μ M sequencing grade dTTP (Amersham Biosciences, Cleveland OH), 0.211M sense primer, 0.2, uM antisense primer, 1.1 μ g/l TaqStart antibody (Clontech, Palo Alto, CA) that had been pre-warmed with 1/6 volumes of TaqStart antibody (1.1 μ g/l) on ice for 5 minutes (Clontech, Palo Alto, CA) and water PCR to 20 μ M genomic PCR. Each series of amplifications included a negative control omitting the DNA template. PCR cycling conditions for both exons were 95 ℃ C2 min, followed by 40 cycles of 95 ℃ 30s, 58 ℃ 30s and 72 ℃ 45 sec; and finally an extension at 72 ℃ for 10min, followed by placement on an MJ-Research PTC-200 or PTC-225 thermocycler (MJ-Research, Waltham MA) at 4 ℃.

The PCR products were resolved by 0.8% agarose gel electrophoresis to ensure amplification from diseased material and no amplification in negative controls. PCR products were purified prior to sequencing by mixing 10. mu.l of each PCR amplicon with 0.5. mu.l of exonuclease I (10U/l) (United states Biochemical, Cleveland, OH), and 1. mu.l of shrimp alkaline phosphatase (IU/. mu.l) (United states Biochemical, Cleveland, OH) and incubated at 37 ℃ for 20 minutes followed by inactivation at 80 ℃ for 15 minutes on a thermal cycler (MJ-Research, Waltham MA). Purified DNA was diluted in water according to amplicon strength and subjected to cycle sequencing using the ABI BigDye Terminator kit v1.1(applied biosystems, Foster City, Calif.) according to the manufacturer's instructions. Cycle sequencing was performed on an MJ-Research thermocycler using the following cycle conditions: exon 19 sense primer, 5'-GCAATATCAGCCTTAGGTGCGGCTC-3' (SEQ ID NO: 505); exon 19 antisense primer, 5'-CATAG AAAGTGAACATTTAGGATGTG-3' (SEQ ID NO: 506); exon 21 sense primer, 5'-CTAACGTTCGCCAG CCATAAGTCC-3' (SEQ ID NO: 507) or 5'-CGTGGAGAGGCTCAGAGCCTGGCATG-3' (SEQ ID NO: 687); exon 21 antisense primer, 5'-GCTGCGAGCTCACCCAGAATGTCTGG-3' (SEQ ID NO: 508). Sequencing reactions were electrophoresed on an ABI3100 genetic Analyzer (Applied Biosystems, Foster City, Calif.). Potential heterozygous locations were marked using the Factura and sequence Navigator (Applied Biosystems, Foster City, Calif.) software program and displayed for evaluation. Nucleotides at positions where the height of the minor peak is greater than or equal to 30% of the height of the major peak are labeled as heterozygous and confirmed by sense and antisense reading. Samples with sequence indicators of the presence of mutations were re-amplified and sequenced for confirmation.

Position of primers used in sequence analysis relative to exons 19 and 21

Intron primers are shown in lower case and underlined.

Intron sequences are shown in lower case letters.

Exon sequences are shown in capital letters.

EGFR exon 19(5 '-3') (SEQ ID NO: 641)

gcaatatcagccttaggtgcggctccacagccccagtgtccctcaccttcggggtgcatcgctggtaacatccacccagatcactgggcagcatgtggcaccatctcacaattgccagttaacgtcttccttctctctctgtcatagGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATgtgagtttctgctttgctgtgtgggggtccatggctctgaacctcaggcccaccttttctcatgtctggcagctgctctgctctagaccctgctcatctccacatcctaaatgttcactttctatg

EGFR exon 21(5 '-3') (SEQ ID NO: 642) or (SEQ ID NO: 687)

ctaacgttcgccagccataagtcctcgacgtggagaggctcagagcctggcatgaacatgaccctgaattcggatgcagagcttcttcccatgatgatctgtccctcacagcagggtcttctctgtttcagGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTGGCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAgtaaggaggtggctttaggtcagccagcattttcctgacaccagggaccaggctgccttcccactagctgtattgtttaacacatgcaggggaggatgctctccagacattctgggtgagctcgcagc

Results

Clinical features of Gefitinib responders

Patients with advanced, refractory chemotherapy NSCLC have been treated with the single agent Gefitinib since 2000 in Massachusetts General Hospital. A total of 275 patients were treated as part of the institutional use expanded access program before they were approved by the FDA at5 months of 2003 and commercial supplies were used after the date of approval. During this period, 25 patients were identified by the physician as having a significant clinical response. Significant clinical response was defined as partial response using RECIST criteria for patients with measurable disease, or evaluable response assessed by two physicians for patients who were unable to quantify tumor burden using these criteria. Table 1 shows the clinical characteristics of 9 cases for which tumor samples were obtained as initial diagnosis. For other Gefitinib responders, no tissue was obtained, most often because diagnostic samples from needle aspirates were cytologically limited. As a group, the 9 patients were substantially benefited by Gefitinib. Median survival from the start of drug treatment was over 18 months, while median treatment period was greater than 16 months. Consistent with previous reports, Gefitinib responders were mostly women, with no history of aspiration, and tumors with bronchoalveolar histology (11, 12). Case 6 is a representative Gefitinib-responsive population. This patient was a 32 year old man with no history of smoking, with multiple brain lesions and disease in the right lung diagnosed as bronchoalveolar carcinoma. He was treated with whole brain radiation therapy followed by a series of chemotherapy regimens that did not respond to his tumor (carboplatin and gemcitabine; docetaxel; vinorelbine). With a constantly declining functional status and a progressive lung tumor burden he started the treatment with 250mg daily Gefitinib. His shortness of breath improved rapidly and pulmonary CT 6 weeks after the start of treatment revealed a significant improvement as shown in figure 1.

EGFR mutations in Gefitinib responders

We hypothesized that NSCLC cases with significant responses to Gefitinib may have somatic mutations of EGFR, suggesting a fundamental role played by this growth factor signaling pathway in these tumors. To look for these mutations, we first tested rearrangements in the extracellular domain of EGFR, which is characteristic of gliomas (15): nothing is detected. We sequenced the entire coding region of the gene using PCR amplification of individual exons. Heterozygous mutations were observed in case 8/9, all of which were clustered within the kinase domain of EGFR (table 2 and figure 2). Four tumors had in-frame deletions with amino acids 746-750(delE 746-A750; case 1), 747-750(delL747-T751 insS; case 2), and 747-752(delL747-P753 insS; case 3, case 4). The latter two deletions are associated with the insertion of a serine residue resulting from the generation of a new codon at the deletion breakpoint. Strikingly, these four deletions overlapped, and the deletion of four amino acids within exon 19 (at codons 747-750, leucine, arginine, glutamic acid and alanine) was common to all cases (see FIG. 4 a). Three other tumors have amino acid substitutions within exon 21: leucine-arginine at codon 858 (L858R; cases 5 and 6), and leucine-glutamine at codon 861 (L861Q; case 7). The L861Q mutation is of particular interest because the same amino acid in the mouse EGFR gene is responsible for the black skin (dsk5) trait, associated with altered EGFR signaling (18). A fourth missense mutation in the kinase domain resulted in a glycine-cysteine substitution at codon 719 within exon 18 (G719C; case 8). Matched normal tissues were obtained for cases 1, 4,5 and 6 and only the wild-type sequence was shown, indicating that the mutation occurred in the body during tumor formation. No mutations were observed in seven NSCLC cases that did not respond to Gefitinib (P ═ 0.0007; 2-lateral Fisher's exact test).

Prevalence of specific EGFR mutations in NSCLC and other cancer types

Unlike gliomas, in which rearrangements affecting the extracellular domain of EGFR have been extensively studied (15), mutations of EGFR in NSCLC have not been defined. We therefore sequenced the complete coding region of the gene for 25 primary cases unrelated to the Gefitinib study, including 15 cases with bronchoalveolar histology, which had been associated with Gefitinib reactivity in previous clinical trials (11, 12). Heterozygous mutations were detected in two cases of bronchoalveolar carcinoma. Both cases had the same in-frame deletion in the kinase domain as in the Gefitinib responder, i.e., delL747-P753ins and delE746-A750 (Table 2). Given the apparent clustering of EGFR mutations, we sequenced exons 19 and 21 for a total of 55 primary tumors and 78 cancer-derived cell lines representing different tumor types (see supplementary material). No mutations were detected suggesting that these only occur in a small group of cancers where EGFR signaling may play an important role in tumorigenesis.

EGF-induced activation and enhancement of Gefitinib inhibition of mutant EGFR proteins

To investigate the functional properties encoded by these mutations, L747-S752insS deletion and L858R missense mutants were expressed in cultured cells. Transient transfection of wild-type and mutant constructs into Cos-7 cells demonstrated equivalent expression levels,indicating that the mutation did not affect protein stability. By measuring tyrosine, commonly used as a marker for receptor autophosphorylation¹⁰⁶⁸Phosphorylation of residues quantifies EGFR activation (19). Neither wild type nor mutant EGFR showed autophosphorylation in the absence of serum and associated growth factors (fig. 3 a). However, addition of EGF results in a 2-3 fold increase in receptor activation of missense and deletion EGFR mutants compared to wild type receptor. Furthermore, although normal EGFR activation was not down-regulated after 15min, consistent with receptor internalization, both mutant receptors showed sustained activation up to 3hrs (fig. 3 a). Similar results were obtained with antibodies measuring overall EGFR phosphorylation after EGF addition (not shown).

