US20170044622A1

US20170044622A1 - Pik3ca fusions

Info

Publication number: US20170044622A1
Application number: US15/304,656
Authority: US
Inventors: Ethan G. CERAMI; Christoph Lengauer; Nicolas Stransky
Original assignee: Blueprint Medicines Corp
Current assignee: Blueprint Medicines Corp
Priority date: 2014-04-18
Filing date: 2015-04-17
Publication date: 2017-02-16
Also published as: EP3132056A1; EP3132056B1; US20190185942A1; WO2015161274A1; US10669590B2

Abstract

The invention provides PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) gene fusions, and fragments of those gene fusions. The invention further provides methods of diagnosing and treating diseases or disorders associated with PIK3CA fusions, such as conditions mediated by PIK3CA aberrant expression or activity, or overexpression of PIK3CA.

Description

This application claims the benefit of U.S. Provisional No. 61/981,546, filed Apr. 18, 2014, which is incorporated herein by reference in its entirety.
This invention relates to PIK3CA gene fusions. The invention further relates to methods of diagnosing and treating diseases or disorders associated with PIK3CA fusions, such as conditions mediated by PIK3CA activity, or conditions associated with aberrant expression or overexpression of PIK3CA.
Many forms of cancer are caused by genetic lesions that give rise to tumor initiation and growth. Genetic lesions may include chromosomal aberrations, such as translocations, inversions, deletions, copy number changes, gene expression level changes, and somatic and germline mutations. Indeed, the presence of such genomic aberrations is a hallmark feature of many cancers, including, for example, B cell cancer, lung cancer, breast cancer, ovarian cancer, pancreatic cancer, and colon cancer. In some models, cancer represents the phenotypic end-point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis.
Recent efforts by The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC), and dozens of other large-scale profiling efforts have generated an enormous amount of new sequencing data for dozens of cancer types—this includes whole-genome DNA, whole-exome DNA, and full-transcriptome RNA sequencing. These efforts have led to the identification of new driver genes and fusion genes within multiple cancer types. Fusions, particularly fusions involving kinases, are of particular interest, as such fusions have been shown to be oncogenic, and have been successfully targeted by new therapeutics. For example, anaplastic lymphoma kinase (ALK), one of the receptor tyrosine kinases, is known to become oncogenic when fused with various genes. See, e.g., M. Soda et al, “Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer,” Nature 444:561-566 (2007).
A need exists for identifying novel genetic lesions associated with cancer. For example, the presence of fusions involving a kinase in samples collected from more than one source can indicate that the kinase is an oncogenic driver. The identification of such fusions can be an effective approach to diagnosis of cancers and development of compounds, compositions, methods, and assays for evaluating and treating cancer patients.
In one aspect, the invention provides methods for detecting the presence of a PIK3CA gene fusion in a biological sample. The methods include the steps of: (a) obtaining a biological sample from a mammal; and (b) contacting the sample with a reagent that detects a PIK3CA gene fusion, to determine whether a PIK3CA gene fusion is present in the biological sample. In some embodiments, the sample can be from a cancer patient, such as, e.g., a breast, uterine, or prostate cancer patient. The fusion can be, e.g., a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion. In some embodiments, the TBL1XR1:PIK3CA fusion comprises all or a part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:1. In some embodiments, the FNDC3B:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:3.
In another aspect, the invention provides methods of diagnosing a patient of having a disease or disorder associated with aberrant PIK3CA activity or expression, or overexpression of PIK3CA; the methods include: (a) obtaining a biological sample from the patient; and (b) contacting the sample with a reagent that detects a PIK3CA gene fusion to determine whether a PIK3CA gene fusion is present in the biological sample, whereby the detection of the PIK3CA gene fusion indicates the presence of a disorder associated with aberrant PIK3CA expression or activity, or overexpression of PIK3CA. In some embodiments, the biological smaple is from a tumor of the patient.
The invention also includes methods of determining a therapeutic regimen for treating a cancer in a human subject; methods of identifying a patient likely to respond to treatment with a PIK3CA inhibitor or a PIK3CA fusion inhibitor; methods of stratifying a patient population by detecting a PIK3CA gene fusion; methods of inhibiting the proliferation of cells containing a PIK3CA fusion methods of treating a condition characterized by overexpression of PIK3CA; methods of treating a condition characterized by aberrant expression or activity of PIK3CA; and method of identifying an agent that modulates the activity of a PIK3CA fusion and methods of monitoring disease burden in a patient having a condition mediated by PIK3CA.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A and 1B show the nucleotide sequence of a TBL1XR1-PIK3CA gene fusion (SEQ ID NO:1) comprising a portion of the TBL1XR1 gene up to and including exon 1 and a portion of the PIK3CA gene starting exon 2. The slash after nucleotide 140 indicates the breakpoint (fusion junction) where the fusion has occurred. The underlined nucleotides are the start codon for PIK3CA transcription.

FIG. 2 shows the amino acid sequence for wild type PIK3CA (SEQ ID NO:2).

FIGS. 3A and 3B show the nucleotide sequence of an FNDC3B-PIK3CA gene fusion (SEQ ID NO:3) comprising a portion of the FNDC3B gene up to and including exon 3 and a portion of the PIK3CA gene starting exon 2. The slash after nucleotide 359 indicates the breakpoint (fusion junction) where the fusion has occurred. The underlined nucleotides 436-438 in the PIK3CA sequence are the start codon for PIK3CA transcription.

FIG. 4A is a graph showing PIK3CA DNA copy number versus the mRNA expression in breast cancer samples; FIG. 4B is a graph showing PIK3CA DNA copy number versus mRNA expression in prostate cancer samples; and FIG. 4C is a graph showings PIK3CA DNA copy number versus mRNA expression in uterine corpus endometrial carcinoma samples.

