METHODS OF DIAGNOSING, CLASSIFYING AND TREATING ENDOMETRIAL CANCER AND PRECANCER
Diagnostic and therapeutic applications for endometrial cancer are described. The diagnostic and therapeutic applications are based on certain activation mutations in the FGFR2 gene and its expression products. The present invention is directed to nucleotide sequences, amino acid sequences, probes, and primers related to FGFR2 activation mutants and kits comprising these mutants to diagnosis and classify endometrial cancer in a subject.
This patent application is a continuation of U.S. patent application Ser. No. 15/088,099, filed Mar. 31, 2016 (published as US20160209417), which is a continuation of U.S. patent application Ser. No. 13/973,614, filed Aug. 22, 2013 (published as US20140057261), which is a continuation-in-part of U.S. patent application Ser. No. 12/532,563 filed Nov. 11, 2009 (published as US20100111944), which is a U.S. National Stage Application of International Patent Application No. PCT/US2008/058065 filed Mar. 24, 2008, which claims priority to U.S. Provisional Application No. 60/896,884, filed Mar. 23, 2007 and U.S. Provisional Application No. 60/982,093, filed Oct. 23, 2007. Each of the foregoing applications is hereby incorporated by reference in its entirety.
INCORPORATION-BY-REFERENCE OF MATERIAL ELECTRONICALLY FILEDIncorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 27,199 byte ASCII (text) file named “Seq_list” created on Aug. 22, 2013.
FIELD OF THE INVENTIONThe present invention is directed to methods and kits for diagnosing, classifying, and treating endometrial cancer.
BACKGROUND OF THE INVENTIONEndometrial cancer is the most commonly diagnosed malignancy of the female reproductive tract in the United States. It was estimated that 39,080 new cases of cancer of the uterine corpus would be diagnosed and 7,400 women would die of this disease in the United States in 2007 (Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun M J. CA Cancer J Clin 2007 January-February; 57(1):43-66). The majority of women presenting with endometrial cancer are surgically cured with a hysterectomy; however, about 15% of women demonstrate persistent or recurrent tumors that are refractory to current chemotherapies. For those women with advanced stage, progressive, or recurrent disease, survival is poor as there are no adjuvant therapies proven to be effective. The median survival after recurrence is ten months (Jereczek-Fossa B, Badzio A, Jassem J., Int J Gynecol Cancer 1999 July; 9(4):285-94) and the five-year survival for patients who have recurred is only 13% (Creutzberg C L, van Putten W L, Koper P C, et al., Lancet 2000 Apr. 22; 355(9213):1404-11).
Malignant carcinomas often display mutations in multiple oncogenes and tumor suppressor genes, exhibit alterations in the expression of hundreds of genes, and contain various chromosomal abnormalities. Despite this genomic complexity, targeting specific molecular abnormalities has been shown to produce rapid regression of human tumors, such as is seen with the selective tyrosine kinase inhibitors Imatinib (Gleevec) and Gefitinib (Iressa). To explain this phenomenon, Bernard Weinstein introduced the term “oncogene addiction”. He proposed that the signaling circuitry of a tumor cell is reprogrammed in the presence of an oncogenic activity such that the tumor cell is dependent on that oncogenic activity for cell survival and growth (Weinstein I B. Science 2002 Jul. 5; 297(5578):63-4). Indeed, experimental and clinical data support this concept of oncogene addiction and, furthermore, suggest that multiple mechanisms of oncogene activation, including mutation, rearrangement, and overexpression, can be involved in oncogene addiction (Weinstein I B, Joe A K., Nat Clin Pract Oncol 2006 August; 3(8):448-57).
A variety of somatic gene defects have been reported in endometrial carcinoma. Well or moderately differentiated endometrioid endometrial carcinomas account for approximately 80% of uterine cancers. They are characterized by a high frequency of inactivating mutations in PTEN (26-80%), activating KRAS2 mutations (13-26%), and gain-of-function β-catenin mutations (25-38%) (Hecht J L, Mutter G L., J Clin Oncol 2006 Oct. 10; 24(29):4783-91, Shiozawa T, Konishi I., Int J Clin Oncol 2006 February; 11(1):13-21). Germline gain-of-function mutations in FGFR1, 2, and 3 have been reported in a variety of craniosynostosis syndromes and chondrodysplasia syndromes. The genotype/phenotype correlations in these disorders are complex, with over 14 distinct clinical syndromes associated with mutations in one of the three receptors and several clinical syndromes e.g., Pfeiffer and Crouzon Syndrome associated with mutations in different receptors (Passos-Bueno M R, Wilcox W R, Jabs E W, Sertie A L, Alonso L G and Kitoh H. (1999), Hum Mutat 14: 115-125, Wilkie A O, Patey S J, Kan S H, van den Ouweland A M and Hamel B C. (2002), Am J Med Genet 112: 266-278.).
Although much progress has been made toward understanding the biological basis of cancer and in its diagnosis and treatment, it is still one of the leading causes of death in the United States. Inherent difficulties in the diagnosis and treatment of cancer include among other things, the existence of many different subgroups of cancer and the concomitant variation in appropriate treatment strategies to maximize the likelihood of positive patient outcome. Furthermore, there are a wide range of endometrial cancer subgroups and variations in the disease's progression. To properly treat the endometrial cancer and to maximize the chances of a successful treatment it is important that the type or subtype of endometrial cancer be identified as early as possible.
Thus, there presently is a need for a method of detecting and classifying endometrial cancer in order to select the appropriate and optimal treatment regimen. Once detected and classified, there is a further need for improved methods of treating endometrial cancer based on the type of endometrial cancer to maximize the chances of successfully treating or inhibiting reoccurrence of the disease in the subject.
SUMMARY OF THE INVENTIONThe present invention provides methods of diagnosing, classifying and treating endometrial cancer. By identifying and correlating fibroblast growth factor receptor 2 (FGFR2) activation mutations with endometrial cancer, the inventors herein provide useful tools for diagnosing, classifying, and treating endometrial cancer in a subject.
In one embodiment, the present invention is a method of detecting and diagnosing endometrial cancer or precancer in a subject, preferably a human subject. The method preferably comprises detecting a receptor mutation in a FGFR2 in a biological sample containing endometrial cells, wherein the mutation is associated with FGFR2 receptor activation. The presence of one or more activation mutations in the FGFR2 is diagnostic of endometrial cancer or precancer in the subject. The activation mutation can be a missense mutation, a deletion, an insertion, and both a deletion and an insertion and often result in enhanced ligand binding, promiscuous ligand binding (e.g, allows the receptor to bind to and be activated by ligands that cannot normally bind to the wildtype receptor) constitutive receptor dimerization, impaired receptor recycling leading to augmentation of signaling, delayed degradation, overexpression, or kinase activation. In a preferred embodiment, the FGFR2 is a constitutively active mutant, which may still require ligand stimulation for optimal signaling.
Preferably, the step of detecting comprises screening the biological sample for at least one nucleotide FGFR2 mutation in at least one nucleic acid of genomic DNA, RNA, or cDNA. In certain embodiments the activation mutation results in an at least one amino acid substitution in FGFR2.
In a preferred embodiment the FGFR2 activation mutation includes at least one mutation selected from the group consisting of: a mutation in the junction between the immunoglobulin-like (Ig) domains II and III (e.g., a S to W, F, or L mutation at position 252; a P to R mutation at position 253; a P to L mutation at position 263; a S to P mutation at position 267, all of SEQ ID NOS:2 or 3); a mutation in the IgIII domain (e.g., a F to V mutation at position 276; a C to Y or F mutation at position 278; a Y to C mutation at position 281; an I to S mutation at position 288; a Q to P mutation at position 289; a Y to C, G. or R mutation at position 290; a K to E mutation at position 292; a K to R mutation at position 310; an A to T mutation at position 315; a D to A mutation at position 321; a Y to C mutation at position 328, all of SEQ ID NOS:2 or 3); a mutation in the junction between the IgIII domain and the transmembrane (TM) domain (e.g., a S to C or T mutation at position 354 or 353; a V to F mutation at position 359 or 358; an A to S mutation at position 362 or 361; a S to C mutation at position 372 or 371; a Y to C mutation at position 375 or 374; a S to C mutation at position 373 or 372; a Y to C mutation at position 376 or 375, all of SEQ ID NOS:2 or 3 respectively); a mutation of the TM domain (e.g., a G to R mutation at position 380 or 379; a C to R mutation at position 383 or 382; a G to R mutation at positions 384 or 383; a M to R mutation at position 392 or 391, all of SEQ ID NOS: 2 or 3 respectively); a mutation in the junction between the TM domain and the tyrosine kinase domain I (e.g., an IVS10+2A>C splicing mutation); a mutation in the tyrosine kinase domain I (e.g., an I to V mutation at position 538 or 537; a N to K mutation at position 540; an I to V mutation at position 548 or 547; a N to H mutation at position 549 or 548; a N to K mutation at position 550 or 549; an E to G mutation at position 565 or 564, all of SEQ ID NOS:2 or 3 respectively); or a mutation in the tyrosine kinase domain II (e.g., a K to R mutation at position 641 or 640; a K to E mutation at position 650 or 649; a K to N mutation at position 659 or 658; a K to E mutation at position 660 or 659; a G to E mutation at position 663 or 662; a R to G mutation at position 678 or 677, all of SEQ ID NOS:2 or 3 respectively; a frame shift mutation caused by the deletion of nucleotide C and T at position 2290-91 of SEQ ID NO:1).
Other examples of preferred activation mutations of the IgIII domain include for example, a N to I mutation at position 331; an A to P mutation at position 337, a G to P or R mutation at position 338; a Y to C or H mutation at position 340; a T to P mutation at position 341; a C to F, G, R, S, W or Y mutation at position 342; an A to G or P mutation at position 344; a S to C mutation at position 347; a S to C mutation at position 351, all of SEQ ID NO:2, and the equivalent mutations in SEQ ID NO:3.
It is important to note that more than one FGFR2 activation mutation may be detected in a biological sample, for example, at least two FGFR2 receptor activation mutations are detected in certain embodiments.
The endometrial cancer detected can be any subtypes, for example, serous, mucinous, and endometrioid histological subtypes. In a preferred embodiment, however, the cancer detected is an endometrioid histologic subtype.
In addition, the invention provides a method diagnosing or classifying endometrial cancer in a subject, which comprises assessing the level of activity of a FGFR2 signal transduction pathway in a test subject and comparing it to the level of activity in a control subject, wherein increased activity of the FGFR2 pathway in the test subject compared to the control subject is indicative of endometrial cancer. The level of activity of the pathway can, for example, be assed by assessing an increase in the level of expression or activity of a FGFR2 protein. Alternatively, the level of expression or activity may, for example, be assessed by determining the amount of mRNA that encodes the FGFR2, preferably a mutated FGFR2 that results in receptor activation. For example, in one embodiment, endometrial cancer is associated with overexpression of FGFR2 due to genomic amplification, and the assay is designed specifically to detect the overexpression of FGFR2.