Since the 7/8EGFR kinase mutation is located in the ATP cleft, which is targeted by Gefitinib, we determined whether the mutant protein has altered sensitivity to inhibitors. EGF-induced autophosphorylation of receptors was measured in cells pretreated with varying concentrations of Gefitinib. Strikingly, both mutant receptors showed increased sensitivity to inhibition by Gefitinib. Wild type EGFR has an IC of 0.1. mu.M₅₀And showed complete inhibition of autophosphorylation on 2. mu.M Gefitinib, while both mutant proteins had an IC of 0.015. mu.M₅₀And shows the elimination of autophosphorylation at 0.2. mu.M (FIG. 3 b). This difference in drug sensitivity may be clinically relevant because pharmacokinetic studies indicate that oral daily administration of 400-600mg of Gefitinib results in mean steady state low trough plasma concentrations of 1.1-1.4 μ M, whereas the currently recommended daily dose of 250mg results in a low trough concentration of 0.4 μ M (20).

Example 2

Tumor cells that have a mutation in the kinase domain of EGFR, and are therefore sensitive to growth inhibition by Gefitinib treatment, can also undergo a "second site" mutation within the kinase domain, which confers resistance to Gefitinib but which are still "active" in the sense that they exhibit increased EGFR signaling relative to wild-type EGFR. These gefitinib resistant mutants were generated from two sporadic human NSCLC cell lines, NCI-1650 and NCI-1975. Each cell line contains a heterozygous mutation in the kinase domain of EGFR and is expected to be sensitive to gefitinib. The EGFR mutation in NCI-1650 consists of an in-frame deletion of 15 nucleotides at position 2235-2249 within exon 19 (delLE746-A750) while NCI-1975 has an in-exon missense mutation replacing G with T on nucleic acid 2573 (L858R). The L858R mutation in NCI-H1975 is shown herein to be active and confer sensitivity to gefitinib in vitro.

After random chemical mutagenesis using EMS (ethyl methanesulfonate) followed by culture in gefitinib-supplemented medium to select for the outgrowth of resistant clones, gefitinib-resistant cell lines derived from NCI-1650 and NCI-1975 were isolated. Following sub-culture of individual clones, nucleotide sequence determination of the EGFR gene was performed after specific PCR-mediated amplification of genomic DNA corresponding to the EGFR kinase domain.

One variant of this strategy involves the spontaneous acquisition of mutations in the EGFR gene conferring resistance to gefitinib by serial passage of both cell lines in the presence of increasing concentrations of gefitinib for a period of several weeks. Selected clones, which continued to proliferate at relatively high concentrations of gefitinib, were isolated as colonies and mutations were identified as described above.

Example 3

To determine whether mutations in receptor tyrosine kinases play an important role in NSCLC, we looked for genetic changes in a panel of 119 primary NSCLC tumors consisting of 58 samples from Nagoya city university host in Japan and 61 samples from Brigham and Women's host in boston, Massachusetts. The tumors included 70 lung adenocarcinoma and 49 other NSCLC tumors, from 74 male and 45 female patients, which were not treated with the EGFR kinase inhibitor treatment.

As an initial screen, we amplified and sequenced 47 exons encoding activation loops from genomic DNA from a subset of 58 NSCLC samples, including 41 lung adenocarcinomas, of 58 human receptor tyrosine kinases (table S1). Three of the tumors, all lung adenocarcinomas, showed no heterozygous missense mutations in EGFR in lung tissue DNA from the same patient (table S2; S0361, S0388, S0389). No mutations were detected in amplicons from other receptor tyrosine kinase genes. All three tumors had the same EGFR mutation, predicted to change leucine ("L") to arginine ("R") at position 858 (fig. 6A; CTG → CGG; "L858R"), where all numbering is with reference to human EGFR.

We next examined the entire 119 NSCLC tumor pools for exons 2 to 25 of EGFR. Exon sequencing of genomic DNA revealed missense and deletion mutations in a total of 16 tumors, all in kinase domain exons 18 to 21. All sequence changes in this group were heterozygous in tumor DNA; in each case, the paired normal lung tissues from the same patient showed wild-type sequence, confirming that the mutation was somatic in origin. The distribution of nucleotide and protein sequence changes, as well as patient characteristics associated with these abnormalities, are summarized in table S2.

Substitution mutations G719S and L858R were detected in two and three tumors, respectively. The "G719S" mutation changed glycine (G) to serine (S) at position 719 (FIG. 6B). These mutations are located in the nucleotide triphosphate binding domain or GXGXXG motif of the P loop (SEQ ID NO: 490) and in the highly conserved DFG motif adjacent to the activation loop, respectively. See, for example, fig. 7. The mutated residues were nearly invariant in all protein kinases and similar residues in the serine-threonine kinases of the B-Raf proteins (G463 and L596) were somatically mutated (41, 53) in colorectal, ovarian and lung cancers (fig. 6A, 6B).

We also detected multiple deletion mutations that accumulated in the region of the EGFR kinase domain spanning codons 746-759. Ten tumors carried one of two overlapping 15 nucleotide deletions that abolished EGFR codon 746-750, starting at nucleotide 2235 or 2236 (Del-1; FIGS. 6C and 8C; Table S2). EGFR DNA from another tumor showed a heterozygous 24-nucleotide gap, resulting in a deletion of codons 752 to 759 (Del-2; FIG. 6C). Representative chromatograms are shown in fig. 8A-8F.

The positions of the substitution mutations and the Del-1 deletions in the three-dimensional structure of the active form of the EGFR kinase domain are shown in fig. 7. Note that sequence changes are clustered around the kinase active site, and substitution mutations are located in the activation loop and the glycine-rich P-loop, which are structural elements already important for the autoregulation of many protein kinases (52).

Two other EGFR mutations were identified in two different tumor types. That is, we identified the EGFR mutation G857V in Acute Myeloid Leukemia (AML) and the EGFR mutation L883S in metastatic sarcoma. The "G857V" mutation has a glycine (G) substituted with a valine (v) at position 857, while the "L883S" mutation has a leucine (L) substituted with a serine (S) at position 883. These findings suggest that mutations in EGFR occur in several tumor types and, most importantly, EGFR inhibitors will be effective in the treatment of patients with these mutations. This extends kinase inhibitors such as, for example, the tyrosine kinase inhibitor gefitinib (marketed as Iressa)^TM) Erlotinib (commercially available as Tarceva)^TM) And the like in the treatment of tumor types other than NSCLC.

EGFR mutations show surprising concordance with the differential patient characteristics described in the japanese and us patent families. As noted above, clinical trials revealed that gefitinib (Iressa), a tyrosine kinase inhibitor, was administered as a tyrosine kinase inhibitor^TM) Significant variability of response, higher response seen in japanese patients than in the population mainly derived from europe (27.5% vs. 10.4%, in the multi-institutional phase II trial) (48); and partial responses are more common in women in the united states, in smokers, and in adenocarcinoma patients (49-51). We show that EGFR mutations are more common in adenocarcinomas (15/70 or 21%) than in other NSCLCs (1/49 or 2%); in women (9/45 or 20%) than in menMore common than (7/74 or 9%); it is more common in patients from japan (15/58 or 26%, and 14/41 adenocarcinoma or 32%) than in patients from the united states (1/61 or 2%, and 1/29 adenocarcinoma or 3%). The highest part of EGFR mutations (8/14 or 57%) was observed in japanese women with adenocarcinoma. Notably, patient characteristics associated with the presence of EGFR mutations appear to be those consistent with clinical response to gefitinib treatment.

To investigate whether EGFR mutations may be a determinant of gefitinib sensitivity, pre-treated NSCLC samples were obtained from 5 patients who responded and 4 patients who had undergone gefitinib treatment, identified from more than 125 patients who were treated after extended program acceptance by the Dana-Farber Cancer Institute or after general approval of gefitinib (49). Four of the patients had a partial radiographic response (50% tumor regression in CT scans after 2 months of treatment), while the fifth patient experienced significant improvement in symptoms in less than two months. All patients were from the united states and caucasian.

Although sequencing of the kinase domain (exons 18 to 24) did not reveal mutations in tumors from four patients, whose tumors developed after gefitinib treatment, all five tumors from gefitinib-responsive patients had EGFR kinase domain mutations. Chi-square test revealed that the difference in EGFR mutation frequency between gefitinib responder (5/5) and non-responder (0/4) was statistically significant with p ═ 0.0027, whereas the difference between gefitinib responder and non-selected us NSCLC patients (5/5vs.1/61) was also significant with p < 10^-12(＊.) mutations of EGFR L858R previously observed in unselected tumors were identified in a gefitinib-sensitive lung adenocarcinoma (FIG. 6A; Table S3A, IR 3T.) three gefitinib-sensitive tumors contained heterozygous in-frame deletions (FIG. 6C and tables S3A and S3B, Del-3 in both cases and Del-4 in one case) and one contained homozygous in-frame deletions (FIG. 6C and tables S3A and S3B, Del-5.) each of these deletions was within the region of codons 746 to 753 of EGFR, where deletions were also found in unselected tumorsThe generations are related (tables S3A-S3C). These mutations were confirmed to be somatic in all four samples of matched normal tissue.

