Inhibitors of alternative alleles of genes encoding products that mediate cell response to environmental changes

Abstract

Disclosed are methods for the treatment of proliferative disorders using compounds and/or environmental conditions which result in a difference in sensitivity of targeted and non-targeted cells. Certain of the methods involve the identification and use of allele-specific inhibitors of conditionally essential genes.

What we claim is:  
     
         1 . A method for identifying an inhibitor potentially useful for treatment of cancer, wherein said inhibitor is active on a conditionally essential gene, and wherein said gene is subject to loss of heterozygosity in a cancer, said method comprising the steps of: 
 (a) determining at least two alleles of a said gene;    (b) testing a potential allele specific inhibitor to determine whether said potential allele specific inhibitor is active on at least one but less than all of said alleles;    wherein inhibition of expression of at least one but less than all of said alleles or reduction of the level of activity of a product of at least one but less than all of said alleles in the presence of said potential allele specific inhibitor is indicative that said potential allele specific inhibitor is a said inhibitor.    
     
     
         2 . An inhibitor potentially useful for treatment of cancer, wherein said inhibitor is active on an allelic form of a conditionally essential gene, said gene has at least two alternative alleles in a population, and 
 wherein said inhibitor targets at least one but less than all of said alternative alleles.    
     
     
         3 . A pharmaceutical composition, comprising 
 at least one allele specific inhibitor targeting at least one but less than all allelic forms of a conditionally essential gene in a population; and    a pharmaceutically acceptable carrier or excipient.    
     
     
         4 . A method for producing an inhibitor potentially useful for cancer treatment, wherein said inhibitor is active on at least one but less than all alternative alleles of a conditionally essential gene having at least two alternative alleles, comprising the steps of: 
 (a) identifying a conditionally essential gene that has alternative allelic forms in a noncancerous cell, wherein one of said alternative allelic forms is deleted in a cancer cell;    (b) screening to identify an inhibitor which inhibits said at least one but less than all of said at least two alternative alleles; and    (c) synthesizing said inhibitor in an amount sufficient to produce a therapeutic effect when administered to a patient suffering from a cancer in whom cancerous cells have only an allele of said gene inhibited by said inhibitor and in whom normal cells are heterozygous for said gene and contain an allelic form not inhibited by said inhibitor.    
     
     
         5 . A method for preventing the development of cancer in a patient having a precancerous condition, comprising the steps of: 
 a. subjecting cells of said precancerous condition to an altered condition such that a first conditionally essential becomes essential;    b. administering to said patient a therapeutic amount of a first allele specific inhibitor targeted to an allele of said first conditionally essential gene present in cells of said precancerous condition, wherein the normal somatic cells of said patient are heterozygous for said first gene, said inhibitor is active on at least one but less than all allelic forms of said gene present in a population and targets only one allelic form present in said normal somatic cells; and    wherein cells of said precancerous condition have undergone LOH of said first gene.    
     
     
         6 . The method of  claim 5 , wherein the cells of said precancerous condition are not clonal from a single cell, further comprising the step of: 
 c. serially administering to said patient at least one additional allele specific inhibitor, wherein each of said at least one additional allele specific inhibitors targets a different allele of a conditionally essential gene or an essential gene than is targeted by said first allele specific inhibitor, wherein said different allele may be a different allele of said first gene or an allele of a different gene, and wherein said patient is heterozygous for each targeted gene and each targeted gene has undergone LOH in cells of said precancerous condition.    
     
     
         7 . A method for treating a patient suffering from a cancer, wherein said patient is heterozygous for a conditionally essential gene, comprising the steps of: 
 a) subjecting cells of said cancer to altered conditions such that said gene is essential; and    administering a therapeutic amount of an allele specific inhibitor active on at least one but less than all allelic forms of said gene present in a population,    wherein said allele specific inhibitor inhibits only one allelic form of said gene present in said patient, and said only one allelic form of said gene is present in cancer cells in said patient.    
     
     
         8 . The method of  claim 7 , further comprising the steps of: 
 (a) determining whether non-cancerous cells of said patient are heterozygous for a particular conditionally essential gene; or    (b) determining whether cancerous cells of said patient have only one allele of said particular gene; or    (c) both (a) and (b).    
     
     
         9 . A method of inhibiting growth of a cell comprising the steps of: 
 a) subjecting said cell to conditions such that said gene is essential; and    b) administering at least one inhibitor active on an allele of said conditionally essential gene,    wherein said inhibitor is less active on at least one other allele of said gene.    
     