EXEMPLARY EMBODIMENTS OF THE INVENTION

The invention is based, at least in part, on the discovery of novel recombination or translocation events in cancer patients that result in at least a fragment of a PIK3CA gene linked to a non-homologous promoter via a recombination or translocation event that may result in aberrant expression (e.g., in a location where the kinase is not typically expressed) or overexpression of at least the kinase domain PIK3CA. Thus, a new patient population is identified, which is characterized by the presence of a PIK3CA fusion. This new patient population suffers from or is susceptible to disorders mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as, e.g., a cancer. In another aspect of the invention, a new subtype of cancer is identified, which is characterized by the presence of the PIK3CA fusions described herein. In some embodiments, the new patient population suffers from or is susceptible to a breast cancer, uterine cancer, or prostate cancer characterized by the presence of a PIK3CA fusion. New methods of diagnosing and treating the patient population and the PIK3CA fusion cancer subtype are also provided.
The phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA), also called p110α protein, is a class I PI 3-kinase catalytic subunit. The human p110α protein is encoded by the PIK3CA gene. PIK3CA is a known oncogene. FIG. 4a shows the DNA copy number versus the mRNA expression (from TCGA) for breast cancer samples; the arrows show the samples in which a PIK3CA fusion has occurred. The only sample with a higher PIK3CA expression is one with a PIK3CA DNA copy number amplification. FIG. 4b shows the DNA copy number versus the mRNA expression (from TCGA) for prostate cancer samples; the arrow shows the sample in which a PIK3CA fusion has occurred. FIG. 4c shows the DNA copy number versus the mRNA expression (from TCGA) for uterine corpus endometrial carcinoma; the arrow shows the sample in which a PIK3CA fusion has occurred. The only sample with a higher PIK3CA expression is one with a PIK3CA DNA copy number amplification. This is evidence that PIK3CA fusions such as the ones described here lead to overexpression of PIK3CA.
The term “PIK3CA fusion” is used generically herein, and includes any fusion molecule (e.g., gene, gene product (e.g., cDNA or mRNA), and variants thereof) that includes a fragment of the nucleotide sequence for PIK3CA, particularly the coding region for the kinase domain of PIK3CA, and a portion of the nucleotide sequence of another protein (e.g, the promoter and/or the coding region of a non-homologous gene, such that the coding region for the kinase domain of PIK3CA is under control of the non-homologous promoter). Depending on where the fusion point is, the protein that is expressed may comprise the full PIK3CA protein sequence. In some embodiments, the PIK3CA fusion is a TBL1XR1:PIK3CA fusion. In some embodiments, the PIK3CA fusion is an FNDC3B:PIK3CA fusion.

