Novel estrogen receptor mutations and uses thereof

Abstract

Novel mutant ESR1 molecules and uses are disclosed.

1 . A reaction mixture comprising:
 a detection reagent; and   a target nucleic acid derived from a breast cancer that is estrogen receptor positive (ER + ), malignant, and resistant to a treatment with a first or second line Selective Estrogen Receptor Modulator (SERM) therapy,   wherein said detection reagent distinguishes a reference nucleotide or amino acid sequence from a nucleotide or amino acid sequence comprising a mutation chosen from one or more of:   a missense mutation at nucleotide position 1609 according to SEQ ID NO: 1;   a missense mutation at nucleotide position 1610 according to SEQ ID NO: 1;   a missense mutation at nucleotide position 1613 according to SEQ ID NO: 1;   a six-nucleotide deletion of nucleotides 1046-1051 (TGGCAG) according to SEQ ID NO: 1, or a deletion that comprises one or more of nucleotides 1046-1051 according to SEQ ID NO: 1;   a three-nucleotide insertion between nucleotide positions 1033 and 1034 according to SEQ ID NO: 1; or   a mutation at an amino acid or nucleotide position identified as mutated in Table 3.   
     
     
         2 .- 3 . (canceled) 
     
     
         4 . The reaction mixture of  claim 1 , wherein the mutation is selected from:
 a missense mutation at amino acid position 537 or 538 of SEQ ID NO: 2;   a tyrosine to asparagine substitution at amino acid position 537 (a Y537N) of SEQ ID NO: 2;   a tyrosine to cysteine substitution at amino acid position 537 (a Y537C) of SEQ ID NO: 2;   an aspartate to glycine substitution at amino acid position 538 (a D538G) of SEQ ID NO: 2;; or   an AT to A replacement at nucleotide position 1609 of SEQ ID NO: 1; or   an A to G replacement at nucleotide position 1610 of SEQ ID NO: 1.   
     
     
         5 . (canceled) 
     
     
         6 . A method of making the reaction mixture of  claim 1 , the method comprising combining the detection reagent with the target nucleic acid. 
     
     
         7 . (canceled) 
     
     
         8 . A purified or isolated preparation of an ESR1 nucleic acid from a breast cancer that is estrogen receptor positive (ER + ), malignant, and resistant to a treatment with a first or second line SERM therapy disposed in a sequencing device or a device for determining a physical or chemical property, or a sample holder for use in such a device, wherein said ESR1 nucleic acid comprises a mutation chosen from:
 a missense mutation at nucleotide position 1609 according to SEQ ID NO: 1;   a missense mutation at nucleotide position 1610 according to SEQ ID NO: 1;   a missense mutation at nucleotide position 1613 according to SEQ ID NO: 1;   a six-nucleotide deletion of nucleotides 1046-1051 (TGGCAG) according to SEQ ID NO: 1, or a deletion that comprises one or more of nucleotides 1046-1051 according to SEQ ID NO: 1;   a three-nucleotide insertion between nucleotides 1033 and 1034 according to SEQ ID NO: 1; or   a mutation at a nucleotide position identified as mutated in Table 3.   
     
     
         9 .- 15 . (canceled) 
     
     
         16 . A method of treating a subject having a breast cancer, the method comprising:
 acquiring knowledge of a presence of a mutant estrogen receptor 1 (ESR1) polypeptide or a nucleic acid molecule encoding the mutant ESR1 polypeptide and an Estrogen Receptor positive (ER+) breast cancer in said subject, wherein the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide comprises a mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide; and   responsive to said knowledge, administering to the subject an effective amount of an estrogen receptor modulator set forth in Table 5,   thereby treating the breast cancer in the subject.   
     
     
         17 . The method of  claim 16 , wherein the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide comprises a mutation chosen from one or more of:
 a missense mutation at amino acid position 537, 538, 311, 341, 350, 394, 414, 433, or 503 of SEQ ID NO: 2,   a deletion of nucleotides 1046-1051 of SEQ ID NO: 3, or   an insertion between amino acid positions 344 and 345 of SEQ ID NO: 2.   
     