The invention is also directed to a kit for diagnosing or classifying endometrial cancer, comprising an oligonucleotide that specifically hybridizes to or adjacent to a site of mutation of a FGFR2 gene that results in increased activity of a FGFR2 protein encoded by the gene, and instructions for use in diagnosing endometrial cancer. The site of mutation may, for example, comprise a nucleotide selected from the group consisting of nucleotides 755, 929, 943, 1118, 1147, 1642, 1650, 1978, and 2290-91 of SEQ ID NO:1 and the equivalent nucleotides of SEQ ID NO:7. In a preferred embodiment, the kit comprises at least one probe comprising the site of mutation.
The invention further is directed to a kit for diagnosing or classifying endometrial cancer, comprising an antibody that specifically recognizes a mutation in a FGFR2 protein, and instructions for use. Optionally, the mutation results in an increased activity as compared to a non-mutated FGFR2 protein, such as that of SEQ ID NOS:2 and 3. Preferably, the antibody is directed against a specific FGFR2 protein mutation selected from the group consisting of: a mutation in the junction between the immunoglobulin-like (Ig) domains II and III; a mutation in the IgIII domain; a mutation in the junction between the IgIII domain and the transmembrane (TM) domain; a mutation in the TM domain; a mutation in the junction between the TM domain and the tyrosine kinase domain I; a mutation in the tyrosine kinase domain I, or a mutation in the tyrosine kinase domain II. More preferably the antibody is directed to a mutation selected from the group consisting of: (a) a S to W mutation at position 252 of SEQ ID NOS:2 (NP 075259.2) or 3 (NP 000132.1); (b) a K to R mutation at position 310 of SEQ ID NOS:2 or 3; (c) an A to T mutation at position 315 of SEQ ID NOS:2 or 3; (d) a S to C mutation at position 373 of SEQ ID NO:2 or position 372 of SEQ ID NO:3; (e) a Y to C mutation at position 376 of SEQ ID NO:2 or position 375 of SEQ ID NO:3; (f) a C to R mutation at position 383 of SEQ ID NO:2 or position 382 of SEQ ID NO:3; (g) a M to R mutation at position 392 of SEQ ID NO:2 or position 391 of SEQ ID NO:3; (h) an I to V mutation at position 548 of SEQ ID NO:2 or position 547 of SEQ ID NO:3; (i) N to K mutation at position 550 of SEQ ID NO:2 or position 549 of SEQ ID NO:3; or (j) a K to E mutation at position 660 of SEQ ID NO:2 or position 659 of SEQ ID NO:3.
The present invention further provides a method of treating endometrial cancer or precancer in a subject. Preferably the subject is a human affected with endometrial cancer (e.g., serous, mucinous, and endometrioid histological subtypes). The method preferably comprises administering an effective amount of a FGFR2 inhibitor with a pharmaceutically acceptable carrier to the subject having endometrial cancer or precancer characterized by FGFR2 activation, for example, a FGFR2 mutated form that is constitutively active in either a ligand-independent or ligand-dependent manner, wherein the FGFR2 inhibitor inhibits FGFR2 expression or activity, thereby effectively inhibiting growth or proliferation of the endometrial cancer in the subject. The FGFR2 inhibitor preferably induces cell cycle arrest and/or apoptosis of the endometrial cancer cells. In one embodiment, the FGFR2 inhibitor is administered to the subject after surgical treatment for endometrial cancer to inhibit the reoccurrence of endometrial cancer after surgery. In another embodiment, the inhibitor is administered to patients with persistent or recurrent endometrial cancer, not amenable to surgical removal.
The FGFR2 inhibitor used may inhibit expression of a FGFR2 gene or a FGFR2 expression product. In one embodiment the agent is a FGFR2 antisense nucleic acid, preferably an antisense nucleic acid hybridizing to a segment of SEQ ID NO:1 comprising at least one nucleotide substitution selected from an A to G substitution at position 929; a T to G substitution at position 1650; a G to A substitution at position 943; a C to G substitution at position 755; a T to A or G substitution at position 1650; an A to G substitution at position 1127; a C to G substitution at position 1175; an A to G substitution at position 1642; an A to G substitution at position 1978; an Intron10 A>C+2; or a deletion of CT at positions 2290-91, and the equivalent substitutions of SEQ ID NO:7.
In another embodiment, the FGFR2 inhibitor inhibits FGFR2 activity by blocking a FGFR2 domain. For example, the FGFR2 inhibitor is an anti-FGFR2 inhibitory antibody directed against the linker region between the immunoglobulin-like (Ig) domains II and III of FGFR2; the IgIII domain of FGFR2; the junction between the IgIII domain and the transmembrane (TM) domain of FGFR2; the TM domain; the junction between the TM domain and the tyrosine kinase domain I of FGFR2; the tyrosine kinase domain I of FGFR2, or the tyrosine kinase domain II of FGFR2. For example, in one embodiment, the FGFR2 inhibitor interferes with the FGFR2 folding, the three dimensional structure of FGFR2, ligand binding, or substrate binding, e.g., ATP.
Preferred examples include an antibody that specifically recognizes a FGFR2 amino acid sequence comprising mutations selected from the following: (a) a S to W mutation at position 252 of SEQ ID NOS:2 (NP 075259.2) or 3 (NP 000132.1); (b) a K to R mutation at position 310 of SEQ ID NOS:2 or 3; (c) an A to T mutation at position 315 of SEQ ID NOS:2 or 3; (d) a S to C mutation at position 373 of SEQ ID NO:2 or position 372 of SEQ ID NO:3; (e) a Y to C mutation at position 376 of SEQ ID NO:2 or position 375 of SEQ ID NO:3; (f) a C to R mutation at position 383 of SEQ ID NO:2 or position 382 of SEQ ID NO:3; (g) a M to R mutation at position 392 of SEQ ID NO:2 or position 391 of SEQ ID NO:3; (h) an I to V mutation at position 548 of SEQ ID NO:2 or position 547 of SEQ ID NO:3; (i) N to K mutation at position 550 of SEQ ID NO:2 or position 549 of SEQ ID NO:3; or (j) a K to E mutation at position 660 of SEQ ID NO:2 or position 659 of SEQ ID NO:3.
In a preferred embodiment, the antibody is directed against a S to W mutation at position 252 of SEQ ID NOS:2 or 3. In another preferred embodiment the antibody is a humanized antibody and preferably a monoclonal antibody.
In an alternative embodiment, the FGFR2 inhibitor is a small inhibitory RNA (siRNA), a small hairpin RNA (shRNA), microRNA (miRNA), or a ribozyme. In a preferred embodiment the FGFR2 inhibitor is a shRNA, preferably a shRNA that targets exon 2 of FGFR2 (SEQ ID NO:4) and/or exon 15 of FGFR2 (SEQ ID NO:5). In another specific nonlimiting embodiment, the FGFR2 inhibitor is PD173074.
The invention further provides a method of classifying endometrial cancer. The method allows a user to properly classify the type of endometrial cancer so that a specific and proper treatment can be used based on the type of endometrial cancer a subject has. The method comprises: screening for a FGFR2 mutation in an endometrial cancer cell; and classifying the type of endometrial cancer as a FGFR2 activation induced endometrial cancer upon finding a FGFR2 activation mutation in the endometrial cancer cell. Preferably the FGFR2 activation mutation is one or more of the FGFR2 mutation identified above. In certain embodiments, the method further comprises determining if the FGFR2 mutation induces FGFR2 activation.
Cells were serum-starved in 0.2% FBS for 18 hours, and then treated with increasing concentrations of PD173074 for three hours. Lysates were collected and evaluated by Western blot analysis for activation of PLCg.
The invention will now be described in reference to the preferred embodiments of the invention for purposes of illustration only. It will be understood by one skilled in the art that numerous modifications or alterations may be made in and to the illustrated embodiments without departing from the spirit and scope of the invention.
The invention, in part, is based on the discovery that mutations in the FGFR2 receptor that induce receptor activation can be used to effectively detect and classify endometrial cancer or precancer in a subject. The present invention is further based on the discovery that inhibition of the FGFR2 gene or its expression products are effective in treating endometrial cancer.
As used herein the term “endometrial cancer” encompasses all forms and subtypes of the disease, including for example, serous, mucinous, and endometrioid histological subtypes. Endometrial cancer is cancer that starts in the endometrium, the lining of the uterus (womb).
In context of the present invention, the FGFR2 gene encompasses a gene, preferably of human origin, a coding nucleotide sequence set forth in SEQ ID NOS:1, 7, or homologs including allelic variants and orthologs. The FGFR2 protein encompasses a protein, also preferably of human origin, having the amino acid sequence set forth in SEQ ID NOS:2 or 3, or homologs, including orthologs thereof.
FGFR2 belongs to a family of structurally related tyrosine kinase receptors (FGFRs 1-4) encoded by four different genes. FGFR2 is a glycoprotein composed of three extra-cellular immunoglobulin-like (Ig) domains, a transmembrane domain, and a split tyrosine kinase domain. Alternative splicing in the IgIII domain is primary determinant of both the patterns of redundancy and specificity in FGF/FGFR binding and signaling. This splicing event is tissue specific and gives rise to the Mb and IIIc receptor isoforms for FGFR1-FGFR3 which possess distinct ligand specificities (Mohammadi M, Olsen S K and Ibrahimi O A. (2005), Cytokine Growth Factor Rev 16: 107-137, Ornitz D M and Itoh N. (2001). Genome Biol 2: REVIEWS3005). For FGFR2, cells of an epithelial lineage only express the “IIIb” isoform encoded by exon 8 (FGFR2b; SEQ ID NO:2; NP_07529.2), while mesenchymally derived cells only express the “IIIc” isoform utilizing exon 9 (FGFR2c; SEQ ID NO:3; NP_000132.1) (Scotet E and Houssaint E. (1995). Biochim Biophys Acta 1264: 238-242). The FGFR2b isoform predominantly binds FGF1, FGF3, FGF7 and FGF10, while FGFR2c does not bind FGF7 and FGF10 but does bind FGF1, FGF2, FGF4, FGF6, and FGF8 with high affinity (Ibrahimi O A, Zhang F, Eliseenkova A V, Itoh N, Linhardt R J and Mohammadi M. (2004), Hum Mol Genet 13: 2313-2324).
An “increased activity” or “activation mutation” of FGFR2 in a test subject or a biological sample refers to higher total FGFR2 activity in the test subject or biological sample in comparison with a control, e.g., a healthy subject or a standard sample. Preferably, although not necessarily, the activity is at least 10%, more preferably at least 50%, even more preferably at least 100%, and still more preferably at least 150% higher in the test subject or sample than in the control. The increased activity, for example, may result from increased basal FGFR2 activity, prolonged stimulation, delayed degradation, or over-expression, e.g., due to enhanced ligand binding, promiscuous or inappropriate ligand binding, constitutive receptor dimerization, impaired recycling resulting in augmentation of signaling, delayed degradation, or kinase activation.
A higher expression level of FGFR2 may result from, for example, a mutation in a non-coding region of a FGFR2 gene or a mutation in a coding or non-coding gene involved in FGFR2 transcription or translation. The expression level of FGFR2 can be determined, for example, by comparing FGFR2 mRNA or the level of FGFR2 protein in a test subject as compared to a control, for example by comparing the tumor to normal endometrium (e.g., a normal adjacent endometrium sample).