     
         10 . A method of identifying a potential patient for treatment with an inhibitor active on at least one but less than all alleles of a conditionally essential gene, wherein said patient is suffering from a cancer, said method comprising the step of: 
 identifying a patient heterozygous for a said gene,    wherein if said patient is heterozygous for said gene, then said patient is a potential patient for said treatment.    
     
     
         11 . The method of  claim 10 , further comprising the step of determining whether cancer cells in said patient contain only a single allele of said gene, 
 wherein if said cancer cells contain only a single allele of said gene, then said patient is a potential patient for said treatment.    
     
     
         12 . A method of identifying a potential patient for treatment with an inhibitor active on at least one but less than all alleles of a conditionally essential gene, wherein said patient is suffering from a cancer, said method comprising the step of: 
 determining whether cancer cells in said patient have undergone LOH of a said gene,    wherein if said cells have undergone LOH of said gene, then said patient is a potential patient for said treatment.    
     
     
         13 . A nucleic acid probe at least 12 nucleotides in length which is perfectly complementary to a portion of a first allelic form of a conditionally essential gene, 
 wherein said portion comprises a sequence variance site, and wherein said probe hybridizes under stringent hybridization conditions to said portion and not to a corresponding portion of a second allelic form having at least one different nucleotide at said sequence variance site.    
     
     
         14 . A method for selecting a patient for treatment with an antiproliferative treatment, comprising the steps of: 
 a) determining whether normal somatic cells in a potential patient are heterozygous for an essential or conditionally essential gene, wherein a first allelic form of said gene is more active than a second allelic form, and wherein a reduction in the activity of said gene in a cell increases the sensitivity of said cell to a said antiproliferative treatment; and    b) determining whether cancer cells of said patient have only said second allelic form of said gene,    wherein if said somatic cells are heterozygous and said cancer cells have only said second allelic form, it is indicative that said patient is suitable for treatment with said antiproliferative treatment.    
     
     
         15 . A method for selecting an antiproliferative treatment for a patient suffering from a cancer, comprising the steps of: 
 a) determining whether normal somatic cells in a potential patient are heterozygous for an essential or conditionally essential gene which reduces the sensitivity of cells to an antiproliferative treatment, wherein a first allelic form of said gene is more active than a second allelic form, and wherein a reduction in the activity of said gene in a cell increases the sensitivity of said cell to a said antiproliferative treatment; and    b) determining whether cancer cells of said patient have only said second allelic form of said gene,    wherein if said somatic cells are heterozygous for said gene and said cancer cells have only said second allelic form, it is indicative that said antiproliferative treatment is suitable for said patient.    
     
     
         16 . The method of any of claims  1 - 15 , wherein said gene is selected from the group consisting of: 
 galactose-1-phosphate uridyltransferase, galactose kinase, UDP galactose-4-epimerase, methionine synthase, asparagine synthase, glutamine synthetase, multidrug resistance gne/Pglycoprotein, multidrug resistance associated proteins 1-5, bleomycin hydrolase, dihydropyrimidine dehydrogenase, β-ureidopropoinase, β-alanine synthetase, cytidine deaminase, thiopurine methyltransferase, CYP1A1, CYP1A2, CYP2A6, CYP2A7, CYP2B6, CYP2B7, CYP2C8, CYP2C9, CYP2C17, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP2F1, CYP3A3, CYP3A4, CYP3A5, CYP3A7, CYP4B1, CYP7, CYP11, CYP17, CYP19, CYP21, CYP27, glutathione transferase alpha, glutathione transferase theta, glutathione transferae mu, glutathione transferase pi, methylguanine methyltransferase, 3-alkylguanine alkyltransferase, 3-methyladenine DNA glucosylase, DNA dependent protein kinase, catalytic subunit of DNA-PK, DNA binding subunit of DNA-PK Ku-70 or Ku-80 subunit, KARP-1, Poly(ADP-ribose) polymerase, Fanconi Anemia genes A, B, C, D, E, F, G, and H, ERCC-1, ERCC2/XPD, ERCC3/XPB, ERCC4, ERCC5, ERCC6, XPA, XPC, XPE, HHR23A, HHR23B, uracil glycosylase, 3-methyl adenine DNA glycosylase, NF-kappa B, XRCC4, XRCC5/Ku80, XRCC6, XRCC7, glutathione-X-transferase, I-kappa B alpha, HSP70, HSP27, and 9-oxoguanine DNA glycosylase.