Example 3A: primer design

The cDNA sequence of the receptor tyrosine kinase was obtained from GenBank (accession numbers listed in S1) and compared to the human genomic arrangement (http:// genome. ucsc. edu) using a BLAT alignment to identify the exon/intron boundaries. The external gene-specific Primer pairs were designed using the Primer3 program (http:// frodo. wi. mit. edu/Primer3/Primer 3. code. html) to amplify on each side the exon sequences and at least 250bp of flanking internal or adjacent exon sequences. The resulting predicted amplicons were then used to design internal primers (typically greater than 50bp from the exon/intron boundary) flanking the exon and comprising the appended forward or reverse primer tails of M13. These nested primer pairs were tested for appropriate amplicon size and high quality sequence from control DNA. Amplicons containing exons encoding the 47 tyrosine kinase activation loops were amplified and sequenced in a panel of 58 primary lung cancer samples from the Nagoya City University Medical School. In addition, amplicons covering full length EGFR were also amplified.

Example 3B: PCR and sequencing method for genomic DNA

Tyrosine kinase exon and flanking intron sequences were amplified using specific primers in a 384 well format nested PCR device. Each PCR reaction contained 5ng of DNA, 1 XHotStar Buffer, 0.8mM dNTPs, 1mM MgCl₂0.2UHotStar Enzyme (Qiagen, Valencia, Calif.), and 0.2. mu.M forward and reverse primers in a 10. mu.L reaction volume. The PCR cycle parameters were: one cycle of 95 ℃ for 15min, 35 cycles of 95 ℃ for 20s, 60 ℃ for 30s and 72 ℃ for 1min, followed by one cycle of 72 ℃ for 3 min.

The resulting PCR product was chemically purified by solid phase reversible immobilization followed by two-way dye-terminator fluorescent sequencing with the universal M13 primer. Sequencing fragments were detected by capillary electrophoresis using an ABI Prism3700DNA analyzer (Applied Biosystems, Foster City, Calif.). PCR and sequencing were performed by Agencour Bioscience Corporation (Beverly, Mass.).

Example 3B: sequence analysis and validation

The forward (F) and reverse (R) chromatograms were batch analyzed by the sequence Mutation Surveyor 2.03(SoftGenetics, State College, Pa.). High quality sequence variations found in one or both directions are scored as candidate mutations. Exons with candidate mutations were re-amplified from the original sample and re-sequenced as above.

Example 3C: patient's health

Lung tumor specimens were obtained from Nagoya city university Hospital and the Brigham and women's Hospital (unselected japanese and gefitinib treated us tumors, respectively) treated non-small cell lung cancer patients under an Institutional Review Board approved study and from the Brigham and women's Hospital anonymous tumor bank (unselected us samples). For most samples there is information on sex, age and histology. Patient samples were also obtained from patients treated in an open label clinical trial at Dana-Farber Cancer Institute (13). Responses to gefitinib are defined using authoritative criteria (see, e.g., A.B.Miller, B.Hoogstraten, M.Staquet, A.winkler, 1981Cancer 47, 207-14). IRB approval was obtained for these studies.

Of the gefitinib-responsive patients, two patients had previously been treated with at least one cycle of chemotherapy, one patient had previously been treated with radiation therapy, one patient was being treated with chemotherapy, and one patient received no other therapy. For patients with gefitinib insensitivity, treatment failure was defined as the appearance of new or growth of existing tumor lesions in the CT scan after 2 months of gefitinib treatment compared to the baseline CT scan.

Example 3D: cDNA sequencing of patient samples

Total RNA was isolated from tissue samples using Trizol (Invitrogen, Carlsbad, Calif.) and purified using the RNeasy mini-elute clean kit (Qiagen, Valencia, Calif.). cDNA was transcribed from 2. mu.g of total RNA using Superscript II reverse transcriptase (Invitrogen Life technologies, Carlsbad, Calif.) according to the manufacturer's recommendations. The cDNA was used as a template for subsequent PCR amplification of EGFR.

The PCR components were: 20rnM Tris-HCl (pH 8.4), 50mM KCl, 1.5mM MgCl₂0.1mM, 0.2mM each of dATP, dCTP, dGTP and dTTP; mu.M of each primer, and 0.05 units/. mu.l of Taq polymerase (TaqPlatinurn, GIBCO BRL, Gaithersburg, Md.). Amplification of fragment "a" requires the addition of 4% DMSO to the reaction. The primer sequences are listed in table S4. The forward and reverse primers were synthesized with 18 base pair bulge M13forward and reverse sequences, respectively. The thermal cycling conditions were: 94 ℃ for 4 min; followed by 11 cycles, a variation step 20 "at 94 ℃, an extension step 20" at 72 ℃, and an annealing step 20 "down by 1 ℃/cycle, from 60 ℃ for cycle 1 to 50 ℃ for cycle 11; cycle 11 was then repeated 25 times. The procedure was ended with 6 min incubation at 72 ℃ followed by 4 ℃.

One aliquot of the PCR reaction was diluted 1: 50 with water. The diluted PCR products were sequenced using the M13Forward Big Dye Primer kit (Perkin-Elmer/Applied Biosystems, Foster City, Calif.) according to the manufacturer's recommendations. The sequencing products were isolated on a fluorescence sequencer (model 3100 from Applied Biosystems, Foster City, CA). Base recognition was performed by instrument software and reviewed by visual inspection. Each sequence was compared to the corresponding normal sequence using Sequencher 4.1 software (Gene Codes Corp.).

Example 3E: tumor types expressing mutant EGFR

Two other EGFR mutations were found in two different tumor types. EGFR mutations replacing glycine (G) with valine (V) at position 857 ("G857V") were identified in Acute Myeloid Leukemia (AML). EGFR mutations were identified in metastatic sarcomas that replaced leucine (L) with serine (S) at position 883 ("L857S").

Example 3F: cell lines

The effect of gefitinib on NSCLC cell lines in vitro was examined. One cell line, H3255, was particularly sensitive to gefitinib, IC₅₀Was 40 nM. Other cell lines have much higher IC_50s. For example, wild type cell line H1666 has an IC of 2. mu.M₅₀It is 50 times higher than the mutant cell line. When EGFR from this cell line was sequenced, it contained a L858R missense mutation, while the other cell lines were wild-type to EGFR. Compared with EGFR wild type cell, gefitinib with much lower concentration is required to inhibit EGFR and AKT and ERK phosphorylation triggered by EGFR, and gefitinib with at least 100 times higher concentration is required to achieve the same effect in wild type cell. These findings suggest that the mutant receptor is more sensitive to the action of gefitinib.

It is also noted here that,

example 3G: combination therapy

Tumor samples from patients with advanced NSCLC treated on a carboplatin/paclitaxel randomization trial with or without erlotinib were analyzed. The clinical part of this trial showed equivalent survival in both treatment adjunctions. Tumor samples for sequencing were obtained from 228 of 1076 patients. The preliminary clinical features of these patients were indistinguishable from this group in terms of baseline demographics, response rates, median and overall survival rates.

Exons 18-21 of the tyrosine kinase domain were sequenced and 29 mutations were identified with a 12.7 percent mutation frequency.

Patients with EGFR mutations as a whole had better survival regardless of whether they received chemotherapy alone or in combination with erlotinib. These differences were statistically significant with p values less than 0.001. These findings raise the possibility of EGFR mutation, and in addition to being a predictor of gefitinib and erlotinib, increased survival can be predicted.

(. o) note that the frequency of EGFR mutations in unselected US patients, 1in 61, appears to be low compared to the reported frequency of 10.4% gefitinib responses. This difference was of moderate statistical significance (chi-square test p ═ 0.025). This result can thus still be attributed to chance, to a fraction of responders without EGFR mutations, or to experimental failure to detect EGFR mutations in this tumor collection. If the frequency of EGFR mutations (5/5) in gefitinib-responsive US patients is compared to the expected frequency of gefitinib response (10.4%), the probability of the chi-square test is again less than 10 "12.

Example 4

Research and design:

from 8 months to 1 month 2005, with reference to EGFR kinase domain sequencing, the sequence was determined in Massachusetts General Hospital (MGH), Dana-Farber Cancer: institute (DFCI), and Brigham and Women's Hospital (BWH), we conducted a retrospective population study of NSCLC patients. These three institutes include Dana-Farber/Partners cancer Care (DF/PCC), an academic Joint temporary cancer Care center, which nurses approximately 1,200 lung cancer patients annually. At 8 months 2004, the EGFR kinase domain can be sequenced at DF/PCC for clinical use. The physician can choose which patient to test for, and the patient needs to have enough and appropriate tumor sample present. The tumor cells must contain at least 50% of the specimen based on histological examination by MGH and BWH reference to a pathologist, and the specimen must be from dissection of primary or metastatic tumors, bronchoscope biopsy, or core needle biopsy, or cell pellets from pleural fluid. In rare cases, fine needle aspiration of the sample was determined to be sufficient. The sample may be paraffin embedded or frozen tissue. Patients with this diagnosis were ineligible to test due to low prevalence of EGFR mutations in squamous cell tumors (62).

We identified patients undergoing EGFR testing using EGFR case records retained in the Laboratory for Molecular Medicine (LMM), of the Harvard medical School/Partners HealthCare Center for Genetics and Genomics (CLIA #22D1005307), which is a diagnostic testing facility that implements and interprets full sequencing. We included all patients who underwent EGFR testing, from DF/PCC, with a diagnosis of NSCLC during the study.

