Mutations of the pik3ca gene in human cancers

Abstract

Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the PI3K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the PI3K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.

1 . A method of inhibiting progression of a tumor in a human, comprising the steps of:
 administering to the human an antisense oligonucleotide or antisense construct to a tumor, wherein the antisense oligonucleotide or RNA transcribed from the antisense construct is complementary to mRNA transcribed from PIK3CA (SEQ ID NO: 2), whereby amount of p110α protein expressed by the tumor is reduced.   
     
     
         2 . The method of  claim 1  wherein the antisense oligonucleotide or RNA transcribed from the antisense construct are complementary to a region of said mRNA which comprises an initial methionine codon of said mRNA. 
     
     
         3 . A method of inhibiting progression of a tumor in a human, comprising the steps of:
 administering to the human siRNA comprising 19 to 21 bp duplexes of a human PIK3CA mRNA with 2 nt 3′ overhangs, wherein one strand of the duplex comprises a contiguous sequence selected from mRNA transcribed from PIK3CA (SEQ ID NO: 2), whereby amount of p110α protein expressed by the tumor is reduced.   
     
     
         4 . The method of  claim 3  wherein the contiguous sequence comprises an initial methionine codon of said mRNA. 
     
     
         5 . A method of inhibiting progression of a tumor, comprising the steps of:
 administering a molecule comprising an antibody binding region to a tumor, wherein the antibody binding region specifically binds to p110α (SEQ ID NO: 3).   
     
     
         6 . The method of  claim 5  wherein the antibody binding region specifically binds to the kinase domain (nt 2095-3096 of SEQ ID NO: 2) of PIK3CA. 
     
     
         7 . The method of  claim 5  wherein the antibody binding region specifically binds to the helical domain (nt 1567-2124 of SEQ ID NO: 2) of PIK3CA. 
     
     
         8 . The method of  claim 5  wherein the antibody binding region specifically binds to the P85BD domain (nt 103-335 of SEQ ID NO: 2) of PIK3CA. 
     
     
         9 . A method of identifying candidate chemotherapeutic agents, comprising the steps of:
 contacting a wild-type or activated mutant p110α (SEQ ID NO: 3) with a test compound;   measuring p110α activity;   identifying a test compound as a candidate chemotherapeutic agent if it inhibits p110α activity.   
     
     
         10 . The method of  claim 9  wherein a mutant form of the p110α is contacted with the test compound, said mutant form comprising a substitution mutation selected from the group consisting of E542K, E545K, Q546K, and H1047R. 
     
     
         11 . The method of  claim 9  wherein the test compound is identified as being a candidate chemotherapeutic agent for treating tumors with an activating mutation of p110α. 
     
     
         12 . The method of  claim 9  wherein the test compound is identified as being a candidate chemotherapeutic agent for treating tumors with a substitution mutation of PIK3 CA. 
     
     
         13 . The method of  claim 9  wherein the test compound is identified as being a candidate chemotherapeutic agent for treating tumors with an activating mutation of PIK3 CA in its kinase domain (nt 2095-3096 of SEQ ID NO: 2). 
     
     
         14 . The method of  claim 9  wherein the test compound is identified as being a candidate chemotherapeutic agent for treating tumors with an activating mutation of PIK3CA in its helical domain (nt 1567-2124 of SEQ ID NO: 2). 
     
     
         15 . The method of  claim 9  wherein the test compound is identified as being a candidate chemotherapeutic agent for treating tumors with an activating mutation of PIK3CA in its P85BD domain (nt 103-335 of SEQ ID NO: 2). 
     
     
         16 . The method of  claim 9  further comprising the steps of:
 contacting the test compound with one or more enzymes selected from the group consisting of: PIK3CB, PIK3CG, PIK3C2A, PIK3C2B, PIK3C2G, PIK3C3, A-TM, ATR, FRAP1, LAT1-3TM, SMG1, PRKDC, and TRRAP; 
 identifying a test compound as a specific candidate chemotherapeutic agent if it inhibits one or more of said enzymes less than it inhibits p110α. 
 
     
     
         17 . The method of  claim 16  wherein a test compound which inhibits PIK3CB, PIK3CG, PIK3C2A, PIK3C2B, PIK3C2G, and PIK3C3 less than it inhibits p110α (PIK3CA) is identified as a highly specific candidate chemotherapeutic agent. 
     
     
         18 . The method of  claim 16  wherein a test compound which inhibits p110α more than it inhibits PIK3CB and PIK3CG is identified as highly specific. 
     
     
         19 . The method of  claim 9  wherein the step of contacting is performed in a cell-free system. 
     
     
         20 . The method of  claim 9  wherein the step of contacting is performed in whole cells. 
     
     
         21 . A method for delivering an appropriate chemotherapeutic drug to a patient in need thereof, comprising:
 determining a non-synonymous, intragenic mutation in a PIK3CA coding sequence (SEQ ID NO: 1) in a body sample of a patient;   administering a p110α inhibitor to the patient.   
     
     
         22 . The method of  claim 21  wherein the p110α inhibitor is LY294002. 
     
     
         23 . The method of  claim 21  wherein the p110α inhibitor is wortmannin. 
     
     
         24 . The method of  claim 21  wherein the p110α inhibitor is a molecule comprising an antibody binding region specific for p110α. 
     
     
         25 . The method of  claim 24  wherein the antibody binding region binds to the kinase domain (nt 2095-3096 of SEQ ID NO: 2). 
     
     
         26 . The method of  claim 24  wherein the antibody binding region binds to the helical domain (nt 1567-2124 of SEQ ID NO: 2). 
     
     
         27 . The method of  claim 24  wherein the antibody binding region binds to the P85BD domain (nt 103-335 of SEQ ID NO: 2). 
     
     
         28 . A set of one or more primers for amplifying and/or sequencing PIK3CA, said primers selected from the group consisting of forward primers, reverse primers and sequencing primers, wherein the forward primers are selected from the group consisting of: SEQ ID NO: 6 to 165, the reverse primers are selected from the group consisting of: SEQ ID NO: 166 to 325, and the sequencing primers are selected from the group consisting of: SEQ ID NO: 326 to 485. 
     
     
         29 . The set of  claim 28  wherein the one or more primers comprise at least one forward and one reverse primer for amplifying a segment of PIK3CA. 
     
     
         30 . The set of  claim 28  wherein the one or more primers comprise at least one forward, one reverse, and one sequencing primer for amplifying and sequencing a segment of PIK3 CA. 
     
     
         31 . The set of  claim 28  wherein the one or more primers comprise all of said forward, reverse, and sequencing primers. 
     
     
         32 . The set of  claim 28  which is in a single divided or undivided container. 
     
     
         33 . The set of  claim 29  which is in a single divided or undivided container. 
     
     
         34 . The set of  claim 30  which is in a single divided or undivided container. 
     
     
         35 . The set of  claim 31  which is in a single divided or undivided container.