“Function-conservative variants” are those in which a given amino acid residue in a protein or enzyme has been changed without altering the overall conformation and function of the polypeptide, including, but not limited to, replacement of an amino acid with one having similar properties (such as, for example, polarity, hydrogen bonding potential, acidic, basic, hydrophobic, aromatic, and the like). Amino acids with similar properties are well known in the art. For example, arginine, histidine and lysine are hydrophilic-basic amino acids and may be interchangeable. Similarly, isoleucine, a hydrophobic amino acid, may be replaced with leucine, methionine or valine. Such changes are expected to have little or no effect on the apparent molecular weight or isoelectric point of the protein or polypeptide.
Amino acids other than those indicated as conserved may differ in a protein or enzyme so that the percent protein or amino acid sequence similarity between any two proteins of similar function may vary and may be, for example, from 70% to 99% as determined according to an alignment scheme such as by the Cluster Method, wherein similarity is based on the MEGALIGN algorithm. A “variant” also includes a polypeptide or enzyme which has at least 60% amino acid identity as determined by BLAST or FASTA algorithms, preferably at least 75% most preferably at least 85%, and even more preferably at least 90%, and still more preferably at least 95%, and which has the same or substantially similar properties or functions as the native or parent protein or enzyme to which it is compared. A particular variant is a “gain-of-function” variant, meaning a polypeptide variant in which the change of at least one given amino acid residue in a protein or enzyme improves a specific function of the polypeptide, including, but not limited to protein activity. The change in amino acid residue can be replacement of an amino acid with one having similar properties.
As used herein, the terms “homologous” and “similar” refer to the relationship between proteins that possess a “common evolutionary origin,” including proteins from superfamilies (e.g., the immunoglobulin superfamily) and homologous proteins from different species. Such proteins (and their encoding genes) have sequence homology, as reflected by their sequence similarity, whether in terms of percent similarity or the presence of specific residues or motifs as conserved positions.
In a specific embodiment, two DNA sequences are “substantially homologous or similar” when at least about 80%, and most preferably at least about 90% or at least 95%) of the nucleotides match over the defined lengths of the DNA sequences, as determined by sequence comparison algorithms, such as, BLAST, FASTA, DNA Strider, etc.
The terms “mutant” and mutation” mean any detectable change in genetic material, e.g., DNA, or any process mechanism, or result of such a change. When compared to a control material, such change may be referred to as an “abnormality.” This includes gene mutations, in which the structure (e.g. DNA sequence of a gene is altered, any gene or DNA arising from any mutation process, and any expression product (e.g., protein) expressed by a modified gene or DNA sequence. The term “variant” may also be used to indicate a modified or altered gene, DNA sequence, enzyme, cell, etc., i.e., any kind of mutant.
As used herein, “sequence-specific oligonucleotides” refers to related sets of oligonucleotides that can be used to detect specific variations or mutations in the FGFR2 gene, preferably a FGFR2 activation mutation.
A “probe” refers to a nucleic acid or oligonucleotide that forms a hybrid structure with a sequence in a target region due to complementarity of at least one sequence in the probe with a sequence in the target protein of the subject.
The present invention provides antisense nucleic acids (including ribozymes), which may be used to inhibit expression of FGFR2. An “antisense nucleic acid” is preferably a single stranded nucleic acid molecule which, on hybridizing under cytoplasmic conditions with complementary bases in an RNA or DNA molecule, inhibits the latter's role. If the RNA is messenger RNA transcript, the antisense nucleic acid is a countertranscript or mRNA-interfering complementary nucleic acid. As presently used, “antisense” broadly includes RNA-RNA interactions, RNA-DNA interactions, ribozymes, RNA-induced silencing complexes, and RNASe-H mediated arrest. Antisense nucleic acid molecules can be encoded by a recombinant gene for expression in a cell (e.g., U.S. Pat. Nos. 5,814,500; 5,811,234), or alternatively they can be prepared synthetically (e.g., U.S. Pat. No. 5,780,607). Synthetic oligonucleotides are suitable for antisense use.
Diagnostic MethodsAccording to the present invention, mutations of the FGFR2 receptor that induce receptor activation, which includes overexpression and delayed degradation, can be detected to diagnose or classify endometrial cancer or precancer in a subject.
As used herein, a “subject” is a human or non-human mammal, e.g., a primate, cow, horse, pig, sheep, goat, dog, cat, or rodent, likely to develop endometrial cancer. In all embodiments human subjects are preferred. Preferably the subject is a human either suspected of having endometrial cancer, having been diagnosed with endometrial cancer, or having a family history of endometrial cancer. Methods for identifying subjects suspected of having endometrial cancer may include physical examination, subject's family medical history, subject's medical history, endometrial biopsy, or a number of imaging technologies such as ultrasonography, computed tomography, magnetic resonance imaging, magnetic resonance spectroscopy, or positron emission tomography. Diagnostic method for endometrial cancer and the clinical delineation of endometrial cancer diagnoses are well known to those of skill in the medical arts.
Accordingly, diagnostic methods may comprise for example, detecting a mutation in the FGFR2 gene, wherein the mutation results in increased FGFR2 receptor activity. The FGFR2 mutation may especially affect a coding region of the FGFR2 gene, such as, for example, a mutation in the IgII or IgIII domain of the FGFR2 gene. The mutation may be a missense mutation, preferably a missense mutation resulting in nucleic acid substitution, or a deletion, or a combination of both. Preferably, the mutation results in one, and sometimes more, amino acid substitutions or deletions, e.g., see Table 2 below.
The diagnostic methods of the invention also encompass detecting a mutation in the FGFR2 protein, in particular a mutation that results in increased activity of the FGFR2 protein. Preferably the mutation is at least one mutation in FGFR2 selected from the group consisting of: a mutation in the junction between the immunoglobulin-like (Ig) domains II and III; a mutation in the IgIII domain; a mutation in the junction between the IgIII domain and the transmembrane (TM) domain; a mutation in the TM domain; a mutation in the junction between the TM domain and the tyrosine kinase domain I; a mutation in the tyrosine kinase domain I, or a mutation in the tyrosine kinase domain II. Most preferably the mutation induces an amino acid substitution in FGFR2, for example, a S to W mutation at position 252 of SEQ ID NOS:2 or 3, or N to K mutation at position 550 of SEQ ID NO:2 or position 549 of SEQ ID NO:3. In another embodiment, the amino acid substitution in FGFR2 is a K to R mutation at position 310 of SEQ ID NOS:2 or 3; or a M to R mutation at position 392 of SEQ ID NO:2 or position 391 of SEQ ID NO:3. In one nonlimiting embodiment, the mutation is consist of a deletion of nucleotide C and T at position 2290-91 of SEQ ID NO:1 (NM-02297.2); SEQ ID NO:7; or an IVS10+2A>C splicing mutation.
Typically, a detected FGFR2 receptor activation mutation increases activation of the receptor by, for example, enhancing ligand binding, altered (promiscuous) ligand affinity, constitutive receptor dimerization, delayed degradation, impaired recycling from the cell membrane, overexpression, or kinase activation, thereby activating the FGFR2 receptor.
As used herein, the term “diagnosis” refers to the identification of the disease at any stage of its development, and also includes the determination of a predisposition of a subject to develop the disease or relapse. The invention further provides a means of confirming and classifying the type of endometrial cancer.
The term “biological sample” refers to any cell source from which DNA may be obtained. Preferably the biological sample are obtained from the uterus area or near thereto to ensure that endometrial cells lining the uterus are present in the biological sample. In one embodiment the biological sample is in the form of blood, for example, uterine blood from menstrual or post menopausal spotting.
In a further embodiment, the diagnosis of endometrial cancer in a subject comprises assessing the level of expression, delayed degradation, or activity of the FGFR2 protein in endometrial cells of a test subject and comparing it to the level of expression or activity in endometrial cells of a control subject, wherein an increased expression and/or activity of FGFR2 protein in the test subject compared to the control subject is indicative of endometrial cancer or precancer.
The level of expression or delayed degradation of FGFR2 may be assessed by determining the amount of mRNA that encodes the FGFR2 protein in a biological sample, or by determining the concentration of FGFR2 protein in a biological sample. The level of FGFR2 activity may be assessed by determining the level of activity in a FGFR2 signaling pathway signaling flux, e.g., by measuring FGFR2 activity in a sample or subject, as described herein.
Nucleic Acid Based AssaysAccording to the invention, mutated forms of FGFR2 nucleic acids, i.e. in the FGFR2 DNA or in its transcripts, as well as a deregulated expression, e.g. overexpression, of FGFR2 or other components of a FGFR2 pathway can be detected by a variety of suitable methods.
Standard methods for analyzing and sequencing the nucleic acid contained in a biological sample and for diagnosing a genetic disorder can be employed, and many strategies for genotypic analysis are known to those of skilled in the art.
In a preferred embodiment, the determination of mutations in the FGFR2 gene encompasses the use of nucleic acid sequences such as specific oligonucleotides, to detect mutations in FGFR2 genomic DNA or mRNA in a biological sample. Such oligonucleotides may be specifically hybridize to a site of mutation, or to a region adjacent to this site of mutation present in a FGFR2 nucleic acid. One may also employ primers that permit amplification of all or part of FGFR2. Alternatively, or in combination with such techniques, oligonucleotide sequencing described herein or known to the skilled artisan can be applied to detect the FGFR2 mutations.
One skilled in the art may use hybridization probes in solution and in embodiments employing solid-phase procedures. In embodiments involving solid-phase procedures, the test nucleic acid is adsorbed or otherwise affixed to a selected matrix or surface. The fixed, single-stranded nucleic acid is then subjected to specific hybridization with selected probes.
In another embodiment, one skilled in the art may use oligonucleotide primers in an amplification technique, such as PCR or reverse-PCR (“reverse polymerase chain reaction”), to specifically amplify the target DNA or mRNA, respectively, which is potentially present in the biological sample.
Useful oligonucleotides include primers that permit amplification of FGFR2 exons.
The present invention is more particularly directed to a method of in vitro diagnosis of endometrial cancer or precancer comprising the steps of:
a) contacting a biological sample containing DNA with specific oligonucleotides permitting the amplification of all or part of the FGFR2 gene, the DNA contained in the sample having being rendered accessible, where appropriate, to hybridization, and under conditions permitting a hybridization of the primers with the DNA contained in the biological sample;
b) amplifying said DNA;
c) detecting the amplification products;
d) comparing the amplified products as obtained to the amplified products obtained with a normal control biological sample, and thereby detecting a possible abnormality in the FGFR2 gene.
In certain embodiments, the DNA a biological sample is sequenced directly with no requirement for amplification. In these embodiments, the sequenced DNA is compared to a control sequence for detecting possible abnormalities in the FGFR2 gene.
The method of the invention can also be applied to the detection of an abnormality in the transcript of the FGFR2 gene, e.g., by amplifying the mRNAs contained in a biological sample, for example by RT-PCR.
Thus another subject of the present invention is a method of in vitro diagnosis of endometrial cancer, as previously defined comprising the steps of:
a) producing cDNA from mRNA contained in a biological sample;
b) contacting said cDNA with specific oligonucleotides permitting the amplification of all or part of the transcript of the FGFR2 gene, under conditions permitting a hybridization of the primers with said cDNA;
c) amplifying said cDNA;
d) detecting the amplification products;
e) comparing the amplified products as obtained to the amplified products obtained with a normal control biological sample, and thereby detecting a possible abnormality in the transcript of the FGFR2 gene.
