Methods for Treating Nucleotide Repeat Expansion Disorders Associated with MSH3 Activity - Patent application

Abstract

The present disclosure features compositions and methods useful for treating a nucleotide repeat expansion disorder, e.g., in a subject in need thereof. In some aspects, the compositions and methods described herein are useful for treating a disorder associated with MSH3 activity.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 63 / 196,896, filed June 4, 2021, entitled “METHODS FOR THE TREATMENT OF NUCLEOTIDE REPEAT EXPANSION DISORDERS ASSOCIATED WITH MSH3 ACTIVITY,” the entire disclosure of which is incorporated herein by reference.

[0002] INCORPORATION BY REFERENCE TO SEQUENCE LISTING The contents of the text file named "4398_056PC01_Seqlisting_ST25", created on June 2, 2022, and having a size of 1,013,261 bytes, are incorporated by reference in their entirety into this specification. [Background technology]

[0003] Nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) is a genetic disorder caused by nucleotide repeat expansion (e.g., trinucleotide repeat). Nucleotide repeat expansion (e.g., trinucleotide repeat expansion) is a type of genetic mutation in which nucleotide repeats in a particular gene or intron exceed the normal stable threshold of the gene. Nucleotide repeats (e.g., trinucleotide repeats) can cause toxic effects by resulting in defective or toxic gene products, impairing RNA transcription, and / or forming toxic mRNA transcripts.

[0004] Nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are generally classified by the type of repeat expansion. For example, type 1 disorders, such as Huntington's disease, are caused by CAG repeats that result in a series of glutamine residues known as polyglutamine tracts, type 2 disorders are caused by heterogeneous expansions that are generally small in size, and type 3 disorders, such as fragile X syndrome, are generally characterized by large repeat expansions that are located outside the protein-coding regions of genes. Nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are characterized by a wide variety of symptoms, including progressive degeneration of nerve cells, which is common to type 1 disorders.

[0005] A subject having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) or a subject considered to be at risk of developing a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) has a constitutive nucleotide expansion in a gene associated with the disease (i.e., a nucleotide repeat expansion is present in the gene during embryogenesis). A constitutive nucleotide repeat expansion (e.g., a trinucleotide repeat expansion) can undergo expansion after embryogenesis (i.e., somatic nucleotide repeat expansion). Both constitutive and somatic nucleotide repeat expansions can be associated with the presence of a disease, the age of onset of the disease, and / or the rate of progression of the disease. Summary of the Invention

[0006] The present disclosure features compositions and methods useful for treating a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), e.g., in a subject in need thereof. In some aspects, the compositions and methods described herein are useful for treating a disorder associated with MSH3 activity.

[0007] Oligonucleotides Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the 17-20 contiguous nucleobases begin at positions 876, 877, 878, 879, 880, 881, 882, 883, 884, or 885 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 876-901 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the 20-23 contiguous nucleobases begin at positions 876, 877, 878, 879, 880, 881, or 882 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0008] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 931, 932, 933, 934, 935, 936, 937, 938, 939, or 940 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at positions 931, 932, 933, 934, 935, 936, 937 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0009] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, or 1321 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, or 1318 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0010] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2151, 2152, or 2153 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, or 2150 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0011] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, or 2276 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2267, 2268, 2269, 2270, 2271, 2272, or 2273 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0012] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, wherein the oligonucleotide is at least 95% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at position 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2560, 2561, 2562, or 2563 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases beginning at position 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, or 2560 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0013] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2151, 2152, or 2153 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, or 2149 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0014] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, or 2276 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2267, 2268, 2269, 2270, 2271, or 2272 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0015] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, 2628, 2629, 2630, or 2631 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, or 2627 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0016] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2685, 2686, 2687, 2688, 2689, 2690, 2691, 2692, 2693, or 2694 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases beginning at position 2685, 2686, 2687, 2688, 2689, 2690, or 2691 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0017] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is complementary to 17-20 contiguous nucleobases beginning at positions 2769, 2770, 2771, 2772, 2773, 2774, 2775, 2776, 2777, 2778, or 2779 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2769, 2770, 2771, 2772, 2773, 2774, 2775, or 2776 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0018] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, (the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151), or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is selected from the group consisting of positions 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, 2825, 2826, 2827, 2828, 2829, 2830, 2831, 2832, 2833, 2834, 2835, 2836, 2837, 2838, 2839, 2840, 2841, 2842, 2843, 2844, 2845, 2846, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2855, 2856, 2857, 2858, 2859, 2860, 2861, 2862, 2863, 2864, 2865, 2866, 2867, 2868, 2869, 2870, 2871, 2872, 2873, 2874, 2875, 2876, 2877, 2878, 287 or a pharmaceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length or a pharmaceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20 to 23 adjacent nucleobases at positions 2798 to 2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20 to 23 adjacent nucleobases at positions 2798 to 2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to positions 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, or a pharma- ceutically acceptable salt thereof, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0019] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2950, ​​2951, 2952, 2953, 2954, 2955, 2956, 2957, 2958, or 2959 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2950, ​​2951, 2952, 2953, 2954, 2955, or 2956 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0020] In some embodiments, the oligonucleotide is not any one of antisense oligo numbers 5152-5176 in Table 3.

[0021] In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-5150 and 5152-5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-5150, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-206 and 5152, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-206, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 207-412 and 5153, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 207-412, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 413-618 and 5154, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 413-618, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 619-824 and 5155, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 619-824, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 825-1030 and 5156, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 825-1030, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1031-1236 and 5157, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1031-1236, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1237-1442 and 5158, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1237-1442, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1443-1648 and 5159, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1443-1648, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1649-1854 and 5160, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1649-1854, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1855-2060 and 5161, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1855-2060, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2061-2266 and 5162, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2061-2266, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2267-2472 and 5163, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2267-2472, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2473-2678 and 5164, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2473-2678, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2679-2884 and 5165, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2679-2884, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2885-3090 and 5166, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2885-3090, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3091-3296 and 5167, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3091-3296, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3297-3502 and 5168, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3297-3502, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3503-3708 and 5169, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3503-3708, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3709-3914 and 5170, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3709-3914, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3915-4120 and 5171, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3915-4120, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4121-4326 and 5172, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4121-4326, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4327-4532 and 5173, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4327-4532, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4533-4738 and 5174, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4533-4738, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4739-4944 and 5175, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4739-4944, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4945-5150 and 5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of a nucleobase sequence selected from the group consisting of any of SEQ ID NOs: 4945-5150, or a pharma- ceutically acceptable salt thereof.

[0022] Some embodiments of the present disclosure relate to a single-stranded oligonucleotide (the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 5150 and 5152 to 5176), or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 5150, or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 206 and 5152, or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 206, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of SEQ ID NOs: 207 to 412 and 5153, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of SEQ ID NOs: 207 to 412, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 413-618 and 5154, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 413-618, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 619-824 and 5155, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 619-824, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 825-1030 and 5156, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 825-1030, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 1031-1236 and 5157, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1031-1236, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1237-1442 and 5158, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1237-1442, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1443-1648 and 5159, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1443-1648, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1649-1854 and 5160, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1649-1854, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1855-2060 and 5161, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1855-2060, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2061-2266 and 5162, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2061-2266, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2267-2472 and 5163, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 2267-2472, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2473-2678 and 5164, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2473-2678, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2679-2884 and 5165, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2679-2884, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2885-3090 and 5166, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2885-3090, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3091-3296 and 5167, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3091-3296, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3297-3502 and 5168, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3297-3502, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3503-3708 and 5169, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3503-3708, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 3709-3914 and 5170, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3709-3914, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3915-4120 and 5171, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3915-4120, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4121-4326 and 5172, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4121-4326, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4327-4532 and 5173, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4327-4532, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4533-4738 and 5174, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4533-4738, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4739-4944 and 5175, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4739-4944, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4945-5150 and 5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 4945-5150, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide consists of a nucleobase sequence selected from the group consisting of any one of SEQ ID NOs: 5152-5176, or a pharma- ceutically acceptable salt thereof.

[0023] In some embodiments, the oligonucleotide does not have a nucleobase sequence consisting of any one of SEQ ID NOs: 5152-5176.

[0024] In some aspects described herein, the oligonucleotide described above comprises: (a) a DNA core sequence comprising linked deoxyribonucleosides; (b) a 5' flanking sequence comprising a linking nucleoside; and (c) a 3' flanking sequence containing a linked nucleoside wherein the DNA core comprises a region of at least 10 contiguous nucleobases located between a 5' flanking sequence and a 3' flanking sequence, the 5' flanking sequence and the 3' flanking sequence each comprising at least two linked nucleosides, and at least one nucleoside of each flanking sequence comprises an alternative nucleoside, or a pharma- ceutically acceptable salt thereof.

[0025] In some embodiments, the oligonucleotide comprises at least one alternative internucleoside linkage, or a pharma- ceutically acceptable salt thereof. In some embodiments, the at least one alternative internucleoside linkage is a phosphorothioate internucleoside linkage. In some embodiments, the at least one alternative internucleoside linkage is a 2'-alkoxy internucleoside linkage. In some embodiments, the at least one alternative internucleoside linkage is an alkylphosphate internucleoside linkage. In some embodiments, the oligonucleotide comprises at least one alternative nucleobase, or a pharma- ceutically acceptable salt thereof. In some embodiments, the alternative nucleobase is 5'-methylcytosine, pseudouridine, or 5-methoxyuridine. In some embodiments, the oligonucleotide comprises at least one alternative sugar moiety, or a pharma- ceutically acceptable salt thereof. In some embodiments, the alternative sugar moiety is 2'-OMe or a bicyclic nucleic acid. In some embodiments, the oligonucleotide further comprises a ligand, or a pharma- ceutically acceptable salt thereof, conjugated to the 5' or 3' end of the oligonucleotide via a monovalent or branched divalent or trivalent linker.

[0026] Some embodiments of the present disclosure relate to an oligonucleotide selected from the group consisting of antisense oligonucleotide numbers 1-5150 and 5152-5176 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-5150 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-206 and 5152 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-206 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 207-412 and 5153 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 207-412 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 413-618 and 5154 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 413-618 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 619-824 and 5155 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 619-824 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 825-1030 and 5156 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 825-1030 of Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1031-1236 and 5157 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1031-1236 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1237-1442 and 5158 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1237-1442 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1443-1648 and 5159 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1443-1648 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1649-1854 and 5160 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1649-1854 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1855-2060 and 5161 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1855-2060 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2061-2266 and 5162 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2061-2266 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2267-2472 and 5163 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2267-2472 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2473-2678 and 5164 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2473-2678 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2679-2884 and 5165 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2679-2884 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2885-3090 and 5166 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2885-3090 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3091-3296 and 5167 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3091-3296 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3297-3502 and 5168 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3297-3502 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3503-3708 and 5169 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3503-3708 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3709-3914 and 5170 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3709-3914 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3915-4120 and 5171 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3915-4120 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4121-4326 and 5172 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4121-4326 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4327-4532 and 5173 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4327-4532 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4533-4738 and 5174 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4533-4738 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4739-4944 and 5175 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4739-4944 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4945-5150 and 5176 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4945-5150 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 5152-5176 in Table 3, or a pharma- ceutically acceptable salt thereof.

[0027] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 60% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 70% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 80% at an oligonucleotide concentration of 10 nM.

[0028] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50% at an oligonucleotide concentration of 1 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 60% at an oligonucleotide concentration of 1 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 70% at an oligonucleotide concentration of 1 nM.

[0029] In some embodiments, MSH3 mRNA expression is assessed in vitro. In some embodiments, MSH3 mRNA expression is assessed in a cell-based assay. In some embodiments, MSH3 mRNA expression is assessed in HeLa cells. In some embodiments, MSH3 mRNA expression is determined by quantitative reverse transcription polymerase chain reaction (RT-qPCR). In some embodiments, MSH3 mRNA expression is normalized relative to the mRNA expression of a reference gene. In some embodiments, MSH3 mRNA expression is normalized relative to the mRNA expression of beta-glucuronidase (GUSB). In some embodiments, the decrease in MSH3 mRNA expression is relative to a control. In some embodiments, the control is MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof. In some embodiments, the control is MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof, but in the presence of a control oligonucleotide, or a salt thereof. In some embodiments, the control oligonucleotide, or a salt thereof, is a scrambled luciferase-targeting oligonucleotide. In some embodiments, the reduction in MSH3 mRNA expression is calculated by the delta-delta Ct (ΔΔCT) method. In some embodiments, the delta-delta Ct (ΔΔCT) method involves normalizing MSH3 mRNA expression relative to the mRNA expression of a reference gene and relative to the MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof, but in the presence of a control oligonucleotide, or a salt thereof. In some embodiments, the reference gene is beta-glucuronidase (GUSB) and / or the control oligonucleotide, or a salt thereof, is a scrambled luciferase-targeted oligonucleotide. In some embodiments, the reduction in MSH3 mRNA expression is determined by the method of Example 1.

[0030] In some embodiments, the oligonucleotide is in free base form. In some embodiments, the oligonucleotide is a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is a sodium salt.

[0031] Pharmaceutical compositions and methods of treatment using same In some aspects, the present application is directed to pharmaceutical compositions comprising one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, and a pharma- ceutically acceptable carrier or excipient.

[0032] In some aspects, the present application is directed to a composition comprising one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and a lipid nanoparticle, a polyplex nanoparticle, a lipoplex nanoparticle, or a liposome.

[0033] In some aspects, the application is directed to a method of inhibiting transcription of MSH3 in a cell, the method comprising contacting a cell with one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, a pharmaceutical composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, or a composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for a time sufficient to obtain degradation of mRNA transcripts of the MSH3 gene, inhibiting expression of the MSH3 gene in the cell.

[0034] In some aspects, the application is directed to a method of treating, preventing, or delaying the progression of a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) in a subject in need thereof, the method comprising contacting a cell with one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, a pharmaceutical composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, or a composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for a time sufficient to obtain degradation of mRNA transcripts of the MSH3 gene that inhibits expression of the MSH3 gene in the cell.

[0035] In some aspects, the application is directed to a method of decreasing the level and / or activity of MSH3 in a cell of a subject identified as having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), the method comprising contacting the cell with one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, a pharmaceutical composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, or a composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for a time sufficient to inhibit expression of the MSH3 gene in the cell and obtain degradation of mRNA transcripts of the MSH3 gene.

[0036] In some aspects, the application is directed to a method of inhibiting expression of the MSH3 gene in a cell, the method comprising contacting a cell with one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, a pharmaceutical composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, or a composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and a lipid nanoparticle, polyplex nanoparticle, lipoplex nanoparticle, or liposome, for a time sufficient to obtain degradation of the mRNA transcript of the MSH3 gene, thereby inhibiting expression of the MSH3 gene in the cell, and maintaining the cell for a time sufficient to obtain degradation of the mRNA transcript of the MSH3 gene, thereby inhibiting expression of the MSH3 gene in the cell.

[0037] In some aspects, the application is directed to a method of reducing a nucleotide repeat expansion (e.g., a trinucleotide repeat expansion) in a cell, the method comprising contacting a cell with one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, a pharmaceutical composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein, or a composition of one or more of the oligonucleotides or pharma- ceutically acceptable salts thereof described herein and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for a time sufficient to obtain degradation of mRNA transcripts of the MSH3 gene, inhibiting expression of the MSH3 gene in the cell.