PIK3CA Gene Fusions

PIK3CA gene fusions are generated by a fusion between at least a part of the PIK3CA gene and a part of another gene as a result of a translocation (including inversion) within a chromosome or between chromosomes. As a result of a translocation, the PIK3CA gene may be placed under the transcriptional control of the partner gene promoter, resulting in aberrant PIK3CA expression or activity, or overexpression of PIK3CA. The overexpression can lead to certain cancers, such as breast cancer, uterine cancer (e.g., uterine corpus endometrial cancer), or prostate cancer. As used herein, the 5′-region is upstream of, and the 3′-region is downstream of, a fusion junction or breakpoint in one of the component genes. PIK3CA and the gene that it is fused to may be referred to as “fusion partners.” In some exemplary embodiments, the fusion partner is TBL1XR1 (transducin (beta)-like 1 X-linked receptor 1). In other exemplary embodiments, the fusion partner is FNDC3B (fibronectin type III domain containing 3B).
Reference to “all or a portion” or “all or part” of a PIK3CA gene fusion or SEQ ID NO:1 or SEQ ID NO:3, means that the nucleotide sequence comprises the entire PIK3CA gene fusion nucleotide sequence or a fragment of that sequence that comprises the fusion junction or breakpoint between PIK3CA and its fusion partner (such as, e.g., TBL1XR1 or FNDC3B). The fragment may comprise 7, 8, 9, 10, 12, 14, 16, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 120, 150, 175, 200, 250, 300, or more nucleotides spanning the fusion junction of the PIK3CA gene fusion.
In one embodiment, a fusion includes all or a portion of the gene TBL1XR1 (e.g., a TBL1XR1 promoter or a functional fragment thereof) and an exon of the PIK3CA gene (e.g., one or more exons encoding a kinase domain of PIK3CA, or a functional fragment thereof). Such a fusion can be referred to as a TBL1XR1:PIK3CA fusion. In one embodiment, the TBL1XR1:PIK3CA fusion causes the PIK3CA protein to be over-expressed.
In a particular embodiment, the invention provides a TBL1XR1:PIK3CA gene fusion comprising the nucleotide sequence depicted in FIG. 1 (SEQ ID NO: 1), or a fragment thereof that includes the fusion junction. SEQ ID NO: 1 comprises TBL1XR1 up to exon number 1, in the untranslated region of TBL1XR1, fused to exon number 2, in the untranslated region of the PIK3CA gene. In some embodiments, the TBL1XR1:PIK3CA gene fusion (such as, e.g., SEQ ID NO: 1) codes for wild type PIK3CA protein. In some embodiments the TBL1XR1:PIK3CA gene fusion comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 97%, or at least 98% identical to all or part of SEQ ID NO: 1.
In another embodiment, a fusion includes all or a portion of gene FNDC3B (e.g., an FNDC3B promoter or a functional fragment thereof) and an exon of PIK3CA (e.g., one or more exons encoding a PIK3CA kinase domain, or a functional fragment thereof). Such a fusion can be referred to as an FNDC3B:PIK3CA fusion. In one embodiment, the FNDC3B:PIK3CA gene fusion causes the PIK3CA protein to be over-expressed.
In a particular embodiment, the invention provides an FNDC3B:PIK3CA gene fusion comprising the nucleotide sequence in FIG. 3 (SEQ ID NO:3), or a fragment thereof that includes the fusion junction. SEQ ID NO:3 includes the nucleotide sequence of FNDC3B, up to exon number 3, fused to exon number 2 in the untranslated region of PIK3CA. In some embodiments, the FNDC3B:PIK3CA gene fusion (such as, e.g., SEQ ID NO:3) codes for wild type PIK3CA protein. In some embodiments the FNDC:PIK3CA gene fusion comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 97%, or at least 98% identical to all or part of SEQ ID NO:3.
The nucleic acid sequences of PIK3CA gene fusions may be used as probes, primers, or bait to identify nucleotides from a biological sample that include, flank, or hybridize to PIK3CA fusions, such as, e.g., TBL1XR1:PIK3CA (for example, all or part of SEQ ID NO: 1) or FNDC3B:PIK3CA (for example, all or part of SEQ ID NO:3), at e.g., the fusion junctions. In certain embodiments, the probe, primer, or bait molecule is an oligonucleotide that allows capture, detection, and/or isolation of a PIK3CA gene fusion from a biological sample. In certain embodiments, the probes or primers derived from the nucleic acid sequences of PIK3CA gene fusions (e.g., from the fusion junctions) may be used, for example, for polymerase chain reaction (PCR) amplification. The oligonucleotide can comprise a nucleotide sequence substantially complementary to a fragment of the PIK3CA gene fusion nucleic acid molecules described herein. The sequence identity between the nucleic acid fragment, e.g., the oligonucleotide and the target PIK3CA gene fusion sequence, need not be exact, so long as the sequences are sufficiently complementary to allow the capture, detection or isolation of the target sequence. In one embodiment, the nucleic acid fragment is a probe or primer that includes an oligonucleotide between about 5 and 25, e.g., between 10 and 20, or 10 and 15 nucleotides in length that includes the fusion junction of a PIK3CA fusion, such as, e.g., TBL1XR1:PIK3CA (for example, all or part of SEQ ID NO: 1) or FNDC3B:PIK3CA (for example, all or part of SEQ ID NO:3). In other embodiments, the nucleic acid fragment is a bait that includes an oligonucleotide between about 100 to 300 nucleotides, 130 and 230 nucleotides, or 150 and 200 nucleotides in length that includes the fusion junction of a PIK3CA fusion, such as, e.g., TBL1XR1:PIK3CA (for example, all or part of SEQ ID NO: 1) or FNDC3B:PIK3CA (for example, all or part of SEQ ID NO:3).
In certain embodiments, the nucleic acid fragments hybridize to a nucleotide sequence that includes a breakpoint or fusion junction, e.g., a breakpoint or fusion junction as identified by a slash (“/”) in FIGS. 1 and 3. For example, the nucleic acid fragment can hybridize to a nucleotide sequence that includes the fusion junction between the TBL1XR1 transcript and the PIK3CA transcript (e.g, nucleotides 139-141 of SEQ ID NO:1), or between the FNDC3B transcript and the PIK3CA transcript (e.g. nucleotides 358-360 of SEQ ID NO:3), i.e., a nucleotide sequence that includes all or a portion of SEQ ID NO: 1 or 3. Examples of such nucleotide sequence may include a portion of SEQ ID NO:1 comprising nucleotides 136-145, 131-150, 116-165, 91-190, 66-215, or 41-240; or a portion of SEQ ID NO:3 comprising nucleotides 355-364, 350-369, 335-384, 310-409, 285-434, or 260-459.
In other embodiments, the nucleic acid fragment includes a bait that comprises a nucleotide sequence that hybridizes to a PIK3CA gene fusion nucleic acid molecule described herein, and thereby allows the detection, capture, and/or isolation of the nucleic acid molecule. In one embodiment, a bait is suitable for solution phase hybridization. In other embodiments, a bait includes a binding entity or detection entity, e.g., an affinity tag or fluorescent label, that allows detection, capture, and/or separation, e.g., by binding to a binding entity, of a hybrid formed by a bait and a nucleic acid hybridized to the bait.
In exemplary embodiments, the nucleic acid fragments used as bait comprise a nucleotide sequence that includes a fusion junction between the TBL1XR1 transcript and the PIK3CA transcript, e.g, a nucleotide sequence within SEQ ID NO: 1 comprising nucleotides 139-141 (such as, e.g., a sequence comprising nucleotides 136-145, 131-150, 116-165, 91-190, 66-215, or 41-240 of SEQ ID NO:1). In other exemplary embodiments, the nucleic acid fragments used as bait comprise a nucleotide sequence that includes a fusion junction between the FNDC3B transcript and the PIK3CA transcript, e.g. a nucleotide sequence within SEQ ID NO:3 comprising nucleotides 358-360 (such as, e.g., a sequence comprising nucleotides 355-364, 350-369, 335-384, 310-409, 285-434, or 260-459 of SEQ ID NO:3).

Detection and Diagnostic Methods

In another aspect, the invention provides a method of determining the presence of a PIK3CA gene fusion, such as, e.g., a TBL1XR1:PIK3CA or FNDC3B:PIK3CA fusion as described herein. The presence of a PIK3CA gene fusion can indicate that the mammal providing the biological sample suffers from or is at risk of developing a disorder mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as, e.g., a cancer. The presence of a PIK3CA gene fusion may also indicate that the cancer is treatable with a PIK3CA inhibitor (such as, e.g., a kinase inhibitor, or an antibody specific to PIK3CA) or a PIK3CA fusion inhibitor. In some embodiments, the cancer is breast cancer. In some embodiments, the cancer is uterine cancer. In some embodiments, the cancer is prostate cancer. In other embodiments, the cancer is a different cancer associated with aberrant expression or activity of PIK3CA or overexpression of PIK3CA.
The method includes detecting whether a PIK3CA fusion nucleic acid molecule is present in a cell (e.g., a circulating cell or a cancer cell), a tissue (e.g., a tumor), or a sample (e.g., a tumor sample), from a subject. In one embodiment, the sample is a nucleic acid sample. In one embodiment, the nucleic acid sample contains DNA, e.g., genomic DNA or cDNA, or RNA. e.g., mRNA.
The methods of the invention may be employed to detect the presence of a PIK3CA fusion polynucleotide in a biological sample of a mammal. In some embodiments, such method comprises the steps of obtaining a biological sample from the mammal and contacting that sample with at least one reagent that detects a PIK3CA fusion, to determine whether a PIK3CA fusion is present in the biological sample. The sample can be chosen from one or more of sample types: such as, e.g., tissue, e.g., cancerous tissue (e.g., a tissue biopsy), whole blood, serum, plasma, buccal scrape, sputum, saliva, cerebrospinal fluid, urine, stool, circulating tumor cells, circulating nucleic acids, or bone marrow.
In some embodiments, the PIK3CA fusion (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein) is detected in a nucleic acid molecule by one or more methods chosen from nucleic acid hybridization assays (e.g. in situ hybridization, comparative genomic hybridization, microarray, Southern blot, northern blot), amplification-based assays (e.g., PCR, PCR-RFLP assay, or real-time PCR), sequencing and genotyping (e.g. sequence-specific primers, high-performance liquid chromatography, or mass-spectrometric genotyping), and screening analysis (including metaphase cytogenetic analysis by karyotype methods).