A control can be any normal endometrial control sample known to those skilled in the art, for example, a normal adjacent endometrium sample or a normal DNA, obtained from blood or buccal swab.
For RNA analysis, the biological sample may be any cell source, as described above, such as a biopsy tissue, from which RNA is isolated using standard methods well known to those of ordinary skill in the art such as guanidium thiocyanate-phenol-chloroform extraction (Chomocyznski et al., Anal. Biochem., 1987, 162:156). The isolated RNA is then subjected to coupled reverse transcription and amplification by polymerase chain reaction (RT-PCR), using specific oligonucleotide primers that are specific for a selected site. Conditions for primer annealing are chosen to ensure specific reverse transcription and amplification; thus, the appearance of an amplification product is diagnostic of the presence of a particular genetic variation. In another embodiment, RNA is reverse-transcribed and amplified, after which the amplified sequences are identified by, e.g., direct sequencing. In still another embodiment, cDNA obtained from the RNA can be cloned and sequenced to identify a mutation.
The FGFR2 nucleic acids of the invention can also be used as probes, e.g., in therapeutic and diagnostic assays. For instance, the present invention provides a probe comprising a substantially purified oligonucleotide, which oligonucleotide comprises a region having a nucleotide sequence that is capable of hybridizing specifically to a region of a FGFR2 gene which differs from that of the wild-type gene (SEQ ID NOS:1 and 7), e.g., a mutant or polymorphic region. Such probes can then be used to specifically detect which mutation of the FGFR2 gene is present in a sample taken from a subject. The mutant or polymorphic region can be located in the promoter, exon, or intron sequences of the FGFR2 gene.
Particularly preferred probes of the invention have a number of nucleotides sufficient to allow specific hybridization to the target nucleotide sequence. Thus, probes of suitable lengths based on SEQ ID NOS:1-3 and complementary to the mutant sequences provided herein can be constructed and tested by the skilled artisan for appropriate level of specificity depending on the application intended. Where the target nucleotide sequence is present in a large fragment of DNA, such as a genomic DNA fragment of several tens or hundreds of kilobases, the size of the probe may have to be longer to provide sufficiently specific hybridization, as compared to a probe which is used to detect a target sequence which is present in a shorter fragment of DNA. For example, in some diagnostic methods, a portion of the FGFR2 gene may first be amplified and thus isolated from the rest of the chromosomal DNA and then hybridized to a probe. In such a situation, a shorter probe will likely provide sufficient specificity of hybridization. For example, a probe having a nucleotide sequence of about 10 nucleotides may be sufficient, although probes of about 15 nucleotides, even more preferably 20 nucleotides, are preferred.
In a preferred embodiment, the probe or primer further comprises a label attached thereto, which preferably is capable of being detected. The label can, for example, be selected from radioisotopes, fluorescent compounds, enzymes, and enzyme co-factors.
In another preferred embodiment of the invention, the isolated nucleic acid, which is used, e.g., as a probe or a primer, is modified, such as to become more stable. Exemplary nucleic acid molecules which are modified include phosphoramidate, phosphothioate and methylphosphonate analogs of DNA (see also U.S. Pat. Nos. 5,176,996; 5,264,564; and 5,256,775).
In yet another embodiment, one may use HPLC or denaturing HPLC (DHPLC) techniques to analyze the FGFR2 nucleic acids. DHPLC was developed when observing that, when HPLC analyses are carried out at a partially denaturing temperature, i.e., a temperature sufficient to denature a heteroduplex at the site of base pair mismatch, homoduplexes can be separated from heteroduplexes having the same base pair length (Hayward-Lester, et al., Genome Research, 1995, 5:494; Underhill, et al., Proc. Natl. Acad. Sci. USA, 1996, 93:193; Doris, et al., DHPLC Workshop, 1997, Stanford University). Thus, the use of DHPLC was applied to mutation detection (Underhill, et al., Genome Research, 1997, 7:996; Liu, et al., Nucleic Acid Res., 1998, 26; 1396). DHPLC can separate heteroduplexes that differ by as little as one base pair. “Matched Ion Polynucleotide Chromatography” (MIPC), or Denaturing “Matched Ion Polynucleotide Chromatography” (DMIPC) as described in U.S. Pat. No. 6,287,822 or 6,024,878, are separation methods that can also be useful in connection with the present invention.
Alternatively, one can use the DGGE method (Denaturing Gradient Gel Electrophoresis), or the SSCP method (Single Strand Conformation Polymorphism) for detecting an abnormality in the FGFR2 gene. DGGE is a method for resolving two DNA fragments of identical length on the basis of sequence differences as small as a single base pair change, using electrophoresis through a gel containing varying concentrations of denaturant (Guldberg et al., Nuc. Acids Res. 1994, 22:880). SSCP is a method for detecting sequence differences between two DNAs, comprising hybridization of the two species with subsequent mismatch detection by gel electrophoresis (Ravnik-Glavac et al., Hum. Mol. Genet. 1994, 3:801). “HOT cleavage”, a method for detecting sequence differences between two DNAs, comprising hybridization of the two species with subsequent mismatch detection by chemical cleavage (Cotton, et al., Proc. Natl. Acad. Sci. USA 1988, 85:4397), can also be used. Such methods are preferably followed by direct sequencing. Advantageously, the RT-PCR method may be used for detecting abnormalities in the FGFR2 transcript, as it allows to visualize the consequences of a splicing mutation such as exon skipping or aberrant splicing due to the activation of a cryptic site. Preferably this method is followed by direct sequencing as well.
Techniques using microarrays, preferably microarray techniques allowing for high-throughput screening, can also be advantageously implemented for detecting an abnormality in the FGFR2 gene or for assaying expression of the FGFR2 gene or the gene of another component in the FGFR2 pathway resulting in increased signaling as described herein. Microarrays may be designed so that the same set of identical oligonucleotides is attached to at least two selected discrete regions of the array, so that one can easily compare a normal sample, contacted with one of said selected regions of the array, against a test sample, contacted with another of said selected regions. These arrays avoid the mixture of normal sample and test sample, using microfluidic conduits. Useful microarray techniques include those developed by Nanogen, Inc (San Diego, Calif.) and those developed by Affymetrix. However, all types of microarrays, also called “gene chips” or “DNA chips”, may be adapted for the identification of mutations. Such microarrays are well known in the art.
The solid support on which oligonucleotides are attached may be made from glass, silicon, plastic (e.g., polypropylene, nylon), polyacrylamide, nitrocellulose, or other materials. One method for attaching the nucleic acids to a surface is by printing on glass plates, as is described generally by Schena et al., Science 1995, 270:467-470. This method is especially useful for preparing microarrays of cDNA. See also DeRisi et al., Nature Genetics 1996, 14:457-460; Shalon et al., Genome Res. 1996, 6:639-645; and Schena et al., Proc. Natl. Acad. Sci. USA 1995, 93:10539-11286.
Other methods for making microarrays, e.g., by masking (Maskos and Southern, Nuc. Acids Res. 1992, 20:1679-1684), may also be used. In principal, any type of array, for example, dot blots on a nylon hybridization membrane (see Sambrook et al., Molecular Cloning A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989) could be used, although, as will be recognized by those of skill in the art, very small arrays will be preferred because hybridization volumes will be smaller. For these assays nucleic acid hybridization and wash conditions are chosen so that the attached oligonucleotides “specifically bind” or “specifically hybridize” to at least a portion of the FGFR2 gene present in the tested sample, i.e., the probe hybridizes, duplexes or binds to the FGFR2 locus with a complementary nucleic acid sequence but does not hybridize to a site with a non-complementary nucleic acid sequence. As used herein, one polynucleotide sequence is considered complementary to another when, if the shorter of the polynucleotides is less than or equal to 25 bases, there are no mismatches using standard base-pairing rules or, if the shorter of the polynucleotides is longer than 25 bases, there is no more than a 5% mismatch. Preferably, the polynucleotides are perfectly complementary (no mismatches). It can easily be demonstrated that specific hybridization conditions result in specific hybridization by carrying out a hybridization assay including negative controls (see, e.g., Shalon et al., supra, and Chee et al., Science 1996, 274:610-614).
A variety of methods are available for detection and analysis of the hybridization events. Depending on the reporter group (fluorophore, enzyme, radioisotope, etc.) used to label the DNA probe, detection and analysis are carried out fluorimetrically, colorimetrically or by autoradiography. By observing and measuring emitted radiation, such as fluorescent radiation or a particle emission, information may be obtained about the hybridization events.
When fluorescently labeled probes are used, the fluorescence emissions at each site of transcript array can, preferably be detected by scanning confocal laser microscopy. In one embodiment, a separate scan, using the appropriate excitation line, is carried out for each of the two fluorophores used. Alternatively, a laser can be used that allows simultaneous specimen illumination at wavelengths specific to the two fluorophores and emissions from the two fluorophores can be analyzed simultaneously (see Shalon et al. Genome Res. 1996, 6:639-695).
Protein Based AssaysAs an alternative to analyzing FGFR2 nucleic acids, one can evaluate FGFR2 on the basis of mutations in the protein, or dysregulated production, e.g., overproduction, of the protein.
In preferred embodiments, FGFR2 are detected by immunoassay. For example, Western blotting permits detection of a specific variant, or the presence or absence of FGFR2. In particular, an immunoassay can detect a specific (wild-type or mutant) amino acid sequence in a FGFR2 protein. Other immunoassay formats can also be used in place of Western blotting, as described below for the production of antibodies. One of these is ELISA assay.
In ELISA assays, an antibody against FGFR2, an epitopic fragment of FGFR2, is immobilized onto a selected surface, for example, a surface capable of binding proteins such as the wells of a polystyrene microtiter plate. After washing to remove incompletely adsorbed polypeptides, a nonspecific protein such as a solution of bovine serum albumin (BSA) may be bound to the selected surface. This allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific bindings of antisera onto the surface. The immobilizing surface is then contacted with a sample, to be tested in a manner conductive to immune complex (antigen/antibody) formation. This may include diluting the sample with diluents, such as solutions of BSA, bovine gamma globulin (BGG) and/or phosphate buffered saline (PBS)/Tween. The sample is then allowed to incubate for from 2 to 4 hours, at temperatures between about 25 to 37 degrees C. Following incubation, the sample-contacted surface is washed to remove non-immunocomplexed material. The washing procedure may include washing with a solution, such as PBS/Tween or borate buffer. Following formation of specific immunocomplexes between the test sample and the bound antibody, and subsequent washing, the occurrence, and an even amount of immunocomplex formation may be determined by subjecting the immunocomplex to a second antibody against FGFR2 mutants, that recognizes a mutated epitope on the protein. To provide detecting means, the second antibody may have an associated activity such as an enzymatic activity that will generate, for example, a color development upon incubating with an appropriate chromogenic substrate. Quantification may then be achieved by measuring the degree of color generation using, for example, a visible spectra spectrophotometer.
Typically the detection antibody is conjugated to an enzyme such as peroxidase and the protein is detected by the addition of a soluble chromophore peroxidase substrate such as tetramethylbenzidine followed by 1 M sulfuric acid. The test protein concentration is determined by comparison with standard curves.