[0038] In some embodiments, the cell is in a subject. In some embodiments, the subject is a human. In some embodiments, the cell is a cell of the central nervous system or a muscle cell.

[0039] In some embodiments, the subject is identified as having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder). In some embodiments, the nucleotide repeat expansion disorder is spinocerebellar ataxia type 36 or frontotemporal dementia. In some embodiments, the nucleotide repeat expansion disorder is a trinucleotide repeat expansion disorder. In some embodiments, the trinucleotide repeat expansion disorder is a polyglutamine disease. In some embodiments, the polyglutamine disease is selected from the group consisting of dentatorubral-pallidoluysian atrophy, Huntington's disease, spinobulbar muscular atrophy, spinocerebellar ataxia type 1, spinocerebellar ataxia type 2, spinocerebellar ataxia type 3, spinocerebellar ataxia type 6, spinocerebellar ataxia type 7, spinocerebellar ataxia type 17, and Huntington's disease-related disease type 2. In some embodiments, the nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) is Huntington's disease.

[0040] In some embodiments, the nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) is a non-polyglutamine disease. In some embodiments, the non-polyglutamine disease is selected from the group consisting of fragile X syndrome, fragile X-associated tremor / ataxia syndrome, fragile XE mental retardation, Friedreich's ataxia, myotonic dystrophy type 1, spinocerebellar ataxia type 8, spinocerebellar ataxia type 12, oculopharyngeal muscular dystrophy, fragile X-associated premature ovarian failure, FRA2A syndrome, FRA7A syndrome, and early infantile epileptic encephalopathy. In some embodiments, the nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) is Friedreich's ataxia. In some embodiments, the nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) is myotonic dystrophy type 1.

[0041] In some aspects, the present application is directed to one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, pharmaceutical compositions of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, or compositions of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for use in the prophylaxis or treatment of a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder). In some aspects, the one or more of the oligonucleotides described herein, or pharma- ceutical compositions of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, or compositions of one or more of the oligonucleotides described herein, or pharma- ceutical acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, are administered intrathecally.

[0042] In some embodiments, one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, a pharmaceutical composition of one or more of the oligonucleotides described herein, or pharma-ceutically acceptable salts thereof, or a composition of one or more of the oligonucleotides described herein, or pharma-ceutically acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, is administered intracerebroventricularly.

[0043] In some embodiments, one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, a pharmaceutical composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, or a composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, is administered intramuscularly.

[0044] In some aspects, the application is directed to a method of treating, preventing, or delaying the progression of a disorder in a subject in need thereof, wherein the subject is afflicted with a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), the method comprising administering to the subject one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, a pharmaceutical composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, or a composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes.

[0045] In some embodiments, the method of treating, preventing, or delaying the progression of a disorder in a subject further comprises administering an additional therapeutic agent, hi some embodiments, the additional therapeutic agent is another oligonucleotide that hybridizes to an mRNA encoding the huntingtin gene, or a pharma- ceutically acceptable salt thereof.

[0046] In some embodiments, the methods of treating, preventing, or delaying the progression of a disorder in a subject delay the progression of a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) by at least 120 days, e.g., at least 6 months, at least 12 months, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years or more, as compared to expected progression.

[0047] In some aspects, the application is directed to one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, a pharmaceutical composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, or a composition of one or more of the oligonucleotides described herein, or pharma- ceutically acceptable salts thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, for use in preventing or delaying the progression of a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) in a subject.

[0048] definition For convenience, the meanings of some terms and phrases used in the specification, examples, and appended claims are provided below. Unless otherwise stated or implied from the context, the following terms and phrases include the meanings provided below. The definitions are provided to help describe certain embodiments and are not intended to limit the claimed technology, since the scope of the technology is limited only by the claims. Unless otherwise specified, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which this technology belongs. If there is an apparent discrepancy between the usage of a term in the art and its definition provided herein, the definition provided herein shall prevail.

[0049] In this application, unless otherwise clear from the context, (i) the term "a" may be understood to mean "at least one," (ii) the term "or" may be understood to mean "and / or," and (iii) the terms "including" and "comprising" may be understood to encompass the listed elements or steps, whether presented by themselves or with one or more additional elements or steps.

[0050] As used herein, the terms "about" and "approximately" refer to values ​​within 10% above and below the stated value. For example, the term "about 5 nM" indicates a range of 4.5 to 5.5 nM.

[0051] The term "at least" before a number or series of numbers is understood to include the number adjacent to the term "at least" and all subsequent numbers or integers that may be logically included, as is clear from the context. For example, the number of nucleotides in a nucleic acid molecule must be an integer. For example, "at least 18 nucleotides of a 21 nucleotide nucleic acid molecule" means that 18, 19, 20, or 21 nucleotides have the indicated property. When at least is present before a series of numbers or a range, it is understood that "at least" can modify each of the numbers in the series or range. "At least" is also not limited to integers (e.g., "at least 5%" includes 5.0%, 5.1%, and 5.18% without considering the number of significant digits).

[0052] As used herein, "less than" or "less than" is understood as the value adjacent to the phrase and the logically lower value or integer to zero, as is logical from the context.For example, an oligonucleotide with "3 or less mismatches to target sequence" has 3, 2, 1 or 0 mismatches to target sequence.When "less than" is present before a series of numbers or a range, it is understood that "less than" can modify each of the numbers in the series or range.

[0053] As used herein, the term "administration" refers to administration of a composition (e.g., a compound or a preparation containing a compound as described herein) to a subject or system. Administration to an animal subject (e.g., to a human) can be by any suitable route, such as those routes described herein.

[0054] As used herein, "combination therapy" or "administered in combination" means that two (or more) different agents or treatments are administered to a subject as part of a defined treatment regimen for a particular disease or condition. The treatment regimen specifies the dose and periodicity of administration of each agent such that the effects of the separate agents on the subject overlap. In some embodiments, the delivery of two or more agents is simultaneous or parallel, and the agents may be co-formulated. In some embodiments, the two or more agents are not co-formulated, but are administered in a sequential manner as part of a given regimen. In some embodiments, the administration of two or more agents or treatments in combination is such that the reduction in symptoms, or other parameters associated with the disorder, is greater than that observed with one agent or treatment delivered alone or in the absence of the other. The effect of the two treatments may be partially additive, fully additive, or greater than additive (e.g., synergistic). Sequential or substantially simultaneous administration of each therapeutic agent may be by any suitable route, including, but not limited to, oral, intraocular, subcutaneous, intracisternal, intravenous, intramuscular, and direct absorption through mucosal tissue. The therapeutic agents may be administered by the same route or by different routes. For example, one therapeutic agent of the combination may be administered by intravenous injection, while an additional therapeutic agent of the combination may be administered orally.

[0055] As used herein, the term "MSH3" refers to MutS homolog 3, a DNA mismatch repair protein, and has an amino acid sequence from any vertebrate or mammalian source, including, but not limited to, for example, human, bovine, chicken, rodent, mouse, rat, porcine, ovine, primate, monkey, and guinea pig, unless otherwise specified. The term also refers to fragments and variants of native MSH3 that maintain at least one in vivo or in vitro activity of native MSH3. The term encompasses unprocessed full-length precursor forms of MSH3 as well as mature forms resulting from post-translational cleavage of the signal peptide. MSH3 is encoded by the MSH3 gene. The nucleic acid sequence of an exemplary Homo sapiens (human) MSH3 gene is set forth in NCBI reference NM_002439.4 or SEQ ID NO: 385. The term "MSH3" also refers to naturally occurring variants of wild-type MSH3 protein, such as proteins having at least 85% identity (e.g., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9% identity or greater) to the amino acid sequence of wild-type human MSH3 (as set forth in NCBI Reference No. NP_002430.3 or SEQ ID NO: 386). An exemplary nucleic acid sequence of a Mus musculus (mouse) MSH3 gene is set forth in NCBI Reference No. NM_010829.2 or SEQ ID NO: 387. An exemplary nucleic acid sequence of a Rattus norvegicus (rat) MSH3 gene is set forth in NCBI Reference No. NM_001191957.1 or SEQ ID NO: 388. An exemplary nucleic acid sequence of a Macaca fascicularis (cynomolgus monkey) MSH3 gene is set forth in NCBI Reference No. XM_005557283.2 or SEQ ID NO:389.

[0056] The term "MSH3" as used herein also refers to a specific polypeptide expressed in cells due to naturally occurring DNA sequence variations of the MSH3 gene, such as single nucleotide polymorphisms of the MSH3 gene. Numerous SNPs within the MSH3 gene have been identified and can be found, for example, in NCBI dbSNP (see, for example, www.ncbi.nlm.nih.gov / snp). Non-limiting examples of SNPs within the MSH3 gene include NCBI dbSNP accession numbers: rs1650697, rs70991108, rs10168, rs26279, ... , rs26282, rs26779, rs26784, rs32989, rs33003, rs33008, rs33013, rs40139, rs181747, rs184967, rs245346, rs245397, rs249633, rs380691, rs408626, rs442767, rs836802, rs836808, rs863221, rs1105525, rs1428030, rs1478834, rs1650694 , rs1650737, rs1677626, rs1677658, rs1805355, rs2897298, rs3045983, rs3797897, rs4703819, rs6151627, rs6151640, rs6151662, rs6151670, rs6151735, rs6151838, rs7709909, rs7712332, rs10079641, rs12513549, and rs12522132.

[0057] As used herein, "target sequence" refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during transcription of the MSH3 gene, including mRNA that is the product of RNA processing of a primary transcript. In one embodiment, the target portion of the sequence is at or near a portion of the nucleotide sequence of an mRNA molecule formed during transcription of the MSH3 gene that is at least long enough to serve as a substrate for oligonucleotide-directed (e.g., antisense oligonucleotide (ASO)-directed) cleavage. The target sequence can be, for example, about 9-36 nucleotides in length, e.g., about 15-30 nucleotides in length. For example, the target sequence may be 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or about 15-30 nucleotides, 15-29, 15-28, 15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-25, 18-26, 18-27, 18-28, 18-29, 18-30, 18-30, 18-4 ... The length may be 22, 18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24, 20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 nucleotides in length. Ranges and lengths intermediate to the ranges and lengths listed above are also contemplated.

[0058] "G", "C", "A", "T" and "U" each generally represent naturally occurring nucleotides containing guanine, cytosine, adenine, thymidine and uracil, respectively, as bases. However, it will be understood that the term "nucleotide" may refer to alternative nucleotides or surrogate replacement moieties, as further detailed below. Those skilled in the art will appreciate that guanine, cytosine, adenine and uracil may be substituted with other moieties without substantially changing the base pairing properties of an oligonucleotide containing such a substituted nucleotide. For example, but not limited to, a nucleotide containing inosine as its base may base pair with a nucleotide containing adenine, cytosine or uracil. Thus, a nucleotide containing uracil, guanine or adenine may be replaced in the nucleotide sequence of an oligonucleotide with, for example, a nucleotide containing inosine. In another example, adenine and cytosine anywhere in an oligonucleotide may be replaced with guanine and uracil, respectively, to form a GU wobble base pair with a target mRNA. Sequences containing such replacement moieties are suitable for the compositions and methods featured herein.

[0059] The terms "nucleobase" and "base" include purine (e.g., adenine and guanine) and pyrimidine (e.g., uracil, thymine, and cytosine) moieties present in nucleosides and nucleotides that form hydrogen bonds during nucleic acid hybridization. The term nucleobase also encompasses alternative nucleobases that may differ from naturally occurring nucleobases but function during nucleic acid hybridization. In this context, "nucleobase" refers to both naturally occurring nucleobases, such as adenine, guanine, cytosine, thymidine, uracil, xanthine, and hypoxanthine, as well as alternative nucleobases. Such variants are described, for example, in Hirao et al (2012) Accounts of Chemical Research vol 45 page 2055 and Bergstrom (2009) Current Protocols in Nucleic Acid Chemistry Suppl.37 1.4.1.

[0060] The term "nucleoside" refers to a monomeric unit of an oligonucleotide or polynucleotide having a nucleobase and a sugar moiety. Nucleosides can include naturally occurring as well as alternative nucleosides, such as those described herein. The nucleobase of a nucleoside can be a naturally occurring nucleobase or an alternative nucleobase. Similarly, the sugar moiety of a nucleoside can be a naturally occurring sugar or an alternative sugar.

[0061] The term "alternative nucleoside" refers to a nucleoside having an alternative sugar or alternative nucleobase, such as those described herein.

[0062] In some aspects, the nucleobase moiety is modified by changing the purine or pyrimidine to a modified purine or pyrimidine, such as a substituted purine or substituted pyrimidine, such as an "alternate nucleobase" selected from isocytosine, pseudoisocytosine, 5-methylcytosine, 5-thiozolo-cytosine, 5-propynyl-cytosine, 5-propynyl-uridine, 5-bromouridine, 5-thiazolo-uridine, 2-thio-uridine, pseudouridine, 1-methylpseudouridine, 5-methoxyuridine, 2'-thio-thymine, inosine, diaminopurine, 6-aminopurine, 2-aminopurine, 2,6-diaminopurine, and 2-chloro-6-aminopurine.

[0063] The nucleobase moieties may be designated by the letter code of the corresponding nucleobase, e.g., A, T, G, C, or U, and each letter may include alternative nucleobases with equivalent functions. In some embodiments, e.g., for gapmers, 5-methylcytosine LNA nucleosides may be used.

[0064] "Sugar" or "sugar moiety" includes naturally occurring sugars having a furanose ring. Sugar also includes "sugar substitutes," defined as structures that can replace the furanose ring of a nucleoside. In some embodiments, the sugar substitute is a non-furanose (or 4'-substituted furanose) ring or ring system or open system. Such structures can include simple changes compared to the natural furanose ring, such as a six-membered ring, or can be more complex, as in the case of the acyclic systems used in peptide nucleic acids. The sugar substitute can include sugar surrogates in which the furanose ring is replaced with another ring system, such as, for example, a morpholino or hexitol ring system. Sugar moieties useful in preparing oligonucleotides bearing the motif include β-D-ribose, β-D-2'-deoxyribose, substituted sugars (such as 2', 5' and bis-substituted sugars), 4'-S-sugars (such as 4'-S-ribose, 4'-S-2'-deoxyribose and 4'-S-2'-substituted ribose), bicyclic sugar surrogates (2'-O-CH 2 -4' or 2'-O-(CH 2 ) 2-4'-bridged ribose derived bicyclic sugars, as well as sugar surrogates, such as where the ribose ring is replaced with a morpholino or hexitol ring system. The type of heterocyclic base and internucleoside linkage used at each position varies and is not a determining factor of the motif. In most nucleosides with alternative sugar moieties, the heterocyclic nucleobase is generally maintained to allow hybridization.

[0065] "Nucleotide" as used herein refers to a monomeric unit of an oligonucleotide or polynucleotide comprising a nucleoside and an internucleoside linkage. The internucleoside linkage may comprise a phosphate linkage. Similarly, a "linked nucleoside" may be linked by a phosphate linkage. Many "alternative internucleoside linkages" are known in the art, including, but not limited to, phosphate, phosphorothioate and boronophosphate linkages. Alternative nucleosides include bicyclic nucleosides (BNAs), such as locked nucleosides (LNAs (e.g., A-LNA, 5mC L-NA, G-LNA, T-LNA) and constrained ethyl (cEt) nucleosides), peptide nucleosides (PNAs), phosphotriesters, phosphorothioates, phosphoramidates, and other variants on the phosphate backbone of natural nucleosides, including those described herein.