(1) Hybridization Methods

In some embodiments, the reagent hybridizes to a PIK3CA gene fusion, such as, e.g., nucleotides 139-141, 136-145, 131-150, 116-165, 91-190, 66-215, or 41-240 of SEQ ID NO:1. In alternate embodiments, the reagent detects the presence of nucleotides 358-360, 355-364, 350-369, 335-384, 310-409, 285-434, or 260-459 of SEQ ID NO:3.
Hybridization, as described throughout the specification, may be carried out under stringent conditions, e.g., medium or high stringency. See, e.g., J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Pr; 2nd edition (1989); T. Brown, Hybridization Analysis of DNA Blots. Current Protocols in Molecular Biology at 21:2.10.1-2.10.16 (2001). High stringency conditions for hybridization refer to conditions under which two nucleic acids must possess a high degree of homology to each other to hybridize. Examples of highly stringent conditions for hybridization include hybridization in 4×sodium chloride/sodium citrate (SSC), at 65 or 70° C., or hybridization in 4×SSC plus 50% formamide at about 42 or 50° C., followed by at least one, at least two, or at least three washes in 1×SSC, at 65 or 70° C. Another example of highly stringent conditions includes hybridization in 2×SSC; 10×Denhardt solution (Fikoll 400+PEG+BSA; ratio 1:1:1); 0.1% SDS; 5 mM EDTA; 50 mM Na₂HPO₄; 250 μg/ml of herring sperm DNA; 50 μg/ml of tRNA; or 0.25 M of sodium phosphate buffer, pH 7.2; 1 mM EDTA7% SDS at 60° C.; followed by washing 2×SSC, 0.1% SDS at 60° C.
The nucleic acid fragments can be detectably labeled with, e.g., a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, an enzyme label, a binding pair label (e.g., biotin/streptavidin), or can include an affinity tag or identifier (e.g., an adaptor, barcode or other sequence identifier). Labeled or unlabeled nucleic acids and/or nucleic acid fragments may be used in reagents for detecting, capturing, and/or isolating PIK3CA gene fusions, such as, e.g. TBL1XR1:PIK3CA (for example, all or part of SEQ ID NO: 1) or FNDC3B:PIK3CA (for example, all or part of SEQ ID NO:3). In some embodiments, the labeled reagent can be detected using, e.g., autoradiography, microscopy (e.g., brightfield, fluorescence, or electron microscopy), enzyme-linked immunosorbent assay (ELISA), or immunohistochemistry.
In one embodiment, the method includes: contacting a nucleic acid sample, e.g., a genomic DNA sample (e.g., a chromosomal sample or a fractionated, enriched or otherwise pre-treated sample) or a gene product (mRNA or cDNA), obtained from the subject, with a nucleic acid fragment. e.g., a probe or primer as described herein (e.g., an exon-specific or a breakpoint-specific probe or primer) under conditions suitable for hybridization, and determining the presence or absence of the PIK3CA gene fusion, such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein.
In some embodiments, the method comprises performing chromosome in situ hybridization with chromosomal DNA from a biological sample to detect the presence of a PIK3CA gene fusion (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein). In some embodiments, the chromosome in situ hybridization comprises the steps of: providing a chromosome (e.g., interphase or metaphase chromosome) preparation (e.g., by attaching the chromosomes to a substrate (e.g., glass)); denaturing the chromosomal DNA (e.g., by exposure to formamide) to separate the double strands of the polynucleotides from each other; exposing the nucleic acid probe to the chromosomes under conditions to allow hybridization of the probe to the target DNA; removing unhybridized or non-specifically hybridized probes by washing; and detecting the hybridization of the probe with the target DNA. In some embodiments, the chromosome in situ hybridization is fluorescence in situ hybridization (FISH). In some embodiments, the probe is labeled directly by a fluorescent label, or indirectly by incorporation of a nucleotide containing a tag or reporter molecule (e.g., biotin, digoxigenin, or hapten) which after hybridization to the target DNA is then bound by fluorescently labeled affinity molecule (e.g., an antibody or streptavidin). In some embodiments, the hybridization of the probe with the target DNA in FISH can be visualized using a fluorescence microscope.
In other embodiments, the method comprises performing Southern blot with DNA polynucleotides from a biological sample to detect the presence of a PIK3CA gene fusion. In some embodiments, the Southern blot comprises the steps of: optionally fragmenting the polynucleotides into smaller sizes by restriction endonucleases; separating the polynucleotides by gel electrophoresis; denaturing the polynucleotides (e.g., by heat or alkali treatment) to separate the double strands of the polynucleotides from each other; transferring the polynucleotides from the gel to a membrane (e.g., a nylon or nitrocellulose membrane); immobilizing the polynucleotides to the membrane (e.g., by UV light or heat); exposing the nucleic acid probe to the polynucleotides under conditions to allow hybridization of the probe to the target DNA; removing unhybridized or non-specifically hybridized probes by washing; and detecting the hybridization of the probe with the target DNA.