These protocols are detailed in Current Protocols in Molecular Biology, V. 2 Ch. 11 and Antibodies, a Laboratory Manual, Ed Harlow, David Lane, Cold Spring Harbor Laboratory (1988) pp 579-593.
Alternatively, a biochemical assay can be used to detect expression, or accumulation of FGFR2, e.g., by detecting the presence or absence of a band in samples analyzed by polyacrylamide gel electrophoresis; by the presence or absence of a chromatographic peak in samples analyzed by any of the various methods of high performance liquid chromatography, including reverse phase, ion exchange, and gel permeation; by the presence or absence of FGFR2 in analytical capillary electrophoresis chromatography, or any other quantitative or qualitative biochemical technique known in the art.
The immunoassays discussed above involve using antibodies directed against the FGFR2 protein or fragments thereof. The production of such antibodies is described below.
Anti-FGFR2 AntibodiesSuch antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments, Fab expression library, and for example, humanized antibodies.
Various procedures known in the art may be used for the production of polyclonal or monoclonal antibodies to FGFR2 polypeptides or derivative or analog thereof. For the production of antibody, various host animals can be immunized by injection with the antigenic polypeptide, including but not limited to rabbits, mice, rats, sheep, goats, etc.
For preparation of monoclonal antibodies directed toward the FGFR2 polypeptides, any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used. These include but are not limited to the hybridoma technique originally developed by Kohler and Milstein (Nature 256:495-497, 1975), as well as the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today 4:72, 1983; Cote et al., Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030, 1983), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96, 1985). In an additional embodiment of the invention, monoclonal antibodies can be produced in germ-free animals (International Patent Publication No. WO 89/12690, published Dec. 28, 1989).
According to the invention, techniques described for the production of single chain antibodies (U.S. Pat. Nos. 5,476,786 and 5,132,405 to Huston; U.S. Pat. No. 4,946,778) can be adapted to produce the FGFR2 polypeptide-specific single chain antibodies. Indeed, these genes can be delivered for expression in vivo. An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse et al., Science 246:1275-1281, 1989) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for a FGFR2 polypeptide, or its derivatives, or analogs.
Antibody fragments which contain the idiotype of the antibody molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′).sub.2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′).sub.2 fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent.
In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), “sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
Diagnostic KitsThe present invention further provides kits for the determination of the sequence within the FGFR2 gene in a subject to diagnose or classify endometrial cancer. The kits comprise a means for determining the sequence at the variant positions, and may optionally include data for analysis of mutations. The means for sequence determination may comprise suitable nucleic acid-based and immunological reagents. Preferably, the kits also comprise suitable buffers, control reagents where appropriate, and directions for determining the sequence at a variant position and for diagnosing or classifying endometrial cancer in a subject.
Nucleic Acid Based Diagnostic KitsThe invention provides nucleic acid-based methods for detecting genetic variations of FGFR2 in a biological sample. The sequence at particular positions in the FGFR2 gene is determined using any suitable means known in the art, including without limitation one or more of hybridization with specific probes for PCR amplification, restriction fragmentation, direct sequencing, SSCP, and other techniques known in the art.
In one embodiment, diagnostic kits include the following components:
a) Probe DNA: The probe DNA may be pre-labeled; alternatively, the probe DNA may be unlabeled and the ingredients for labeling may be included in the kit in separate containers; and
b) Hybridization reagents: The kit may also contain other suitably packaged reagents and materials needed for the particular hybridization protocol, including solid-phase matrices, if applicable, and standards.
In another embodiment, diagnostic kits include:
a) Sequence determination primers: Sequencing primers may be pre-labeled or may contain an affinity purification or attachment moiety; and
b) Sequence determination reagents: The kit may also contain other suitably packaged reagents and materials needed for the particular sequencing protocol.
In one preferred embodiment, the kit comprises a panel of sequencing primers, whose sequences correspond to sequences adjacent to variant positions.
Antibody Based Diagnostic KitsThe invention also provides antibody-based methods for detecting mutant (or wild type) FGFR2 proteins in a biological sample. The methods comprise the steps of: (i) contacting a sample with one or more antibody preparations, wherein each of the antibody preparations is specific for mutant (or wild type) FGFR2 under conditions in which a stable antigen-antibody complex can form between the antibody and FGFR2 in the biological sample; and (ii) detecting any antigen-antibody complex formed in step (i) using any suitable means known in the art, wherein the detection of a complex indicates the presence of mutant (or wild type) FGFR2.
Typically, immunoassays use either a labeled antibody or a labeled antigenic component (e.g., that competes with the antigen in the sample for binding to the antibody). Suitable labels include without limitation enzyme-based, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays that amplify the signals from the probe are also known, such as, for example, those that utilize biotin and avidin, and enzyme-labeled immunoassays, such as ELISA assays.
Diagnostic kits typically include one or more of the following components:
(i) FGFR2-specific antibodies: The antibodies may be pre-labeled; alternatively, the antibody may be unlabeled and the ingredients for labeling may be included in the kit in separate containers, or a secondary, labeled antibody is provided; and
(ii) Reaction components: The kit may also contain other suitably packaged reagents and materials needed for the particular immunoassay protocol, including solid-phase matrices, if applicable, and standards.
The kits referred to above preferably includes instructions for conducting and reading the test to diagnose or classify endometrial cancer. Furthermore, in preferred embodiments, the diagnostic kits are adaptable to high-throughput and/or automated operation.
Methods of Treating Endometrial CancerThe present invention further provides a method of treating endometrial cancer characterized by FGFR2 activation. The treatment method preferably comprises inhibition of the FGFR2 activity in a subject. Generally the method comprises administering to a patient in need of such treatment an effective amount of an agent that modulates FGFR2 expression or activity, with a pharmaceutically acceptable carrier. For example, the therapeutic agent may be a FGFR2 antisense nucleic acid, an anti-FGFR2 intracellular inhibitory antibody or a small molecule inhibitor.
The treatment compositions comprise, as active principle agents a FGFR2 inhibitor. Examples of suitable inhibitors includes those inhibitors that inhibit FGFR2 DNA synthesis and its expression products (e.g., FGFR2 RNA or protein). In one exemplary embodiment the inhibitor is a small molecule FGFR2 inhibitor, e.g., PD173074. In another exemplary embodiment RNA interference is used, wherein the inhibitor is a reagent that inhibits RNA synthesis and/or translation, e.g., a small inhibitory RNA (siRNA), a small hairpin RNA (shRNA), microRNA (miRNA), or a ribozyme.
In yet another embodiment the inhibitor comprises antibodies directed against FGFR2, preferably a mutated FGFR2, and particularly against at least one Ig domain thereof. Preferably the antibodies are specific for a mutated linker region between IgII and IgIII domains of FGFR2, e.g., against the S252W mutation. Generally, preferred antibodies are monoclonal ones, and particularly antibodies modified so that they do not induce immunogenic reactions in a human subject (e.g., humanized antibodies). Antibodies that block the activity of FGFR2 may be produced and selected according to any standard method well-known by one skilled in the art, such as those described above in the context of diagnostic applications.
Intracellular antibodies (sometime referred to as “intrabodies”) have been used to regulate the activity of intracellular proteins in a number of systems (see, Marasco, Gene Ther. 1997, 4:11; Chen et al., Hum. Gene Ther. 1994, 5:595), e.g., viral infections (Marasco et al., Hum. Gene Ther. 1998, 9:1627) and other infectious diseases (Rondon et al., Annu. Rev. Microbiol. 1997, 51:257), and oncogenes, such as p21 (Cardinale et al., FEBS Lett. 1998, 439:197-202; Cochet et al., Cancer Res. 1998, 58:1170-6), myb (Kasono et al., Biochem Biophys Res Commun. 1998, 251:124-30), erbB-2 (Graus-Porta et al., Mol Cell Biol. 1995, 15:1182-91), etc. This technology can be adapted to inhibit FGFR2 activity by expression of an anti-FGFR2 intracellular antibody.
Other inhibitors that would be suitable include antisense oligonucleotides directed against FGFR2, more preferably a mutated FGFR2 isoform. Vectors comprising a sequence encoding an antisense nucleic acid according to the invention may be administered by any known methods, such as the methods for gene therapy available in the art. For general reviews of the methods of gene therapy, see, Goldspiel et al., Clinical Pharmacy 1993, 12:488-505; Wu and Wu, Biotherapy 1991, 3:87-95; Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 1993, 32:573-596; Mulligan, Science 1993, 260:926-932; and Morgan and Anderson, Ann. Rev. Biochem. 1993, 62:191-217; May, TIBTECH 1993, 11:155-215. Methods commonly known in the art of recombinant DNA technology that can be used are described in Ausubel et al., (eds.), 1993, Current Protocols in Molecular Biology, John Wiley & Sons, NY; Kriegler, 1990, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY; and in Chapters 12 and 13, Dracopoli et al., (eds.), 1994, Current Protocols in Human Genetics, John Wiley & Sons, NY.
The term “treatment” as used herein is to therapeutically intervene in the development or progression of a endometrial cancer in a subject. The term “treatment” also encompasses prevention of the development or reoccurence of endometrial cancer in a subject diagnosed as having a known FGFR2 activation mutation.
The term “therapeutically effective amount” is used herein to mean an amount or dose sufficient to modulate, e.g., decrease the level of FGFR2 activity e.g., by about 10 percent, preferably by about 50 percent, and more preferably by about 90 percent. Preferably, a therapeutically effective amount can ameliorate or present a clinically significant deficit in the activity, function and response of the subject. Alternatively, a therapeutically effective amount is sufficient to cause an improvement in a clinically significant condition in the subject.
The FGFR2 inhibitor inhibits FGFR2 activity or expression and is advantageously formulated in a pharmaceutical composition, with a pharmaceutically acceptable carrier. This substance may be then called an active ingredient or a therapeutic agent against endometrial cancer.
The concentration or amount of the active ingredient depends on the desired dosage and administration regimen, as discussed below. Suitable dose ranges largely depend on the FGFR2 inhibitor used, but may include, for purposes of exemplifying only, from about 0.01 mg/kg to about 100 mg/kg of body weight per day.
The pharmaceutical compositions may also include other biologically active compounds. The phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human. Preferably, as used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, particularly for injectable solutions. Suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.
According to the invention, the pharmaceutical composition of the invention can be introduced parenterally, transmucosally, e.g., orally (per os), nasally, vaginally, or rectally, or transdermally. Parental routes include intravenous, intra-arteriole, intramuscular, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial administration. Targeting the uterus directly, e.g. by direct administration to uterus or uterus lining, may be advantageous.
In one embodiment, the therapeutic compound can be delivered in a controlled release system. For example, a polypeptide may be administered using intravenous infusion with a continuous pump, in a polymer matrix such as polylactic/glutamic acid (PLGA), a pellet containing a mixture of cholesterol and the active ingredient (SilasticR™; Dow Corning, Midland, Mich.; see U.S. Pat. No. 5,554,601) implanted subcutaneously, an implantable osmotic pump, a transdermal patch, liposomes, or other modes of administration.
Examples of the invention are provided, and are understood to be exemplary only, and do not limit the scope of the invention or the appended claims. A person of ordinary skill in the art will appreciate the invention can be practiced in any forms according to the claims and disclosure here.