[0066] "Alternative nucleotide," as used herein, refers to a nucleotide having an alternative nucleoside or sugar and internucleoside linkage, which may include alternative nucleoside linkages.

[0067] The terms "oligonucleotide" and "polynucleotide" as used herein are defined as molecules that contain two or more covalently linked nucleosides as generally understood by those skilled in the art. Such covalently linked nucleosides may be referred to as nucleic acid molecules or oligomers. Oligonucleotides are usually produced in a laboratory by solid-phase chemical synthesis followed by purification. When referring to the sequence of an oligonucleotide, it refers to the sequence or order of the nucleobase moieties of the covalently linked nucleotides or nucleosides, or modifications thereof. An oligonucleotide may be artificial. For example, an oligonucleotide may be chemically synthesized and purified or isolated. Oligonucleotides are also intended to include compounds with (i) one or more furanose moieties replaced by furanose derivatives or any cyclic or acyclic structure that can be used as a covalent attachment point for the base moiety, (ii) one or more phosphodiester linkages that are either modified as in the case of phosphoramidate or phosphorothioate linkages, or completely replaced with a suitable linkage moiety as in the case of formacetal or riboacetal linkages, and / or (iii) one or more linked furanose-phosphodiester linkages that are replaced by any cyclic or acyclic structure that can be used as a covalent attachment point for the base moiety. Oligonucleotides may include one or more alternative nucleosides or nucleotides (e.g., including those described herein). It is further understood that oligonucleotides include compositions that lack sugar moieties or nucleobases, but can still pair with or hybridize to a target sequence. "Oligonucleotide" refers to short polynucleotides (e.g., 100 or fewer linked nucleosides).

[0068] As used herein, the term "oligonucleotide comprising a nucleobase sequence" refers to an oligonucleotide that comprises a chain of nucleotides or nucleosides described by a sequence referenced using standard nucleotide nomenclature.

[0069] The term "contiguous nucleobase region" refers to a region of an oligonucleotide that is complementary to a target nucleic acid. This term may be used interchangeably herein with the term "contiguous nucleotide sequence" or "contiguous nucleobase sequence". In some embodiments, all nucleotides of an oligonucleotide are present within a contiguous nucleotide or nucleoside region. In some embodiments, an oligonucleotide comprises a contiguous nucleotide region and may further comprise a nucleotide linker region that may be used to attach a nucleotide(s) or nucleoside(s), e.g., a functional group, to the contiguous nucleotide sequence. The nucleotide linker region may be complementary to a target nucleic acid. In some embodiments, the internucleoside linkages present between the nucleotides of the contiguous nucleotide region are all phosphorothioate internucleoside linkages. In some embodiments, the contiguous nucleotide region comprises one or more sugar-modified nucleosides.

[0070] The term "gapmer," as used herein, refers to an oligonucleotide that includes a region of an RNase H recruiting oligonucleotide (the gap or DNA core) flanked on the 5' and 3' sides by regions that include one or more affinity-enhancing alternative nucleosides (wing or flanking sequences). Various gapmer designs are described herein. Headmers and tailmers are oligonucleotides capable of recruiting RNase H that lack one of the flanks, i.e., only one end of the oligonucleotide contains the affinity-enhancing alternative nucleosides. In the case of a headmer, the 3' flanking sequence is lacking (i.e., the 5' flanking sequence includes the affinity-enhancing alternative nucleosides), and in the case of a tailmer, the 5' flanking sequence is lacking (i.e., the 3' flanking sequence includes the affinity-enhancing alternative nucleosides). A "mixed flanking sequence gapmer" refers to a gapmer in which the flanking sequence comprises at least one alternative nucleoside, such as at least one DNA nucleoside or at least one 2'-substituted alternative nucleoside, such as 2'-O-alkyl-RNA, 2'-O-methyl-RNA, 2'-alkoxy-RNA, 2'-O-methoxyethyl-RNA (MOE), 2'-amino-DNA, 2'-fluoro-RNA, 2'-F-ANA nucleoside(s), or bicyclic nucleosides (e.g., locked or constrained ethyl (cEt) nucleosides). In some embodiments, a mixed flanking sequence gapmer has one flanking sequence (e.g., on the 5' or 3' side) that comprises an alternative nucleoside and the other flanking sequence (on the 3' or 5' side, respectively) comprises the 2'-substituted alternative nucleoside(s).

[0071] A "linker" or "linking group" is a bond between two atoms that connects one chemical group or segment of interest to another chemical group or segment of interest by one or more covalent bonds. The oligonucleotides disclosed herein may contain one or more linkers that can link one or more oligonucleotides disclosed herein to one or more other oligonucleotides disclosed herein, and / or to any other oligonucleotides disclosed herein, and / or to any conjugate moiety. For example, linkers can be used to link oligonucleotides disclosed herein to oligonucleotides that target the huntingtin gene.

[0072] The linker may be susceptible to cleavage ("cleavable linker"), thereby facilitating the release of different oligonucleotides and / or different conjugate moieties disclosed herein. Such cleavable linkers may be susceptible under suitable conditions, for example, to nuclease-induced cleavage, acid-induced cleavage, light-induced cleavage, peptidase-induced cleavage, esterase-induced cleavage, and disulfide bond cleavage. Suitable cleavable linkers for use in cleavable linkers include linkers that are sufficiently stable outside a cell, but are cleaved upon entry into a target cell to release the two moieties held together by the linker.

[0073] Alternatively, the linker may be substantially resistant to cleavage ("non-cleavable linker"). Such non-cleavable linker may be any chemical moiety capable of linking one or more different oligonucleotides disclosed herein to one or more other oligonucleotides disclosed herein and / or any complex moiety that is stably covalently linked, and does not fall into the categories listed above for cleavable linkers. Thus, non-cleavable linkers are substantially resistant to acid-induced cleavage, nuclease-induced cleavage, light-induced cleavage, peptidase-induced cleavage, esterase-induced cleavage, and disulfide bond cleavage. Furthermore, "non-cleavable" refers to the ability of the chemical bond in or adjacent to the linker to resist cleavage induced by acid, nuclease, photocleavable cleavage agent, peptidase, esterase, or chemical or physiological compound that cleaves disulfide bonds, provided that the oligonucleotides disclosed herein do not lose their activity or intended purpose.

[0074] The conjugate moiety can be attached to the oligonucleotide directly or via a linking moiety (e.g., a linker or tether). The linker serves to covalently link the third region, e.g., the conjugate moiety, to the oligonucleotide (e.g., at the end of region A or C). In some embodiments, the conjugate or oligonucleotide conjugate can include a linker region disposed between the oligonucleotide and the conjugate moiety. In some embodiments, the linker between the conjugate and the oligonucleotide is biochemically cleavable. Phosphodiester containing biochemically cleavable linkers are described in more detail in WO2014 / 076195 (incorporated herein by reference).

[0075] In some embodiments, two or more linkers may be linked in tandem. When multiple linkers connect one or more oligonucleotides disclosed herein to one or more other oligonucleotides disclosed herein and / or to any conjugate moiety, each of the linkers may be the same or different.

[0076] As used herein, unless otherwise indicated, the term "complementary," when used to describe a first nucleotide or nucleoside sequence in relation to a second nucleotide or nucleoside sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide or nucleoside sequence to hybridize to form a double-stranded structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as would be understood by one of skill in the art. Such conditions may be, for example, stringent conditions, which may include 400 mM NaCl, 40 mM PIPES (pH 6.4), 1 mM EDTA, at 50°C or 70°C for 12-16 hours, followed by washing (see, for example, "Molecular Cloning: A Laboratory Manual, Sambrook, et al. (1989) Cold Spring Harbor Laboratory Press). Other conditions, such as those that may occur inside an organism, such as physiologically relevant conditions, may be used. Those skilled in the art will be able to determine the optimal set of conditions for testing the complementarity of two sequences according to the ultimate use of the hybridized nucleotide or nucleoside.

[0077] "Complementary" sequences, as used herein, may include or be formed entirely of non-Watson-Crick base pairs and / or base pairs formed from non-natural and alternative nucleotides or nucleosides, so long as the above requirements regarding their ability to hybridize are met. Such non-Watson-Crick base pairs include, but are not limited to, G:U wobble base pairing or Hoogsteen base pairing. Complementary sequences between an oligonucleotide and a target sequence as described herein include base pairing over the entire length of one or both nucleotide or nucleoside sequences of an oligonucleotide or polynucleotide containing a first nucleotide or nucleoside sequence and an oligonucleotide or polynucleotide containing a second nucleotide or nucleoside sequence. Such sequences may be referred to herein as "fully complementary" to each other. However, when a first sequence is referred to as "substantially complementary" to a second sequence herein, the two sequences may be completely complementary, or they may form one or more, but generally no more than five, four, three or two mismatched base pairs upon hybridization into a duplex of up to 30 base pairs, while retaining the ability to hybridize under conditions most relevant to their ultimate use, e.g., inhibition of gene expression by the RNase H-mediated pathway. "Substantially complementary" may refer to a polynucleotide that is substantially complementary to a contiguous portion of an mRNA of interest (e.g., an mRNA encoding MSH3). For example, a polynucleotide is complementary to at least a portion of an MSH3 mRNA if the sequence is substantially complementary to a non-interrupted portion of an mRNA encoding MSH3.

[0078] As used herein, the term "region of complementarity" refers to a region on an oligonucleotide that is substantially complementary to all or a portion of a gene, primary transcript, sequence (e.g., a target sequence, e.g., an MSH3 nucleotide sequence), or mRNA processed to interfere with the expression of an endogenous gene (e.g., MSH3). When the region of complementarity is not completely complementary to the target sequence, mismatches may occur in the internal or terminal regions of the molecule. In general, mismatches are most tolerated in the terminal regions, e.g., within 5, 4, 3, or 2 nucleotides of the 5' and / or 3' ends of the oligonucleotide.

[0079] As used herein, an "agent that decreases the level and / or activity of MSH3" refers to any polynucleotide agent (e.g., an oligonucleotide, e.g., ASO) that decreases the level or inhibits the expression of MSH3 in a cell or subject. The phrase "inhibiting expression of MSH3" as used herein includes inhibition of expression of any MSH3 gene (e.g., mouse MSH3 gene, rat MSH3 gene, monkey MSH3 gene, or human MSH3 gene, etc.), as well as variants or mutants of the MSH3 gene that encode the MSH3 protein. Thus, the MSH3 gene can be a wild-type MSH3 gene, a mutant MSH3 gene, or a transgenic MSH3 gene in the context of a genetically engineered cell, cell population, or organism.

[0080] "Reducing the activity of MSH3" means decreasing the level of activity associated with MSH3 (e.g., by decreasing the amount of nucleotide repeats in a gene associated with a nucleotide repeat expansion disorder, e.g., a trinucleotide repeat expansion disorder, associated with MSH3 activity). The activity level of MSH3 can be measured using any method known in the art (e.g., by directly sequencing a gene associated with a nucleotide repeat expansion disorder and measuring the level of nucleotide repeats).

[0081] "Decreasing the level of MSH3" means lowering the level of MSH3 in a cell or subject, for example, by administering an oligonucleotide, or a pharma- ceutically acceptable salt thereof, to the cell or subject. The level of MSH3 can be measured using any method known in the art (e.g., by measuring the level of MSH3 mRNA or the level of MSH3 protein in the cell or subject).

[0082] "Modulating the activity of a MutSβ heterodimer containing MSH3" means changing the level of activity associated with the MutSβ heterodimer or associated downstream effect. The activity level of the MutSβ heterodimer can be measured using any method known in the art.

[0083] As used herein, the term "inhibitor" refers to any agent that reduces the level and / or activity of a protein (e.g., MSH3). Non-limiting examples of inhibitors include polynucleotides (e.g., oligonucleotides, e.g., ASOs). The term "inhibit" as used herein is used interchangeably with "reduce," "silence," "downregulate," "suppress," and other similar terms, and includes any level of inhibition.

[0084] The phrase "contacting a cell with an oligonucleotide", such as an oligonucleotide, as used herein includes contacting a cell by any possible means.Contacting a cell with an oligonucleotide includes contacting a cell with an oligonucleotide in vitro or contacting a cell with an oligonucleotide in vivo.Contacting can be performed directly or indirectly.Thus, for example, the oligonucleotide can be physically contacted with the cell by the individual who performs the method, or alternatively, the oligonucleotide agent can be in a situation that allows or causes it to contact the cell later.

[0085] Contacting cells in vitro can be performed, for example, by incubating cells with oligonucleotide. Contacting cells in vivo can be performed, for example, by injecting oligonucleotide into or near the tissue where the cells are located, or by injecting oligonucleotide agent into another area, for example, bloodstream or subcutaneous space, so that the agent will then reach the tissue where the contacted cells are located. For example, the oligonucleotide can contain and / or be bound to a ligand, for example, GalNAc3, that guides the oligonucleotide to the site of interest, for example, liver. A combination of in vitro and in vivo contacting methods is also possible. For example, cells can be contacted with oligonucleotide in vitro and then transplanted into a subject.

[0086] In one aspect, contacting a cell with an oligonucleotide includes "introducing" or "delivering" an oligonucleotide into a cell by promoting or causing uptake or absorption into the cell. Absorption or uptake of the ASO can occur through unassisted diffusive or active cellular processes, or by auxiliary agents or devices. Introduction of the oligonucleotide into a cell can be in vitro and / or in vivo. For example, in in vivo introduction, the oligonucleotide can be injected into a tissue site or administered systemically. In vitro introduction into a cell includes methods known in the art, such as electroporation and lipofection. Further approaches are described herein below and / or known in the art.

[0087] As used herein, "lipid nanoparticles" or "LNPs" are vesicles that contain a lipid layer that encapsulates medicamentously active molecules, such as nucleic acid molecules, such as oligonucleotides. LNPs refer to stable nucleic acid-lipid particles. LNPs usually contain cationic lipids, non-cationic lipids, and lipids that prevent particle aggregation (e.g., PEG-lipid conjugates). LNPs are described, for example, in U.S. Patent Nos. 6,858,225, 6,815,432, 8,158,601, and 8,058,069, the entire contents of which are incorporated herein by reference.

[0088] As used herein, the term "liposome" refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one or more bilayers. Liposomes include unilamellar and multilamellar vesicles with a membrane formed from lipophilic material and an aqueous interior. The aqueous portion contains the oligonucleotide composition. The lipophilic material separates the aqueous interior from the aqueous exterior, which usually does not contain the oligonucleotide composition, but in some instances may. Liposomes also include "sterically stabilized" liposomes, which term, as used herein, refers to liposomes that contain one or more specialized lipids, which, when incorporated into the liposome, provide an extended circulation life compared to liposomes that lack such specialized lipids.

[0089] A "micelle" is defined herein as a particular type of molecular assembly in which amphiphilic molecules are arranged in a spherical structure such that all the hydrophobic portions of the molecule face inward, while the hydrophilic portions remain in contact with the surrounding aqueous phase. The reverse arrangement exists when the environment is hydrophobic.

[0090] The term "antisense" as used herein refers to a nucleic acid comprising an oligonucleotide or polynucleotide that is sufficiently complementary to all or a portion of a gene, primary transcript, or processed mRNA so as to interfere with the expression of an endogenous gene (e.g., MSH3). A "complementary" polynucleotide is one that can base pair according to the standard Watson-Crick complementarity rules. Specifically, purines will base pair with pyrimidines to form combinations of guanine paired with cytosine (G:C) and either adenine paired with thymine (A:T) in the case of DNA, or adenine paired with uracil (A:U) in the case of RNA. It is understood that two polynucleotides can hybridize to each other, even if they are not completely complementary to each other, provided that each has at least one region that is substantially complementary to the other.