Patient age, gender, and race were collected by an electronic medical record system. The smoking status, cancer history, EGFR kinase domain sequencing results, and subsequent EGFR-TKI treatment plan were recorded using structured physicalanchart review. In particular, smoking status and cancer history are obtained from doctors and care notes. Former smokers were defined as patients who had quit smoking at least one year prior to their lung cancer diagnosis and never smokers were defined as patients who had drawn less than 100 cigarettes during their lifetime. Smokers who quit smoking within one year of their diagnosis or who are smoking at the time of diagnosis are classified as current smokers. The pack-years of smoking are calculated by multiplying the number of packs drawn per day by the number of years smoked. Tumor histology and EGFR kinase domain sequencing results were obtained from pathology reports. All pathological samples were examined centrally at MGH or BWH and histology was classified using the World Health Organization (WHO) classification system (63). Subsequent treatment plans are obtained from doctor notes.

There is complete data on age, sex, tumor histology, and EGFR mutation status. For ethnicity (12%), tumor stage at time of testing (4%), smoking status (6%), prior treatment (5%), and subsequent EGFR-TKI treatment plan (11%) there is missing data. The study was approved by Institutional Review Board at DF/PCC.

EGFR gene sequencing:

serial sections of frozen or formalin-fixed, paraffin-embedded (FFPE) tumor tissue were excised and placed on glass slides. A pathologist identified a tumor tissue region consisting of at least 50% viable tumor cells. The FFPE samples were extracted with xylene and ethanol to remove paraffin. Both FFPE and frozen tissue samples were digested overnight with proteinase K. Genomic deoxyribonucleic acid (DNA) was extracted from tissues and peripheral blood using standard methods. Using DNASTEK-Oragene^TMThe saliva kit extracts genomic DNA from saliva.

The kinase domain of EGFR (exons 18-24 and flanking intron regions) was amplified in a set of individual nested Polymerase Chain Reactions (PCR). The primers used in nested PCR amplification are described in tables S1A and B and SEQ ID 1-424, with the addition of the universal sequence (5 'tgtaaaacgacggccagt) (SEQ ID NO.645) to the 5' end of the primers. The PCR products were directly sequenced by dye-terminator sequencing. PCR was performed in 384 well plates in 15. mu.l volumes containing 5ng genomic DNA, 2mM MgCl₂0.75. mu.l DMSO, 1M Betaine, 0.2mM dNTPs, 20pmol primer, 0.2. mu.l(Applied Biosystems), 1 Xbuffer (AmpliTaqgold was supplied). The thermal cycling conditions were as follows: 10 minutes at 95 ℃; 30 cycles of 95 ℃ for 30 seconds, 60 ℃ for 30 seconds, and 72 ℃ for 1 minute; and 72 ℃ for 10 minutes. By usingMagnetic beads (Agencourt) purified PCR products.

By usingThe sequencing products were purified by magnetic beads (Agencourt) and separated by capillary electrophoresis on an ABI 3730DNA analyzer (Applied Biosystems). By means of a Mutation Surveyor (SoftGenetics, S)te College, PA) and sequence analysis was performed manually by two reviewers. Nonsynonymous DNA sequence variants were confirmed by analysis of 3-5 PCR reactions of the original genomic DNA sample. Blood or saliva samples with nonsynonymous DNA sequence variants were analyzed to investigate whether the sequence changes were specific for tumor tissue.

Statistical analysis:

we constructed logistic regression models to assess univariate associations between patient demographics and clinical characteristics and EGFR mutation status. To identify significant predictors of mutation positivity, we constructed multivariate logistic regression models that included independent variables identified in previous studies as predictors of mutation, specifically gender, race, histology, and smoking status. Six patients were excluded from these analyses due to the lack of EGFR mutation data as a result of PCR failure. The entire analysis was performed using SAS statistical software (version 8.02, SAS Institute, Cary, NC).

As a result:

the characteristics of the patients are as follows:

of the 100 patients with NSCLC who underwent somatic EGFR kinase domain sequencing as part of clinical cancer during the study, the mean age was 60.7 years, 63% of women (table 4). Most patients were white (76%) or asian (7%) and had metastatic disease at the time of scheduled testing (67%). Almost all patients tested for EGFR mutation (94%) had adenocarcinoma, adenocarcinoma with characteristics of bronchioloalveolar carcinoma (BAC), or pure BAC. About one third of the patients are never smokers. Therapies administered between EGFR tests include surgery (50%), chest radiotherapy (22%), chemotherapy (47%), and EGFR targeted therapy (11%).

Identified mutations:

the average length of time from the test to the results was 12 working days. Most of the samples submitted were paraffin-embedded (74%). 6 of the 74 paraffin-embedded specimens (8%) failed to be PCR amplified, while all 26 frozen samples were successfully amplified. Of the 94 patients with demonstrable results, 23 (24%) were found to have at least one mutation in the EGFR kinase domain, and two of these patients showed two point mutations per person, for a total of 25 mutations identified (table 5). Of the 23 patients with mutations, 9 (39%) had one or more point mutations, 12 (52%) had an in-frame overlapping deletion in exon 19 and two patients (9%) had a duplication in exon 20. Point mutations are in exons 18 and 21, and include five each of 2573T > G (L858R), 2126A > T (E709V), 2155G > a (G719S), 2156G > C (G719A), 2327G > a (R776H), 2543C > T (P848L), and 2582T > a (L861Q). One of the point mutations (P848L) was detected in both tumor samples and in mononuclear cells obtained from oral swabs. No mutations were detected in exon s22, 23, or 24.

Predictor of mutation:

in our samples, there was no clear association between EGFR mutation status and age (p 0.61), female gender (p 0.92), asian race (p 0.08), or metastatic disease at the time of medical schedule. None of the 6 patients with non-adenocarcinoma tumor histology had a leap found to have a mutation. Among patients with adenocarcinoma, adenocarcinoma with BAC signature and pure BAC had no association between BAC/BAC signature and EGFR mutation status (p 0.35).

None of the 17 current smokers were found to have mutations. Never smokers are clearly more likely to have EGFR mutations than previous smokers (probability [ OR ] ═ 3.08, 95% confidence in care [ CI ] 1.09-8.76). The mean pack-year number of smokes was significantly lower (0.7 pack-year) in EGFR mutation positive patients compared to EGFR mutation negative patients (25.0 pack-year, p < 0.001). There was a 4% reduction in the probability of having a mutation every other puff-year (OR ═ 0.96, 95% CI0.93-0.99)

The package-years of smoking after control of sex, race, and tumor histology remain meaningful predictors of the mutation status (OR ═ 0.96, 95% CI 0.93-0.99).

Subsequent use of the test information:

EGFR mutation positive patients are significantly more likely to have a documented plan to receive subsequent EGFR-TKI treatment (86%) than EGFR mutation negative patients (11%, p < 0.001). Clinicians demonstrate that the results of EGFR affect their preferred recommended therapies in 38% of cases. These cases included 14 out of 23 mutation-positive patients (61%) for whom EGFR-TKI therapy was recommended earlier than in patients who tested negative, while 24 out of 71 mutation-negative patients (34%) did not recommend EGFR-TKI therapy, or recommended later than in patients who tested positive.

EGFR mutation status is more likely to change treatment choice preferences in patients with metastatic disease (54%) than in patients with localized or locally advanced disease (19%, p 0.003%). Given this finding, we further analyzed the process of making decisions in metastatic patients (fig. 10). Of the 31 patients with metastatic disease whose test results affected treatment recommendations, five mutation-positive patients were given first-line EGFR-TKI treatment and six mutation-positive patients were given second-line EGFR-TKI treatment at the chemotherapy site. Based on their negative EGFR test results, twenty mutation-negative patients were encouraged to postpone EGFR-TKI treatment until three-line treatment or later. Of the 26 patients with metastatic disease whose test results did not affect the treatment recommendation, two mutation-negative patients received first-line EGFR-TKI treatment, although they were negative results, nine patients including four mutation-positive patients received second-line or third-line EGFR-TKI treatment, and 15 patients including two mutation-positive patients did not receive the recommendation for EGFR-TKI. Three of the patients with metastatic disease are participating in a trial evaluating first-line EGFR-TKI therapy. Nine of the patients with metastatic disease had previously received EGFR-TKIs or were receiving EGFR-TKIs at the time of EGFR testing.

Discussion:

we studied the first 100 patients with NSCLC, and conducted a screening of somatic EGFR mutations as part of the clinical cancer care performed at our institute and found that the test was feasible and significantly affected the treatment of NSCLC patients. Patients with EGFR mutations are significantly more likely to receive recommendations for EGFR-TKI therapy than patients without mutations. Roots of medicine adjusted their treatment recommendations according to test results in one third of the cases, and are more likely to do so in patients with metastatic disease. In our patient samples, physicians use positive EGFR test results to help make decisions about some patients' chemotherapeutic preferences for EGFR-TKIs, particularly with first or second line treatments. However, negative EGFR testing results do not prevent physicians from administering EGFR-TKIs to selected patients. Many of the test results do not affect patients who make clinical decisions who have early, resective disease or who have been undergoing EGFR-TKI for metastatic disease at the time of testing. This is reasonable because the use of EGFR-TKIs as an adjunct therapy is not known and there is benefit to EGFR-TKI therapy in a small number of patients without identified EGFR mutations (65, 66-70, 71).