Example 1 Detection of Activating FGFR2 Mutations in Endometrial CancerOur findings show that activation and overexpression of FGFR2 plays a role in endometrial tumorigenesis. Exon 8 is three nucleotides longer than exon 9, hence the FGFR2b isoform is one codon longer than the FGFR2c isoform. Specificity of signaling is also provided by tissue specific expression of receptors, ligands and heparin sulphate proteoglycans (Allen et al., 2001; Fiore, 2001). Due to the differences in length of the FGFR2 “b” and “c” isoforms, all mutations will be numbered relative to the epithelially expressed FGFR2b isoform (SEQ ID NO:2; NP_075259.2). For those occurring downstream of exon 8 we provide herein the equivalent mutation numbered relative to the FGFR2c isoform (SEQ ID NO:3; NP_000132.1) in brackets and in Table 2. The N550K (N549K) variant identified in two of the endometrial cell lines was likely to result in receptor activation as identical or similar germline missense changes had been reported in FGFR2 and FGFR3 in patients with Crouzon syndrome (Kan et al., 2002) and hypochondroplasia (Bellus et al., 1995) (
Next we sought to determine the spectrum and frequency of activating FGFR2 mutations in primary uterine cancers. Direct sequencing of the exons in which activating mutations in FGFR2 and FGFR3 had previously been identified in the germline (exons 7, 8, 10, 13 and 15) was performed for 187 primary uterine cancers, representing all grades and stages of tumors and the major histologic subtypes of endometrial carcinoma (Table 1).
It should be noted that the A315T reported in ESS-1 derived from an endometrial stromal sarcoma occurred in the mesenchymally expressed isoform (FGFR2c) and all carcinosarcomas (tumors with both malignant epithelial and stromal elements) were also screened for mutations in exon 9 (NM 000141). For a subset of tumors (32 endometrioid endometrial cancers plus 17 carcinosarcomas) exons 5-18 encompassing the second and third immunoglobulin domains (hereafter referred to as D2 and D3), transmembrane domain and the entire kinase domain were sequenced to determine the relative occurrence of novel somatic mutations. In addition to the mutations found in exons 7, 10, 13 and 15, one additional mutation was identified in this more extensive mutational screen, a 2 bp deletion in exon 18. Mutations were identified in 19 cases (10%). Eighteen of 115 endometrioid endometrial cancers (16%) had mutations and a single serous carcinoma (1 of 45, 2%) harbored a mutation. No mutations were seen in carcinosarcomas or clear cell cancers.
For all mutations, constitutional DNA was sequenced to confirm that the mutation arose somatically. Among the endometrioid cases, there was an excess of FGFR2 mutations in cases with mismatch repair deficiency (11 of 49, 22%) compared with cases with normal mismatch repair (6 of 61, 10%), although it did not reach statistical significance (p=0.10). It should be noted that microsatellite instability (MSI) status was not determined for five tumors. We did not include the 2 bp deletion in an MSI positive case as it is unlikely to be activating and thus may represent a bystander mutation. Although there is an excess of mutations in tumors demonstrating microsatellite instability, we would argue that these mutations in FGFR2 are pathogenic due to the fact that the same mutations are observed in both MSI positive and microsatellite stable (MSS) primary tumors and that the majority of the mutations are identical to those activating mutations identified in the germline, a coincidence one would not expect if they were bystander mutations associated with microsatellite instability.
Of the 11 different mutations we identified, 7 had previously been reported associated with craniosynostosis or skeletal dysplasia syndromes, one (A315T) occurred at a FGFR2c residue at which a similar missense mutation had been reported (A315S) and four mutations were novel (
A combination of studies utilizing biochemical, structural and biological assays have shown that the S252W mutation demonstrates increased ligand binding and ligand promiscuity (Ibrahimi et al., 2001; Ibrahimi et al., 2004; Yu et al., 2000). Extensive in vitro affinity studies have been performed with both the S252W FGFR2c and S252W FGFR2b mutant receptors showing that this mutation increases the binding affinity of the receptor for multiple FGFs from 2-8 fold, in addition to violating the ligand binding specificities attributed to the alternatively spliced isoforms (Ibrahimi et al., 2004).
The prevalence of the S252W mutation in this panel of tumors suggests positive selection for this mutant in endometrioid endometrial cancers. Although the expression of all FGF ligands has not been examined in normal cycling endometrium and endometrial cancers, there are several studies reporting the expression of FGF2 predominantly in the basal part of luminal and glandular epithelium (Moller et al., 2001; Sangha et al., 1997). Several studies have also shown an increase in FGF2 expression in the glandular epithelia associated with complex hyperplasia and adenocarcinoma (Gold et al., 1994). Endometrial epithelial cells normally express only the FGFR2b isoform which cannot bind FGF2. However, the acquisition of the S252W mutation in these cells would be anticipated to result in autocrine activation of the S252W FGFR2b receptor. The S252W mutation also enables the mutant receptor to bind FGF9 which is highly expressed in the endometrial stroma (Tsai et al., 2002). The prevalence of the S252W mutation suggests that the different FGFR2 isoforms play important roles in mediating directional epithelial-mesenchymal signaling in the endometrium.
Four additional extracellular domain mutations were identified, K310R and A315T in the cell lines and S373C (S372C) and Y376C (Y375C) in primary tumors, the latter mutation seen in two independent tumors (
We identified two mutations; C383R (C382C) and M392R (M391E) within the transmembrane domain. The C383R mutation we identified is similar to a non conservative missense mutation at the paralogous position in FGFR3 (G380R) that accounts for over 95% of patients with achondroplasia (Shiang et al., 1994). The FGFR3 G380R mutation has been reported to increase receptor half-life and render the receptor resistant to ligand-induced internalization (Monsonego-Ornan et al., 2000). A more recent study showed that whereas wildtype receptor undergoes lysosomal degradation following ligand stimulation, the mutant G380R mutant receptor is recycled back from the lysosomes to the plasma membrane thus augmenting FGF signaling (Cho et al., 2004). The novel M392R mutation is two residues proximal to the well-studied FGFR3 A391E mutation associated with Crouzon syndrome with acanthosis nigricans (Meyers et al., 1995). Biophysical analysis of the A391E mutation demonstrated a change in the dimerization free energy of the FGFR3 transmembrane domain consistent with stabilization of the dimer (Li et al., 2006). Although the C382R mutation in FGFR2c has previously been shown to result in constitutive receptor phosphorylation and transformation of NIH3T3 cells (Li et al., 1997), elucidation of the exact mechanism of receptor activation by these transmembrane FGFR2b mutations remains to be explored.
In addition to the extracellular and transmembrane domain mutations, four different mutations in the FGFR2 kinase domain were identified. While two of these, N550K (N549K) and K660E (K659E), have not been identified as germline mutations in any craniosynostosis syndromes, the similar N549H mutation in FGFR2c has been associated with Crouzon Syndrome (Kan et al., 2002) and identical mutations at the paralogous positions have been seen in FGFR3 associated with hypochondroplasia (N540K) and thanatophoric dysplasia II (K650E) (Naski et al., 1996). Crystal structures of N549H and K650N mutant FGFR2c kinases show that these mutations activate the kinase by loosening a novel autoinhibitory molecular brake at the kinase hinge region (M. Mohammadi, unpublished results).
The pathological consequence of the novel IVS10+2A>C splicing mutation is unknown, however it is tempting to speculate that this would result in increased receptor signaling. There is alternative splicing in the intracellular juxtamembrane region in FGFR1-3 leading to the inclusion or exclusion of two amino acids, valine and threonine (VT) downstream of exon 10. The IVS10+2A>C mutation results in a GCAAGT non-canonical splice donor site and given that the non canonical GC-AG donor/receptor pair is observed 15-30× more frequently in the genome than the GA-AG donor/receptor pair (Burset et al., 2000; Chong et al., 2004) the IVS10+2A>C mutation may result in an increase in the relative proportion of the +VT isoform. The FRS2 adaptor signaling protein that links FGFRs to the MAPK and PI3K pathways binds to a sequence in the juxtamembrane domain of murine FGFR1 that includes the alternatively splicing VT (Burgar et al., 2002). As such, the IVS10+2A>C mutation likely results in a more efficient splice donor site that increases the levels of the +VT transcript, this in turn would result in increased FRS2a mediated signaling.
One endometrial tumor was shown to carry a novel 2 bp deletion 2287-88 CT, leading to a frameshift and change from LTTNE to LTHNQStop with a premature truncation at codon 766, the last codon of exon 18. This 2 bp deletion may result in a truncated FGFR2 receptor that is constitutively activated in a similar manner to the similarly truncated C3 transcript of FGFR2 (Moffa et al., 2004) or alternatively it may simply represent a bystander mutation.
Two endometrial samples were shown to carry two mutations, the AN3 CA MSI positive cell line which carried N550K (N549K) and K310R and the MSI negative tumor 1492 which carried S252W and Y376C (Y375C). The discovery of two presumably dominantly activating mutations in the same tumor was unexpected. It is interesting to note that in each case there is a mutation that is known to result in constitutive ligand-independent receptor activation, along with either the ligand-dependent S252W or the uncharacterized K310R, suggesting additional selective pressure may exist for increased FGFR2 activation in endometrial epithelia.
Example 2 Treatment of Endometrial Cancer by Inhibition of FGFR2 Materials and Methods Sequencing AnalysisMutation analysis was performed as previously described (8). PCR primer sequences were M13 tailed and sequencing performed in two directions. Primer sequences are available by request from the author.
Cell Culture and ReagentsThe human endometrial MFE296 cell line was purchased from the European Collection of Cell Cultures (Salisbury, Wiltshire, UK). The human endometrial cell lines AN3CA, HEC1A, Ishikawa, RL952, and KLE were provided by Dr. Paul Goodfellow (Washington University, St. Louis, Mo.). MFE296 cells were grown in MEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and penicillin-streptomycin. AN3CA cells were cultured in DMEM supplemented with 10% FBS, non-essential amino acids, 2 mM L-glutamine, and penicillin-streptomycin. HEC1A cells were cultured in 50% DMEM and 50% RPMI 1640, supplemented with 10% FBS and penicillin-streptomycin. Ishikawa and RL952 cells were grown in DMEM supplemented with 10% FBS, non-essential amino acids, and penicillin-streptomycin. KLE cells were grown in 50% DMEM and 50% F-12 media supplemented with 10% FBS and penicillin-streptomycin. All media, FBS, and supplements were purchased from Invitrogen (Carlsbad, Calif.). All cells were grown at 37 C in a humidified atmosphere containing 5% CO2. PD173074 was purchased from Sigma-Aldrich (St. Louis, Mo.), reconstituted in DMSO at a stock concentration of 1 mM, and stored at −20 C. The KH1-LV lentivector plasmid was kindly provided by Dr. Maria S. Soengas (University of Michigan, Ann Arbor, Mich.), and the pNHP, pVSV-G, and pTAT lentiviral packaging plasmids were kindly provided by Dr. Matthew Huentelman (Translational Genomics Research Institute, Phoenix, Ariz.).
shRNA Design
Two independent shRNA constructs, targeting two different exons of FGFR2 (exon 2 and exon 15), were designed against the following sequences: shRNA targeting exon 2: TTAGTTGAGGATACCACATTA (SEQ ID NO:4; nucleotides 79-99, NM_022970); shRNA targeting exon 15: ATGTATTCATCGAGATTTA (SEQ ID NO:5; nucleotides 1866-1884, NM_022970). A nonsilencing shRNA construct was also designed based on a nonsilencing siRNA sequence from Qiagen (SEQ ID NO:6; AATTCTCCGAACGTGTCACGT), and was used as a negative control. The corresponding oligonucleotides were annealed and cloned into the KH1-LV lentivector. The KH1-LV self-inactivating lentiviral vector allows expression of short hairpin sequences under the control of the H1 promoter and GFP expression under the control of the human ubiquitin-C promoter, enabling easy monitoring of transduction efficiency. Cloning strategies are available from the authors upon request.
