Methods and compositions for manipulating translation of protein isoforms from alternative initiation start sites

Abstract

Provided herein are antisense oligonucleotides, compositions comprising antisense oligonucleotides, and methods for the use of antisense oligonucleotides in manipulating translation. Expression of isoforms of proteins expressed from different start codons of the same transcript are inhibited by antisense oligonucleotides, which may also enhance expression of non-target isoforms.

1 .- 35 . (canceled) 
     
     
         36 . An isolated antisense oligonucleotide of 12 to 40 nucleotides in length comprising a sequence substantially complementary to a translation start codon of an mRNA that encodes at least two cellular protein isoforms translated from at least two translation start codons of said mRNA, wherein said mRNA encodes a protein consisting of TAR DNA binding protein-43 (TDP-43); or a pharmaceutically acceptable salt thereof. 
     
     
         37 . The isolated antisense oligonucleotide or pharmaceutically acceptable salt thereof of  claim 36 , wherein the oligonucleotide is substantially complementary to the sequence AAGGAAAAUGG AUG AGACAGA (SEQ ID NO: 31) or a portion thereof comprising the  AUG  of Met85. 
     
     
         38 . The isolated antisense oligonucleotide or pharmaceutically acceptable salt thereof of  claim 37 , wherein the antisense oligonucleotide comprises a phosphorodiamidate morpholino oligonucleotide (PMO), a PMO comprising one or more piperazine-containing intersubunit linkages (PMOplus), a PMO-X oligonucleotide, a boronic acid conjugate, a peptide-nucleic acid (PNA), a locked-nucleic acid (LNA), or a 2′-O-methyl oligoribonucleotide. 
     
     
         39 . The isolated antisense oligonucleotide of  claim 38 , wherein the antisense oligonucleotide is a phosphorodiamidate morpholino oligonucleotide comprising one or more piperazine-containing intersubunit linkages (PMOplus). 
     
     
         40 . A pharmaceutical composition, comprising an isolated antisense oligonucleotide of 12 to 40 nucleotides in length comprising a sequence substantially complementary to a translation start codon of an mRNA that encodes at least two cellular protein isoforms translated from at least two translation start codons of said mRNA, wherein said mRNA encodes a protein consisting of TAR DNA binding protein-43 (TDP-43); or a pharmaceutically acceptable salt thereof; and a pharmaceutically acceptable carrier. 
     
     
         41 . The pharmaceutical composition of  claim 40 , wherein the oligonucleotide is substantially complementary to the sequence AAGGAAAAUGG AUG AGACAGA (SEQ ID NO: 31) or a portion thereof comprising the  AUG  of Met85. 
     
     
         42 . A method of inhibiting translation of an isoform of a cellular protein translated from a start codon of an mRNA that comprises at least two start codons, comprising specifically hybridizing to said mRNA an antisense oligonucleotide of any one of  claims 36 - 39  or a pharmaceutical composition of  claim 40  or  41 . 
     
     
         43 . A method of inhibiting translation of an isoform of a cellular protein translated from a start codon of an mRNA that comprises at least two start codons, wherein the isoform is associated with a disease, comprising contacting a cell that expresses the mRNA with an antisense oligonucleotide of any one of  claims 36 - 39 . 
     
     
         44 . A method of inhibiting translation of an isoform of a cellular protein translated from a start codon of an mRNA that comprises at least two start codons, wherein the isoform is associated with a disease, comprising contacting a cell that expresses the mRNA with a pharmaceutical composition of  claim 40  or  41 . 
     
     
         45 . The method of  claim 43 , wherein the disease is a TDP-43 proteinopathy. 
     
     
         46 . The method of  claim 44 , wherein the disease is a TDP-43 proteinopathy.