Our studies also provide evidence that molecular diagnostics can improve the clinical ability to identify patients with EGFR mutations. Many oncologists currently use clinical features associated with EGRR mutations and responses to EGFR-TKIs to guide the process of making a decision on patients with NSCLC. Indeed, our cohort of patients who underwent EGFR testing demonstrated an enhanced prevalence of these features. For example, 95% of related patients have adenocarcinoma or BAC tumor histology (72) compared to 45% in the general NSCLC population. Although never smokers account for 29% of our population, the prevalence of never smokers in the general NSCLC population is reported to be 2-10% and can be as high as 27% in women with NSCLC (73-75). Similarly, our population contains only 17% of current smokers compared to the 38-75% ratio of current smokers in newly diagnosed NSCLC patients. Thus our clinically selected population had an EGFR mutation rate of 24% which was substantially higher than the rates recorded by our and other american research groups testing unselected existing NSCLC tumor samples (65-66, 81). It is important to note, however, that although clinicians seem to attempt to select patients for testing with clinical characteristics of EGFR mutations, the mutation frequency is still only 24%, emphasizing the fact that molecular diagnostics add information that can be used to make clinical decisions.

After the control was a predictor of the mutation status described previously, the smoking status was the strongest predictor of EGFR mutation status in our patients, and the increased smoking history correlated with a significantly decreased likelihood of having EGFR mutations. Our results are consistent with other safety series that record the importance of smoking status in the EGFR mutation potential (66, 69, 70, 81, 82). Just as the very low prevalence of EGFR mutations in squamous cell tumors (62) has turned testing efforts to adenocarcinoma tumors, it may be appropriate to focus future efforts on patients with a low or no history of smoking. However, EGFR mutation reports in patients without typical clinical features suggest strict test limits (83). When examining other clinical features thought to be associated with mutations, we found that asian ethnicity and BAC tumor histology had an insignificant trend to predict EGFR mutation status. The lack of statistical significance in these associations may be due to the small sample.

The test is feasible and fits within the time constraints of clinical cancer care. Almost all tumors submitted for analysis produced enunciable results. All six samples that failed to be PCR amplified were paraffin-embedded, while the samples without freezing failed to PCR amplify. When available, fresh frozen tissue is the preferred EGFR mutation test substrate.

To date, partial or complete EGFR sequence analysis has been reported for nearly 2,500NSCLC samples. Our patients showed similar mutations to those previously reported, overlapping exon 19 deletions of 9-23 base pairs and point mutations that resulted in single amino acid substitutions in exons 18 and 21. Five of the point mutations we found have been described above (E709V, G719S, G719A, L858R, and L861Q). One of the point mutations we found initiates an amino acid substitution at the codon at which a different amino acid substitution was previously described (R776H). The E709V and R776H variants were each found with a known gefitinib sensitizing mutation involving codon 719. The P848L mutation in exon 21 was found in both somatic and oral samples, suggesting that it may be a germline variant of uncertain significance. The patient was a never-smoking female with adenocarcinoma, she had stable disease for 15 months after gefitinib treatment prior to EGFR mutation testing. When the P848L mutation was found, she was recently found to have progressive disease and began erlotinib therapy. No information exists about the response to erlotinib at this time.

(2253-2276 del) deletions overlapped the previously described exon 19 deletions. Deletions in our patients can be divided into one of two groups: the minimum crossing codon 747-749 deletion (amino acid sequence LRE), and the crossing codon 752-759 deletion (FIG. 11). Analysis of all exons 19 reported to date suggests that many amino acids can be deleted from the TK region spanning codons 747-759. It appears that no essential common codons have been deleted; however, all deletions we detected retained a lysine residue at position 745.

One of our two exon 20 mutations is in never-smoked women with recurrent adenocarcinoma, who were treated with erlotinib after the EGFR test and had stable disease for two months at this time. The other is a pre-smoker with metastatic gonadal cancer who is treated with EGFR-TKI but cannot tolerate it due to severe rash. The identification of clinically relevant EGFR mutations in exon 20 underscores the importance of comprehensive sequencing of the TK region of EGFR.

In summary, this study demonstrates the feasibility and utility of a comprehensive screen for somatic mutations in the TK region of the EGFR gene in NSCLC patients as part of clinical cancer care. The test results provide useful information about clinical predictors of EGFR-TKI response. Current smokers are unlikely to have a mutation, as were previous smokers with a history of high pack-year smoking.

Example 5

EGFR gene testing of non-small cell lung cancer, standard protocols.

Clinical indications:

this test indicates individuals with non-small cell lung cancer.

Principle of analysis

EGFR gene sequencing is a genetic test to detect mutations in the EGFR kinase domain. DNA was first obtained from tumor biopsies. The DNA sequence of the 7 exons (18, 19, 20, 21, 22, 23, 24) of EGFR was then determined by direct bidirectional gene sequencing. The obtained sequence was then compared to known EGFR sequences to identify DNA sequence changes. If a DNA sequence change is detected in the tumor tissue, the test will be repeated on the original tumor sample. If the change has not been previously reported in gefitinib-or erlotinib-responders, the test will also be performed on a blood sample from the individual to investigate whether the mutation is constitutive (and thus likely a normally occurring polymorphism) or somatically in tumor tissue.

Sample requirement

A minimum of 100ng of DNA is required from the tumor sample.

Note that: very small amounts of DNA can be extracted from tissue samples. The concentration of such DNA may not be precisely quantified.

Quality control:

controls used

Two negative controls (water) and one positive control (human DNA) were included for each exon in the PCR reaction. Negative controls should be performed in their entirety to ensure that the sequence obtained is not a result of contamination. pGEM positive control and ABI array control were included in the sequencing step.

Control preparation and preservation:

the positive control for PCR was Clontech human DNA or human DNA from anonymous blood samples and stored at 4 ℃. The negative control for the PCR reaction was high purity molecular biological grade water stored at room temperature. Positive controls and ABI array controls were stored at-20 ℃.

Tolerance and steps to be taken if individual controls fail:

if the positive PCR control fails but the negative control and sample pass, the PCR result is designated as pass and sequencing will be performed. If the negative control shows evidence of DNA amplification, the entire reaction will be repeated with a new copy of patient DNA. If the pGEM control fails and the test reaction fails, the sequencing will be repeated with a second PCR product. If the sequencing control fails but the test reaction passes, no repetition of the sequencing is required. Note that: due to the low yield of DNA extracted from paraffin-embedded tissue samples, external PCR reactions often do not produce visible products. The internal PCR reaction should be product-visible. The size of the product detected on the gel should be compared to the expected size (see below) to ensure that a suitable PCR product is obtained. Exon-specific PCR failure reactions should be repeated if the internal PCR product is not visible on the gel

If the PCR amplification fails for an individual sample, a new round of PCR should be performed with the addition of a DNA template concentration that is increased by two times. If the PCR amplification fails again, a new DNA sample, if any, should be obtained for the patient. If the sample is a paraffin embedded tissue sample, additional slides should be scraped. More slides, if any, than were used to generate the original sample should be scraped and digestion in proteinase K should be allowed to proceed for three nights.

Equipment and reagents (unless otherwise noted all reagents were stable for one year)

PCR and sequencing(generally, PCR and sequencing equipment and reagents are known to those skilled in the art and can be used herein, also as noted above).

Primer: (see tables 6 and 7)

Table 6: external PCR primers:

table 7: internal PCR primers:

preventive measures

TABLE 8

Preparation of PCR reaction mixtures for external PCR.

All manipulations were performed on genomic DNA in a PCR fume hood, not a clean fume hood.

1. The Taq Gold and dNTPs were thawed out on ice.

2. Master mixtures were prepared in tubes (eppendorf or 15mL tubes) using the following table. Water, betaine, 10 Xbuffer, MgCl₂DMSO, Taq Gold and dNTP should be added in the order listed. It is very important to add each reagent while mixing the reagents by gentle up and down pumping.

DNA should be added to the master mix before aliquoting. After the bulk of the master mix was made, 96 μ l (sufficient for 8rxns) was dispensed into separate tubes for each patient or control. Mu.l of DNA was added to 96. mu.l of the master mix at5 ng/. mu.l. 13 μ l can then be added to each well of the plate or placed in a strip of test tubes with a multichannel pipettor and pipetted.

4. For the entire 384-well plate of the reaction, enough master mix to perform about 415 reactions was made.

5. The plates of the master mix were centrifuged to remove air bubbles.

6. If a large set of primers is used, it will be helpful to have them in separate plates together with the forward and reverse primers in a 96-well plate.

7. Primers were added using a multichannel pipettor. Mixing was confirmed by gentle pipetting up and down.

8. The plate was centrifuged to remove any air bubbles.

9. Amplification was performed using the following cycle.

Note: PCR was performed in 384-well plates.

TABLE 9

Reagent	Volume per reaction (μ L)
		Autoclaving ddH2O	4.90
5M betaine	3.00
		10 Xbuffer solution	1.50
Magnesium chloride	1.50
		DMSO	0.75
Taq	0.20
		Dntp	0.15
PCR Forward primer 1 (concentration 20pmol/uL)	1.00
		PCR reverse primer 2 (concentration 20pmol/uL)	1.00
DNA (concentration 5ng/uL)	1.00
		Total volume of PCR reaction	15.00

Table 10: PCR amplification cycle

Note: no purification is necessary after the external PCR.

Preparation of PCR reaction mixture for internal PCR

The internal PCR setup is almost identical to the external PCR with a slight exception.

1. Bulk master mix was made in a PCR fume hood as described for external PCR.

2. MM was aliquoted into 7 strip tubes and 12 μ l was pipetted into 384 well plates using a multichannel pipettor.

3. 12 μ l of each of the forward and reverse inner primers were added. And (5) temporarily closing the plate.

4. Removed from the fume hood, the plate was centrifuged down and into the post-PCR device area.

5. Mu.l of external PCR product was aliquoted into each reaction using a dedicated pipette.

6. Heat sealed and centrifuged again.

7. The same amplification cycle was run as the external PCR.

PCR products were run on a 1% gel before purification. Determination of pass/fail exons repeat PCR.