[0091] As used herein, the terms "effective amount," "therapeutically effective amount," and "sufficient amount" of an agent that decreases the level and / or activity of MSH3 described herein (e.g., in a cell or a subject) refer to an amount sufficient to effect a beneficial or desired result, including a clinical result, when administered to a subject, including a human, and thus, "effective amount" or its synonyms will depend on the context in which it is being applied. For example, in the context of treating a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), the amount is the amount of an agent that decreases the level and / or activity of MSH3 sufficient to effect a therapeutic response when compared to the response obtained without administering the agent that decreases the level and / or activity of MSH3. The amount of a given agent that decreases the level and / or activity of MSH3 described herein that would correspond to such an amount will vary depending on a variety of factors, such as the given agent, pharmaceutical formulation, route of administration, type of disease or disorder, identity of the subject or host being treated (e.g., age, sex, and / or weight), etc., but may nevertheless be routinely determined by one of skill in the art. Also, as used herein, a "therapeutically effective amount" of an agent that decreases the level and / or activity of MSH3 of the present disclosure is an amount that produces a beneficial or desired result in a subject when compared to a control. As defined herein, a therapeutically effective amount of an agent that decreases the level and / or activity of MSH3 of the present disclosure can be readily determined by one of skill in the art by routine methods known in the art. Dosage regimens can be adjusted to provide an optimal therapeutic response.

[0092] A "prophylactically effective amount," as used herein, is intended to include an amount of oligonucleotide sufficient to prevent or ameliorate a disease or one or more symptoms of a disease when administered to a subject having or predisposed to having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder). Ameliorating a disease includes slowing the progression of the disease or reducing the severity of a disease that subsequently develops. A "prophylactically effective amount" may vary depending on the oligonucleotide, the method of administration of the agent, the degree of disease risk, and the medical history, age, weight, family history, genetic makeup, type of prior or concomitant treatment, if any, and other individual characteristics of the patient being treated. A prophylactically effective amount may refer, for example, to an amount of an agent that reduces the level and / or activity of MSH3 (e.g., in a cell or a subject) as described herein, or may refer to an amount that, when administered to a subject, including a human, is sufficient to delay the onset of one or more of the nucleotide repeat disorders (e.g., trinucleotide repeat expansion disorders) described herein by at least 120 days, e.g., at least 6 months, at least 12 months, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years or more, as compared to expected onset.

[0093] A "therapeutically effective amount" or a "prophylactically effective amount" also includes an amount of oligonucleotide (either administered in single or multiple doses) that produces some desired local or systemic effect, at a reasonable benefit / risk ratio applicable to any treatment. The oligonucleotides used in the methods herein may be administered in an amount sufficient to produce a reasonable benefit / risk ratio applicable to such treatment.

[0094] As used herein, the term "region of complementarity" refers to a region on an oligonucleotide that is substantially complementary to all or a portion of a gene, primary transcript, sequence (e.g., a target sequence, e.g., an MSH3 nucleotide sequence), or mRNA processed to interfere with the expression of an endogenous gene (e.g., MSH3). When the region of complementarity is not completely complementary to the target sequence, mismatches may occur in the internal or terminal regions of the molecule. In general, mismatches are most tolerated in the terminal regions, e.g., within 5, 4, 3, or 2 nucleotides of the 5' and / or 3' ends of the oligonucleotide.

[0095] An "amount effective to reduce a nucleotide repeat expansion" of a particular gene refers to an amount of an agent that reduces the level and / or activity of MSH3 as described herein (e.g., in a cell or a subject), or an amount that, when administered to a subject, including a human, is sufficient to reduce a nucleotide repeat expansion of a particular gene (e.g., a gene associated with a nucleotide repeat expansion disorder as described herein, e.g., a trinucleotide repeat expansion disorder).

[0096] As used herein, the term "subject identified as having a nucleotide repeat expansion disorder" refers to a subject who has been identified as having a disease or condition of, or of a molecular or pathological condition associated with, a nucleotide repeat expansion disorder, such as identification of a nucleotide repeat expansion disorder or a symptom thereof, or identification of a subject having or suspected of having a nucleotide repeat expansion disorder who may benefit from a particular treatment regimen.

[0097] As used herein, "trinucleotide repeat expansion disorder" refers to a classification of genetic diseases or disorders characterized by excess trinucleotide repeats (e.g., trinucleotide repeats such as CAG) in a target gene or intron that exceed the normal stable threshold of the gene or intron. Nucleotide repeats are common in the human genome and are not usually associated with disease. However, in some cases, expansion of the repeat number beyond a stable threshold leads to disease, and the severity of symptoms can generally be correlated with the number of repeats. Nucleotide repeat expansion disorders include "polyglutamine" disorders and "non-polyglutamine" disorders.

[0098] "Determining the level of a protein" refers to detecting the protein, or the mRNA encoding the protein, by methods known in the art, either directly or indirectly. "Directly determining" refers to performing a process to obtain a physical entity or value (e.g., performing an assay or test on a sample, or "analyzing a sample" as that term is defined herein). "Indirectly determining" refers to receiving a physical entity or value from another party or source (e.g., a third party laboratory that obtains the physical entity or value directly). Methods for measuring protein levels generally include, but are not limited to, Western blotting, immunoblotting, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunofluorescence, surface plasmon resonance, chemiluminescence, fluorescence polarization, phosphorescence, immunohistochemistry, matrix-assisted laser desorption / ionization time-of-flight (MALDI-TOF) mass spectrometry, liquid chromatography (LC) mass spectrometry, microcytometry, microscopy, fluorescence-activated cell sorting (FACS), and flow cytometry, as well as assays based on protein properties, including, but not limited to, enzyme activity or interaction with other protein partners.Methods for measuring mRNA levels are known in the art.

[0099] "Percent sequence identity" with respect to a reference polynucleotide or polypeptide sequence is defined as the percentage of nucleic acids or amino acids in a candidate sequence that are identical to those in the reference polynucleotide or polypeptide sequence after aligning the sequences and introducing gaps (DNA core sequences) if necessary to obtain the maximum percent sequence identity. Alignment to determine percent nucleic acid or amino acid sequence identity can be achieved in a variety of ways that are within the capabilities of those skilled in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine the appropriate parameters for aligning sequences, including any algorithms required to achieve maximum alignment over the entire length of the sequences being compared. For example, percent sequence identity values ​​can be generated using the sequence comparison computer program BLAST. As an illustration, the percent sequence identity of a given nucleic acid or amino acid sequence A to, with, or against a given nucleic acid or amino acid sequence B (which can be translated as a given nucleic acid or amino acid sequence A having a certain percent sequence identity to, with, or against a given nucleic acid or amino acid sequence B) is calculated as follows: 100×(fraction X / Y) where X is the number of nucleotides or amino acids that a sequence alignment program (e.g., BLAST) scores as identical matches in that program's alignment of A and B, and Y is the total number of nucleic acids in B. It will be understood that if the length of nucleic acid or amino acid sequence A is not equal to the length of nucleic acid or amino acid sequence B, then the percent sequence identity of A to B will not be equal to the percent sequence identity of B to A.

[0100] "Level" refers to the level or activity of a protein, or an mRNA encoding a protein (e.g., MSH3), optionally as compared to a reference. The reference can be any useful reference, as defined herein. A "decreased level" or "increased level" of a protein refers to a decrease or increase in protein level (e.g., about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, about 150%, about 200%, about 300%, about 400%, about 500% or more decrease or increase, when compared to a reference. By "protein level" is meant a 10%, 15%, 20%, 50%, 75%, 100%, or greater than 200% decrease or increase, less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold decrease or increase, or greater than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold increase, or greater, when compared to a control. Protein levels can be expressed as mass / volume (e.g., g / dL, mg / mL, μg / mL, or ng / mL) or as a percentage compared to the total protein or mRNA in the sample.

[0101] The term "pharmaceutical composition" as used herein refers to a composition containing a compound described herein, formulated with a pharmaceutically acceptable excipient, which may be manufactured or sold by approval of a government regulatory agency as part of a therapeutic regimen for treating a disease in a mammal.The pharmaceutical composition may be formulated, for example, for oral administration in unit dosage form (e.g., tablet, capsule, caplet, gelcap, or syrup), for topical administration (e.g., as a cream, gel, lotion, or ointment), for intravenous administration (e.g., as a sterile solution free of particulate embolic material and in a solvent system suitable for intravenous use), for intrathecal injection, for intraventricular injection, for intraparenchymal injection, for intraocular administration (e.g., for intravitreal or subretinal administration), or any other pharmaceutically acceptable formulation.

[0102] "Pharmaceutically acceptable excipient" as used herein refers to any component other than the compounds described herein (e.g., a vehicle that can suspend or dissolve active compounds), and has the property of being substantially non-toxic and non-inflammatory in patients.Excipients can include, for example, anti-adhesive agents, antioxidants, binders, coating agents, compression aids, disintegrants, dyes (colors), emollients, emulsifiers, fillers (diluents), film-forming or coating agents, flavors, fragrances, flow agents (glidants), lubricants, preservatives, printing inks, adsorbents, suspending or dispersing agents, sweeteners, and hydration water. Exemplary excipients include, but are not limited to, butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, cross-linked polyvinylpyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropylcellulose, hydroxypropylmethylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine, methylcellulose, methylparaben, microcrystalline cellulose, polyethylene glycol, polyvinylpyrrolidone, povidone, pregelatinized starch, propylparaben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethylcellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C, and xylitol.

[0103] As used herein, the term "pharmaceutically acceptable salt" refers to any pharmaceutically acceptable salt of a compound for any of the compounds described herein. For example, pharmaceutically acceptable salts of any of the compounds described herein include those that are suitable for use in contact with human and animal tissues without causing undue toxicity, irritation, or allergic response within the scope of sound medical judgment, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in Berge et al., J. Pharmaceutical Sciences 66:1-19, 1977, and Pharmaceutical Salts: Properties, Selection, and Use, (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008. Salts can be prepared in situ during the final isolation and purification of the compounds described herein, or separately by reacting a free base group with a suitable organic acid.

[0104] The compounds described herein may have ionic groups so that they can be prepared as pharmaceutically acceptable salts.These salts may be acid addition salts, including inorganic or organic acids, or salts may be prepared from inorganic or organic bases in the case of the acidic form of the compounds described herein.In many cases, compounds are prepared or used as pharmaceutically acceptable salts prepared as addition products of pharmaceutically acceptable acids or bases.Suitable pharmaceutically acceptable acids and bases and methods for preparing suitable salts are well known in the art.Salts may be prepared from pharmaceutically acceptable non-toxic acids and bases, including inorganic and organic acids and bases. Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecyl sulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, and magnesium, as well as non-toxic ammonium, quaternary ammonium, and amine cations, including, but not limited to, ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, and ethylamine.

[0105] By "reference" is meant any useful reference used to compare protein or mRNA levels or activity. A reference can be any sample, standard, calibration curve, or level used for comparison purposes. A reference can be a normal reference sample or a reference standard or level. A "reference sample" can be, for example, a control, e.g., a predefined negative control value such as a "normal control" or a previous sample taken from the same subject, a sample from a normal healthy subject, e.g., a normal cell or normal tissue, a sample (e.g., cell or tissue) from a subject without a disease, a sample from a subject diagnosed with a disease but not yet treated with a compound described herein, a sample from a subject being treated with a compound described herein, or a sample of a known normal concentration of purified protein (e.g., any described herein). By "reference standard or level" is meant a value or number obtained from a reference sample. A "normal control value" is a predefined value indicative of a non-disease state, e.g., a value expected in a healthy control subject. Typically, a normal control value is expressed as a range ("X to Y"), a high threshold value ("below X"), or a low threshold value ("above X"). A subject having a measurement value within the normal control value for a particular biomarker is usually referred to as being "within the normal range" for that biomarker. The normal reference standard or level can be a value or value obtained from a normal subject without a disease or disorder (e.g., a nucleotide or trinucleotide repeat expansion disorder) and a subject treated with a compound described herein. In some embodiments, the reference sample, standard, or level is matched to the sample subject sample by at least one of the following criteria: age, weight, sex, stage of disease, and overall health. A standard curve of purified protein within the normal reference range, for example any of the levels described herein, can be used as a reference.

[0106] As used herein, the term "subject" refers to any organism to which a composition may be administered, e.g., for experimental, diagnostic, prophylactic, and / or therapeutic purposes. Typical subjects include any animal (e.g., mammals, such as mice, rats, rabbits, non-human primates, and humans). A subject may be a human or animal that is seeking or in need of treatment, is in need of treatment, is undergoing treatment, will be undergoing treatment in the future, or is under the care of a professional trained in a particular disease or condition.

[0107] As used herein, the terms "treat", "treated" and "treating" refer to both therapeutic treatment and prophylactic or preventative measures, the purpose of which is to prevent or slow (reduce) an undesirable physiological condition, disorder or disease, or to obtain beneficial or desired clinical results. Beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, reduction in the extent of the condition, disorder or disease, stabilization (i.e., not worsening) of the condition, disorder or disease, delay in onset of the condition, disorder or disease or slowing of its progression, improvement or remission (whether partial or total) of the condition, disorder or disease state, whether detectable or undetectable, improvement in at least one measurable physical parameter, not necessarily discernible by the patient, or improvement or amelioration of the condition, disorder or disease. Treatment includes eliciting a clinically significant response without causing an excessive level of side effects. Treatment also includes extending survival as compared to expected survival in the absence of treatment.

[0108] As used herein, the terms "variant" and "derivative" are used interchangeably and refer to naturally occurring, synthetic, and semi-synthetic analogs of the compounds, peptides, proteins, or other substances described herein. Variants or derivatives of the compounds, peptides, proteins, or other substances described herein may retain or improve the biological activity of the original material.

[0109] The details of one or more embodiments are set forth in the description below. Other features, objects, and advantages will be apparent from the description, and from the claims. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0110] The present inventors have found that inhibiting or depleting MSH3 levels and / or activity in cells is effective in treating nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders). Accordingly, useful compositions and methods for treating nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders), e.g., in a subject in need thereof, are provided herein.

[0111] I. Nucleotide Repeat Expansion Disorders Nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are a group of genetic disorders characterized by pathogenic expansion of repeat regions within a genomic region. In such disorders, the number of repeats expands beyond the normal stable threshold number of the gene to the disease range.

[0112] Nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) can generally be classified as "polyglutamine" or "non-polyglutamine". Polyglutamine disorders, including Huntington's disease (HD) and some spinocerebellar ataxias, are caused by CAG (glutamine) repeats in the protein coding regions of certain genes. Non-polyglutamine disorders are more heterogeneous and can be caused by CAG nucleotide repeat expansions in non-coding regions, as in myotonic dystrophy, or by nucleotide repeat expansions other than CAG, which can be in coding or non-coding regions, such as the CGG repeat expansions that cause fragile X syndrome.

[0113] Nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are dynamic in the sense that the number of repeats can vary between generations, or even between cells within the same individual. Repeat expansion is thought to be caused by polymerase "slippage" during DNA replication. Tandem repeats in DNA sequences can "loop out" while maintaining complementary base pairing between parent and daughter strands. If a loop structure is formed from the daughter strand, the number of repeats will increase.