(2) Amplification-Based Assays

In certain embodiments, the method of determining the presence of a PIK3CA gene fusion, comprises (a) performing a PCR amplification reaction with polynucleotides from a biological sample, wherein the amplification reaction utilizes a pair of primers which will amplify at least a fragment of the PIK3CA gene fusion, wherein the fragment comprises the fusion junction, wherein the first primer is in sense orientation and the second primer is in antisense orientation; and (b) detecting an amplification product, wherein the presence of the amplification product is indicative of the presence of a PIK3CA fusion polynucleotide in the sample. In specific exemplary embodiments, the PIK3CA gene fusion is TBL1XR1:PIK3CA, such as, e.g., the gene fusion of SEQ ID NO: 1, or a fragment thereof, e.g., a nucleotide sequence comprising nucleotides 139-141, 136-145, 131-150, 116-165, 91-190, 66-215, or 41-240 of SEQ ID NO: 1. In other exemplary embodiments, the gene fusion is FNDC3B:PIK3CA, such as, e.g. the gene fusion of SEQ ID NO:3 or a fragment thereof, e.g., a nucleotide sequence comprising nucleotides 358-360, 355-364, 350-369, 335-384, 310-409, 285-434, or 260-459 of SEQ ID NO:3.
In some embodiments, step (a) of performing a PCR amplification reaction comprises: (i) providing a reaction mixture comprising the polynucleotides (e.g., DNA or cDNA) from the biological sample, the pair of primers which will amplify at least a fragment of the PIK3CA gene fusion wherein the first primer is complementary to a sequence on the first strand of the polynucleotides and the second primer is complementary to a sequence on the second strand of the polynucleotides, a DNA polymerase, and a plurality of free nucleotides comprising adenine, thymine, cytosine, and guanine (dNTPs); (ii) heating the reaction mixture to a first predetermined temperature for a first predetermined time to separate the double strands of the polynucleotides from each other; (iii) cooling the reaction mixture to a second predetermined temperature for a second predetermined time under conditions to allow the first and second primers to hybridize with their complementary sequences on the first and second strands of the polynucleotides, and to allow the DNA polymerase to extend the primers; and (iv) repeating steps (ii) and (iii) for a predetermined number of cycles (e.g., 10, 15, 20, 25, 30, 35, 40, 45, or 50 cycles).
In some embodiments, the polynucleotides from the biological sample comprise RNA, and the method further comprises performing a RT-PCR amplification reaction with the RNA to synthesize cDNA as the template for subsequent or simultaneous PCR reactions. In some embodiments, the RT-PCR amplification reaction comprises providing a reaction mixture comprising the RNA, a primer which will amplify the RNA (e.g., a sequence-specific primer, a random primer, or oligo(dT)s), a reverse transcriptase, and dNTPs, and heating the reaction mixture to a third predetermined temperature for a third predetermined time under conditions to allow the reverse transcriptase to extend the primer.