Internal PCR purification Using Ampure Magnetic Bead Clean-up

Purification of

1. The plate of Ampure magnetic beads was shaken until no beads were deposited.

2. It is very important that the temperature of the Ampure beads is at room temperature.

3. A 384-well Ampure protocol was used on Biomek and the reaction volume was changed to 12 μ l to accommodate reagents for purification. If this is not done, an error will be generated.

4. After completion of the procedure, the plates were autoclaved with 20. mu.l of ddH2O per well. Upon addition of water, mixing was ensured by gentle up-down suction.

5. The plate was centrifuged to remove any air bubbles.

6. The plate was placed on a magnet to isolate the beads. You should now be able to remove 1. mu.l of DNA for the sequencing reaction. The remainder was stored at-20 ℃ for future use.

Sequencing protocol

Preparation of sequencing reaction mixture

1. BigDye 3.1 was melted out on ice in a dark room.

2. Master mixtures were prepared in tubes (eppendorf or 15mL tubes) using the following table. Water, buffer, DMSO, Taq Gold and BigDye 3.1 should be added in the order listed.

3. It is very important to add each reagent while mixing the reagents by gentle up and down pumping.

4. When sequencing is performed using a usual primer, the primer may also be added to the master mix at this time. If the primer is unique it should be added separately after the master mix is placed in a 384 well plate.

5. Typically, enough master mix to perform about 415 reactions is made for the entire 384-well plate of reactions.

6. Once the master mix was made, the mix was divided into 8 wells of strip tubes. (no reservoir is used to aliquot the master mix-that would waste the reagents).

7. The master mix can now be aliquoted into 384-well plates using a multichannel pipettor.

8. The plates of the master mix were centrifuged to remove air bubbles.

9. Sequencing PCR products were added using a multichannel pipettor and the like. Ensure mixing of the reagents by pumping up and down.

10. The plate was centrifuged to remove any air bubbles.

11. Amplification was performed using the following cycle.

TABLE 11

Reagent	Volume per reaction (μ L)
		Autoclaving ddH2O	4.38
5xABI buffer	3.65
		DMSO	0.50
ABI BigDye 3.1	0.35
		Concentration of sequencing primer	0.12
DNA from an internal PCR reaction	1.00
		Total volume of reaction	10.00

Table 12: performing amplification cycles of sequencing

Purification by Clean Magnetic Bead Clean-up 1

1. The plate of clean magnetic beads was shaken until no beads were deposited.

2. Samples were purified on Biomek using the clean 384-well plate program.

3. After completion of the procedure, the original plate was stored at-20 ℃. New plates with purified samples can be used on ABI 3730.

(Note: if the PCR product is less than 300bps you may have to dilute the sample before placing it on 3730)

Mutation check templates for EGFR testing were generated and included on LMM/sequencing/sequence-MS check/EGFR.

Criteria for duplicate results

All positive results were repeated by amplifying and sequencing specific exons in which DNA sequence changes were detected from a second patient DNA derived from the original tissue sample. Furthermore, the DNA extracted from the patient's blood sample should be manipulated in parallel for comparison with the tumor tissue if the detected sequence changes have not been detected in the past in gefitinib-or erlotinib-responders.

Based on the specific technical problem, any exon that does not produce a clear sequence will be repeated by extraction, PCR or sequencing.

Measuring parameters

Sensitivity tested-somatic EGFR kinase domain mutations were found in approximately 13% of individuals with NSCLC (Paez JG et al, 2004). Furthermore, somatic EGFR kinase domain mutations were found in gefitinib-reactive 13/14 (92.8%) individuals with NSCLC (Paez JG et al, 2004, Lynch et al, 2004). The confirmation of sensitivity of the test technique showed 100% sensitivity to known mutations and the confirmation of 100% sensitivity on our laboratory sequencing platform (see "accuracy of technique" below). The sensitivity of mutation detection in combination samples has been determined to be 25% (i.e., heterozygous mutations can be detected when present as 50% of the cell mixture). We found that up to 20% of paraffin-embedded tissues did not produce high quality DNA. We were unable to obtain sequence information from these samples.

Specificity of test-to date, published literature indicates that individuals with somatic mutations in EGFR do not respond to gefitinib (11/11). The chance of finding a mutation due to artifacts of bidirectional sequencing is nearly 0% (see "accuracy of technology" below). Thus, the specificity of the test was approximately 100%.

Technical accuracy-DNA sequencing technology is the gold standard in molecular diagnostics. The laboratory used an ABI 3730DNA analyzer with a reported accuracy of 98.5%. Combining this with two-way sequencing, automated chromatography with a Mutation Surveyor, and manual analysis of false positives, we achieved 100% accuracy. This is based on the analysis of 100,000 bases of the original sequence, see our handbook of quality assurance protocols.

Note: we do not assume that these results guarantee 100% accuracy for this platform. Given that sequencing errors can occur, we report our accuracy as 99-99%, which has been found by large scale sequencing protocols (Hill et al 2000).

Reproducibility of the test-due to the accuracy of the test, when results were obtained, they were reproducible, equivalent to the accuracy of the test (99.99%). Occasionally, however, the test may fail due to the factors listed below (see limitations of the method) or due to PCR or sequencing failures due to unclear technical reasons. In these cases, no results are obtained and the assay is repeated until a result is obtained or the patient sample is unacceptable. The specific failure rate for each assay step and sample can be found in our validation report of the quality assurance protocol manual.

Normal range of results-using GenBank accession number: NT-033968.5 (genomic sequence) and NM-005228.3 (mRNA sequence) allow the online discovery of normal sequences of the EGFR gene.

Limitation of the method:

large deletions spanning one or more exons will not be detected by sequencing methods, particularly if present as heterozygosity. Mutations outside the kinase domain of the EGFR gene will not be detected by this assay. Inhibitors may be present in the DNA sample that prevent amplification by PCR. Degraded DNA may not yield analyzable data and may require resubmission of the sample. Rare sequence variations or secondary structure of the targeting primer sequence can affect PCR amplification, so mutations can be missed in this region of one allele.

Example 6

Gefitinib (iressa) is a tyrosine kinase inhibitor that targets the Epidermal Growth Factor Receptor (EGFR) and induces a significant clinical response in non-small cell lung cancers (NSCLCs) that have activating mutations within the EGFR kinase domain. We report that these mutant EGFRs selectively activate Akt and STAT signaling pathways, which promote cell survival, but have no effect on the proliferation-inducing Erk/MAPK signaling. Nsclc expressing mutant EGFRs undergo extensive apoptosis following siRNA-mediated depression of mutant EGFR or treatment with pharmaceutical inhibitors of Akt and STAT signaling, and are relatively resistant to apoptosis induced by conventional chemotherapeutic drugs. Thus, mutant EGFRs selectively transduce survival signals on which NSCLCs depend; therefore, inhibition of those signals by Gefitinib may be the basis for fighting clinical responses.

Receptor tyrosine kinases of the EGFR family regulate basic cellular functions including proliferation, survival, migration and differentiation and appear to play a central role in the etiology and progression of solid tumors (r.n. jorissen et al, exp. cellres.284, 31(2003), h.s. earp, t.l. dawson, x.li, h.yu, Breast Cancer res.treat.35, 115 (1995)). EGFR is frequently overexpressed in breast, lung, colon, ovarian, and brain tumors, facilitating the development of specific pharmaceutical inhibitors such as Gefitinib, which destroy EGFR kinase activity by binding to the ATP pocket within the catalytic domain (a-e.wakeling et al, Cancer res.62, 5749 (2002)). Gefitinib induces a significant clinical response in approximately 10% of patients with chemotherapy-refractory NSCLC (j.baselga et al, j.clin.oncol.20, 4292(2002), m.fukuoka et al, j.clin.oncol.21, 2237(2003), g.giaccone et al, J Clin oncol.22, 777(2004), m.g.kris et al, TAMA 290, 2149 (2003)). Virtually all Gefitinib-responsive lung cancers have somatically mutated in the EGFR kinase domain, while no mutations are seen in non-responsive cases (t.j.lynch et al, n.engl.j.med.350, 2129(2004), j.g.paez et al, Science 304, 1497 (2004)). These heterozygous mutations include small in-frame deletions and missense substitutions that accumulate within ATP-binding pockets.

Transient transfection with mutant EGFRs we previously shown that both types of mutations result in enhanced EGF-dependent receptor activation as measured by autophosphorylation of Y1068, one of the prominent C-terminal phosphorylation sites of EGFR (t.j.lynch et al, n.engl.j.med.350, 2129 (2004)).

To be able to study the qualitative differences in the signals generated by mutant EGFRs, we generated stable lines of non-transformed mouse mammary epidermal cells (NMuMg) expressing wild-type or mutant EGFRs and analyzed EGF-mediated autophosphorylation of various tyrosine residues associated with different downstream effectors (r.n.jorissen et al, exp.cell res.284, 31 (2003)). Cell lines were made that expressed either wild-type EGFR or one of two recurrent mutations detected in tumors from Gefitinib-responsive patients: missense mutation L858R and an in-frame deletion of 18bp, delL747-P753 insS. Significantly different tyrosine phosphorylation patterns were observed at several C-terminal sites between the wild-type and two mutant EGFRs. EGF-induced phosphorylation of Y1045 and Y1173 was completely indistinguishable between wild-type and mutant EGFRs, whereas Y992 and Y1068 were substantially increased in both mutants. Interestingly, Y845 was highly phosphorylated in L858R missense mutants, but not in wild-type or deletion mutations, and thus appeared to be unique in distinguishing between the two types of EGFR mutations. The different EGF-induced tyrosine phosphorylation patterns seen in the wild-type and mutant receptors were reproducible in cis-transfected COS7 cells, ensuring targeting potential cell-type specific effects.