[0114] Conversely, if loop structures are formed from the parental strand, the number of repeats will decrease. Expansion rather than reduction appears to be more common. In general, the length of the repeat expansion is negatively correlated with prognosis, with longer repeats being correlated with a lower age of onset and worsening disease severity. Thus, nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are "predictive," meaning that the severity and / or age of onset of symptoms will worsen with successive generations of affected families due to these repeat expansions from one generation to the next.

[0115] Nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) is well known in the art.For example, frontotemporal dementia (FTD) is a hexanucleotide repeat string of nucleotide GGGGCC that repeats much more in individuals than individuals without FTD.Furthermore, individuals with spinocerebellar ataxia type 36 (SCA36) have much more GGCCTG repeats than individuals without SCA36.

[0116] Exemplary trinucleotide repeat expansion disorders and the genetic trinucleotide repeats commonly associated with them are included in Table 1.

[0117] [Table 1-1]

[0118] [Table 1-2]

[0119] Proteins associated with nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) are usually selected based on the experimental association of proteins associated with nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) with nucleotide repeat expansion disorders. For example, the production rate or circulating concentration of proteins associated with nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) may be elevated or decreased in a population with a nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder) compared to a population lacking a nucleotide repeat expansion disorder (e.g., trinucleotide repeat expansion disorder). Differences in protein levels may be assessed using protein techniques, including but not limited to Western blot, immunohistochemical staining, enzyme-linked immunosorbent assay (ELISA), and mass spectrometry. Alternatively, proteins associated with nucleotide repeat expansion disorders (e.g., trinucleotide repeat expansion disorders) can be identified by obtaining gene expression profiles of genes encoding the proteins using genomic techniques, including, but not limited to, DNA microarray analysis, sequence analysis of gene expression (SAGE), and quantitative real-time polymerase chain reaction (qPCR).

[0120] II. Evidence for the involvement of the mismatch repair pathway in nucleotide repeat expansion. There is increasing evidence that DNA repair pathways, especially mismatch repair (MMR), are involved in the expansion of nucleotide repeats (e.g., trinucleotide repeats). A recent genome-wide association (GWA) analysis identified loci harboring genetic variants that alter the age at neurological onset of Huntington's disease (HD) (GEM-HD Consortium, Cell. 2015 Jul 30; 162(3): 516-26). This study identified MLH1, a human homolog of the E. coli DNA mismatch repair gene mutL. ​​Subsequent GWA studies in patients with polyglutamine diseases found significant associations of specific SNPs in FAN1 and PMS2 with disease, in addition to a significant association of age at onset, when all polyglutamine diseases (HD and SCA) with DNA repair genes were classified as a group (Bettencourt et al., (2016) Ann. Neurol., 79: 983-990). These results were consistent with the results of a previous study comparing the differences in repeat expansion in two different mouse models of Huntington's disease, which identified Mlh1 and Mlh3 as novel key modifiers of CAG instability (Pinto et al.,(2013)Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice:Genome-Wide and Candidate Approaches.PLoS Genet 9(10):e1003930). Another member of the mismatch repair pathway, 8-oxo-guanine glycosylase (OGG1), has also been implicated in the expansion, as transgenic mice lacking OGG1 showed reduced somatic expansion (Kovtun IVet al.(2007)Nature 447,447-452). However, in another study, human subjects containing the Ser326Cys polymorphism in hOGG1 (resulting in reduced OGG1 activity) were found to have an increase in mutant huntingtin (Coppede et al., (2009) Toxicol., 278:199-203).Similarly, complete inactivation of Fan1, another component of the DNA repair pathway, in a mouse HD model leads to somatic CAG expansions (Long et al. (2018) J. Hum Genet., 103:1-9). Another component of the mismatch repair pathway, MSH3, has been reported to be involved in somatic expansions, and polymorphisms in Msh3 have been associated with somatic instability of expanded CTG trinucleotide repeats in myotonic dystrophy type 1 (DM1) patients (Morales et al., (2016) DNA Repair 40:57-66). Furthermore, natural polymorphisms in Msh3 and Mlh1 have been identified as mediators of mouse strain-specific differences in CTG·CAG repeat instability (Pinto et al. (2013) ibid., Tome et al., (2013) PLoS Genet. 9 e1003280). Further evidence for the involvement of Msh2 and Msh3 in expanded repeats was reported in a study in which slow short hairpin RNA (shRNA) knockdown of either MSH2 or MSH3 and ectopic expression of either MSH2 or MSH3 induced GAA trinucleotide repeat expansion of the FRDA gene in fibroblasts derived from patients with Friedreich's ataxia (FRDA) (Halabi et al., (2012) J. Biol. Chem. 287, 29958-29967). Despite some of the contradictory results provided above, there is strong evidence that the MMR pathway plays a role in trinucleotide repeat expansion in various disorders. Moreover, they are the first studies to recognize that inhibition of the MMR pathway allows for the treatment or prevention of these repeat expansion disorders, however, no therapies modulating MMR to treat or prevent these repeat expansion disorders are currently available or in development.

[0121] III. Oligonucleotide Agents The agents described herein that decrease the level and / or activity of MSH3 in a cell can be, for example, a polynucleotide, e.g., an oligonucleotide, or a pharma- ceutically acceptable salt thereof, that decrease the level of an activity associated with MSH3, or an associated downstream effect, or that decrease the level of MSH3 in a cell or subject.

[0122] In some embodiments, the agent that decreases the level and / or activity of MSH3 is a polynucleotide. In some embodiments, the polynucleotide is, for example, a single stranded oligonucleotide that acts via an RNase H mediated pathway. Oligonucleotides include DNA and DNA / RNA chimeric molecules, typically about 10-30 nucleotides in length, that recognize a polynucleotide target sequence or sequence portion by hydrogen bonding interactions with the nucleotide bases of the target sequence (e.g., MSH3). The oligonucleotide molecule can decrease the expression level (e.g., protein level or mRNA level) of MSH3. For example, the oligonucleotide includes an oligonucleotide that targets full length MSH3. In some embodiments, the oligonucleotide molecule recruits an RNase H enzyme resulting in target mRNA degradation.

[0123] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, decreases the level and / or activity of a positive regulator of function. In other embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, increases the level and / or activity of an inhibitor of a positive regulator of function. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, increases the level and / or activity of a negative regulator of function.

[0124] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, decreases the level and / or activity or function of MSH3. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, inhibits expression of MSH3. In other embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, increases the degradation of MSH3 and / or decreases the stability (i.e., half-life) of MSH3. The oligonucleotide, or a pharma- ceutically acceptable salt thereof, may be chemically synthesized.

[0125] The oligonucleotides, or pharma- ceutically acceptable salts thereof, can be synthesized by standard methods known in the art, as further described below, for example, by use of an automated DNA synthesizer, such as those commercially available from Biosearch, Applied Biosystems, Inc.

[0126] Oligonucleotide, or its pharmaceutically acceptable salt, can be prepared using liquid phase or solid phase organic synthesis or both.Organic synthesis provides the advantage that the oligonucleotide, or its pharmaceutically acceptable salt, containing non-natural or alternative nucleotides can be easily prepared.Single-stranded oligonucleotide, or its pharmaceutically acceptable salt, can be prepared using liquid phase or solid phase organic synthesis or both.

[0127] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 876-901 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the 17-20 contiguous nucleobases begin at positions 876, 877, 878, 879, 880, 881, 882, 883, 884, or 885 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 876-901 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the 20-23 contiguous nucleobases begin at positions 876, 877, 878, 879, 880, 881, or 882 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0128] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 931, 932, 933, 934, 935, 936, 937, 938, 939, or 940 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 931-956 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at positions 931, 932, 933, 934, 935, 936, 937 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0129] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, or 1321 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 1310-1337 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, or 1318 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0130] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2151, 2152, or 2153 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, or 2150 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0131] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, or 2276 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2267, 2268, 2269, 2270, 2271, 2272, or 2273 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0132] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, wherein the oligonucleotide is at least 95% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at position 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2560, 2561, 2562, or 2563 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2543-2579 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases beginning at position 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, or 2560 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0133] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2151, 2152, or 2153 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2141-2169 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, or 2149 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0134] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, or 2276 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2267-2292 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2267, 2268, 2269, 2270, 2271, or 2272 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0135] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, 2628, 2629, 2630, or 2631 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2620-2647 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, or 2627 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0136] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2685, 2686, 2687, 2688, 2689, 2690, 2691, 2692, 2693, or 2694 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases at positions 2685-2710 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is complementary to 20-23 contiguous nucleobases beginning at position 2685, 2686, 2687, 2688, 2689, 2690, or 2691 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0137] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is complementary to 17-20 contiguous nucleobases beginning at positions 2769, 2770, 2771, 2772, 2773, 2774, 2775, 2776, 2777, 2778, or 2779 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2769-2795 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2769, 2770, 2771, 2772, 2773, 2774, 2775, or 2776 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0138] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2798-2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is selected from the group consisting of positions 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, 2825, 2826, 2827, 2828, 2829, 2830, 2831, 2832, 2833, 2834, 2835, 2836, 2837, 2838, 2839, 2840, 2841, 2842, 2843, 2844, 2845, 2846, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2855, 2856, 2857, 2858, 2859, 2860, 2861, 2862, 2863, 2864, 2865, 2866, 2867, 2868, 2869, 2870, 2871, 2872, 2873, 2874, 2875, 2876, 2877, 2878, 287 or a pharmaceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length or a pharmaceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20 to 23 adjacent nucleobases at positions 2798 to 2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20 to 23 adjacent nucleobases at positions 2798 to 2868 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to positions 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, or a pharma- ceutically acceptable salt thereof, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0139] Some embodiments of the present disclosure relate to single-stranded oligonucleotides of 15-30 linked nucleotides in length, where the oligonucleotide, or a portion thereof, is at least 95% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 98% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is at least 99% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is 100% complementary to at least 15 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma-ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-23 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 17-20 contiguous nucleobases beginning at positions 2950, ​​2951, 2952, 2953, 2954, 2955, 2956, 2957, 2958, or 2959 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 17-20 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases at positions 2950-2975 of SEQ ID NO:5151, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide, or a portion thereof, is complementary to 20-23 contiguous nucleobases beginning at position 2950, ​​2951, 2952, 2953, 2954, 2955, or 2956 of SEQ ID NO: 5151, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is 20-23 linked nucleotides in length, or a pharma- ceutically acceptable salt thereof.

[0140] In some embodiments, the oligonucleotide is not any one of antisense oligo numbers 5152-5176 in Table 3.

[0141] In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-5150 and 5152-5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-5150, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-206 and 5152, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1-206, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 207-412 and 5153, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 207-412, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 413-618 and 5154, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 413-618, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 619-824 and 5155, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 619-824, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 825-1030 and 5156, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 825-1030, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1031-1236 and 5157, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1031-1236, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1237-1442 and 5158, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1237-1442, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1443-1648 and 5159, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1443-1648, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1649-1854 and 5160, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1649-1854, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1855-2060 and 5161, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 1855-2060, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2061-2266 and 5162, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2061-2266, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2267-2472 and 5163, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2267-2472, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2473-2678 and 5164, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2473-2678, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2679-2884 and 5165, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2679-2884, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2885-3090 and 5166, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 2885-3090, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3091-3296 and 5167, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3091-3296, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3297-3502 and 5168, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3297-3502, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3503-3708 and 5169, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3503-3708, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3709-3914 and 5170, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3709-3914, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3915-4120 and 5171, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 3915-4120, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4121-4326 and 5172, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4121-4326, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4327-4532 and 5173, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4327-4532, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4533-4738 and 5174, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4533-4738, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4739-4944 and 5175, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4739-4944, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises a nucleic acid base sequence selected from the group consisting of any of SEQ ID NOs: 4945-5150 and 5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of a nucleobase sequence selected from the group consisting of any of SEQ ID NOs: 4945-5150, or a pharma- ceutically acceptable salt thereof.

[0142] Some embodiments of the present disclosure relate to a single-stranded oligonucleotide (the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 5150 and 5152 to 5176), or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 5150, or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 206 and 5152, or a pharma- ceutically acceptable salt thereof. In some embodiments, the nucleic acid base sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 206, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of SEQ ID NOs: 207 to 412 and 5153, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of SEQ ID NOs: 207 to 412, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 413-618 and 5154, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 413-618, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 619-824 and 5155, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 619-824, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 825-1030 and 5156, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 825-1030, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 1031-1236 and 5157, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1031-1236, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1237-1442 and 5158, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1237-1442, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1443-1648 and 5159, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1443-1648, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1649-1854 and 5160, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1649-1854, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1855-2060 and 5161, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 1855-2060, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2061-2266 and 5162, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2061-2266, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 2267-2472 and 5163, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 2267-2472, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2473-2678 and 5164, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2473-2678, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2679-2884 and 5165, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2679-2884, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2885-3090 and 5166, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 2885-3090, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3091-3296 and 5167, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3091-3296, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3297-3502 and 5168, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3297-3502, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3503-3708 and 5169, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of any one of the nucleic acid base sequences of SEQ ID NOs: 3503-3708, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 3709-3914 and 5170, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3709-3914, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3915-4120 and 5171, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 3915-4120, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4121-4326 and 5172, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4121-4326, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4327-4532 and 5173, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4327-4532, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4533-4738 and 5174, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4533-4738, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4739-4944 and 5175, or a pharma- ceutically acceptable salt thereof. The oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4739-4944, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide comprises any one of the nucleic acid base sequences of SEQ ID NOs: 4945-5150 and 5176, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide consists of the nucleobase sequence of any one of SEQ ID NOs: 4945-5150, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide consists of a nucleobase sequence selected from the group consisting of any one of SEQ ID NOs: 5152-5176, or a pharma- ceutically acceptable salt thereof.

[0143] Some embodiments of the present disclosure relate to an oligonucleotide selected from the group consisting of antisense oligonucleotide numbers 1-5150 and 5152-5176 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-5150 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-206 and 5152 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1-206 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 207-412 and 5153 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 207-412 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 413-618 and 5154 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 413-618 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 619-824 and 5155 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 619-824 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 825-1030 and 5156 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 825-1030 of Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1031-1236 and 5157 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1031-1236 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1237-1442 and 5158 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1237-1442 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1443-1648 and 5159 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1443-1648 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1649-1854 and 5160 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1649-1854 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1855-2060 and 5161 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 1855-2060 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2061-2266 and 5162 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2061-2266 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2267-2472 and 5163 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2267-2472 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2473-2678 and 5164 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2473-2678 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2679-2884 and 5165 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2679-2884 of Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2885-3090 and 5166 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 2885-3090 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3091-3296 and 5167 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3091-3296 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3297-3502 and 5168 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3297-3502 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3503-3708 and 5169 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3503-3708 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3709-3914 and 5170 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3709-3914 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3915-4120 and 5171 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 3915-4120 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4121-4326 and 5172 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4121-4326 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4327-4532 and 5173 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4327-4532 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4533-4738 and 5174 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4533-4738 in Table 3, or a pharma- ceutically acceptable salt thereof.In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4739-4944 and 5175 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4739-4944 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4945-5150 and 5176 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 4945-5150 in Table 3, or a pharma- ceutically acceptable salt thereof. In some embodiments, the oligonucleotide is selected from the group consisting of antisense oligonucleotide numbers 5152-5176 in Table 3, or a pharma- ceutically acceptable salt thereof.