(3) Sequencing and Genotyping

Another method for determining the presence of a PIK3CA gene fusion molecule (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein) includes: sequencing a portion of the nucleic acid molecule (e.g., sequencing the portion of the nucleic acid molecule that comprises the fusion junction of a PIK3CA gene fusion), thereby determining that the PIK3CA gene fusion is present in the nucleic acid molecule. In some exemplary embodiments, the gene fusion is TBL1XR1:PIK3CA. In other exemplary embodiments, the gene fusion is FNDC3B:PIK3CA. Optionally, the sequence acquired is compared to a reference sequence, or a wild type reference sequence. In one embodiment, the sequence is determined by a next generation sequencing method. In some embodiments, the sequencing is automated and/or high-throughput sequencing. The method can further include acquiring, e.g., directly or indirectly acquiring, a sample. e.g., a tumor or cancer sample, from a patient.
In some embodiments, the sequencing comprises chain terminator sequencing (Sanger sequencing), comprising: providing a reaction mixture comprising a nucleic acid molecule from a biological sample, a primer complementary to a region of the template nucleic acid molecule, a DNA polymerase, a plurality of free nucleotides comprising adenine, thymine, cytosine, and guanine (dNTPs), and at least one chain terminating nucleotide (e.g., at least one dideoxynucleotide (ddNTPs) chosen from ddATP, ddTTP, ddCTP, and ddGTP), wherein the at least one chain terminating nucleotide is present in a low concentration so that chain termination occurs randomly at any one of the positions containing the corresponding base on the DNA strand; annealing the primer to a single strand of the nucleic acid molecule; extending the primer to allow incorporation of the chain terminating nucleotide by the DNA polymerase to produce a series of DNA fragments that are terminated at positions where that particular nucleotide is used; separating the polynucleotides by electrophoresis (e.g., gel or capillary electrophoresis); and determining the nucleotide order of the template nucleic acid molecule based on the positions of chain termination on the DNA fragments. In some embodiments, the sequencing is carried out with four separate base-specific reactions, wherein the primer or the chain terminating nucleotide in each reaction is labeled with a separate fluorescent label. In other embodiments, the sequencing is carried out in a single reaction, wherein the four chain terminating nucleotides mixed in the single reaction are each labeled with a separate fluorescent label.
In some embodiments, the sequencing comprises pyrosequencing (sequencing by synthesis), comprising: (i) providing a reaction mixture comprising a nucleic acid molecule from a biological sample, a primer complementary to a region of the template nucleic acid molecule, a DNA polymerase, a first enzyme capable of converting pyrophosphate into ATP, and a second enzyme capable using ATP to generates a detectable signal (e.g., a chemiluminescent signal, such as light) in an amount that is proportional to the amount of ATP; (ii) annealing the primer to a single strand of the nucleic acid molecule; (iii) adding one of the four free nucleotides (dNTPs) to allow incorporation of the correct, complementary dNTP onto the template by the DNA polymerase and release of pyrophosphate stoichiometrically; (iv) converting the released pyrophosphate to ATP by the first enzyme; (v) generating a detectable signal by the second enzyme using the ATP; (vi) detecting the generated signal and analyzing the amount of signal generated in a pyrogram; (vii) removing the unincorporated nucleotides; and (viii) repeating steps (iii) to (vii). The method allows sequencing of a single strand of DNA, one base pair at a time, and detecting which base was actually added at each step. The solutions of each type of nucleotides are sequentially added and removed from the reaction. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The order of solutions which produce detectable signals allows the determination of the sequence of the template.
In some embodiments, the method of determining the presence of a PIK3CA fusion (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein) comprises analyzing a nucleic acid sample (e.g., DNA, cDNA, or RNA, or an amplification product thereof) by HPLC. The method may comprise: passing a pressurized liquid solution containing the sample through a column filled with a sorbent, wherein the nucleic acid or protein components in the sample interact differently with the sorbent, causing different flow rates for the different components; separating the components as they flow out the column at different flow rates. In some embodiments, the HPLC is chosen from, e.g., reverse-phase HPLC, size exclusion HPLC, ion-exchange HPLC, and bioaffinity HPLC.
In some embodiments, the method of determining the presence of a PIK3CA fusion (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein) comprises analyzing a nucleic acid sample (e.g., DNA, cDNA, or RNA, or an amplification product thereof) by mass spectrometry. The method may comprise: ionizing the components in the sample (e.g., by chemical or electron ionization); accelerating and subjecting the ionized components to an electric or magnetic field; separating the ionized components based on their mass-to-charge ratios; and detecting the separated components by a detector capable of detecting charged particles (e.g., by an electron multiplier).
Detection of a PIK3CA gene fusion in a patient can lead to assignment of the patient to the newly identified patient population that bears the PIK3CA fusion. Because this patient population can suffer from or be susceptible to a disorder associated with an aberrant PIK3CA expression or activity, or overexpression of PIK3CA, detection of the PIK3CA fusion can also lead to diagnosis of such disorder. Thus, a further aspect of the invention provides a method of stratifying a patient population (e.g., assigning a patient, to a group or class) and/or diagnosing a patient, comprising: obtaining a biological sample from the patient, contacting the sample to at least one reagent that detects a PIK3CA gene fusion to determine whether a PIK3CA fusion is present in the biological sample. The detection of a PIK3CA fusion indicates that the patient belongs to the newly identified patient population that bears the PIK3CA fusion, and/or the presence of a disorder associated with aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as e.g., a cancer (e.g., breast cancer, uterine cancer, or prostate cancer). The detection of a PIK3CA fusion also identifies a new subtype of cancer, which is characterized by the presence of the PIK3CA fusion, such as, e.g., certain cancers (e.g., certain breast cancer, uterine cancer, or prostate cancer). In certain embodiments, the PIK3CA fusion is TBL1XR1:PIK3CA. In some embodiments, the TBL1XR1:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO: 1. In other embodiments, the PIK3CA fusion is FNDC3B:PIK3CA. In some embodiments, the FNDC3B:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:3.
In some embodiments, the PIK3CA gene fusion is detected prior to initiating, during, and/or after a treatment of a patient with, e.g., a PIK3CA inhibitor (e.g., a kinase inhibitor, or an antibody specific to PIK3CA) or a PIK3CA fusion inhibitor. In one embodiment, the PIK3CA gene fusion is detected at the time the patient is diagnosed with a cancer. In other embodiment, the PIK3CA fusion is detected at a pre-determined interval, e.g., a first point in time and at least at a subsequent point in time. In certain embodiments, in response to detection of a PIK3CA fusion, such as, e.g., TBL1XR1:PIK3CA, FNDC3B:PIK3CA, the method further includes one or more of:
(1) stratifying a patient population (e.g., assigning a patient, to a group or class);
(2) identifying or selecting the patient as likely or unlikely to respond to a treatment, e.g., PIK3CA inhibitor treatment (e.g., a kinase inhibitor treatment) or a PIK3CA fusion inhibitor treatment as described herein;
(3) selecting a treatment regimen, e.g., administering or not administering a preselected therapeutic agent, such as, e.g., a PIK3CA inhibitor or a PIK3CA fusion inhibitor;
(4) prognosticating the time course of the disease in the patient (e.g., evaluating the likelihood of increased or decreased patient survival); or
(5) monitoring the effectiveness of treatment (e.g., by detecting a reduction in the level of PIK3CA gene fusion in a patient sample).
In certain embodiments, upon detection of a PIK3CA gene fusion in a patient's biological sample, the patient is identified as likely to respond to a treatment that comprises a PIK3CA inhibitor or a PIK3CA fusion inhibitor. In some embodiments, the PIK3CA fusion detected is a TBL1XR1:PIK3CA fusion. In some embodiments, the TBL1XR1:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO: 1. In alternate embodiments, the PIK3CA fusion detected is an FNDC3B:PIK3CA fusion. In some embodiments, the FNDC3B:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:3.
A further aspect of the invention provides a method of selecting a treatment option by detecting a PIK3CA fusion. The method comprises obtaining a biological sample from a patient and exposing the sample to at least one reagent that detects a PIK3CA gene fusion to determine whether a PIK3CA fusion is present in the biological sample. The detection of the PIK3CA gene fusion indicates the likelihood of the patient responding to treatment with a PIK3CA inhibitor or a PIK3CA fusion inhibitor. The method may be augmented or personalized by evaluating the effect of a variety of PIK3CA inhibitors or PIK3CA fusion inhibitors on the biological sample shown to contain a PIK3CA fusion to determine the most appropriate inhibitor to administer. In certain embodiments, the PIK3CA fusion is TBL1XR1:PIK3CA. In some embodiments, the TBL1XR1:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:1. In other embodiments, the PIK3CA fusion is FNDC3B:PIK3CA. In some embodiments, the FNDC3B:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:3.