     
         18 . The method of  claim 16 , wherein the mutant ESR1 polypeptide comprises a mutation chosen from one or more of:
 a tyrosine to asparagine substitution at amino acid position 537 (a Y537N) of SEQ ID NO: 2;   a tyrosine to cysteine substitution at amino acid position 537 (a Y537C) of SEQ ID NO: 2;   an aspartate to glycine substitution at amino acid position 538 (a D538G) of SEQ ID NO: 2;   a deletion of amino acids Leu-Ala-Asp (LAD) at positions 349-351 of SEQ ID NO: 4;   an insertion of a histidine at amino acid position 349 of SEQ ID NO: 3;   a threonine to methionine substitution at amino acid position 311 (a T311M) of SEQ ID NO: 2;   a serine to leucine substitution at amino acid position 341 (a S341L) of SEQ ID NO: 2;   an alanine to glutamate substitution at amino acid position 350 (a A350E) of SEQ ID NO: 2;   an arginine to histidine substitution at amino acid position 394 (a R394H) of SEQ ID NO: 2;   a glutamine substitution at amino acid position 414 of SEQ ID NO: 2;   a serine to proline substitution at amino acid position 433 (a S433P) of SEQ ID NO: 2;   an arginine to tryptophan substitution at amino acid position 503 (a R503W) of SEQ ID NO: 2; or   an insertion of a cysteine between amino acid positions 344 and 345 of SEQ ID NO:2.   
     
     
         19 . The method of  claim 16 , wherein said subject has one or more of the following:
 (i) previously received a treatment with a SERM;   (ii) has failed a first or second line of treatment with a SERM;   (iii) has a late stage, metastatic progressive breast cancer;   (iv) is post-menopausal or pre-menopausal;   (v) stops a treatment with a SERM and begins a treatment with an anti-cancer agent that is not a SERM; or   (vi) is premenopausal and receives an oophorectomy.   
     
     
         20 .- 24 . (canceled) 
     
     
         25 . The method of  claim 19 , wherein the SERM is chosen from raloxifene, EM652, GW7604, keoxifene, toremifene, tamoxifen, lasofoxifene, levormeloxifene, bazedoxifene, or arzoxifene. 
     
     
         26 . The method of  claim 16 , further comprising administering to the subject an anti-cancer agent chosen from a Selective Estrogen Receptor Degrader (SERD), an aromatase inhibitor, an mTOR pathway inhibitor, or a chemotherapeutic agent. 
     
     
         27 . (canceled) 
     
     
         28 . The method of  claim 16 , further comprising administering to the subject fulvestrant. 
     
     
         29 . The method of  claim 26 , wherein the aromatase inhibitor is chosen from aminoglutethimide, testolactone, anastrozole, letrozole, exemestane, vorozole, formestane, fadrozole, 4-hydroxyandrostenedione, 1,4,6-androstatrien-3, 17-dione (ATD), or 4-Androstene-3,6,17-trione (“6-OXO”). 
     
     
         30 . The method of  claim 26 , wherein the mTOR pathway inhibitor is chosen from rapamycin, temsirolimus, everolimus, ridaforolimus, AP23573, AZD8055, BEZ235, BGT226, XL765, PF-4691502, GDC0980, SF1126, OSI-027, GSK1059615, KU-0063794, WYE-354, INK128, temsirolimus (CCI-779), Palomid 529 (P529), PF-04691502, or PKI-587. 
     
     
         31 . (canceled) 
     
     
         32 . The method of  claim 16 , wherein the estrogen receptor modulator is administered in combination with a different therapeutic agent or a different therapeutic modality. 
     