Thus, Gefitinib-sensitive mutant EGFRs transduce signals that are qualitatively different from signals mediated by wild-type EGFR. These differences may result directly from structural changes within the catalytic pocket that affect substrate specificity, or from interactions with changes in accessory proteins that modulate the EGFR signaling pathway.

Establishing cell lines stably transfected with mutant EGFRs makes it possible to compare the phosphorylation states of major downstream targets of EGFR in a common cellular context. EGF-induced activation of Erkl and Erk2 by Ras, Akt by PLC γ/PI3K, and STAT3 and STAT5 by JAK2 are the basic downstream pathways mediating EGFR carcinogenesis (r.n. jorissen et al, exp.cell res.284, 31 (2003)). EGF-induced Erk activation is essentially indistinguishable in cells expressing either wild-type EGFR or both activating EGFR mutants. In contrast, phosphorylation of Akt and STAT5 was substantially increased in cells expressing either mutant EGFRs. Enhanced phosphorylation of STAT3 was similarly observed in cells expressing mutant EGFRs. Invariable Erk activation by mutant EGFRs is consistent with enhanced phosphorylation in the absence of Y1173, an important docking site for Shc and Grb-2 linkers that leads to Ras activation and subsequent Erk phosphorylation (r.n. jorissen et al, exp. cell res.284, 31 (2003)). Enhanced Akt and STAT phosphorylation following activation of mutant EGFRs is consistent with enhancement of Y992 and Y1068 phosphorylation, both of which were previously associated with Akt and STAT activation (r.n. jorissen et al, exp. cell res.284, 31 (2003)). Thus, selective EGF induction of C-terminal tyrosine residues within mutant EGFRs induces autophosphorylation in good agreement with selective activation of downstream signaling pathways.

To extend these observations to lung cancer cells where EGFR mutations appear to drive tumor formation, we investigated cell lines derived from five NSCL tumors. NCI-H1975 carries a recurrent missense mutation L858R while NCI-H1650 has an in-frame deletion of del 746-A750, while NCI-358, NCI-H1666, and NCI-H1734 express wild-type EGFR. In transfected cells, EGF-induced autophosphorylation of Y992 and Y1068 was significantly improved in both cell lines with endogenous EGFR mutations, as was phosphorylation of Akt and STAT5, but not Erk.

Oncogenic activity of EGFR reflects activation of signaling pathways that promote cell proliferation and cell survival (s.grant, l.qiao, p.dent, fro7zt.biosc.7, d376 (2002)). Although these pathways show overlap, Ras-mediated activation of Erk kinase essentially confers proliferative activity on EGFR, whereas activation of Akt and STAT are largely linked to anti-apoptotic function (s.grant, l.qiao, p.dent, front.biosci.7, d376(2002), f.chang et al, leukamia 17, 1263(2003), f.chang et al, leukamia 17, 590(2003), f.chang et al, int.j.oncol.22, 469(2003), v.calo et al, j.cell physio.197, 157(2003), t.j.ahonen et al, j.biol.chem.278, 27287 (2003)). Two lung cancer cells with EGFR mutations showed proliferative responses to EGF at low serum concentrations, which was not observed in cells with wild type receptor. However, their proliferation rates and cell confluence codes were comparable at normal serum concentrations.

SiRNA

In contrast, the apoptotic pathway is markedly different in lung cancer cells with mutant EGFRs: siRNA-mediated specific activation of mutant EGFR in these cell lines results in rapid and massive apoptosis. Approximately 90% of the NCI-H1975 cells transfected with L858R-specific siRNA died within 96 hours, as did the NCI-H1650 cells transfected with del 746-A750-specific siRNA. Sirnas specific for both EGFR mutations had no effect on cells expressing the other mutations, sirnas targeting wild-type and mutant EGFR had minimal effect on the viability of cells expressing only the wild-type receptor, but induced rapid cell death in cell lines expressing EGFR mutants. The ability of siRNAs to specifically target the corresponding EGFR alleles was confirmed by immunoblotting in COS7 cells. Thus, expression of mutant EGFRs in lung cancers with these mutations appears to be essential for inhibition of pro-apoptotic signals. The fact that lung cancer cells expressing only wild-type receptor do not show a similar dependence on EGFR expression may also indicate the relative Gefitinib insensitivity of human tumors overexpressing wild-type EGFR.

The effectiveness of Gefitinib in lung cancers with mutant EGFRs may reflect its inhibition of critical anti-apoptotic pathways that these cells depend heavily on, as well as the altered biochemical properties of mutant receptors. We previously reported that mutant EGFRs are more sensitive to inhibition by EGF-dependent autophosphorylation Gefitinib than the wild-type receptor (t.j.lynch et al, n.engl.j.med.350, 2129 (2004)). This increased drug sensitivity by mutant receptors was also observed for Erk and STAT5 activation. Thus, although EGF-induced signaling pathways generated by mutant receptors demonstrate selective activation of downstream effectors through distinct autophosphorylation events, their enhanced inhibition by Gefitinib is consistent and likely reflects changes in drug binding to the mutant ATP pocket.

To determine the relevance of enhanced Akt and STAT signals in EGFR-mediated NSCLC survival, we targeted these pathways with specific pharmaceutical inhibitors. Lung cancer cells with EGFR mutations are 100-fold more sensitive to Gefitinib than cells with wild-type receptors. Cells expressing mutant EGFRs are also more sensitive to drug inhibition of Akt or STAT signaling than cells expressing wild-type EGFR alone. Although EGFR mutant lung cancer cells exhibit increased sensitivity to disruption of Akt/STAT-mediated anti-apoptotic signals, they show significantly increased resistance to cell death signals induced by the commonly used chemotherapeutic agents doxorubicin and cisplatin, as well as pro-apoptotic Fas ligand.

Enhanced Akt/STAT signaling in cells with mutant EGFR may therefore provide additional therapeutic targets, while increasing the likelihood that conventional chemotherapy may be less effective against these tumors.

"oncogene preference" has been proposed to explain apoptosis of cancer cell-dependent proliferative signals after their inhibition (I.B. Weinstein, Science 297, 63 (2002)). Interestingly, imatinib (gleevec) effectively triggers cell death in chronic myeloid Leukemia expressing BCR-ABL translocation products and in gastrointestinal mucosal tumors expressing activating c-Kit mutations, both of which often exhibit constitutive STAT activation, which is effectively inhibited by drugs (t.kindler et al, leukamia 17, 999(2003), g.p.paner et al, Anticancer res.23, 2253 (2003)). Similarly, in lung cancer cells with EGFR kinase mutations, Gefitinib-reactivity may be due in large part to its potent inhibition of the essential anti-apoptotic signals transduced by mutant receptors.

Materials and methods

Immunoblotting

Lysates from cultured cells were prepared in ice-cold RIPA lysis solution (1% Triton X-100, 0.1% SDS, 50mM Tris-HCl, pH 7.4, 150mM NaCl, 1mM EDTA, 1mM EGTA, 10mM β -glycero-phosphate, 10mM NaF, 1mM Na-orthovanadate, containing protease inhibitors). Debris was removed by centrifugation in a centrifuge tube at 12,000x g4 ℃ for 10 min. The clarified lysates were boiled in gel loading buffer and separated by 10% SDS-PAGE. Proteins were electrotransferred onto nitrocellulose membranes and detected with specific antibodies, followed by incubation with horseradish peroxidase conjugated goat secondary antibody (Beverly, MA; 1: 2000) and development with amplified chemo-chemistry (DuPont NEN) followed by autoradiography phosphorus-EGFR Y845, Y992, Y1045, Y1068, phosphorus-STAT 5(Tyr694), phosphorus-AKT (Ser473), phosphorus-ERKl/2 (Thr202/Tyr204), AKT, STAT5, and ERK1/2 antibodies were obtained from New England Biolabs (Beverly, MA), all EGFR Ab-20 antibodies were obtained from NeoMarkers (Frost, CA), phosphorus-EGFreEGFr1173 antibodies were from static Biotechnology (Laake, Laccid, NY) and all phosphorus tyrosine antibodies PY-20 were from transactions Laboratories (Lexions, KY. diluted with 1000 antibodies.

EGFR expression vector

Full-length EGFR expression constructs encoding wild-type, L858 or del L747-P753insS mutations were subcloned into plasmid pUSeamp using standard methods. All constructs were confirmed by DNA sequence analysis.

Cell lines and transfections

COS7 cells and NMuMg (normal mouse mammary gland epidermis) cells were grown in DMEM (Dulbecco's modified Eagle's media) with 10% fetal bovine serum in the presence of 2mM L-glutamine and 50U/ml Penicillium/streptomycin. The NCI-H358, NCI-H1650, NCI-H1734, NCI-H1666, and NCI-H1975 human lung cancer cell lines were obtained from the American type culture Collection and grown in RPMI1640 with 10% fetal bovine serum, 2mM L-glutamine, 50U/Penicillium/streptomycin, and 1mM sodium pyruvate. They are referred to herein in abbreviated form as H358, H1650, H1734, H1666, and H1975, respectively. Transient transfection of COS7 cells was performed using Lipofectamine2000 (Invitrogen; Carlsbad, Calif.). Plasmid (1. mu.g) was transfected into 80% confluent cells on 10cm dishes. After 12 hours, cells were collected and re-seeded in 12-well plates without serum. The following day, cells were stimulated with 30ng/ml EGF. Stable NMuMg cell lines were prepared by co-transfection of EGFR expression constructs with pBABE puro as a selectable drug followed by selection in puromycin at 3. mu.g/ml. The drug-resistant cell pool was used for analysis. Expression of EGFR in stably transfected cells was confirmed by immunoblotting.

