US20170044622A1 - Pik3ca fusions - Google Patents

Pik3ca fusions Download PDF

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US20170044622A1
US20170044622A1 US15/304,656 US201515304656A US2017044622A1 US 20170044622 A1 US20170044622 A1 US 20170044622A1 US 201515304656 A US201515304656 A US 201515304656A US 2017044622 A1 US2017044622 A1 US 2017044622A1
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pik3ca
fusion
cancer
seq
patient
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Ethan G. CERAMI
Christoph Lengauer
Nicolas Stransky
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Blueprint Medicines Corp
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Blueprint Medicines Corp
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • C—CHEMISTRY; METALLURGY
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • 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.
  • cancer is 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.
  • cancer represents the phenotypic end-point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • FIG. 4C is a graph showings PIK3CA DNA copy number versus mRNA expression in uterine corpus endometrial carcinoma samples.
  • 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.
  • 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.
  • a new subtype of cancer is identified, which is characterized by the presence of the PIK3CA fusions described herein.
  • 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.
  • PIK3CA phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
  • PIK3CA phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
  • the human p110 ⁇ protein is encoded by the PIK3CA gene.
  • PIK3CA is a known oncogene.
  • FIG. 4 a 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. 4 a 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
  • FIG. 4 b 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. 4 c 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.
  • 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).
  • fusion molecule e.g., gene, gene product (e.g., cDNA or mRNA), and variants thereof
  • a fragment of the nucleotide sequence for PIK3CA particularly the coding region for the kinase domain of PIK3CA
  • another protein e.g, the promoter and/or the
  • the protein that is expressed may comprise the full PIK3CA protein sequence.
  • the PIK3CA fusion is a TBL1XR1:PIK3CA fusion.
  • the PIK3CA fusion is an FNDC3B:PIK3CA fusion.
  • 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.
  • 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.
  • 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.”
  • the fusion partner is TBL1XR1 (transducin (beta)-like 1 X-linked receptor 1).
  • the fusion partner is FNDC3B (fibronectin type III domain containing 3B).
  • 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.
  • 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).
  • TBL1XR1 e.g., a TBL1XR1 promoter or a functional fragment thereof
  • an exon of the PIK3CA gene e.g., one or more exons encoding a kinase domain of PIK3CA, or a functional fragment thereof.
  • TBL1XR1:PIK3CA fusion causes the PIK3CA protein to be over-expressed.
  • 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.
  • the TBL1XR1:PIK3CA gene fusion (such as, e.g., SEQ ID NO: 1) codes for wild type PIK3CA protein.
  • 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.
  • a fusion in another embodiment, 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).
  • FNDC3B FNDC3B promoter or a functional fragment thereof
  • PIK3CA e.g., one or more exons encoding a PIK3CA kinase domain, or a functional fragment thereof.
  • the FNDC3B:PIK3CA gene fusion causes the PIK3CA protein to be over-expressed.
  • 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.
  • the FNDC3B:PIK3CA gene fusion (such as, e.g., SEQ ID NO:3) codes for wild type PIK3CA protein.
  • 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.
  • 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.
  • the probes or primers derived from the nucleic acid sequences of PIK3CA gene fusions 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.
  • 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).
  • 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).
  • 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).
  • 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).
  • 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 .
  • 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.
  • 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.
  • 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.
  • a bait is suitable for solution phase hybridization.
  • 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.
  • 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).
  • 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.
  • 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).
  • 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.
  • 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.
  • a PIK3CA inhibitor such as, e.g., a kinase inhibitor, or an antibody specific to PIK3CA
  • the cancer is breast cancer.
  • the cancer is uterine cancer.
  • the cancer is prostate cancer.
  • 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.
  • a cell e.g., a circulating cell or a cancer cell
  • tissue e.g., a tumor
  • sample e.g., a tumor sample
  • the sample is a nucleic acid sample.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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,
  • 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.
  • 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 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.
  • SSC 4 ⁇ sodium chloride/sodium citrate
  • 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 Na 2 HPO 4 ; 250 ⁇ g/ml of herring sperm DNA; 50 ⁇ g/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.
  • 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.
  • microscopy e.g., brightfield, fluorescence, or electron microscopy
  • ELISA enzyme-linked immunosorbent assay
  • 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.
  • 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
  • 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).
  • a PIK3CA gene fusion such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, as disclosed herein.
  • 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.
  • a chromosome e.g., interphase or metaphase chromosome
  • a substrate e.g., glass
  • denaturing the chromosomal DNA e.g., by exposure to formamide
  • the chromosome in situ hybridization is fluorescence in situ hybridization (FISH).
