Targeting bcl11a distal regulatory elements for fetal hemoglobin reinduction

Abstract

Provided herein are methods and compositions for increasing fetal hemoglobin levels in a cell by disrupting BCL11A expression at the genomic level. Also provided herein are methods and compositions relating to the treatment of hemoglobinopathies by reinduction of fetal hemoglobin levels.

What is claimed: 
     
         1 . A method for treating a hemoglobinopathy in a mammal comprising the steps of:
 a. providing hematopoietic progenitor cells or hematopoietic stem cells,   b. contacting the cells with an effective amount of a composition comprising a DNA-targeting endonuclease, or a vector carrying the coding sequence thereof, wherein the endonuclease cleaves the genomic DNA of the cell on chromosome 2 between positions 60,716,189 and 60,728,612 causing at least one genetic modification therein, wherein fetal hemoglobin expression is increased in the mammal relative to expression prior to the contacting; and   c. administering the cells of step (b) into the mammal.   
     
     
         2 . The method of  claim 1 , wherein the vector is introduced into the isolated human hematopoietic progenitor cell ex vivo. 
     
     
         3 . The method of  claim 1 , wherein the isolated human hematopoietic progenitor is a cell of the erythroid lineage. 
     
     
         4 . The method of  claim 1 , wherein the isolated human hematopoietic progenitor cell comprises at least one genetic modification. 
     
     
         5 . The method of  claim 4 , wherein the at least one genetic modification is a deletion. 
     
     
         6 . The method of  claim 5 , wherein the deletion removes the entire region between chromosome 2 location 60,716,189-60,728,612 or removes one or more DHSs in the region. 
     
     
         7 . The method of  claim 5 , wherein the deletion removes the entire region between chromosome 2 location 60,716,189-60,728,612. 
     
     
         8 . The method of  claim 5 , wherein the deletion disrupts DHS +62. 
     
     
         9 . The method of  claim 5 , wherein the deletion disrupts DHS +58. 
     
     
         10 . The method of  claim 5 , wherein the deletion disrupts DHS +55. 
     
     
         11 . A method for treating a hemoglobinopathy in a mammal comprising the steps of:
 a. providing hematopoietic progenitor cells or hematopoietic stem cells,   b. contacting the cells with an effective amount of an RNA encoding a DNA-targeting endonuclease into an isolated hematopoietic progenitor cell that cleaves genomic DNA of the cell on chromosome 2 between position 60,716,189 and 60,728,612 (according to UCSC Genome Browser hg 19 human genome assembly) in DNAse hypersensitive sites +62, +58, or +55, thereby causing a genetic modification therein and reducing the mRNA and protein expression of BCL11A; and   c. administering the cells of step (b) into the mammal.   
     
     
         12 . The method of  claim 11 , wherein the RNA encoding the DNA-targeting endonuclease is introduced into the isolated human hematopoietic progenitor cell ex vivo. 
     
     
         13 . The method of  claim 11 , wherein the isolated human hematopoietic progenitor is a cell of the erythroid lineage. 
     
     
         14 . The method of  claim 11 , wherein the isolated human hematopoietic progenitor cell comprises at least one genetic modification. 
     
     
         15 . The method of  claim 14 , wherein the at least one genetic modification is a deletion. 
     
     
         16 . The method of  claim 15 , wherein the deletion removes the entire region between chromosome 2 location 60,716,189-60,728,612 or removes one or more DHSs in the region. 
     
     
         17 . The method of  claim 15 , wherein the deletion removes the entire region between chromosome 2 location 60,716,189-60,728,612. 
     
     
         18 . The method of  claim 15 , wherein the deletion disrupts DHS +62. 
     
     
         19 . The method of  claim 15 , wherein the deletion disrupts DHS +58. 
     
     
         20 . The method of  claim 15 , wherein the deletion disrupts DHS +55.