Methods of Treatment

Alternatively, or in combination with the detection and diagnostic methods described herein, the invention provides method for treating the newly identified patient population and the new PIK3CA fusion cancer subtype, which are characterized by the presence of a PIK3CA fusion. The patient population and cancer subtype can be associated with or predict the onset of a condition mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as, e.g., a cancer or a tumor harboring a PIK3CA fusion (such as, e.g., breast cancer, unterine cancer, or prostate cancer). The methods comprise administering a therapeutic agent, e.g., a PIK3CA inhibitor or a PIK3CA fusion inhibitor, alone or in combination with e.g., other chemotherapeutic agents or procedures, in an amount sufficient to treat a condition mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA by one or more of the following: e.g., impeding growth of a cancer, causing a cancer to shrink by weight or volume, extending the expected survival time of the patient, inhibiting tumor growth, reducing tumor mass, reducing size or number of metastatic lesions, inhibiting the development of new metastatic lesions, prolonging survival, prolonging progression-free survival, prolonging time to progression, and/or enhancing quality of life.
In certain embodiments, the PIK3CA fusions of the invention may be inhibited by a PIK3CA inhibitor or a PIK3CA fusion inhibitor. In some embodiments, the therapeutic agent is a PIK3CA inhibitor, such as, e.g., a compound, biological or chemical, which inhibits, directly or indirectly, the expression and/or activity of PIK3CA. For example, the PIK3CA inhibitors may be an antibody (such as, e.g., antibodies specific to PIK3CA) or a small molecule inhibitor. In some embodiments, the inhibitors may act directly on PIK3CA itself, modify the activity of PIK3CA, or inhibit the expression of PIK3CA. In other embodiments, the inhibitors may indirectly inhibit PIK3CA activity by inhibiting the activity of proteins or molecules other than PIK3CA itself. For example, the inhibitors may modulate the activity of regulatory kinases that phosphorylate or dephosphorylate PIK3CA, interfere with binding of ligands, or inhibit the activity of interacting or downstream proteins or molecules. Exemplary small molecule inhibitors include pan-kinase inhibitors with activity against several different kinases (including PIK3CA) or specific kinase inhibitors (i.e., kinase inhibitors specific to PIK3CA). In one embodiment, the PIK3C2G fusion, such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, is inhibited by a kinase inhibitor.
In some embodiments, the PIK3CA fusion is inhibited by a PIK3CA fusion inhibitor. In some embodiments, the PIK3CA fusion is inhibited by an agent that inhibits transcription or translation of the fusion, e.g., an RNA inhibitor that recognizes the PIK3CA coding sequence, the binding partner (e.g., TBL1XR1 or FNDC3B), or the binding partner: PIK3CA fusion junction, including but not limited to small interfering RNA (siRNA), double stranded RNA (dsRNA), short-hairpin RNA (shRNA), or any other antisense nucleic acid inhibitor. Examples of PIK3CA fusion inhibitors also include other nucleic acid molecules, for example, ribozymes or triple helix molecules, that hybridize to a nucleic acid encoding a PIK3CA fusion or a transcription regulatory region, and blocks or reduces expression of the PIK3CA fusion. In some embodiments, the PIK3CA fusion inhibited is selected from all or a portion of SEQ ID NO: 1 or SEQ ID NO:3.
As used herein, and unless otherwise specified, a “therapeutically effective amount” of a compound is an amount sufficient to provide a therapeutic benefit in the treatment or management of a condition mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as, delaying or minimizing one or more symptoms associated with a cancer or a tumor harboring a PIK3CA fusion (such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein). A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapeutic agents, which provides a therapeutic benefit in the treatment or management of the cancer. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the condition mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, or enhances the therapeutic efficacy of another therapeutic agent.
In certain embodiments, the cancer or tumor harboring a PIK3CA fusion is breast cancer. In certain embodiments, the cancer or tumor harboring a PIK3CA fusion is uterine cancer. In other embodiments the cancer or tumor harboring a PIK3CA fusion is prostate cancer.
In some embodiments, the patient to be treated is suffering from breast cancer, and the method for treating the condition comprises administering to the patient a therapeutically effective amount of a PIK3CA inhibitor or a PIK3CA fusion inhibitor. In some embodiments, the patient to be treated is suffering from uterine cancer, and the method for treating the condition comprises administering to the patient a therapeutically effective amount of a compound of a PIK3CA inhibitor or a PIK3CA fusion inhibitor. In some embodiments, the patient to be treated is suffering from prostate cancer, and the method for treating the condition comprises administering to the patient a therapeutically effective amount of a compound of a PIK3CA inhibitor or a PIK3CA fusion inhibitor.

Screening Methods

Therapeutic agents, such as e.g., PIK3CA inhibitors or PIK3CA fusion inhibitors, used in the therapeutic methods of the invention can be evaluated using the screening assays described herein. Thus, the invention provides a method of identifying an agent useful for treating a condition mediated by aberrant PIK3CA expression activity, or overexpression of PIK3CA, such as, e.g., cancer or a tumor harboring a PIK3CA fusion (such as e.g., breast cancer, uterine cancer, or prostate cancer), comprising contacting a cell expressing a PIK3CA gene fusion with a candidate agent and determining whether the expression level of the fusion is decreased or a biological function associated with the fusion is altered. In one embodiment, therapeutic agents can be evaluated in a cell-free system, e.g., a cell lysate or in a reconstituted system. In other embodiments, the therapeutic agents are evaluated in a cell in culture, e.g., a cell expressing a PIK3CA fusion (e.g., a mammalian cell, a tumor cell or cell line, a recombinant cell). In yet other embodiments, the therapeutic agents are evaluated in vivo (a PIK3CA fusion-expressing cell present in a subject, e.g., an animal subject (e.g., an in vivo animal model)).
Exemplary parameters to evaluate in determining the efficacy of a therapeutic agent for treating a condition mediated by aberrant PIK3CA expression or activity, or overexpression of PIK3CA, such as, e.g., a cancer or a tumor harboring a PIK3CA fusion include one or more of:

- (i) a change in an activity of a cell containing a PIK3CA fusion (e.g., a tumor cell or a recombinant cell), e.g., a change in proliferation, morphology or tumorigenicity of the cell;
- (ii) a change in tumor present in an animal subject. e.g., size, appearance, proliferation, of the tumor;
- (iii) a change in the level, e.g., expression level, of a PIK3CA gene fusion; or
- (iv) a change in an activity of a signaling pathway involving PIK3CA, e.g., phosphorylation or activity of a interacting or downstream target, or expression level of a target gene.

