RNAi MODULATION OF MLL-AF4 AND USES THEREOF

Abstract

The invention relates to compositions and methods for modulating the expression of the MLL-AF4 fusion gene, and more particularly to the downregulation of MLL-AF4 by chemically modified oligonucleotides.

1 . A method for treating a disorder associated with MLL-AF4 fusion expression comprising administering to a subject having or at risk for developing the disorder a composition comprising a double stranded iRNA agent, wherein the iRNA agent comprises a sense strand and an antisense strand each 15-30 nucleotides in length and a double stranded region 15-30 basepairs in length, wherein the antisense strand comprises a region of complementarity to a mRNA encoding an MLL-AF4 fusion gene, wherein the region of complementarity is less than 30 nucleotides in length, and the antisense strand comprises at least 15 contiguous nucleotides from an antisense sequence of agents 1-12 provided in Table 1 (SEQ ID NOs 6, 7, 11, 13, 15, 19, 21, 23, 25, 27, 31, and 33). 
     
     
         2 . The method of  claim 1 , wherein the iRNA agent is selected from the group consisting of agents 1-12 provided in Table 1. 
     
     
         3 . The method of  claim 1 , wherein the disorder is a proliferative disorder, cancer, leukemia, or acute lymphoblastic leukemia and/or is characterized by the presence of a t(4;11) chromosomal translocation and/or the presence of an MLL-AF4 fusion gene. 
     
     
         4 . The method of  claim 1 , wherein the subject is human. 
     
     
         5 . The method of  claim 1 , wherein the iRNA agent comprises at least one nucleotide modification. 
     
     
         6 . The method of  claim 5 , wherein the nucleotide modification is a phosphorothioate or a 2′ modified nucleotide. 
     
     
         7 . The method of  claim 5 , wherein the nucleotide modification is a 2′ sugar modification, a modification in a single strand overhang, a 5′-modification which includes one or more phosphate groups or one or more analogs of phosphate groups. 
     
     
         8 . The method of  claim 5 , wherein the nucleotide modification is a 5′-uridine-adenine-3′ (5′-UA-3′) dinucleotide wherein the uridine is a 2′-modified nucleotide; a 5′-uridineguanine-3′ (5′-UG-3′) dinucleotide, wherein the 5′-uridine is a 2′-modified nucleotide; a 5′-cytidine-adenine-3′ (5′-CA-3′) dinucleotide, wherein the 5′-cytidine is a 2′-modified nucleotide; or a 5′-uridine-uridine-3′ (5′-UU-3′) dinucleotide, wherein the 5′-uridine is a 2′-modified nucleotide. 
     
     
         9 . The method of  claim 5 , wherein the 2′-modification is chosen from the group consisting of: 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), and 2′-O—N-methylacetamido (2′-O-NMA). 
     
     
         10 . The method of  claim 1 , wherein the iRNA agent comprises a cholesterol moiety. 
     
     
         11 . The method of  claim 10 , wherein the cholesterol moiety is conjugated to the 3′-end of the sense strand of the iRNA agent. 
     
     
         12 . The method of  claim 1 , wherein the iRNA agent comprises at least one nucleotide overhang having 1 to 4 unpaired nucleotides. 
     
     
         13 . The method of  claim 12 , wherein the nucleotide overhang is a two nucleotide overhang at the 3′ end of the antisense strand. 
     
     
         14 . The method of  claim 1 , wherein the composition comprises a pharmaceutically acceptable carrier. 
     
     
         15 . The method of  claim 14 , wherein the pharmaceutically acceptable carrier comprises a polycation or a lipid or a lipid based molecule. 
     
     
         16 . The method of  claim 1 , wherein the composition comprises a ligand. 
     
     
         17 . The method of  claim 16 , wherein the ligand is a lipid or lipid-based molecule. 
     
     
         18 . The method of  claim 1 , wherein the method (a) reduces MLL-AF4 fusion gene expression in a cell or tissue of the subject by at least 2%; (b) does not substantially reduce wildtype MLL and/or AF4 mRNA levels of the subject; (c) does not trigger an interferon response; (d) inhibits leukemic proliferation; (e) is accompanied by an increase in apoptosis; (f) is accompanied by a decrease in expression of Hoxa7, Hoxa9, and Meis-1; and/or (g) reduces leukemic engraftment of t(4;11)-positive cells. 
     
     
         19 . A double-stranded iRNA agent wherein the iRNA agent comprises a sense strand and an antisense strand each 15-30 nucleotides in length and a double stranded region 15-30 basepairs in length and the antisense strand comprises a region of complementarity to a mRNA encoding an MLL-AF4 fusion gene, wherein the region of complementarity is less than 30 nucleotides in length, and the antisense strand comprises at least 15 contiguous nucleotides from an antisense sequence of agents 1-12 provided in Table 1 (SEQ ID NOs 6, 7, 11, 13, 15, 19, 21, 23, 25, 27, 31, and 33). 
     
     
         20 . The iRNA agent of  claim 19 , selected from the group consisting of agents 1-12 provided in Table 1.