Compositions and methods for selecting a treatment for b-cell neoplasias

Abstract

The present invention features compositions and methods for identifying a subject having a B cell neoplasia or related condition responsive to treatment with lenalidomide and lenalidoinide-related compounds.

1 . A method of characterizing the lenalidomide- or lenalidomide analog sensitivity of a subject having a neoplasia characterized by increased IKZF1 or IKZF3 polypeptide expression, the method comprising
 (a) contacting a cell derived from the neoplasia with lenalidomide or a lenalidomide analog; and   (b) detecting the level of an IKZF1 or IKZF3 polypeptide or polypeptide ubiquitination in the cell relative to the level in an untreated control cell, wherein detection of a decrease in IKZF1 or IKZF3 polypeptide level identifies the neoplasia as sensitive to lenalidomide or a lenalidomide analog and the absence of a decrease in IKZF1 or IKZF3 polypeptide level or polypeptide ubiquitination identifies the neoplasia as lenalidomide- or lenalidomide analog resistant.   
     
     
         2 . The method of  claim 1 , wherein the lenalidomide analog is thalidomide or pomalidomide. 
     
     
         3 . The method of  claim 1 , wherein the neoplasia is a B or T cell neoplasia. 
     
     
         4 . The method of  claim 3 , wherein the B or T cell neoplasia is mantle cell lymphoma, chronic lymphocytic leukemia, multiple myeloma, or B cell lymphoma. 
     
     
         5 . The method of  claim 1 , wherein the decrease in IKZF1 or IKZF3 polypeptide level is by at least about 20% or is undetectable by Western blot. 
     
     
         6 . The method of  claim 1 , wherein IKZF1 or IKZF3 polypeptide level is detected by immunoassay, radioimmunoassay, immunohistochemistry, FACS analysis, or quantitative fluorescent microscopy. 
     
     
         7 - 9 . (canceled) 
     
     
         10 . The method of  claim 1 , the method further comprising detecting binding of CRBN to an IKZF1 or IKZF3 polypeptide in a biological sample of the subject relative to the level present in a reference, wherein detection of binding is indicative of lenalidomide- or lenalidomide analog sensitivity and a reduction in binding is indicative of lenalidomide- or lenalidomide analog resistance. 
     
     
         11 . The method of  claim 1 , the method further comprising detecting the sequence of an IKZF1 or IKZF3 polypeptide or polynucleotide in a biological sample obtained from the subject relative to a IKZF1 or IKZF3 reference sequence, wherein detection of a mutation in the IKZF1 or IKZF3 polypeptide or polynucleotide sequence is indicative of lenalidomide resistance and failure to detect a mutation is indicative of lenalidomide sensitivity. 
     
     
         12 - 19 . (canceled) 
     
     
         20 . A method of reducing the proliferation of a cell characterized by increased IKZF1 or IKZF3 polypeptide expression, the method comprising contacting the cell with lenalidomide or a lenalidomide analog and an inhibitory nucleic acid molecule that reduces the expression or activity of an IKZF1 or IKZF3 polypeptide or casein kinase 1. 
     
     
         21 . The method of  claim 20 , wherein the inhibitory nucleic acid molecule is an antisense nucleic acid molecule, shRNA, siRNA molecule, or Crispr. 
     
     
         22 - 23 . (canceled) 
     
     
         24 . The method of  claim 20 , wherein the inhibitory nucleic acid molecule is an antisense nucleic acid molecule, shRNA, siRNA molecule, or CRISPRi. 
     
     
         25 . (canceled) 
     
     
         26 . A recombinant murine cell, transgenic mouse, or knock-in mouse comprising a polynucleotide encoding a human CRBN polypeptide 
     
     
         27 . (canceled) 
     
     
         28 . The recombinant murine cell of  claim 26 , wherein the CRBN polypeptide comprises at least one substitution selected from the group consisting of S369C, V380E, and I391V. 
     
     
         29 - 33 . (canceled) 
     
     
         34 . A method for assessing teratogenicity of lenalidomide or an analog thereof, the method comprising contacting the mouse of  claim 26  with lenalidomide or an analog thereof, and assessing teratogenicity in pups produced by said mouse. 
     
     
         35 . (canceled) 
     
     
         36 . A method of assessing lenalidomide sensitivity in the murine cell, transgenic mouse, or knock-in mouse of  claim 26 , the method comprising contacting the murine cell, transgenic mouse, or knock-in mouse of  claim 26  with lenalidomide or an analog thereof, and assessing lenalidomide sensitivity. 
     
     
         37 - 38 . (canceled) 
     
     
         39 . A derivative of lenalidomide of formula 1: 
       
         
           
           
               
               
           
         
       
     
     
         40 . A method of screening for agents that bind lenalidomide, the method comprising contacting the derivative of  claim 39  with the agent and detecting binding to said derivative. 
     
     
         41 . A method of screening for agents that increase lenalidomide binding to CRBN, the method comprising contacting the derivative of  claim 39  and CRBN with an agent, and detecting increased binding of CRBN to the derivative. 
     
     
         42 . The method of  claim 40 , wherein binding to CRBN is assayed by detecting the affinity of binding, by detecting ubiquination of IKZF1 or IKZF3, by detecting degradation of IKZF1 or IKZF3. 
     
     
         43 . A method of screening for agents that activate ubiquitin ligase, the method comprising contacting a ubiquitin ligase with the agent in the presence of IKZF1 or IKZF3, and detecting ubiquitin ligase activation. 
     
     
         44 - 48 . (canceled) 
     
     
         49 . A method of identifying an agent that treats a myelodysplastic syndrome, the method comprising contacting the cell with the agent and detecting a decrease in casein kinase 1A1 polypeptide level in the cell relative to the level present in a reference, thereby identifying the agent as treating myelodysplastic syndrome. 
     
     
         50 . (canceled) 
     
     
         51 . A method of characterizing the lenalidomide or lenalidomide analog sensitivity of a subject having myelodysplastic syndrome, the method comprising
 (a) contacting a biological sample of the subject with lenalidomide or a lenalidomide analog; and   (b) detecting altered casein kinase 1A1 polypeptide ubiquitination relative to the level present in a reference.   
     
     
         52 . (canceled)