     
         33 . The method of  claim 32 , wherein the different therapeutic agent or modality is selected according to a determination of a presence of a mutation other than the mutation in the mutant ESR1 polypeptide or in the nucleic acid molecule encoding the mutant ESR1 polypeptide, and wherein the mutation other than the mutation in the mutant ESR1 polypeptide and in the nucleic acid molecule encoding the mutant ESR1 polypeptide is chosen from a HER2 mutation, a p53 mutation, a BRCA mutation, an NF1 mutation, an EGFR/myc gain, a PIK3CA mutation, a CCND1 mutation, a CDH1 mutation, or a combination thereof. 
     
     
         34 . The method of  claim 16 , wherein the acquiring knowledge step comprises determining the presence of the mutation in the mutant ESR1 polypeptide or in the nucleic acid molecule encoding the mutant ESR1 polypeptide by sequencing. 
     
     
         35 . The method of  claim 16 , wherein the subject was previously tested for the presence of the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide, wherein the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was not detected during the testing,
 and wherein the subject was administered a SERM based on the knowledge that the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was not detected during the testing.   
     
     
         36 . The method of  claim 16 , wherein the subject was tested at intervals for the presence of the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide, and wherein the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was not detected during the testing,
 and wherein the subject continued a treatment with a SERM based on the knowledge that the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was not detected during the testing.   
     
     
         37 . The method of  claim 16 , wherein the subject was previously tested or is currently being tested for the presence of the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide at six-month or one-year intervals. 
     
     
         38 . The method of  claim 16 , wherein the subject was tested at intervals for the presence of the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide, and wherein the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was detected during the testing,
 and wherein the subject stopped a treatment with a SERM based on the knowledge that the mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide was detected during the testing.   
     
     
         39 . A method of determining a presence of a mutant ESR1 polypeptide or a nucleic acid molecule encoding the mutant ESR1 polypeptide, comprising:
 directly acquiring knowledge that the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide is present in a sample from a subject,   wherein the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide comprises a mutation in the ligand binding domain of the mutant ESR1 polypeptide or in the encoded ligand binding domain of the nucleic acid molecule encoding the mutant ESR1 polypeptide,   wherein the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide comprises a mutation chosen from one or more of:   a missense mutation at amino acid position 537, 538, 311, 341, 350, 394, 414, 433, or 503 of SEQ ID NO: 2;   a deletion of nucleotides 1046-1051 of SEQ ID NO: 3; or   an insertion between amino acid positions 344 and 345 of SEQ ID NO: 2.   
     
     
         40 .- 65 . (canceled) 
     
     
         66 . An isolated or purified mutant ESR1 polypeptide or a mutation-comprising fragment thereof, wherein the mutant ESR1 polypeptide or mutation-comprising fragment thereof comprises a mutation in the ligand binding domain of ESR1, and wherein the mutation is chosen from one or more of:
 a missense mutation at amino acid position 537, 538, 311, 341, 350, 394, 414, 433, or 503 of SEQ ID NO: 2;   a mutation resulted from a deletion of nucleotides 1046-1051 of SEQ ID NO: 3; or   an insertion between amino acid positions 344 and 345 of SEQ ID NO: 2.   
     
     
         67 .- 85 . (canceled) 
     
     
         86 . An isolated or purified nucleic acid molecule encoding the mutant ESR1 polypeptide or the mutation-comprising fragment thereof of  claim 66 . 
     
     
         87 .- 89 . (canceled) 
     
     
         90 . An isolated or purified antibody molecule that binds the mutant ESR1 polypeptide or mutation-comprising fragment thereof of  claim 66 . 
     
     
         91 .- 109 . (canceled) 
     
     
         110 . The method of  claim 16 , further comprising:
 identifying, selecting, or obtaining information or knowledge that the subject has participated in a clinical trial or has been treated for cancer;   acquiring genotype information that identifies the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide as being in the subject,   wherein the presence of the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide identifies the subject as having an increased risk for, or having, a cancer associated with the mutant ESR1 polypeptide or the nucleic acid molecule encoding the mutant ESR1 polypeptide.   
     
     
         111 .- 122 . (canceled)