[0144] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 60% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 70% at an oligonucleotide concentration of 10 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 80% at an oligonucleotide concentration of 10 nM.

[0145] In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50% at an oligonucleotide concentration of 1 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 60% at an oligonucleotide concentration of 1 nM. In some embodiments, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 70% at an oligonucleotide concentration of 1 nM.

[0146] The cell assay may include transfecting mammalian cells, such as HEK293, NIH3T3, or HeLa cells, with a desired concentration of oligonucleotide (e.g., 1 nM or 10 nM) using Lipofectamine2000 (Invitrogen), and comparing the MSH3 mRNA levels of the transfected cells to the MSH3 levels of control cells. The control cells may be transfected with an oligonucleotide that is not specific for MSH3, or may be mock transfected. The mRNA levels may be determined using RT-qPCR, and the MSH3 mRNA levels may be normalized to GAPDH mRNA levels. The inhibition rate may be calculated as the ratio of the MSH3 mRNA concentration to the MSH3 concentration of the control cells.

[0147] In some embodiments, MSH3 mRNA expression is assessed in vitro. In some embodiments, MSH3 mRNA expression is assessed in a cell-based assay. In some embodiments, MSH3 mRNA expression is assessed in HeLa cells. In some embodiments, MSH3 mRNA expression is determined by quantitative reverse transcription polymerase chain reaction (RT-qPCR). In some embodiments, MSH3 mRNA expression is normalized relative to the mRNA expression of a reference gene. In some embodiments, MSH3 mRNA expression is normalized relative to the mRNA expression of beta-glucuronidase (GUSB). In some embodiments, the decrease in MSH3 mRNA expression is relative to a control. In some embodiments, the control is MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof. In some embodiments, the control is MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof, but in the presence of a control oligonucleotide, or a salt thereof. In some embodiments, the control oligonucleotide, or a salt thereof, is a scrambled luciferase-targeting oligonucleotide. In some embodiments, the reduction in MSH3 mRNA expression is calculated by the delta-delta Ct (ΔΔCT) method. In some embodiments, the delta-delta Ct (ΔΔCT) method involves normalizing MSH3 mRNA expression relative to the mRNA expression of a reference gene and relative to the MSH3 mRNA expression in the absence of the oligonucleotide, or a pharma- ceutically acceptable salt thereof, but in the presence of a control oligonucleotide, or a salt thereof. In some embodiments, the reference gene is beta-glucuronidase (GUSB) and / or the control oligonucleotide, or a salt thereof, is a scrambled luciferase-targeted oligonucleotide. In some embodiments, the reduction in MSH3 mRNA expression is determined by the method of Example 1. In some embodiments, in the same assay, antisense oligonucleotide number 1 reduces MSH3 mRNA expression by approximately 58% at an oligonucleotide concentration of 10 nM.In some embodiments, in the same assay, antisense oligo no. 1 reduces MSH3 mRNA expression by approximately 14% at an oligonucleotide concentration of 1 nM.

[0148] In some embodiments, the oligonucleotide, or its adjacent nucleotide regions, has a gapmer design or structure, also referred to herein simply as a "gapmer." In a gapmer structure, the oligonucleotide comprises at least three distinct structural regions in a "5->3" orientation: a 5' flanking sequence (also known as a 5' wing), a DNA core sequence (also known as a gap), and a 3' flanking sequence (also known as a 3' wing). In this design, the 5' and 3' flanking sequences comprise at least one alternative nucleoside adjacent to the DNA core sequence, and in some embodiments may comprise a continuous stretch of 2-7 alternative nucleosides, or a continuous stretch of alternative and DNA nucleosides (mixed flanking sequences that include both alternative and DNA nucleosides).

[0149] The length of the 5' flanking sequence region can be at least two nucleosides long (e.g., at least two, at least three, at least four, at least five, at least six, or more nucleosides long). The length of the 3' flanking sequence region can be at least two nucleosides long (e.g., at least two, at least three, at least four, at least five, at least six, or more nucleosides long). The 5' and 3' flanking sequences can be symmetric or asymmetric with respect to the number of nucleosides they contain. In some embodiments, the DNA core sequence comprises about 10 nucleosides adjacent to the 5' and 3' flanking sequences, each of which comprises about five nucleosides. In some embodiments, the DNA core sequence comprises about 11 nucleosides adjacent to the 5' and 3' flanking sequences, each of which comprises about five or about six nucleosides. In some embodiments, the DNA core sequence comprises about 12 nucleosides flanked by a 5' sequence comprising about 5 nucleosides and a 3' flanking sequence comprising about 6 nucleosides. In some embodiments, the DNA core sequence comprises about 12 nucleosides flanked by a 5' sequence comprising about 6 nucleosides and a 3' flanking sequence comprising about 5 nucleosides. In some embodiments, the DNA core sequence comprises about 12 nucleosides flanked by 5' and 3' flanking sequences each comprising about 6 nucleosides.

[0150] Thus, the nucleosides of the 5' and 3' flanking sequences flanking the DNA core sequence are alternative nucleosides, such as 2' alternative nucleosides. The DNA core sequence comprises a contiguous stretch of nucleotides that can recruit RNase H when the oligonucleotide is duplexed with an MSH3 target nucleic acid. In some embodiments, the DNA core sequence comprises a contiguous stretch of 5-16 DNA nucleosides. In other embodiments, the DNA core sequence comprises a region of at least 10 contiguous nucleobases having at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 99%) complementarity to the MSH3 gene. In some embodiments, the gapmer comprises a region complementary to at least 17 contiguous nucleotides, 19-23 contiguous nucleotides, or 19 contiguous nucleotides of the MSH3 gene. The gapmer can be a contiguous nucleoside region of the oligonucleotide, as it is complementary to the MSH3 target nucleic acid. In some embodiments, a gapmer comprises a region complementary to at least 21 contiguous nucleotides, 20-25 contiguous nucleotides, or 23 contiguous nucleotides of the MSH3 gene. A gapmer can be a contiguous nucleoside region of an oligonucleotide that is complementary to an MSH3 target nucleic acid.

[0151] The 5' and 3' flanking sequences adjacent to the 5' and 3' ends of the DNA core sequence may comprise one or more affinity enhancing surrogate nucleosides. In some embodiments, the 5' and / or 3' flanking sequences comprise at least one 2'-O-methoxyethyl (MOE) nucleoside. In some embodiments, the 5' and / or 3' flanking sequences contain at least two MOE nucleosides. In some embodiments, the 5' flanking sequences comprise at least one, at least two, at least three, at least four, at least five, or at least six or more MOE nucleosides. In some embodiments, the 5' flanking sequences comprise at least one, at least two, at least three, at least four, at least five, or at least six or more MOE nucleosides. In some embodiments, both the 5' and 3' flanking sequences comprise MOE nucleosides. In some embodiments, all nucleosides in the flanking sequences are MOE nucleosides. In other embodiments, the flanking sequences can include both MOE nucleosides and other nucleosides (mixed flanking sequences), such as DNA nucleosides and / or non-MOE surrogate nucleosides, such as bicyclic nucleosides (BNAs) (e.g., LNA nucleosides (e.g., A-LNA, 5mCL-NA, G-LNA, T-LNA) or cET nucleosides), or other 2'-substituted nucleosides. In this case, the DNA core sequence is defined as a flanking sequence of at least five RNase H recruiting nucleosides (e.g., 5-16 DNA nucleosides) flanked on the 5' and 3' ends by affinity enhancing surrogate nucleosides, such as MOE nucleosides.

[0152] In other embodiments, the 5' and / or 3' flanking sequences comprise at least one BNA (e.g., at least one LNA nucleoside (e.g., A-LNA, 5mCL-NA, G-LNA, T-LNA) or a cET nucleoside). In some embodiments, the 5' and / or 3' flanking sequences comprise at least two bicyclic nucleosides. In some embodiments, the 5' flanking sequence comprises at least one BNA. In some embodiments, both the 5' and 3' flanking sequences comprise BNAs. In some embodiments, all nucleosides in a flanking sequence are BNAs. In other embodiments, a flanking sequence may comprise both BNAs and other nucleosides (mixed flanking sequences), such as DNA nucleosides and / or non-BNA alternative nucleosides, such as 2' substituted nucleosides. In this case, the DNA core sequence is defined as a flanking sequence of at least five RNase H recruiting nucleosides (e.g., 5-16 DNA nucleosides) flanked at the 5' and 3' ends by affinity enhancing surrogate nucleosides such as BNAs, e.g., LNAs, e.g., beta-D-oxy-LNAs.

[0153] The 5' flank attached to the 5' end of the DNA core sequence comprises, contains or consists of at least one alternative sugar moiety (e.g., at least three, at least four, at least five, at least six, at least seven, or more alternative sugar moieties). In some embodiments, the flanking sequence comprises or consists of 1-7 alternative nucleobases, such as 2-6 alternative nucleobases, such as 2-5 alternative nucleobases, such as 2-4 alternative nucleobases, such as 1-3 alternative nucleobases, such as 1, 2, 3, or 4 alternative nucleobases. In some embodiments, the flanking sequence comprises or consists of at least one alternative internucleoside linkage (e.g., at least three, at least four, at least five, at least six, at least seven, or more alternative internucleoside linkages).

[0154] The 3' flank attached to the 3' end of the DNA core sequence comprises, contains or consists of at least one alternative sugar moiety (e.g., at least three, at least four, at least five, at least six, at least seven, or more alternative sugar moieties). In some embodiments, the flanking sequence comprises or consists of 1-7 alternative nucleobases, such as 2-6 alternative nucleobases, such as 2-5 alternative nucleobases, such as 2-4 alternative nucleobases, such as 1-3 alternative nucleobases, such as 1, 2, 3, or 4 alternative nucleobases. In some embodiments, the flanking sequence comprises or consists of at least one alternative internucleoside linkage (e.g., at least three, at least four, at least five, at least six, at least seven, or more alternative internucleoside linkages).

[0155] In one aspect, one or more or all of the alternative sugar moieties in the flanking sequences are 2' alternative sugar moieties.

[0156] In a further aspect, one or more of the 2' alternative sugar moieties in the wing region are selected from a 2'-O-alkyl-sugar moiety, a 2'-O-methyl-sugar moiety, a 2'-amino-sugar moiety, a 2'-fluoro-sugar moiety, a 2'-alkoxy-sugar moiety, an MOE sugar moiety, an LNA sugar moiety, an arabinonucleic acid (ANA) sugar moiety, and a 2'-fluoro-ANA sugar moiety.

[0157] In one embodiment, all alternative nucleosides in the flanking sequences are bicyclic nucleosides. In a further embodiment, the bicyclic nucleosides in the flanking sequences are independently selected from the group consisting of oxy-LNA, thio-LNA, amino-LNA, cET, and / or ENA, or combinations thereof, in either the beta-D or alpha-L configuration.

[0158] In some embodiments, one or more alternative internucleoside linkages in the flanking sequences are phosphorothioate internucleoside linkages. In some embodiments, the phosphorothioate linkages are stereochemically pure phosphorothioate linkages. In some embodiments, the phosphorothioate linkages are Sp phosphorothioate linkages. In other embodiments, the phosphorothioate linkages are Rp phosphorothioate linkages. In some embodiments, the alternative internucleoside linkages are 2'-alkoxy internucleoside linkages. In other embodiments, the alternative internucleoside linkages are alkylphosphate internucleoside linkages.

[0159] The DNA core sequence may comprise, contain, or consist of at least 5-16 consecutive DNA nucleosides capable of recruiting RNase H. In some embodiments, all of the nucleosides of the DNA core sequence are DNA units. In further embodiments, the DNA core region may consist of a mixture of DNA and other nucleosides capable of mediating RNase H cleavage. In some embodiments, at least 50% of the nucleosides of the DNA core sequence are DNA, such as at least 60%, at least 70%, or at least 80%, or at least 90% are DNA. In some embodiments, all of the nucleosides of the DNA core sequence are RNA units.

[0160] The oligonucleotide comprises a flanking region that is complementary to the target nucleic acid. In some embodiments, the oligonucleotide may further comprise additional linked nucleosides located 5' and / or 3' to either the 5' and 3' flanking sequences. These additional linked nucleosides may be attached to the 5' end of the 5' flanking sequence or the 3' end of the 3' flanking sequence, respectively. The additional nucleosides may form part of the flanking sequence that is complementary to the target nucleic acid in some embodiments, or may be non-complementary to the target nucleic acid in other embodiments.

[0161] The inclusion of additional nucleosides in either or both of the 5' and 3' flanking sequences can independently include 1, 2, 3, 4, or 5 additional nucleotides, which can be complementary or non-complementary to the target nucleic acid. In this regard, the oligonucleotide can, in some embodiments, include adjacent sequences that can modulate the target adjacent to the additional nucleotides at the 5' and / or 3' ends. Such additional nucleosides can function as biochemically cleavable linkers that are sensitive to nucleases, and can be used to attach functional groups, such as conjugate moieties, to the oligonucleotide. In some embodiments, the additional nucleosides at the 5' and / or 3' ends are linked with phosphodiester bonds and can be DNA or RNA. In other embodiments, the additional nucleosides at the 5' and / or 3' ends are alternative nucleosides that can be included, for example, to enhance nuclease stability or to facilitate synthesis.

[0162] In other embodiments, the oligonucleotides utilize an "altimer" design, which contains alternating 2'-fluoro-ANA and DNA regions that alternate every three nucleosides. Altimer oligonucleotides are described in more detail in Min, et al., Bioorganic & Medicinal Chemistry Letters, 2002, 12(18):2651-2654 and Kalota, et al., Nuc. Acid Res. 2006, 34(2):451-61, which are incorporated herein by reference.

[0163] In other embodiments, the oligonucleotides utilize a "hemimer" design, which contains a single 2' modified flanking sequence adjacent (either 5' or 3' to) a DNA core sequence. Hemimer oligonucleotides are described in detail by Geary et al., 2001, J. Pharm. Exp. Therap., 296:898-904, incorporated herein by reference.

[0164] In some embodiments, the oligonucleotide has a nucleic acid sequence having at least 50% (e.g., at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%) sequence identity to any one of the nucleic acid sequences of SEQ ID NOs: 1 to 384 and 390 to 613. In some embodiments, the oligonucleotide has a nucleic acid sequence having at least 85% sequence identity to any one of the nucleic acid sequences of SEQ ID NOs: 1 to 384 and 390 to 613.

[0165] It will be understood that the oligonucleotides, e.g., the nucleosides of the oligonucleotides, may include any one of the sequences set forth in any one of SEQ ID NOs: 1-384, conjugated or linked with alternative nucleosides as described in detail below.

[0166] In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 1 to 384 of Table 3 or antisense oligo numbers 390 to 613 of Table 4. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 1 to 384 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of one of antisense oligo numbers 1 to 96 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 97 to 192 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 193 to 288 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 289-384 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 390-613 of Table 4. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 390-480 of Table 4. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 481-501 of Table 4. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 502-592 of Table 4.In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 593-613 of Table 4.

[0167] In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 1, 6, 13, 17, 21, 24, 26, 29, 33-34, 37, 44, 49-55, 57, 60-73, 75-76, 79-82, 84-86, 88-92, or 94-96 of Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of the nucleobase sequence of antisense oligo number 6 of Table 3.

[0168] In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 97, 100, 103, 105, 108, 110-111, 113-117, 122-123, 127, 129-130, 133-136, 138-139, 141, 143-145, 147-148, 154-155, 157-165, 168-170, 172, 174-180, 184, 187, or 191 in Table 3.

