Modifiers of cftr-directed therapy

Abstract

Described herein is a genetic modifier of cystic fibrosis (CF), which may serve as a predictor of the efficacy of a CFTR-directed therapy. SNPs rs7512462 or rs2869027 in non-coding regions of SLC26A9 are shown to correlate with CF lung disease severity in patients having CFTR mutations that leave protein at the cell surface, e.g. gating mutations such as G551D. It is also shown that patient response to Ivacaftor correlates with SLC26A9 genotype. Given the biology of SLC26A9, risk alleles of LC26A9 should correlate with reduced SLC26A9. SLC26A9 activity (marked by e.g. genotype or expression level) is therefore a predictor of treatment efficacy for any CFTR-directed therapeutic, such as Ivacaftor or Lumacaftor. Associated methods of selecting and treating patients are described, along with related kits, uses, and drug discovery platforms.

1 . A method of selecting a cystic fibrosis patient for treatment with a CFTR-directed therapy, the method comprising steps of:
 determining an activity level of SLC26A9 in a sample obtained from said patient and   selecting said patient for treatment with said CFTR-directed therapy based on the activity level.   
     
     
         2 . A method of predicting treatment response of a cystic fibrosis patient to a CFTR-directed therapy, the method comprising steps of:
 determining an activity level of SLC26A9 in a sample obtained from said patient and   predicting the treatment response based on the activity level.   
     
     
         3 . A method of treating a cystic fibrosis patient with a CFTR-directed therapy, the method comprising steps of:
 determining an activity level of SLC26A9 in a sample obtained from said patient;   selecting said patient for treatment with said CFTR-directed therapy based on the activity level; and   treating said selected patient with said CFTR-directed therapy.   
     
     
         4 . The method of  claim 2 , further comprising:
 clinically monitoring a patient predicted to have a poor treatment response.   
     
     
         5 . The method of  claim 2 , further comprising:
 treating a patient predicted to have a poor treatment response with another therapy.   
     
     
         6 . The method of any one of  claims 1  to  5 , wherein the treatment is a treatment of CF lung disease. 
     
     
         7 . The method of any one of  claims 1  to  6 , wherein the method comprises:
 measuring an expression level of SLC26A9 protein or mRNA; and 
 selecting said patient for treatment or predicting a positive response to treatment if said expression level exceeds a threshold. 
 
     
     
         8 . The method of  claim 7 , wherein the SLC26A9 protein is measured by an immunoassay. 
     
     
         9 . The method of  claim 7 , wherein the SLC26A9 mRNA is measured by an assay comprising primer extension or nucleic acid hybridization. 
     
     
         10 . The method of any one of  claims 1  to  6 , wherein said activity level of SLC26A9 is determined by:
 determining a genotype of a single nucleotide polymorphism (SNP) indicative of SLC26A9 activity. 
 
     
     
         11 . The method of  claim 10 , wherein said SNP is rs7512462, and said patient is selected for treatment or predicted to have a positive response to treatment if the rs7512462 genotype is determined to be CC or TC. 
     
     
         12 . The method of  claim 11 , wherein said patient is selected for treatment or predicted to have a positive response to treatment if the rs7512462 genotype is determined to be CC. 
     
     
         13 . The method of  claim 10 , wherein said SNP is rs2869027, and said patient is selected for treatment or predicted to have a positive response to treatment if the rs2869027 genotype is determined to be GG or GC. 
     
     
         14 . The method of  claim 13 , wherein the patient is selected for treatment or predicted to have a positive response to treatment if the rs2889027 genotype is determined to be GG. 
     
     
         15 . The method of any one of  claims 10  to  14 , wherein the genotype of the SNP is directly determined. 
     
     
         16 . The method any one of  claims 10  to  14 , wherein the genotype of the SNP is indirectly determined by directly determining the genotype of a proxy SNP in linkage disequilibrium with said SNP. 
     
     
         17 . The method of any one of  claims 10  to  16 , wherein SNP genotyping is accomplished using a method comprising hybridization of a probe or primer extension. 
     
     
         18 . The method of any one of  claims 1  to  17 , wherein the CF patient comprises at least one CFTR mutation resulting in residual CFTR protein at the cell surface. 
     
     
         19 . The method of  claim 18 , wherein the at least one mutation comprises a gating mutation. 
     
     
         20 . The method of  claim 19 , wherein the gating mutation is G551D. 
     
     
         21 . The method of any one of  claims 1  to  20 , wherein the patient comprises a Phe508del mutation in CFTR. 
     