75-cm2 culture flasks were coated with 50 mg/ml poly-D-lysine (Sigma-Aldrich, St. Louis, Mo.) and HEK293FT cells (Invitrogen, Carlsbad, Calif.) seeded at a density of 8×106 cells per flask. The following day, the cells were transfected with 7.1 μg pNHP, 2.8 μg pVSV-G, 0.5 μg pTAT, and 3.5 μg KH1-LV using SuperFect transfection reagent (Qiagen, Valencia, Calif.) at a 4:1 ratio of SuperFect (μl) to DNA (μg), according to the manufacturer's protocol. Media containing the virus was collected 24 and 40 hours later, combined, filtered through a 0.45-mm low-protein-binding Durapore filter (Millipore Corporation, Billerica, Mass.) to remove cell debris, and the viral preparation aliquoted and stored at −80° C. until use.
Lentiviral TransductionCells were plated at a density of 4×105 cells per well in a 6 well plate. The next day, cells were infected with lentiviral stocks in the presence of 6 μg/ml polybrene (Sigma-Aldrich, St. Louis, Mo.). Empty vector and nonsilencing shRNA infections were used as controls for each experiment. Greater than 90% transduction efficiency was achieved in each shRNA experiment, as determined by eGFP visualization (data not shown).
Growth Inhibition AssayTwenty-four hours after infection, cells were trypsinized and plated in 96 well plates in full growth medium at a density of 5,000 cells per well, in triplicate, and proliferation assessed using the Sulforhodamine B (SRB) assay (Sigma-Aldrich, St. Louis, Mo.). At the indicated time points, wells were fixed with 10% (wt/vol) trichloroacetic acid, stained with SRB for 30 min, and washed with 1% (vol/vol) acetic acid. The protein-bound dye was dissolved in 10 mM Tris base solution, and absorbance measured at 510 nm. For PD173074 drug studies, cells were plated in full growth medium at a density of 5,000 cells per well in a 96 well plate. The next day, increasing concentrations of PD173074 were added and proliferation assessed 72 hours later using the SRB assay.
Annexin V-FITC Labeling of Apoptotic CellsAnnexin V-FITC staining was used to measure phosphatidylserine exposure on cells undergoing apoptosis, according to the manufacturer's instructions (BioVision, Inc. Mountain View, Calif.). Knockdown was achieved with siRNAs rather than the shRNA constructs as the latter also expressed GFP, which has an overlapping emission spectra with FITC. 2.5×105 cells were plated per well in a 6 well plate. Twenty-four hours later, cells were transfected with 25 nM nonsilencing (NS) siRNA or FGFR2 siRNA X2 using Lipofectamine 2000 transfection reagent. The siRNA duplex was allowed to form a complex with Lipofectamine 2000 for 20 minutes at room temperature, and transfection carried out at 37° C. for 24 hours. 48 hours after transfection, floating and attached cells were collected, washed in cold PBS, resuspended in Annexin binding buffer (10 mM Hepes (pH 7.4), 140 mM NaCl, 2.5 mM CaCl2), stained with 500 ng/mL annexinV-FITC and 1 μg/mL propidium iodide (Sigma-Aldrich, St. Louis, Mo.), and analyzed for annexin positive cells using a CyAn ADP flow cytometer and Summit software, version 4.3 (Dako Cytomation, Carpinteria, Calif.). For PD173074 studies, cells were plated at a density of 1×105 cells per well in a 6 well plate. 24 hours later, cells were treated with 1 μM PD173074 or DMSO (vehicle control), and, at the indicated time point, stained with AnnexinV-FITC and analyzed by flow cytometry.
Cell Cycle AnalysisCells were plated at a density of 1×105 cells per well in a 6 well plate. The next day, cells were treated with 1 μM PD173074 or DMSO (vehicle control). 72 hours later, cells were stained with propidium iodide as described {Krishan, 1975 #28} and analyzed by flow cytometry. Cell cycle analysis was performed using ModFit software (Verity Software House, Inc. Topsham, Me.).
Western Blot AnalysisCells were plated in 60 mm2 dishes at a density of 2×106 cells per dish. The next day cells were starved overnight for 18 hours in 0.2% FBS or maintained in full growth media, and then incubated with increasing concentrations of PD173074 for three hours. Cells were washed in ice cold PBS, lysed in kinase buffer [20 mM Hepes pH7.4, 2 mM EGTA, 1% Triton X100, 10% glycerol, 1 mM Na3VO4, 1 mM NaF, 100 uM AEBSF, and 1 tablet/10 mL of Mini Complete Protease Inhibitor (Roche Molecular Biochemicals, Indianapolis, Ind.)], briefly sonicated on ice, and protein concentrations estimated using Quick Start Bradford Reagent with bovine gamma-globulin standards (Bio-Rad Laboratories, Hercules, Calif.). Equal amounts of protein were separated by SDS-PAGE on 4-12% gradient gels and transferred to polyvinylidene difluoride membranes (Invitrogen, Carlsbad, Calif.). Membranes were immunoblotted with antibodies to phosphorylated and total AKT, ERL1/2, p38, STAT-3 and STAT-5, PLCγ and total PTEN (Cell Signaling Technology, Beverly, Mass.). FGFR2 expression was detected with BekC17 antibody (Santa Cruz Biotechnology, Inc., Santa Cruz, Calif.). Horseradish peroxidase-conjugated goat anti-mouse or anti-rabbit secondary antibodies (Biomeda, Foster City, Calif.), were used, followed by chemiluminescence staining. For shRNA studies, lysates were collected 48 hours after shRNA transduction and processed as described above.
Statistical AnalysisStatistical analyses were performed using GraphPad Prism version 4.0 for Macintosh (GraphPad Software, San Diego, Calif.). IC50 values were calculated by dose-response analysis using nonlinear regression of sigmoidal dose response with variable slope. Apoptosis data were analyzed by one-way ANOVA. Significant differences between treatment groups were determined using a Student's t test. All P values were considered significant when P<0.05. Data were expressed as mean±SE.
ResultsPatterns of FGFR2, PTEN and KRAS2 mutations in primary endometrial cancers: concomitant FGFR2 and PTEN mutation and mutually exclusive FGFR2 and KRAS2 mutation.
Given that PTEN and KRAS2 mutations are common in endometrioid endometrial cancer, we first sought to determine whether FGFR2 activation occurred in tumors that harbor loss-of-function mutations in PTEN and/or gain-of-function mutations in KRAS. We sequenced all nine exons of PTEN and exon one of KRAS in 116 endometrial tumors for which we knew the FGFR2 mutation status. Due to the limiting amount of DNA available, we only sequenced exon one of KRAS, as mutations in exon one account for greater than 96% of KRAS mutations in endometrioid endometrial cancer (The Catalog of Somatic Mutations in Cancer). Mutation analysis revealed PTEN mutations in 70% (82/116) of tumors. Of those tumors with FGFR2 mutations, 77% (14/18) also carried a PTEN mutation, demonstrating that mutations in FGFR2 frequently occur alongside PTEN mutations in endometrioid endometrial tumors. KRAS mutations were identified in 12% (15/116) of tumors. Activating mutations in GFR2 and KRAS were mutually exclusive. Of note, one tumor possessed a frameshift mutation in FGFR2 (2290-91 del CT) and contained a KRAS mutation. However, as the pathogenic nature of this FGFR2 mutation is unknown, we concluded that activating mutations in FGFR2 were mutually exclusive with activating mutations in KRAS. PTEN inactivating mutations occurred alongside both KRAS and FGFR2 mutations (Table 3).
Given the occurrence of activating FGFR2 mutations within the context of PTEN inactivation in endometrial cancer and the known role of the PI3K/AKT pathway in promoting cell survival, we next sought to determine whether inhibition of FGFR2 could induce cell death in the presence of PTEN inactivation. The impact of shRNA knockdown of FGFR2 expression on cell proliferation was assessed in AN3CA and MFE296 endometrial cancer cells, both of which carry an activating FGFR2 mutation. In addition, AN3CA has mutations in both PTEN alleles and does not express PTEN (
To confirm that the cell death observed following FGFR2 knockdown was due to induction of apoptosis, AN3CA cells were transfected with siRNA targeted towards FGFR2 and labeled with Annexin V-FITC to detect exposed phosphatidylserine by flow cytometry. An increase in Annexin V-FITC positive staining was evident 48 hours following transfection with FGFR2 siRNA compared to the nonsilencing siRNA control, indicating that these cells were undergoing apoptosis (
Six endometrial cancer cell lines (2 mutant N550K FGFR2, and 4 wildtype FGFR2) were treated with increasing concentrations of PD173074, a pan-FGFR tyrosine kinase inhibitor. This inhibitor demonstrates high selectivity against FGFRs (FGFR1, 1050-25 nM) and VEGFs (VEGFR2, IC50=˜100 nM) and has been shown to induce apoptosis in myeloma cells with an activating t(4;14) translocation and activating mutations in FGFR3 (10). As shown in
Inhibition of phosphorylation of ERL1/2, AKT, and STAT3/5, coupled with delayed activation of p38, has been reported to be a common feature associated with the induction of cell death in cells demonstrating oncogene addiction (17). To determine whether PD173074 treatment resulted in a similar inhibition of these pathways, ERL1/2, AKT, STAT3/5, and p38 phosphorylation levels were evaluated by Western blot in three cell lines (two sensitive and one resistant to PD173074). STATS expression was not detectable by Western blot in these three cell lines (data not shown). As shown in
PD173074 treatment also resulted in a moderate reduction in phosphorylation of AKT at Threonine 308 and Serine 473 in AN3CA and MFE296 cells. No decrease in activation of AKT was evident in HEC1A cells. Notably, PD173074 treatment had no effect on STAT3 or p38 phosphorylation in any of the cell lines tested (
Though no change in STAT3 or p38 activation was evident three hours following PD173074 treatment, previous models of oncogene addiction have shown that activation of p38 is delayed, peaking at 8-24 hours following oncogene inhibition {Sharma, 2006 #17}. Therefore, we evaluated ERL1/2, AKT, STAT3, and p38 activation at various time points ranging from 0 to 72 hours following PD173074 treatment. Consistent with data presented in
Notably, no change in STAT3 or p38 activation was detected in AN3CA and MFE296 cells throughout the time course (
Understanding the molecular basis of tumor progression has led to the development and success of targeted therapies in variety of cancer types ({Pickering, 2008 #27}. There is increasing evidence that activating mutations in genes involved in various signaling pathways can result in “addiction” of tumor cells to these pathways {Sharma, 2007 #31}. Furthermore, these activating mutations serve not only to identify potential therapeutic targets but their presence can also predict clinical response to pathway inhibition {Lynch, 2004 #30}. However, it has become increasingly clear that the response to target inhibition is influenced by the molecular context wherein these mutations occur. As we have previously identified activating mutations in FGFR2 in ˜16% of endometrioid endometrial tumors, here we sought to investigate the genetic context in which FGFR2 mutations occur in endometrial cancer. We also sought to evaluate the therapeutic potential of targeting activated FGFR2 by investigating the biological consequence of inhibiting FGFR2 in endometrial cancer cells possessing activating mutations in FGFR2.