[0169] In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 193-200, 202-230, 232-246, 248-253, 255, 258-261, 265, 270, 274-276, or 285-286 in Table 3. In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 226-227, 234, 240, or 243-244 in Table 3.

[0170] In some embodiments, the oligonucleotide is an oligonucleotide having at least 15 contiguous bases of a nucleobase sequence selected from the group consisting of antisense oligo numbers 289-290, 292, 305, 307, 313, 318, 323-324, 326, 329-330, 332, 338-339, 341, 344, or 346 in Table 3.

[0171] An oligonucleotide agent as described herein may contain one or more mismatches in the target sequence. In one embodiment, an oligonucleotide as described herein contains no more than three mismatches. When an oligonucleotide contains mismatches to a target sequence, in some embodiments, the region of mismatch is not located in the center of the region of complementarity. When an oligonucleotide contains mismatches to a target sequence, in some embodiments, the mismatch must be confined to within the last five nucleotides at either the 5' or 3' end of the region of complementarity. For example, in the case of a 30 linked nucleoside oligonucleotide agent, the adjacent nucleobase regions complementary to the MSH3 gene region generally do not contain any mismatches within the central 5-10 linked nucleosides. Methods described herein or known in the art can be used to determine whether an oligonucleotide containing mismatches in a target sequence is effective in inhibiting expression of the MSH3 gene. Considerations regarding the effectiveness of oligonucleotides with mismatches in inhibiting expression of the MSH3 gene are important, especially when a particular region of complementarity of the MSH3 gene is known to have polymorphic sequence diversity within the population.

[0172] The construction of vectors for expressing polynucleotides can be accomplished using conventional techniques that do not require detailed explanation to those skilled in the art. The creation of an efficient expression vector requires the presence of regulatory sequences that control the expression of the polynucleotide. These regulatory sequences include promoter and enhancer sequences, are influenced by specific cellular factors that interact with these sequences, and are well known in the art.

[0173] A. Alternative Oligonucleosides In one embodiment, one or more of the linked nucleosides or internucleoside bonds of the oligonucleotide are naturally occurring and do not include, for example, chemical modifications and / or conjugation, as known in the art and described herein.In another embodiment, one or more of the linked nucleosides or internucleoside bonds of the oligonucleotide are chemically modified to enhance stability or other beneficial properties.Without being bound by theory, it is believed that certain modifications can increase nuclease resistance and / or serum stability or reduce immunogenicity.For example, oligonucleotides can contain nucleotides (e.g., adenine, thymidine, guanosine, cytidine, uridine, or inosine) found to occur naturally in DNA or RNA, or alternative nucleosides or internucleoside bonds that have one or more chemical modifications to one or more components of the nucleotide (e.g., nucleobase, sugar, or phospholinker moiety). The oligonucleotides may be linked to each other via naturally occurring phosphodiester bonds or may contain alternative linkages (e.g., phosphorothioate (e.g., Sp phosphorothioate or Rp phosphorothioate), 3'-methylene phosphonate, 5'-methylene phosphonate, 3'-phosphoamidate, 2'-5' phosphodiester, guanidinium, S-methylthiourea, 2'-alkoxy, alkyl phosphate, or covalently linked via peptide bonds).

[0174] In some embodiments, substantially all of the nucleosides or internucleotide bonds of the oligonucleotide are alternative nucleosides.In other embodiments, substantially all of the nucleosides or internucleotide bonds of the oligonucleotide are alternative nucleosides.The oligonucleotides in which "substantially all of the nucleosides are alternative nucleosides" are mostly, but not completely, modified and can contain 5, 4, 3, 2, or 1 or less naturally occurring nucleosides.In still other embodiments, the oligonucleotides can contain 5, 4, 3, 2, or 1 or less alternative nucleosides.

[0175] Nucleic acids can be synthesized and / or modified by methods well established in the art, such as those described in "Current protocols in nucleic acid chemistry," Beaucage, SLet al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is incorporated herein by reference. Alternative nucleotides and nucleosides include those that include modifications, such as terminal modifications, such as 5'-end modifications (phosphorylation, conjugation, reverse linkage) or 3'-end modifications (conjugation, DNA nucleotides, reverse linkage, etc.), base modifications, such as replacement with stabilizing bases, destabilizing bases, or bases that base pair with a broad repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases, sugar modifications (e.g., at the 2' or 4' position) or sugar substitutions, and / or backbone modifications, including modification or substitution of phosphodiester linkages. The nucleobase may be an isonucleoside in which the nucleobase is moved from the C1 position of the sugar moiety to a different position (e.g., C2, C3, C4, or C5). Specific examples of oligonucleotide compounds useful in the embodiments described herein include, but are not limited to, alternative nucleosides containing modified backbones or non-natural internucleoside linkages. Nucleotides and nucleosides with modified backbones include, among others, those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referred to in the art, alternative RNAs that do not have a phosphorus atom in the internucleoside backbone of RNA can be considered to be oligonucleosides. In some embodiments, the oligonucleotide will have a phosphorus atom in its internucleoside backbone.

[0176] Alternative internucleoside linkages include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl phosphotriesters, methyl and other alkyl phosphonates, including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates, including 3'-amino phosphoramidates and aminoalkyl phosphoramidates, thionophosphoramidates, thionoalkyl phosphonates, thionoalkyl phosphotriesters, and boronophosphates with normal 3'-5' linkages, 2'-5' linked analogs of these, and those with inverted polarity where adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Also included are various salts, mixed salts, and free acid forms.

[0177] Representative United States patents which teach the preparation of the above phosphorus-containing linkages include U.S. Pat. Nos. 3,687,808, 4,469,863, 4,476,301, 5,023,243, 5,177,195, 5,188,897, 5,264,423, 5,276,019, 5,278,302, 5,286,717, 5,321,133, and 5,476,201. No. 1, No. 5,399,676, No. 5,405,939, No. 5,453,496, No. 5,455,233, No. 5,466,677, No. 5,476,925, No. 5,5 19,126, 5,536,821, 5,541,316, 5,550,111, 5,563,253, 5,571,799, 5,587,361, No. 5,625,050, No. 6,028,188, No. 6,124,445, No. 6,160,109, No. 6,169,170, No. 6,172,209, No. 6,239,2 No. 65, No. 6,277,603, No. 6,326,199, No. 6,346,614, No. 6,444,423, No. 6,531,590, No. 6,534,639, No. 6,6 Nos. 6,683,167, 6,858,715, 6,867,294, 6,878,805, 7,015,315, 7,041,816, 7,273,933, 7,321,029, and U.S. Patent No. RE39464, the contents of each of which are incorporated herein by reference in their entirety.

[0178] Alternative internucleoside linkages that do not include a phosphorus atom in the linkage have backbones formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatom or heterocyclic internucleoside linkages. These include morpholino linkages (formed in part from the sugar portion of the nucleoside), siloxane backbones, sulfide, sulfoxide and sulfone backbones, formacetyl and thioformacetyl backbones, methyleneformacetyl and thioformacetyl backbones, alkene-containing backbones, sulfamate backbones, methyleneimino and methylenehydrazino backbones, sulfonate and sulfonamide backbones, amide backbones, and those with mixed N, O, S, and CH 2 Others have component parts.

[0179] Representative U.S. patents which teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506, 5,166,315, 5,185,444, 5,214,134, 5,216,141, 5,235,033, 5,64,562, 5,264,564, 5,405,938, 5,434,257, 5,466,677, 5,470,967, and 5,489,677. Nos. 5,541,307, 5,561,225, 5,596,086, 5,602,240, 5,608,046, 5,610,289, 5,618,704, 5,623,070, 5,663,312, 5,633,360, 5,677,437, and 5,677,439, the contents of each of which are incorporated herein by reference in their entirety.

[0180] In other aspects, suitable oligonucleotides include those in which both the sugar and the internucleoside linkage of the nucleotide units, i.e., the backbone, are replaced. The base units are maintained for hybridization with the appropriate nucleic acid target compound. One such oligomeric compound mimetic that has been shown to have excellent hybridization properties is called peptide nucleic acid (PNA). In PNA compounds, the sugar of the nucleoside is replaced with an amide-containing backbone, particularly an aminoethylglycine backbone. The nucleobase is retained and is directly or indirectly linked to the aza nitrogen atom of the amide portion of the backbone. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Patent Nos. 5,539,082, 5,714,331, and 5,719,262, the contents of each of which are incorporated herein by reference in their entirety. Additional PNA compounds suitable for use in oligonucleotides are described, for example, in Nielsen et al., Science, 1991, 254, 1497-1500.

[0181] Some embodiments include oligonucleotides with phosphorothioate backbones and oligonucleotides with heteroatom backbones, and in particular -CH 2 -NH-CH 2 -, -CH 2 -N(CH 3 )-O-CH 2 - [known as the methylene (methylimino) or MMI backbone], the -CH 2 -ON(CH 3 )-CH 2 -, -CH 2 -N(CH 3 )-N(CH 3 )-CH 2 - and -N(CH 3 )-CH 2 -CH 2 - [wherein the natural phosphodiester backbone is -OPO-CH 2-], as well as the amide backbone of the above-mentioned U.S. Patent No. 5,602,240. In some embodiments, the oligonucleotides featured herein have the morpholino backbone structure of the above-mentioned U.S. Patent No. 5,034,506. In other embodiments, the oligonucleotides described herein include phosphorodiamidate morpholino oligomers (PMOs), in which the deoxyribose moiety is replaced by a morpholine ring and the charged phosphodiester intersubunit bond is replaced by an uncharged phosphorodiamidate bond, as described in Summerton, et al., Antisense Nucleic Acid Drug Dev. 1997, 7:63-70.

[0182] Alternative nucleosides and nucleotides can contain one or more substituted sugar moieties. Oligonucleotides, such as those featured herein, can include one of the following at the 2' position: OH, F, O-, S-, or N-alkyl, O-, S-, or N-alkenyl, O-, S-, or N-alkynyl, or O-alkyl-O-alkyl, where alkyl, alkenyl, and alkynyl are substituted or unsubstituted C 1 ~C 10 Alkyl or C 2 ~C 10 Exemplary and preferred modifications include -O[(CH 2 ) n O] m CH 3 , -O(CH 2 ) n OCH 3 , -O(CH 2 ) n -NH 2 , -O(CH 2 ) n CH 3 , -O(CH 2 ) n -ONH 2 , and -O(CH 2 ) n -ON[(CH 2 ) n CH 3 ] 2(wherein n and m are from 1 to about 10). In other embodiments, the oligonucleotide comprises one of the following at the 2' position: 1 ~C 10 Lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , S.O. 2 CH 3 , O.N.O. 2 , NO 2 , N 3 , N.H. 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, RNA cleaving groups, reporter groups, intercalators, groups for improving the pharmacokinetic properties of oligonucleotides, or groups for improving the pharmacodynamic properties of oligonucleotides, and other substituents with similar properties. In some embodiments, the modification is 2'-methoxyethoxy (2'-O-CH 2 CH 2 OCH 3 (also known as 2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chin. Acta, 1995, 78:486-504), i.e., an alkoxy-alkoxy group. MOE nucleosides confer several beneficial properties to oligonucleotides, including, but not limited to, increased nuclease resistance, improved pharmacokinetic properties, reduced nonspecific protein binding, reduced toxicity, reduced immunostimulatory properties, and enhanced target affinity compared to unmodified oligonucleotides.

[0183] Another exemplary alternative is —O(CH), also known as 2′-dimethylaminooxyethoxy, i.e., 2′-DMAOE, as described in the Examples herein below. 2 ) 2 ON(CH 3 ) 2groups, and 2'-dimethylaminoethoxyethoxy (also known in the art as 2'-O-dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-O-(CH 2 ) 2 -O-(CH 2 ) 2 -N(CH 3 ) 2 Further exemplary alternatives include 5'-Me-2'-F nucleotides, 5'-Me-2'-OMe nucleotides, 5'-Me-2'-deoxynucleotides (both the R and S isomers in these three families), 2'-alkoxyalkyls, and 2'-NMA (N-methylacetamide).

[0184] Other alternatives include 2'-methoxy (2'-OCH 3 ), 2'-aminopropoxy (2'-OCH 2 CH 2 CH 2 NH 2) and 2'-fluoro (2'-F). Similar modifications can be made at other positions on the nucleosides and nucleotides of oligonucleotides, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of the 5' terminal nucleotide. Oligonucleotides can have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugar structures include U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; Nos. 5,576,427, 5,591,722, 5,597,909, 5,610,300, 5,627,053, 5,639,873, 5,646,265, 5,658,873, 5,670,633, and 5,700,920, several of which are commonly owned with the present application. The entire contents of each of the aforementioned patents are incorporated herein by reference.

[0185] Oligonucleotides may contain nucleobase (often simply referred to in the art as "base") alternatives (e.g., modifications or substitutions). Unmodified or natural nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U). Alternative nucleobases include other synthetic and natural nucleobases, such as 5-methylcytidine, 5-hydroxymethylcytidine, 5-formylcytidine, 5-carboxycytidine, pyrrolocytidine, dideoxycytidine, uridine, 5-methoxyuridine, 5-hydroxydeoxyuridine, dihydrouridine, 4-thiouridine, pseudouridine, 1-methyl-pseudouridine, deoxyuridine, 5-hydroxyuridine, 5-hydroxy-1,1-dimethyl ... Sibutinyl-2'-deoxyuridine, xanthine, hypoxanthine, 7-deaza-xanthine, thienoguanine, 8-aza-7-deazaguanosine, 7-methylguanosine, 7-deazaguanosine, 6-aminomethyl-7-deazaguanosine, 8-aminoguanine, 2,2,7-trimethylguanosine, 8-methyladenine, 8-azidoadenine, 7-methyladenine, 7-deazaadenine, 3-deazaadenosine purine, 2,6-diaminopurine, 2-aminopurine, 7-deaza-8-aza-adenine, 8-amino-adenine, thymine, dideoxythymine, 5-nitroindole, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouridine, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyluridine and cytidine, 6-azouridine, cytidine and thymine, 4-thiouridine, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo, especially 5-bromo, 5-trifluoromethyl and other 5-substituted uridines and cytidines, 8-azaguanine and 8-azaadenine, and 3-deazaguanine.Further nucleobases include those disclosed in U.S. Patent No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, JL, ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., (1991) Angewandte Chemie, International Edition, 30:613, and those disclosed by Sanghvi, Y S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, ST and Lebleu, B., Ed., CRC Press, 1993. Some of these nucleobases are particularly useful for increasing the binding affinity of oligonucleotides. These include 5-substituted pyrimidines, 6-azapyrimidines, and N-2, N-6, and O-6 substituted purines, including, for example, 2-aminopropyladenine, 5-propynyluracil, and 5-propynylcytosine. 5-Methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, YS, Crooke, ST and Lebleu, B., Eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278), and are an exemplary base substitution, especially when combined with a 2′-O-methoxyethyl sugar modification.