     
         22 . The method of any one of  claims 1  to  21 , wherein the CFTR-directed therapy comprises gene therapy. 
     
     
         23 . The method of any one of  claims 1  to  21 , wherein the CFTR-directed therapy comprises Ivacaftor. 
     
     
         24 . The method of any one of  claims 1  to  21 , wherein the CFTR-directed therapy comprises Lumacaftor. 
     
     
         25 . The method of any one of  claims 1  to  21 , wherein the CFTR-directed therapy comprises Ivacaftor and Lumacaftor. 
     
     
         26 . The method of any one of  claims 1  to  21 , wherein the CFTR-directed therapy comprises Ataluren. 
     
     
         27 . A kit for use in selecting a cystic fibrosis patient for treatment with a CFTR-directed therapy, the kit comprising:
 reagents for determining an activity level of SLC26A9 in a sample obtained from said patient; and   instructions for selecting said patient for treatment with the CFTR-directed therapy based on the activity.   
     
     
         28 . A kit for use in predicting treatment response of a cystic fibrosis patient to a CFTR-directed therapy, the kit comprising:
 reagents for determining an activity level of SLC26A9 In a sample obtained from said patient; and   instructions for predicting the treatment response based on the activity.   
     
     
         29 . A kit for use in treating a cystic fibrosis patient for with a CFTR-directed therapy, the kit comprising:
 reagents for determining an activity level of SLC26A9 in a sample obtained from said patient; and   instructions for:
 selecting said patient for treatment with said CFTR-directed therapy based on the activity, and 
 treating said selected patient with said CFTR-directed therapeutic agent. 
   
     
     
         30 . The kit of  claim 28 , wherein the instructions indicate that a patient predicted to have a poor treatment response should be clinically monitored. 
     
     
         31 . The kit of  claim 28 , wherein the instructions indicate that a patient predicted to have a poor treatment response should be treated with another therapy. 
     
     
         32 . The kit according to any one of  claims 27  to  31 , wherein the treatment is a treatment of CF lung disease. 
     
     
         33 . The kit of any one of  claims 27  to  32 , wherein said reagents comprise reagents for measuring an expression level of SLC26A9 protein or mRNA, and said instructions indicate to select said patient for treatment or predict a positive treatment response if said expression level exceeds a threshold. 
     
     
         34 . The kit of  claim 33 , wherein said reagents comprise an antibody specific to the SLC26A9 protein. 
     
     
         35 . The kit of  claim 33 , wherein said reagents comprise a nucleic acid probe or primer for measuring SLC26A9 mRNA. 
     
     
         36 . The kit of any one of  claims 27  to  32 , wherein said reagents comprise reagents for genotyping a single nucleotide polymorphism (SNP) indicative of SLC26A9 activity. 
     
     
         37 . The kit of  claim 36 , wherein said reagents comprise reagents for genotyping rs7512462, and said instructions indicate that said patient is to be selected for treatment or that a positive treatment response is to be predicted if the rs7512462 genotype is determined to be CC or TC. 
     
     
         38 . The kit of  claim 37 , wherein said instructions indicate that said patient is to be selected for treatment or that a positive treatment response is to be predicted if the rs7512462 genotype is determined to be CC. 
     
     
         39 . The kit of  claim 36 , wherein said reagents comprise reagents for genotyping rs2869027, and said instructions indicate that said patient is to be selected for treatment or that a positive treatment response is to be predicted if the rs28869027 genotype is determined to be GG or GC. 
     
     
         40 . The kit of  claim 39 , wherein said instructions indicate that said patient is to be selected for treatment or that a positive treatment response is to be predicted if the rs2889027 genotype is determined to be GG. 
     
     
         41 . The kit of any one of  claims 36  to  40 , wherein the reagents are for directly genotyping the SNP. 
     
     
         42 . The kit any one of  claims 36  to  40 , wherein the reagents are for indirectly genotyping the SNP by directly genotyping a proxy SNP in linkage disequilibrium with said SNP. 
     
     
         43 . The kit of any one of  claims 36  to  42 , wherein reagents comprise a nucleic acid probe or primer. 
     
     
         44 . The kit of any one of  claims 27  to  43 , wherein the CF patient comprises at least mutation resulting in residual CFTR protein at the cell surface. 
     
     
         45 . The kit of  claim 44 , wherein the at least one mutation comprises a gating mutation. 
     
