MEK1 Mutation Conferring Resistance to RAF and MEK Inhibitors

Abstract

Nucleic acids and proteins having a mutant MEK sequence, and methods concerning identification of patients having resistance to treatment with anti-cancer agents, specifically inhibitors of RAF or MEK are provided. Methods of treatment and for optimizing treatment for patients having a mutation in a MEK1 sequence are also provided.

1 . An isolated nucleic acid molecule encoding a mutant MEK1 protein having MEK1 activity, wherein said mutant MEK1 protein comprises an amino acid substitution at position 121 of wild-type MEK1 shown in SEQ ID NO: 2, the amino acid substitution conferring resistance to one or more RAF or MEK inhibitors on a cell expressing the mutant MEK1 protein. 
     
     
         2 . The nucleic acid molecule of  claim 1 , wherein the RAF inhibitor is selected from the group consisting of PLX4720, PLX4032, BAY 43-9006 (Sorafenib), ZM 336372, RAF 265, AAL-881, LBT-613, and CJS352. 
     
     
         3 . The nucleic acid molecule of  claim 1 , wherein the MEK inhibitor is selected from the group consisting of CI-1040, AZD6244, PD318088, PD98059, PD334581, RDEA119, Compound A, and Compound B. 
     
     
         4 . The nucleic acid molecule of  claim 1 , wherein the amino acid substitution is a 121C>S amino acid substitution. 
     
     
         5 . The nucleic acid molecule of  claim 1 , wherein the mutant MEK1 protein comprises the amino acid sequence of SEQ ID NO: 4. 
     
     
         6 . The nucleic acid molecule of  claim 1 , which comprises the nucleotide sequence of SEQ ID NO: 3. 
     
     
         7 . An expression vector comprising the nucleic acid of  claim 1 . 
     
     
         8 . A host cell comprising the expression vector of  claim 7 . 
     
     
         9 . A method of producing a mutant MEK1 protein comprising culturing the host cell of  claim 8  such that a mutant MEK1 protein is produced by the cell. 
     
     
         10 . An isolated mutant MEK1 protein having MEK1 activity, wherein said mutant MEK1 protein comprises an amino acid substitution at position 121 of wild-type MEK1 protein shown in SEQ ID NO: 2, the amino acid substitution conferring resistance to one or more RAF or MEK inhibitors on a cell expressing the mutant MEK1 protein. 
     
     
         11 . The mutant MEK1 protein of  claim 10 , wherein the RAF inhibitor is selected from the group consisting of PLX4720, PLX4032, BAY 43-9006 (Sorafenib), ZM 336372, RAF 265, AAL-881, LBT-613, and CJS352. 
     
     
         12 . The mutant MEK1 protein of  claim 10 , wherein the MEK inhibitor is selected from the group consisting of CI-1040, AZD6244, PD318088, PD98059, PD334581, RDEA119, Compound A, and Compound B. 
     
     
         13 . The mutant MEK1 protein of  claim 10 , wherein the amino acid substitution is a 121C>S amino acid substitution 
     
     
         14 . The mutant MEK1 protein of  claim 10 , which comprises the amino acid sequence of SEQ ID NO: 4. 
     
     
         15 . A method of identifying a subject having cancer as having a high risk of relapse during treatment or being unresponsive to treatment—with a RAF inhibitor, comprising:
 (a) extracting nucleic acid from cells of the cancer; and 
 (b) sequencing a nucleic acid molecule encoding a MEK1 protein; 
 wherein the presence of nucleotides that produce a 121C>S amino acid substitution in the MEK1 protein, as compared to wild-type MEK1 protein, identifies the subject as having a high risk of relapse during treatment with a RAF inhibitor or identifies the subject as being unresponsive to treatment with a RAF inhibitor. 
 
     
     
         16 . (canceled) 
     
     
         17 . The method according to  claim 15 ,
 wherein the presence of nucleotides that produce a 121C>S amino acid substitution in the MEK1 protein, as compared to wild-type MEK1 protein, indicates a need to treat the subject with a RAF inhibitor and a MEK inhibitor wherein the MEK inhibitor targets a mutant MEK1 protein having a 121C>S amino acid substitution.   
     
     
         18 . A method of treating a subject having cancer, comprising:
 (a) extracting nucleic acid from cells of the cancer;   (b) sequencing a nucleic acid molecule encoding a MEK1 protein or subjecting the sample to PCR and identifying the nucleotide sequence of a nucleic acid molecule encoding a MEK1 protein; and   (c) administering a RAF inhibitor and administering a MEK inhibitor that targets a mutant MEK1 protein having a 121C>S amino acid substitution. to the subject when the nucleic acid molecule contains nucleotides that produce a 121C>S amino acid substitution in the MEK1 protein, as compared to wild-type MEK1 protein.   
     
     
         19 . (canceled) 
     
     
         20 . A method of identifying a subject having cancer who is likely to benefit from treatment with a RAF inhibitor and a MEK inhibitor that targets a mutant MEK1 protein having a 121C>S amino acid substitution, comprising:
 (a) assaying a nucleic acid sample obtained from the cancer for the presence one or more mutations in a nucleic acid molecule encoding a MEK1 protein that produce a 121C>S amino acid substitution in the MEK1 protein, as compared to wild-type MEK1 protein; and   (b) correlating the presence of the one or more mutations in a nucleic acid molecule encoding a MEK1 protein that produce a 121C>S amino acid substitution in the MEK1 protein with a subject who is likely to benefit from treatment with a RAF inhibitor and a MEK inhibitor that targets a mutant MEK1 protein having a 121C>S amino acid substitution; and treating the subject with a MEK inhibitor that targets a mutant MEK1 protein having a 121C>S amino acid substitution.   
     
     
         21 . (canceled) 
     
     
         22 . The method of  claim 18 , wherein the RAF inhibitor is selected from the group consisting of PLX4720, PLX4032, BAY 43-9006 (Sorafenib), ZM 336372, RAF 265, AAL-881, LBT-613, and CJS352. 
     
     
         23 . The method of  claim 22 , wherein the RAF inhibitor is PLX4720 or PLX4032. 
     
     
         24 . The method of  claim 18 , wherein the cancer is melanoma. 
     
     
         25 . The method of  claim 18 , wherein the cancer is selected from the group consisting of leukemias, lymphomas, myelomas, carcinomas, metastatic carcinomas, sarcomas, adenomas, nervous system cancers and geritourinary cancers.