In the present study, we evaluated the KRAS and PTEN mutation status of endometrioid endometrial tumors with known FGFR2 mutation status. Activating KRAS and FGFR2 mutations did not occur together in the same tumor, consistent with FGFR2 driving tumorigenesis through the MAPK pathway. FGFR2 activation occurred alongside PTEN inactivation, suggesting that, at least in endometrial cells, FGFR2 does not mediate its biological effect through PI3K/AKT. This is supported by one previous report where FGF7 or FGF10 stimulation of endometrial cells resulted in ERL1/2, but not AKT, activation (19). PTEN and KRAS mutations occurred within the same tumor, consistent with a previous report (20).
We have also shown that FGFR2 signaling is essential for survival and proliferation of AN3CA and MFE296 endometrial cancer cell lines, which is highly suggestive of oncogene addiction. This is supported by the PD173074 IC50 studies in which we demonstrated the two cell lines with activated FGFR2 were selectively sensitive to the pan-FGFR inhibitor, PD173074. It is noteworthy that the AN3CA cells were the most sensitive to PD173074 and are mutant for PTEN. This is of particular importance given the high incidence of PTEN mutations in endometrioid endometrial cancer. It has been suggested that PTEN inactivation may transfer the cell's “oncogene addiction” from an activated receptor pathway to constitutively activated PI3K-AKT signaling, and thus lead to resistance to receptor inhibition (21). Indeed, ErbB2-overexpressing breast tumors with reduced or absent PTEN are relatively resistant to trastuzumab-containing chemotherapy regimens (22, 23). Of note, despite the loss of PTEN, inhibition of FGFR2 with a pan-FGFR inhibitor induced cell death and cell cycle arrest in AN3CA cells. The AN3CA cells are thus still addicted to the oncogenic signal of FGFR2. Interestingly, PD173074 treatment induced cell cycle arrest but did not result in enhanced Annexin V staining in MFE296 cells (data not shown). It remains to be determined whether cell cycle arrest alone is responsible for the efficacy of PD173074 in MFE296 cells, or whether induction of Annexin V negative cell death through an unknown mechanism is also involved.
It has been suggested that oncogene addiction resulting from Src, BCR-ABL and EGFR activation share a common signaling cascade, as oncogene inactivation is associated with a rapid loss of phosphorylated ERK, AKT and STAT3/5 and delayed activation of p38 (17). We report here that inhibition of FGFR2 in full growth media is associated with a loss in phosphorylated ERK and partial inhibition of AKT, but has no effect on the phosphorylation status STAT3 or p38. The mechanism underlying addiction to activated FGFR2 in AN3CA and MFE296 cells is therefore distinct from other models of oncogene addiction.
The cell death induced by pan-FGFR inhibition with PD173074 correlated with complete inhibition of ERL1/2 activation in media supplemented with both 10% FBS and 0.2% FBS. Unexpectedly, given the mutant PTEN status in AN3CA cells, PD173074 treatment resulted in a partial loss of AKT phosphorylation in 10% FBS containing media. It is therefore possible that FGFR2 mediates AKT phosphorylation downstream of PTEN. Indeed, in mouse keratinocytes, insulin-like growth factor-I has been shown to alter AKT phosphorylation through a PI3K-independent mechanism involving protein kinase C-mediated protein phosphatase regulation (24). The mechanism responsible for the decreased AKT phosphorylation observed following PD173074 treatment of AN3CA and MFE296 cells remains to be determined. However, the PD173074 induced cell death observed in AN3CA cells is likely independent of this dephosphorylation of AKT. Concentration-response curves performed in 0.2% FBS generated a similar IC50 for AN3CA cells to those generated in 10% FBS (data not shown). As AN3CA cells grown in 0.2% FBS did not exhibit pronounced dephosphorylation of AKT, together these data suggest that dephosphorylation of AKT is not required for PD173074 induced cell death in this cell line.
In summary, we have shown that FGFR2 mutations are coincident with PTEN inactivation and mutually exclusive with KRAS2 mutations in primary endometrioid endometrial cancers.
Blockade of FGFR2 signaling by shRNA knockdown or treatment with a pan-FGFR inhibitor, PD173074, resulted in cell cycle arrest and cell death of endometrial cancer cell lines expressing activated FGFR2. The cellular pathways altered following inhibition of FGFR2, however, were distinct from those observed following inhibition of other oncogenes for which oncogene addiction has been demonstrated. A novel mechanism of oncogene addiction associated with FGFR2 activation in endometrial cancer appears likely. Together these data shows inhibition of constitutively active mutant FGFR2 is therapeutically beneficial for endometrial cancer patients despite the frequent inactivation of PTEN in this cancer type.
Example 3 Activating-FGFR2 Mutations Promote Endometrial Cell Migration Materials and MethodsTo determine the ability of FGFR2 mutations to alter the phenotype of primary endometrial epithelial cells, HPV/TERT immortalized primary human endometrial epithelial cells were transduced with wild type FGFR2b or mutant FGFR2b (N550K) and FGF-stimulated migration evaluated.
Briefly, 3×105 cells were seeded on top of 8 μm pore size polycarbonate membranes (Cell Biolabs, Inc) in full growth media containing 1 nM FGF10. 24 hours later, the media was aspirated from inside the insert and non-migratory cells were removed from the top of the insert using cotton-tipped swabs. Migratory cells (those that had passed through the membrane) were stained and the membranes were photographed (5 random fields per insert). The stained cells on the inserts were then solubilized and quantified by measuring absorbance at 570 nm.
ResultsEach FGFR2 construct was assessed in quadruplicate and the results are presented along with representative pictures of the stained cells (see
The N550K FGFR2b mutation considerably increases the migratory capability of primary endometrial epithelial cells and addition of a soluble ligand-trap antibody against FGF10 markedly inhibits the migration of the N550K mutant cells.
These data indicate that activating-FGFR2b mutations can promote endometrial cell migration and thus support a role for FGFR2 mutations in driving endometrial tumorigenesis and tumor progression.
Example 4 Endometrial Tumors with Activating-FGFR2 Mutations Are Selectively Sensitive to FGFR Inhibition Materials and MethodsTo determine the importance of activating-FGFR2 mutations to endometrial tumor growth, xenograft tumors of Hec1A (FGFR2 wt) and AN3CA (FGFR2 N550K mutant) endometrial cancer cells were established and the effect of PD173074, a small molecule FGFR inhibitor, was evaluated.
Briefly, mice were inoculated subcutaneously with 0.1 ml of a 50% RPMI/50% Matrigel™ mixture containing a suspension of tumor cells (1×107 cells/mouse). Once the established tumors reached a mean of approximately 100-150 mg, administration of PD173074 was initiated (25 mg/kg PD173074 twice daily by oral gavage). Tumor weight measurements were recorded three times a week.
ResultsPD173074 treatment suppressed growth of all eight AN3CA xenograft tumors and caused tumor regression of six of the eight AN3CA tumors with a mean tumor shrinkage of 51%. PD173074 treatment had minimal effect on Hec1A (FGFR2 wild type) xenograft tumors (see
These data demonstrate that endometrial tumors with activating-FGFR2 mutations are selectively sensitive to FGFR inhibition, suggesting that tumors with FGFR2 mutations are “addicted” to the oncogenic FGFR2 signal. Tumors with activating-FGFR2 mutations are dependent on the oncogenic FGFR2 activity.
The present invention is not to be limited in scope by the specific embodiments described herein. Various modification of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description and the accompanying figures. Such modifications are intended to fall within the scope of the claims. It is also understood that all values are approximate, and are provided for description purposes only.
All patents, patent application, publications, product descriptions, and protocols cited throughout this application are incorporated herein by reference in their entireties for all purposes.
Claims
1. A method of classifying endometrial cancer, the method comprising:
- screening for a FGFR2 mutation in an endometrial cancer cell and classifying the type of endometrial cancer as a FGFR2 activation induced endometrial cancer upon finding a FGFR2 activation mutation in the endometrial cancer cell.
2. The method of claim 1, wherein the classification is used to develop a treatment for a subject having endometrial cancer, and the method further comprises the step of determining if the FGFR2 mutation induces FGFR2 activation.
3. The method of claim 1, wherein the mutation in FGFR2 is a mutation in the junction between the immunoglobulin-like (Ig) domains II and III; a mutation in the IgIII domain; a mutation in the junction between the IgIII domain and the transmembrane (TM) domain; a mutation in the TM domain; a mutation in the junction between the TM domain and the tyrosine kinase domain I; a mutation in the tyrosine kinase domain I, or a mutation in the tyrosine kinase domain II.
4. The method of claim 3, wherein the mutation results in an at least one amino acid substitution in FGFR2.
5. The method of claim 4, wherein the amino acid substitution in FGFR2 is selected from the group consisting of: (a) a S to W mutation at position 252 of SEQ ID NOS:2 (NP_075259.2) or 3 (NP_000132.1); (b) a K to R mutation at position 310 of SEQ ID NOS:2 or 3; (c) an A to T mutation at position 315 of SEQ ID NOS:2 or 3; (d) a S to C mutation at position 373 of SEQ ID NO:2 or position 372 of SEQ ID NO:3; (e) a Y to C mutation at position 376 of SEQ ID NO:2 or position 375 of SEQ ID NO:3; (f) a C to R mutation at position 383 of SEQ ID NO:2 or position 382 of SEQ ID NO:3; (g) a M to R mutation at position 392 of SEQ ID NO:2 or position 391 of SEQ ID NO:3; (h) an I to V mutation at position 548 of SEQ ID NO:2 or position 547 of SEQ ID NO:3; (i) N to K mutation at position 550 of SEQ ID NO:2 or position 549 of SEQ ID NO:3; or (j) a K to E mutation at position 660 of SEQ ID NO:2 or position 659 of SEQ ID NO:3.
6. The method of claim 1, wherein the mutation results in enhanced ligand binding, promiscuous ligand affinity, constitutive receptor dimerization, delayed degradation, impaired recycling, or kinase activation, thereby activating the FGFR2 receptor.
7. The method of claim 1, wherein the mutation is a deletion of nucleotide C and T at position 2290-91 of SEQ ID NO:1; or an IVS10+2A>C splicing mutation.
8. The method of claim 1, wherein the cancer is an endometrioid histologic subtype.
9. The method of claim 1, wherein the subject is a human and the FGFR2 is a constitutively active mutant.
Type: Application
Filed: Dec 7, 2018
Publication Date: Mar 28, 2019
Inventors: Pamela Pollock (Phoenix, AZ), Paul Goodfellow (Columbus, OH)
Application Number: 16/213,924