     
         46 . The kit of  claim 45 , wherein the gating mutation is G551D. 
     
     
         47 . The kit of any one of  claims 27  to  46 , wherein the patient comprises a Phe508del mutation in CFTR. 
     
     
         48 . The kit of any one of  claims 27  to  47 , wherein the CFTR-directed therapy comprises gene therapy. 
     
     
         49 . The kit of any one of  claims 27  to  47 , wherein the CFTR-directed therapy comprises Lumacaftor. 
     
     
         50 . The kit of any one of  claims 27  to  47 , wherein the CFTR-directed therapy comprises Ivacaftor. 
     
     
         51 . The kit of any one of  claims 27  to  47 , wherein the CFTR-directed therapy comprises Lumacaftor and Ivacaftor. 
     
     
         52 . The kit of any one of  claims 27  to  47 , wherein the CFTR-directed therapy comprises Ataluren. 
     
     
         53 . A use of a CFTR-directed therapy for treatment of a cystic fibrosis patient having an SLC26A9 activity that exceeds a threshold. 
     
     
         54 . A use of a CFTR-directed therapy for preparation of a medicament for treatment of a cystic fibrosis patient having an SLC26A9 activity that exceeds a threshold. 
     
     
         55 . A CFTR-directed therapy for use in treatment of a cystic fibrosis patient having an SLC26A9 activity that exceeds a threshold. 
     
     
         56 . The use of  claim 53  or  54 , or the therapeutic for use of  claim 55 , wherein the cystic fibrosis patient has a measured expression level of SLC26A9 that exceed a threshold. 
     
     
         57 . The use of  claim 53  or  54 , or the therapeutic for use of  claim 55 , wherein the cystic fibrosis patent has a SNP genotype indicative of SLC26A6 activity that exceeds the threshold. 
     
     
         58 . The use or therapeutic for use of  claim 57 , wherein the SNP genotype is CC or TC at rs7512462. 
     
     
         59 . The use or therapeutic for use of  claim 58 , wherein the SNP genotype is CC at rs7512462. 
     
     
         60 . The use or therapeutic for use of  claim 57 , wherein the SNP genotype is GG or GC at rs2869027. 
     
     
         61 . The use or therapeutic for use of  claim 60 , wherein the SNP genotype is GG at rs2869027. 
     
     
         62 . The use or therapeutic for use of any one of  claims 53  to  54 , wherein the patient has at least one gating mutation in CFTR. 
     
     
         63 . The use or therapeutic for use of  claim 62 , wherein said at least one gating mutation is G551D. 
     
     
         64 . The use or therapeutic for use of any one of  claims 53  to  63 , wherein the patient comprises a Phe508del mutation in CFTR. 
     
     
         65 . The use or therapy for use of any one of  claims 53  to  64 , wherein the CFTR-directed therapy comprises a reagent for gene therapy. 
     
     
         66 . The use or therapeutic for use of any one of  claims 53  to  64 , wherein the CFTR-directed therapy comprises Ivacaftor. 
     
     
         67 . The use or therapeutic for use of any one of  claims 53  to  64 , wherein the CFTR-directed therapy comprises Lumacaftor. 
     
     
         68 . The use or therapeutic for use of any one of  claims 53  to  64 , wherein the CFTR-directed therapy comprises Ivacaftor and Lumacaftor. 
     
     
         69 . The use or therapeutic for use of any one of  claims 53  to  64 , wherein the CFTR-directed therapy comprises Ataluren. 
     
     
         70 . The use or therapeutic for use of any one of  claims 53  to  64 , wherein the treatment is treatment of CF lung disease. 
     
     
         71 . A method of identifying a candidate compound for treating cystic fibrosis (CF) comprising:
 measuring a first level CFTR activity in a cell,   contacting the cell with a test compound,   measuring a second level of CFTR activity in the cell, and   identifying said compound as a candidate compound for treating CF if the second level of CFTR activity exceeds the first level,   wherein the cell exhibits Increased SLC26A9 activity relative to a control.   
     
     
         72 . The method of  claim 71 , wherein the cell exhibits increased SLC26A9 expression compared to the control. 
     
     
         73 . The method of  claim 71 , wherein the cell has a genotype CC or CT at rs7512462. 
     
     
         74 . The method of  claim 73 , wherein the cell has the genotype CC at rs7512462. 
     
     
         75 . The method of  claim 71 , wherein the cell has a genotype GG or GC at rs2869027. 
     