In some embodiments, the PIK3CA fusion is a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion. In some embodiments, the TBL1XR1:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:1. In some embodiments, the FNDC3B:PIK3CA fusion comprises all or part of the nucleotide sequence (such as, e.g., the fusion junction) set forth in SEQ ID NO:3.
In other embodiments, a change in an activity of a cell expressing a PIK3CA fusion, such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein, (e.g., a mammalian cell, a tumor cell or cell line, a recombinant cell) is detected in a cell in culture. In one embodiment, the cell is a recombinant cell that is modified to express a PIK3CA fusion nucleic acid, e.g., is a recombinant cell transfected with a PIK3CA fusion nucleic acid. The transfected cell can show a change in response to the expressed PIK3CA fusion, e.g., increased proliferation, changes in morphology, increased tumorigenicity, and/or acquired a transformed phenotype. A change in any of the activities of the cell, e.g., the recombinant cell, in the presence of the candidate agent can be detected. For example, a decrease in one or more of: proliferation, tumorigenicity, transformed morphology, in the presence of the candidate agent can be indicative of an inhibitor of a PIK3CA fusion. In other embodiments, a change in binding activity or phosphorylation of PIK3CA or its interacting or downstream proteins or molecules as described herein is detected.
In yet other embodiment, a change in a tumor present in an animal subject (e.g., an in vivo animal model) is detected. In one embodiment, a tumor containing animal or a xenograft comprising cells expressing a PIK3CA fusion (e.g., tumorigenic cells expressing a PIK3CA fusion) is employed. The therapeutic agents can be administered to the animal subject and a change in the tumor is evaluated. In one embodiment, the change in the tumor includes one or more of a tumor growth, tumor size, tumor burden, survival, is evaluated. A decrease in one or more of tumor growth, tumor size, tumor burden, or an increased survival is indicative that the candidate agent is an inhibitor or modulator.
In another aspect of the invention provides a method or assay for screening for agents that modulate (e.g., inhibit) the expression or activity of a PIK3CA fusion as described herein. The method includes contacting e.g., a PIK3CA fusion, or a cell expressing a PIK3CA fusion, with a candidate agent; and detecting a change in a parameter associated with a PIK3CA fusion, e.g., a change in the expression or an activity of the PIK3CA fusion. The method can, optionally, include comparing the treated parameter to a reference value, e.g., a control sample (e.g., comparing a parameter obtained from a sample with the candidate agent to a parameter obtained from a sample without the candidate agent). In one embodiment, if a decrease in expression or activity of the PIK3CA fusion is detected, the candidate agent is identified as an inhibitor. In another embodiment, if an increase in expression or activity of the PIK3CA fusion is detected, the candidate agent is identified as an activator. In certain embodiments, the fusion is a PIK3CA gene fusion, where in the fusion is e.g., a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion.
In one embodiment, the contacting step is detected in a cell-free system, e.g., a cell lysate or in a reconstituted system. In other embodiments, the contacting step is detected in a cell in culture, e.g., a cell expressing a PIK3CA fusion (e.g., a mammalian cell, a tumor cell or cell line, a recombinant cell). In yet other embodiments, the contacting step is detected in a cell in vivo (e.g., a PIK3CA expressing cell present in a subject, e.g., an animal subject (e.g., an in vivo animal model)).
Exemplary parameters evaluated in identifying an agent that modulates the activity of a PIK3CA fusion (e.g., a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion) include one or more of:

- (i) a change in an activity of a cell containing a PIK3CA fusion (e.g., a tumor cell or a recombinant cell), e.g., a change in proliferation, morphology or tumorigenicity of the cell;
- (ii) a change in tumor present in an animal subject. e.g., size, appearance, proliferation, of the tumor; or
- (iii) a change in the level, e.g., expression level, of a PIK3CA fusion; or
- (iv) a change in an activity of a signaling pathway involving PIK3CA, e.g., phosphorylation or activity of a interacting or downstream target, or expression level of a target gene.

All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification will supersede any contradictory material. Unless otherwise required by context, singular terms shall include the plural and plural terms shall include the singular. The use of “or” means “and/or” unless stated otherwise. The use of the term “including.” as well as other forms, such as “includes” and “included,” is not limiting. All ranges given in the application encompass the endpoints unless stated otherwise.
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

1-45. (canceled)

46. A method for detecting in a patient a PIK3CA gene fusion selected from TBL1XR1:PIK3CA and FNDC3B:PIK3CA, wherein the gene fusion results in aberrant activity or expression of PIK3CA or overexpression of PIK3CA, said method comprising:

a) contacting a biological sample from the patient with an oligonucleotide that hybridizes under stringent conditions to the fusion junction of the PIK3CA gene fusion; and

b) detecting hybridization between the PIK3CA fusion and the oligonucleotide.

47. The method of claim 46, wherein the oligonucleotide hybridizes under stringent conditions to:

a) a fragment of SEQ ID NO:1 comprising nucleotides 136-145 of SEQ ID NO:1;

b) a fragment of SEQ ID NO:3 comprising 355-364 of SEQ ID NO:3; or

c) a complement of a) or b).

48. The method of claim 46, wherein the patient is suffering from or susceptible to a cancer.

49. The method of claim 48, wherein the cancer is chosen from breast cancer, uterine cancer, and prostate cancer.

50. A method for treating cancer in a patient in which a PIK3CA gene fusion selected from TBL1XR1:PIK3CA and FNDC3B:PIK3CA has been detected, said method comprising administering to the patient a therapeutically effective amount of an agent that inhibits PIK3CA activity or expression of the PIK3CA gene fusion, wherein the PIK3CA gene fusion has been detected in the patient by a method comprising:

b) detecting hybridization between the PIK3CA fusion and the oligonucleotide.

51. The method of claim 50, wherein the agent inhibits expression of the PIK3CA gene fusion and is an oligonucleotide that hybridizes under stringent conditions to:

a) a fragment of SEQ ID NO:1 comprising nucleotides 136-145 of SEQ ID NO:1;

b) a fragment of SEQ ID NO:3 comprising 355-364 of SEQ ID NO:3; or

c) a complement of a) or b).

52. The method of claim 50, wherein the patient is suffering from or susceptible to a cancer.

53. The method of claim 52, wherein the cancer is chosen from breast cancer, uterine cancer, and prostate cancer.

54. A method for diagnosing cancer in a patient comprising:

b) diagnosing the patient with cancer when hybridization of the oligonucleotide to the PIK3CA gene fusion is detected.

55. An RNA molecule that hybridizes under stringent conditions to a nucleic acid encoding at least the fusion junction of a TBL1XR1:PIK3CA or FNDC3B:PIK3CA gene fusion.

56. The RNA molecule of claim 55, wherein the RNA molecule inhibits aberrant expression or overexpression of PIK3CA.

57. The RNA molecule of claim 55, wherein the RNA molecule hybridizes to a nucleic acid encoding:

a) a fragment of SEQ ID NO:1 comprising nucleotides 136-145 of SEQ ID NO:1;

b) a fragment of SEQ ID NO:3 comprising 355-364 of SEQ ID NO:3; or

c) a complement of a) or b).