Genetic alterations in isocitrate dehydrogenase and other genes in malignant glioma

Abstract

We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in gliblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

1 . (canceled) 
     
     
         2 . A method of treating a mutant isocitrate dehydrogenase 2 (IDH2) enzyme-associated cancer in a subject comprising:
 detecting the presence of an isocitrate dehydrogenase 2 (IDH2) mutation in a nucleic acid present in a sample obtained from the subject; and   administering to the subject an anti-cancer agent selected from the group consisting of a chemotherapeutic agent and a biological agent to treat the tumor, wherein the anti-cancer agent inhibits the activity of the mutant IDH2 enzyme.   
     
     
         3 . The method of  claim 2 , wherein the IDH2 mutation is present in a mutant codon that corresponds to a wild type codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131. 
     
     
         4 . The method of  claim 3 , wherein the mutant codon that includes the IDH2 mutation encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G). 
     
     
         5 . The method of  claim 2 , wherein the presence of an IDH2 mutation in the sample is detected using an amplification primer, a hybridization probe, or both. 
     
     
         6 . The method of  claim 5 , wherein:
 the amplification primer comprises at least 10 but fewer than 600 contiguous nucleotide residues of a coding sequence of a IDH2 protein found in a tumor of the subject, or its complement, the at least 10 contiguous nucleic acid residues comprising:   a first nucleotide that is present at a position in a mutant codon that corresponds to a wild type codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131, wherein the mutant codon comprising the first nucleotide encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G), wherein the amplification primer is labeled with a detectable label;   the hybridization probe comprises at least 10 but fewer than 600 contiguous nucleotide residues of a coding sequence of a IDH2 protein found in a tumor of the subject, or its complement, the at least 10 contiguous nucleic acid residues comprising:   a second nucleotide that is present at a position in a mutant codon that corresponds to a wild type codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131, wherein the mutant codon comprising the second nucleotide encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G), wherein the hybridization probe is labeled with a detectable label; or   both.   
     
     
         7 . The method of  claim 2 , wherein the anti-cancer agent is a chemotherapeutic agent. 
     
     
         8 . The method of  claim 7 , wherein the chemotherapeutic agent is a small molecule. 
     
     
         9 . The method of  claim 8 , wherein the small molecule inhibits a mutant IDH2 polypeptide comprising a mutation in codon 172. 
     
     
         10 . The method of  claim 9 , wherein the small molecule is specific for the mutant IDH2 polypeptide. 
     
     
         11 . The method of  claim 2 , wherein the anti-cancer agent is a biological agent. 
     
     
         12 . The method of  claim 11 , wherein the biological agent is selected from an antibody, an antibody derivative, a siRNA, a microRNA, or an antisense oligonucleotide. 
     
     
         13 . The method of  claim 11 , wherein the biological agent is an antibody or antibody derivative, and wherein the antibody or antibody derivative preferentially or specifically binds to the mutant IDH2 enzyme over the wild type IDH2 enzyme. 
     
     
         14 . The method of  claim 2 , wherein the IDH2 mutation results in the subject expressing a mutant IDH2 polypeptide comprising an amino acid substitution at position 172. 
     
     
         15 . The method of  claim 14 , wherein the mutant IDH polypeptide comprises a R172K amino acid substitution. 
     
     
         16 . A method of treating a mutant isocitrate dehydrogenase 2 (IDH2) enzyme-associated cancer in a subject identified as having an isocitrate dehydrogenase 2 (IDH2) mutation that is present in a nucleic acid, the method comprising:
 administering to the subject an anti-cancer agent selected from the group consisting of a chemotherapeutic agent and a biological agent to treat the tumor, wherein the anti-cancer agent inhibits the activity of the mutant IDH2 enzyme.   
     
     
         17 . The method of  claim 16 , wherein the IDH2 mutation is present in a mutant codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131 
     
     
         18 . The method of  claim 17 , wherein the mutant codon that includes the IDH2 mutation encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G). 
     
     
         19 . The method of  claim 16 , wherein the subject is identified as having an isocitrate dehydrogenase 2 (IDH2) mutation by a method that employs an amplification primer, a hybridization probe, or both. 
     
     
         20 . The method of  claim 19 , wherein:
 the amplification primer comprises at least 10 but fewer than 600 contiguous nucleotide residues of a coding sequence of a IDH2 protein found in a tumor of the subject, or its complement, the at least 10 contiguous nucleic acid residues comprising:   a first nucleotide that is present at a position in a mutant codon that corresponds to a wild type codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131, wherein the mutant codon comprising the first nucleotide encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G), wherein the amplification primer is labeled with a detectable label;   the hybridization probe comprises at least 10 but fewer than 600 contiguous nucleotide residues of a coding sequence of a IDH2 protein found in a tumor of the subject, or its complement, the at least 10 contiguous nucleic acid residues comprising:   a second nucleotide that is present at a position in a mutant codon that corresponds to a wild type codon that encodes amino acid 172 in the wild type IDH2 polypeptide of SEQ ID NO: 131, wherein the mutant codon comprising the second nucleotide encodes an amino acid selected from the group consisting of: methionine (M), lysine (K), and glycine (G), wherein the hybridization probe is labeled with a detectable label; or   both.   
     
     
         21 . The method of  claim 16 , wherein the anti-cancer agent is a chemotherapeutic agent. 
     
     
         22 . The method of  claim 21 , wherein the chemotherapeutic agent is a small molecule. 
     
     
         23 . The method of  claim 22 , wherein the small molecule inhibits a mutant IDH2 polypeptide comprising a mutation in codon 172. 
     
     
         24 . The method of  claim 23 , wherein the small molecule is specific for the mutant IDH2 polypeptide. 
     
     
         25 . The method of  claim 16 , wherein the anti-cancer agent is a biological agent. 
     
     
         26 . The method of  claim 25 , wherein the biological agent is selected from an antibody, an antibody derivative, a siRNA, a microRNA, or an antisense oligonucleotide. 
     
     
         27 . The method of  claim 25 , wherein the biological agent is an antibody or antibody derivative, and wherein the antibody or antibody derivative preferentially or specifically binds to the mutant IDH2 enzyme over the wild type IDH2 enzyme. 
     
     
         28 . The method of  claim 16 , wherein the IDH2 mutation results in the subject expressing a mutant IDH2 polypeptide comprising an amino acid substitution at position 172. 
     
     
         29 . The method of  claim 28 , wherein the mutant IDH polypeptide comprises a R172K amino acid substitution.