SiRNA-mediated "depression" of EGFR expression

The SiRNA of EGFRL858R was designed to target nucleotide sequence CACAGATTTTGGGCGGGCCAA (SEQ ID NO.: 688), while the GCTATCAAAACATCTCCGAAA (SEQ ID NO.: 689) sequence was used for del E745-A750 (Qiagen; Valencia, Calif.). To target all forms of EGFR, commercially prepared sirnas corresponding to human wild-type EGFR were obtained from Dharmacon (Lafayette, CO). Transfection of siRNAs was performed using Lipofectamine2000(Invitrogen) according to the manufacturer's instructions. Cells were assayed for viability using the MTT assay after 96 hours.

Apoptosis assay

10,000 cells were seeded into each well of a 96-well plate. After 6 hours, the medium was changed and the cells were maintained in the presence of increasing concentrations of doxorubicin (Sigma; St. Louis, MO), cisplatin (Sigma), Fas-ligand (human activating, clone CH 11; Upstate Biotechnology), Ly294002(Sigma), or AG490 (Calbiochem; La Jolla, Calif.). After 96 hours, the viability of the cells was determined using the MTT assay. For caspase immunostaining, 10,000 cells were seeded onto 10mm coverslips. They were transfected with siRNA the following day (details see preceding paragraph). After 72 hours the cells were fixed in 4% paraformaldehyde for 10min at room temperature. They were then soaked in 0.5% Triton X-100 for 5min and blocked in 5% Normal Goat Serum (NGS) for 1 hr. The coverslips were then incubated overnight at 4 ℃ in primary antibody (sheared caspase-3Asp 1755A 1 from CellSignaling) at a 1: 100 dilution. The next day, the coverslips were washed three times in PBS and incubated with a secondary antibody (Texas Red conjugated goat anti-rabbit; from Jackson Immunoresearch; West Grove, Pa.) diluted 1: 250 in 5% normal goat serum and 0.5ug/ml DAPI (4', 6-diamidine-2-phenylindole). After 3 washes in PBS, the coverslips were loaded with Prolonggold anti-attenuation reagents from Molecular Probes (Eugene, OR).

Cell viability assay

Mu.l of a 5mg/ml MTT (Thiazolyl blue; Sigma) solution was added to each well of a 96-well plate. After 2 hours incubation at 37 ℃, the medium was removed and MTT was solubilized by adding 100 μ l of acidic isopropanol (0.1N HCL) to each well. Absorbance was measured at 570nm with a spectroscopic scale.

Growth curve

Growth curves for H-358, H-1650, H-1734, and H-1975 cells were obtained by seeding 1000 cells in each well of a 96-well plate. Each cell line was seeded in 8 independent wells. At the day after the ligation, the cells were fixed in 4% formaldehyde and stained with 0.1% (w/v) crystal violet solution. The crystal violet was then dissolved in 100 μ l of acetic acid and the relative cell number was determined by measuring the absorbance at 570nm using a plate reader.

Identification of mutations

To identify sporadic NSCLC cell lines with mutations in EGFR, we sequenced exons 19 and 21 within a set of 15 NSCLC cell lines, as described above. Cell lines were selected for analysis based on their origin from bronchoalveolar histology regardless of whether there was a history of smoking, (NCI-H358, NCI-H650, NCI-H1650), or from sources of adenocarcinoma that developed in non-smokers (NCI-H1435, NCI-H1563, NCI-H1651, NCI-H1734, NCI-H1793, NCI-H1975, NCI-H2291, NCI-H2342, NCI-H2030, NCI-H1838, NCI-H2347, NCI-H2023). NCI-H1666 has been reported to have only wild-type EGFR (see examples above). All cell lines are available from the American type culture Collection.

The references cited herein and throughout the specification are incorporated by reference in their entirety.

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TABLE 1 characteristics and response to Gefitinib in nine patients with non-small cell Lung cancer

Adenocarcinoma (Adeno) with any element of bronchoalveolar carcinoma (BAC) is listed as BAC.

The smoking status is defined as before if the patient did not smoke any cigarettes within 12 months prior to entry (former), and never if the patient did not smoke 100 cigarettes before they were a single serving(never)。

Overall survival was measured from the start of gefitinib treatment to death.

EGFR means epidermal growth factor receptor gene.

Partial responses were assessed in solid tumors using response assessment criteria, with greater and lesser responses being assessed by two physicians in patients who were unable to measure responses using these criteria.

TABLE 2 somatic mutations in the EGFR tyrosine kinase domain in non-small cell lung cancer patients

Bronchoalveolar carcinoma-bearing EGFR mutations in 2 (patients a and B) of 25 patients who had not been exposed to gefitinib (15 with bronchoalveolar carcinoma, 7 with adenocarcinoma, 3 with large cell carcinoma). Representing different histological types: no mutations were found in non-small cell lung cancer (6 specimens), bronchial tumors (1 specimen), and 14 lung cancer cell lines of an unknown type (1 specimen). Polymorphic variants identified within EGFR include the following: within the tyrosine kinase domain, a substitution of a for G at nucleotide 1562, a substitution of a for T at nucleotide 1887, and a germline variant of unknown functional significance, a substitution of a for G at nucleotide 2885.

Table 4: population characteristics in 100 patients tested for EGFR mutation as part of NSCLC care

Feature(s)	Frequency of
		Mean age, year (standard deviation)	63
Female with a view to preventing the formation of wrinkles
		Race of a ethnic group	76
White people	7
		Asian	5
Others	12
		Is unknown
State under test	15
		I	4
II	10
		III	67
IV	4
		Is unknown
Histology	1
		Pure BAC	24
Adenocarcinoma with BAC profile	69
		Adenocarcinoma	6
NSCLC, all other subtypes
		Smoking status	17
At present	48
		From the front	29
Never use	6
		Is unknown
Average amount of smoking by current and previous smokers, bag-year (standard deviation)	39.0(32.3)
		Mean time from diagnosis to EGFR test, month (standard deviation)	18.7(78.4)
Previous chemotherapy treatment	47
		Previous EGFR targeting treatments	11

BAC and EGFR

Table S1A: amplification primers for selected EGFR and receptor tyrosine kinase exons (SEQ ID NOS: 1-212)

Table S1A: continuously for

Table S1B: amplification primers for selected EGFR and receptor tyrosine kinase exons (SEQ ID NOS: 213-424)

Table S1B: continuously for

Table S4: primers for cDNA sequencing

Claims (6)

1. A kit, comprising:

a. at least one probe designed to anneal to a nucleic acid region within exon 19 of the EGFR kinase domain, wherein said probe specifically binds under selective binding conditions to a nucleic acid sequence comprising at least one variation in exon 19 in the erbB1 gene, wherein said variation is a mutation that results in:

i) an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID NO.512 resulting in an amino acid change comprising a deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID NO. 512;

b. products and reagents necessary for carrying out the annealing reaction; and

c. and (6) instructions.

2. A kit, comprising:

a. at least one pair of degenerate primers designed to anneal to a nucleic acid region at the border of or within exon 19 of the EGFR kinase domain, wherein said pair of primers specifically amplifies a nucleic acid sequence comprising at least one variation in exon 19 in the EGFR gene, wherein said variation is a mutation that results in:

i) an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID NO.512 resulting in an amino acid change comprising a deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID NO. 512;

b. products and reagents necessary for performing PCR amplification; and

c. and (6) instructions.

3. A kit, comprising:

a. at least one nucleic acid probe designed to detect a variation in exon 19 of the EGFR kinase domain, wherein said nucleic acid probe detects at least one variation in exon 19 in the EGFR gene, wherein said variation is a mutation that results in:

i) an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID No.512 resulting in an amino acid change comprising a deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID No.512, wherein said detection is based on specific hybridization to a nucleotide variant sequence;

b. products and reagents necessary for carrying out the annealing reaction; and

c. and (6) instructions.

4. A probe that specifically binds under selective binding conditions to a nucleic acid sequence comprising at least one variation in exon 19 of the erbB1 gene, wherein the variation is a mutation that results in:

a) an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID NO.512 resulting in an amino acid change comprising a deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID NO. 512.

5. A nucleic acid probe designed to detect a variation in exon 19 in the EGFR gene, wherein the variation is:

a) a mutation resulting in an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID No.512, which results in an amino acid change comprising a deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID No.512, wherein the detection is based on specific hybridization to a nucleotide variant sequence.

6. A primer pair designed to anneal to a nucleic acid region at the border or within exon 19 of the EGFR kinase domain, wherein said primer pair specifically amplifies a nucleic acid sequence comprising at least one variation in exon 19 in the EGFR gene, wherein said variation is:

a) a mutation resulting in an in-frame deletion in exon 19 of the EGFR gene consisting of the deletion in codons 746-753 in SEQ ID NO.512 which results in an amino acid change comprising the deletion of at least the amino acids leucine, arginine and glutamic acid at positions 747, 748 and 749 in SEQ ID NO. 512.