  • FISH fluorescence in situ hybridization
  • 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).
  • a nucleotide containing a tag or reporter molecule e.g., biotin, digoxigenin, or hapten
  • affinity molecule e.g., an antibody or streptavidin
  • the method comprises performing Southern blot with DNA polynucleotides from a biological sample to detect the presence of a PIK3CA gene fusion.
  • 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
  • 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.
  • 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.
  • the gene fusion is FNDC3B:PIK3CA, such as, e.g.
  • SEQ ID NO:3 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.
  • 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
  • the polynucleotides from the biological sample comprise RNA
  • 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.
  • 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.
  • Another method for determining the presence of a PIK3CA gene fusion molecule 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.
  • the gene fusion is TBL1XR1:PIK3CA.
  • the gene fusion is FNDC3B:PIK3CA.
  • the sequence acquired is compared to a reference sequence, or a wild type reference sequence.
  • the sequence is determined by a next generation sequencing method.
  • 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.
  • 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
  • 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.
  • 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
  • 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.
  • the method of determining the presence of a PIK3CA fusion 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.
  • the HPLC is chosen from, e.g., reverse-phase HPLC, size exclusion HPLC, ion-exchange HPLC, and bioaffinity HPLC.
  • the method of determining the presence of a PIK3CA fusion comprises analyzing a nucleic acid sample (e.g., DNA, cDNA, or RNA, or an amplification product thereof) by mass spectrometry.
  • a nucleic acid sample e.g., DNA, cDNA, or RNA, or an amplification product thereof
  • 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.
  • 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).
  • 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).
  • 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.
  • 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.
  • a PIK3CA inhibitor e.g., a kinase inhibitor, or an antibody specific to PIK3CA
  • the PIK3CA gene fusion is detected at the time the patient is diagnosed with a cancer.
  • 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.
  • the method in response to detection of a PIK3CA fusion, such as, e.g., TBL1XR1:PIK3CA, FNDC3B:PIK3CA, the method further includes one or more of:
  • stratifying a patient population e.g., assigning a patient, to a group or class
  • PIK3CA inhibitor treatment e.g., a kinase inhibitor treatment
  • PIK3CA fusion inhibitor treatment as described herein;
  • 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;
  • monitoring the effectiveness of treatment e.g., by detecting a reduction in the level of PIK3CA gene fusion in a patient sample).
  • the patient 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.
  • the PIK3CA fusion detected is a TBL1XR1:PIK3CA fusion.
  • 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.
  • the PIK3CA fusion detected is an FNDC3B:PIK3CA fusion.
  • 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.
  • 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.
  • 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, underine 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.
  • 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
  • the PIK3CA fusions of the invention may be inhibited by a PIK3CA inhibitor or a PIK3CA fusion inhibitor.
  • 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.
  • the PIK3CA inhibitors may be an antibody (such as, e.g., antibodies specific to PIK3CA) or a small molecule inhibitor.
  • the inhibitors may act directly on PIK3CA itself, modify the activity of PIK3CA, or inhibit the expression of PIK3CA.
  • the inhibitors may indirectly inhibit PIK3CA activity by inhibiting the activity of proteins or molecules other than PIK3CA itself.
  • 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).
  • the PIK3C2G fusion such as, e.g., TBL1XR1:PIK3CA or FNDC3B:PIK3CA, is inhibited by a kinase inhibitor.
  • the PIK3CA fusion is inhibited by a PIK3CA fusion inhibitor.
  • 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.
  • siRNA small interfering RNA
  • dsRNA double stranded RNA
  • shRNA short-hairpin RNA
  • 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.
  • the PIK3CA fusion inhibited is selected from all or a portion of SEQ ID NO: 1 or SEQ ID NO:3.
  • 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.
  • terapéuticaally 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • therapeutic agents can be evaluated in a cell-free system, e.g., a cell lysate or in a reconstituted system.
  • 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).
  • 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:
  • the PIK3CA fusion is a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion.
  • 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.
  • 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 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.
  • 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.
  • 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.
  • a change in binding activity or phosphorylation of PIK3CA or its interacting or downstream proteins or molecules as described herein is detected.
  • a change in a tumor present in an animal subject is detected.
  • 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.
  • 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.
  • 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).
  • a reference value e.g., a control sample
  • the candidate agent if a decrease in expression or activity of the PIK3CA fusion is detected, the candidate agent is identified as an inhibitor.
  • the candidate agent if an increase in expression or activity of the PIK3CA fusion is detected, the candidate agent is identified as an activator.
  • the fusion is a PIK3CA gene fusion, where in the fusion is e.g., a TBL1XR1:PIK3CA fusion or an FNDC3B:PIK3CA fusion.
  • the contacting step is detected in a cell-free system, e.g., a cell lysate or in a reconstituted system.
  • 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).
  • 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 include one or more of:

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