     
         76 . The method of  claim 75 , wherein the cell has the genotype GG at rs2869027. 
     
     
         77 . The method of any one of  claims 71  to  76 , wherein the control is a control cell having a genotype TT at rs7512462 and/or CC at rs2869027. 
     
     
         78 . The method of any one of  claims 71  to  77 , wherein the cell comprises mutations in both copies of the CFTR gene. 
     
     
         79 . The method of any one of  claims 71  to  78 , wherein the cell comprises at least one gating mutation. 
     
     
         80 . The method of  claim 79 , wherein the at least one gating mutation is G551D. 
     
     
         81 . The method of any one of  claims 71  to  80 , wherein the cell comprises a Phe508del mutation in CFTR. 
     
     
         82 . The method of any one of  claims 71  to  81 , wherein the method is for identifying a candidate compound for treating CF lung disease. 
     
     
         83 . A method of treating a cystic fibrosis (CF) patient comprising:
 administering to the patient an SLC26A9-directed therapy.   
     
     
         84 . The method of  claim 83 , wherein the SLC26A-directed therapy increases the expression of SLC26A9. 
     
     
         85 . The method of  claim 83  or  84 , wherein the method further comprises:
 administering to the patient a CFTR-directed therapy. 
 
     
     
         86 . The method of  claim 85 , wherein the CFTR-directed therapy comprises Ivacaftor, Lumacaftor, Ataluren, or a combination thereof. 
     
     
         87 . The method of any one of  claims 83  to  88 , wherein the patient has at least one gating mutation in CFTR. 
     
     
         88 . The method of  claim 87 , wherein the at least one gating mutation is G551D. 
     
     
         89 . The method of any one of  claims 83  to  88 , wherein the patient has a Phe50del mutation in CFTR. 
     
     
         90 . The method of any one of  claims 83  to  89 , wherein the patient has a genotype of CC or CT at rs7512462. 
     
     
         91 . The method of any one of  claims 83  to  89 , wherein the patient has a genotype of TT at rs7512462. 
     
     
         92 . The method of any one of  claims 83  to  89 , wherein the patient has a genotype GG or GC at rs2869027. 
     
     
         93 . The method of any one of  claims 83  to  89 , wherein the patient has a genotype CC at rs2869027. 
     
     
         94 . The method of any one of  claims 83  to  93 , wherein the method is for treating CF lung disease. 
     
     
         95 . A use of an SLC26A6-directed therapy for treatment of cystic fibrosis (CF) in a patient. 
     
     
         96 . A use of an SLC26A6-directed therapy for preparation of a medicament for treatment of cystic fibrosis (CF) in a patient. 
     
     
         97 . An SLC26A6-directed therapy for use in treatment of cystic fibrosis (CF) in a patient. 
     
     
         98 . The use of  claim 95  or  96 , or the therapy for use of  claim 97 , wherein the SLC26A-directed therapy increases the expression of SLC26A9. 
     
     
         99 . The use or therapeutic for use of any one of  claims 95  to  98 , wherein the patient is receiving a CFTR-directed therapy. 
     
     
         100 . The use or therapeutic for use of  claim 99 , wherein the CFTR-directed therapy comprises Ivacaftor, Lumacaftor, Ataluren, or a combination thereof. 
     
     
         101 . The use or therapy for use of any one of  claims 96  to  100 , wherein the patient has at least one gating mutation in CFTR. 
     
     
         102 . The use or therapy for use of  claim 101 , wherein the at least one gating mutation is a G551D. 
     
     
         103 . The use or therapy for use of any one of  claims 96  to  102 , wherein the patient has a Phe508del mutation in CFTR. 
     
     
         104 . The use or therapy for use of any one of  claims 96  to  103 , wherein the patient has a genotype of CC or CT at rs7512462. 
     
     
         105 . The use or therapy for use of any one of  claims 96  to  103 , wherein the patient has a genotype of TT at rs7512482. 
     
     
         106 . The use or therapy for use of any one of  claims 96  to  103 , wherein the patient has a genotype GG or GC at rs2869027. 
     
     
         107 . The use or therapy for use of any one of  claims 96  to  103 , wherein the patient has a genotype CC at rs2889027. 
     
     
         108 . The use or therapy for use of any one of  claims 96  to  103 , wherein the treatment is treatment of CF lung disease. 
     
     
         109 . The use or therapy for use of any one of  claims 96  to  108 , wherein the treatment is treatment of CF lung disease. 
     
     
         110 . The invention as herein described.