[0186] Representative United States patents that teach the preparation of other alternative nucleobases, in addition to some of the alternative nucleobases mentioned above, include the above-mentioned U.S. Patent Nos. 3,687,808, 4,845,205, 5,130,30, 5,134,066, 5,175,273, 5,367,066, 5,432,272, 5,457,187, 5,459,255, 5,484,908, 5,502,177, 5,525,711, 5,552,540, 5,587,469, 5,594,121, 5,587,469, 5,594,121, 5,595,121, 5,596,121, 5,597,121, 5,598,121, 5,599,122, 5,600, 5,601, 5,610, 5,611, 5,612, 5,613, 5,614, 5,615, 5,616, 5,617, 5,618, 5,619, 5,620, 5,621, 5,625, 5,630, 5,631, 5,632, 5,635, 5,640, 5,641, 5,642, 5,643, 5,645, 5,650, 5,651, 5,652, 5,655, 5,656, 5,657, 5,658, 5,65 Nos. 5,596,091, 5,614,617, 5,681,941, 5,750,692, 6,015,886, 6,147,200, 6,166,197, 6,222,025, 6,235,887, 6,380,368, 6,528,640, 6,639,062, 6,617,438, 7,045,610, 7,427,672, and 7,495,088, the contents of each of which are incorporated herein by reference in their entirety.

[0187] In other embodiments, the sugar moiety in a nucleotide can be a ribose molecule, optionally having a 2'-O-methyl, 2'-O-MOE, 2'-F, 2'-amino, 2'-O-propyl, 2'-aminopropyl, or 2'-OH modification.

[0188] An oligonucleotide may contain one or more bicyclic sugar moieties. A "bicyclic sugar" is a furanosyl ring modified by a bridge of two atoms. A "bicyclic nucleoside" ("BNA") is a nucleoside having a sugar moiety that includes a bridge connecting two carbon atoms of the sugar ring, thereby forming a bicyclic ring system. In some embodiments, the bridge connects the 4'-carbon and the 2'-carbon of the sugar ring. Thus, in some embodiments, an oligonucleotide may contain one or more locked nucleosides. A locked nucleoside is a nucleoside having a modified ribose moiety, where the ribose moiety includes an additional bridge connecting the 2'-carbon and the 4'-carbon. In other words, a locked nucleoside is a nucleoside having a 4'-CH2 A locked nucleoside is a nucleoside that contains a bicyclic sugar moiety that contains an -O-2' bridge. This structure effectively "locks" the ribose in a 3'-endo structural conformation. The addition of locked nucleosides to oligonucleotides has been shown to increase oligonucleotide stability in serum and reduce off-target effects (Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193). Examples of bicyclic nucleosides for use in polynucleotides include, but are not limited to, nucleosides that contain a bridge between the 4' and 2' ribosyl ring atoms. In some embodiments, a polynucleotide agent includes one or more bicyclic nucleosides that contain a 4' to 2' bridge. Examples of such 4' to 2' bridged bicyclic nucleosides include 4'-(CH 2 )-O-2'(LNA), 4'-(CH 2 )-S-2',4'-(CH 2 ) 2 -O-2'(ENA), 4'-CH(CH 3 )-O-2' (also referred to as "constrained ethyl" or "cEt") and 4'-CH(CH 2 OCH 3 )-O-2' (and analogs thereof, see, e.g., U.S. Pat. No. 7,399,845), 4'-C(CH 3 )(CH 3 )-O-2' (and analogs thereof, see, e.g., U.S. Pat. No. 8,278,283), 4'-CH 2 -N(OCH 3 )-2' (and analogs thereof, see, e.g., U.S. Pat. No. 8,278,425), 4'-CH 2 -ON(CH 3 ) 2 -2' (see, e.g., U.S. Patent Publication No. 2004 / 0171570), 4'-CH 2 -N(R)-O-2' (wherein R is H, C 1 ~C 12 alkyl, or a protecting group) (see, e.g., U.S. Pat. No. 7,427,672), 4'-CH 2 -C(H)(CH 3)-2' (see, e.g., Chattopadhyaya et al., J. Org. Chem., 2009, 74, 118-134), as well as 4'-CH 2 -C(=CH 2 )-2' (and analogs thereof, see, e.g., U.S. Pat. No. 8,278,426). The entire contents of each of the foregoing patents are incorporated herein by reference.

[0189] Additional representative U.S. patents and U.S. patent publications that teach the preparation of locked nucleic acid nucleotides include the following: U.S. Patent Nos. 6,268,490, 6,525,191, 6,670,461, 6,770,748, 6,794,499, 6,998,484, 7,053,207, 7,034,133, 7,084,125, 7,399,845, 7,420,117, and 7,525,191. Nos. 7,427,672, 7,569,686, 7,741,457, 8,022,193, 8,030,467, 8,278,425, 8,278,426, 8,278,283, US2008 / 0039618, and US2009 / 0012281, the contents of each of which are incorporated herein by reference in their entirety.

[0190] Any of the foregoing bicyclic nucleosides may be prepared with one or more stereochemical sugar configurations, including, for example, α-L-ribofuranose and β-D-ribofuranose (see WO 99 / 14226).

[0191] Oligonucleotides can be modified to include one or more constrained ethyl nucleosides. As used herein, "constrained ethyl nucleoside" or "cEt" refers to a 4'-CH(CH 3 )-O-2' bridge. In one embodiment, the constrained ethyl nucleoside is in the S configuration, referred to herein as "S-cEt."

[0192] An oligonucleotide may contain one or more "conformationally restricted nucleosides" ("CRNs"). CRNs are nucleoside analogs with a linker connecting the C2' and C4' carbons of ribose or the C3 and --C5' carbons of ribose. The CRNs lock the ribose ring into a stable conformation and increase hybridization affinity to mRNA. The linker is of sufficient length to place the oxygen in an optimal position for stability and affinity, resulting in reduced puckering of the ribose ring.

[0193] Representative publications that teach the preparation of some of the above-mentioned CRNs include, but are not limited to, U.S. Patent Publication No. 2013 / 0190383, and PCT Publication WO2013 / 036868, the entire contents of each of which are incorporated herein by reference.

[0194] In some embodiments, the oligonucleotide comprises one or more monomers that are UNA (unlocked nucleosides) nucleosides. UNA is an unlocked acyclic nucleoside, in which any of the sugar bonds have been removed to form an unlocked "sugar" residue. In one example, UNA also encompasses monomers in which the C1'-C4' bond (i.e., the covalent carbon-oxygen-carbon bond between the C1' and C4' carbons) has been removed. In another example, the C2'-C3' bond (i.e., the covalent carbon-carbon bond between the C2' and C3' carbons) of the sugar has been removed (see Nuc. Acids Symp. Series, 52, 133-134 (2008) and Fluiter et al., Mol. Biosyst., 2009, 10, 1039, which are incorporated herein by reference).

[0195] Representative U.S. publications that teach the preparation of UNAs include, but are not limited to, U.S. Patent No. 8,314,227, and U.S. Patent Publication Nos. 2013 / 0096289, 2013 / 0011922, and 2011 / 0313020, the contents of each of which are incorporated by reference in their entirety herein.

[0196] The ribose molecule may be modified with a cyclopropane ring to produce tricyclodeoxynucleic acid (tricycloDNA). The ribose moiety may be replaced with another sugar, such as 1,5-anhydrohexitol, threose to produce threose nucleosides (TNAs), or arabinose to produce arabinonucleosides. The ribose molecule may be replaced with a non-sugar, such as cyclohexene to produce cyclohexene nucleosides, or glycol to produce glycol nucleosides.

[0197] Stabilizing modifications to the termini of the nucleoside molecules can potentially include N-(acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2'-O-deoxythymidine (ether), N-(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3''-phosphate, inverted base dT (idT), and the like. Disclosure of this modification can be found in PCT Publication No. WO2011 / 005861.

[0198] Other alternative chemistries for oligonucleotides include 5' phosphates or 5' phosphate mimetics of oligonucleotides, such as 5' terminal phosphates or phosphate mimetics.Suitable phosphate mimetics are disclosed, for example, in US Patent Publication No. 2012 / 0157511, the entire contents of which are incorporated herein by reference.

[0199] Exemplary oligonucleotides include nucleosides with alternative sugar moieties and may include DNA or RNA nucleosides. In some embodiments, oligonucleotides include nucleosides with alternative sugar moieties and DNA nucleosides. The incorporation of alternative nucleosides into oligonucleotides may enhance the affinity of the oligonucleotide to a target nucleic acid. In this case, the alternative nucleosides may be referred to as affinity enhancing alternative nucleotides.

[0200] In some embodiments, the oligonucleotide comprises at least one alternative nucleoside, such as at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, or at least 16 alternative nucleosides. In other embodiments, the oligonucleotide comprises 1-10 alternative nucleosides, such as 2-9 alternative nucleosides, such as 3-8 alternative nucleosides, such as 4-7 alternative nucleosides, such as 6 or 7 alternative nucleosides. In one embodiment, the oligonucleotide can comprise alternatives, which are independently selected from these three types of alternatives (alternative sugar moieties, alternative nucleobases, and alternative internucleoside linkages), or combinations thereof. In one embodiment, the oligonucleotide comprises one or more nucleosides that comprise an alternative sugar moiety, such as a 2' sugar alternative nucleoside. In some embodiments, the oligonucleotide comprises one or more 2' sugar surrogate nucleosides independently selected from the group consisting of 2'-O-alkyl-RNA, 2'-O-methyl-RNA, 2'-alkoxy-RNA, 2'-O-methoxyethyl-RNA, 2'-amino-DNA, 2'-fluoro-DNA, arabinonucleic acid (ANA), 2'-fluoro-ANA, and BNA (e.g., LNA (e.g., A-LNA, 5mC L-NA, G-LNA, T-LNA)) nucleosides. An exemplary structure of an LNA is as follows (with protecting groups removed):

[0201] [ka]

[0202] In some embodiments, one or more of the substituted nucleosides is a BNA.

[0203] In some embodiments, at least one of the alternative nucleosides is a BNA (e.g., an LNA), such as at least two of the alternative nucleosides, such as at least three, at least four, at least five, at least six, at least seven, or at least eight, etc. In still further embodiments, all of the alternative nucleosides are BNAs.

[0204] In further embodiments, the oligonucleotide comprises at least one alternative internucleoside bond. In some embodiments, the internucleoside bond in adjacent nucleotide sequence is phosphorothioate or boronophosphate internucleoside bond. In some embodiments, all internucleoside bonds in adjacent sequences of oligonucleotide are phosphorothioate bond. In some embodiments, phosphorothioate bond is stereochemically pure phosphorothioate bond. In some embodiments, phosphorothioate bond is Sp phosphorothioate bond. In other embodiments, phosphorothioate bond is Rp phosphorothioate bond.

[0205] In some embodiments, the oligonucleotide comprises at least one alternative nucleoside that is 2'-MOE-RNA, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 2'-MOE-RNA nucleoside units. In some embodiments, the 2'-MOE-RNA nucleoside units are linked by phosphorothioate bonds. In some embodiments, at least one of the alternative nucleosides is 2'-fluoro-DNA, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 2'-fluoro-DNA nucleoside units. In some embodiments, the oligonucleotide comprises at least one BNA unit and at least one 2'-substituted modified nucleoside. In some embodiments, the oligonucleotide comprises both 2' sugar modified nucleosides and DNA units. In some embodiments, the oligonucleotide or its adjacent nucleotide region is a gapmer oligonucleotide.

[0206] B. Oligonucleotides conjugated to ligands Oligonucleotides can be chemically linked to one or more ligands, moieties, or conjugates that enhance the activity, cellular distribution, or cellular uptake of the oligonucleotide. Such moieties include lipid moieties, such as cholesterol moieties (Letsinger et al., (1989) Proc. Natl. Acid. Sci. USA, 86:6553-6556), cholic acid (Manoharan et al., (1994) Biorg. Med. Chem. Let., 4:1053-1060), thioethers, such as beryl-S-tritylthiol (Manoharan et al., (1992) Ann. NY Acad. Sci., 660:306-309; Manoharan et al., (1993) Biorg. Med. Chem. Let., 3:2765-2770), thiocholesterol (Oberhauser et al., (1992) Nucl. Acids, 1:106-1070), and cholic acid (Manoharan et al., (1994) Biorg. Med. Chem. Let., 4:1053-1060). Res., 20:533-538), aliphatic chains such as dodecanediol or undecyl residues (Saison-Behmoaras et al., (1991) EMBO J, 10:1111-1118; Kabanov et al., (1990) FEBS Lett., 259:327-330; Svinarchuk et al., (1993) Biochimie, 75:49-54), phospholipids such as di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-phosphonate (Manoharan et al., (1995) Tetrahedron Lett., 36:3651-3654; Shea et al., (1990) Nucl. Acids, 75:49-54). Res., 18:3777-3783), polyamine or polyethylene glycol chains (Manoharan et al., (1995) Nucleosides & Nucleotides, 14:969-973), or adamantane acetic acid (Manoharan et al., (1995) Tetrahedron Lett., 36:3651-3654), palmityl moieties (Mishra et al., (1995) Biochim. Biophys.Acta, 1264:229-237), or octadecylamine or hexylamino-carbonyloxycholesterol moieties (Crooke et al., (1996) J. Pharmacol. Exp. Ther., 277:923-937).

[0207] In one aspect, a ligand alters the distribution, targeting, or lifetime of an oligonucleotide agent into which it is incorporated. In some aspects, a ligand provides enhanced affinity for a selected target, e.g., a molecule, a cell or cell type, a compartment, e.g., a cell or organ compartment, a tissue, an organ, or a body site, e.g., when compared to a species in which such ligand is not present.

[0208] Ligands can include naturally occurring substances, such as proteins (e.g., human serum albumin (HSA), low density lipoprotein (LDL), or globulins), carbohydrates (e.g., dextran, pullulan, chitin, chitosan, inulin, cyclodextrin, N-acetylglucosamine, N-acetylgalactosamine, or hyaluronic acid), or lipids. Ligands can be recombinant or synthetic molecules, such as synthetic polymers, such as synthetic polyamino acids. Examples of polyamino acids include polylysine (PLL), poly-L-aspartic acid, poly-L-glutamic acid, styrene-maleic anhydride copolymer, poly(L-lactide-co-glycolide) copolymer, divinyl ether-maleic anhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacrylic acid), N-isopropylacrylamide polymer, or polyphosphazine. Examples of polyamines include polyethyleneimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine, amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of polyamine, or alpha-helical peptide.

[0209] The ligand may comprise a targeting group, e.g., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a particular cell type, such as a kidney cell. The targeting group may be thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, mucin carbohydrate, polyvalent lactose, polyvalent galactose, N-acetyl-galactosamine, N-acetyl-glucosamine polyvalent mannose, polyvalent fucose, glycosylated polyamino acids, polyvalent galactose, transferrin, bisphosphonate, polyglutamic acid, polyaspartic acid, lipid, cholesterol, steroid, bile acid, folic acid, vitamin B12, vitamin A, biotin, or an RGD peptide or RGD peptide mimetic.

[0210] Other examples of ligands include dyes, intercalating agents (e.g., acridine), crosslinkers (e.g., psoralens, mitomycin C), porphyrins (TPPC4, texaphyrin, sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial endonucleases (e.g., EDTA), lipophilic molecules such as cholesterol, cholic acid, adamantane acetic acid, 1-pyrenebutyric acid, dihydrotestosterone, 1,3-bis-O(hexadecyl)glycerol, gelatin, and the like. nyloxyhexyl, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG] 2 , polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g., biotin), transport / absorption enhancers (e.g., aspirin, vitamin E, folic acid), synthetic ribonucleases (e.g., imidazole, bis-imidazole, histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.

[0211] The ligand may be a protein, e.g., a glycoprotein, or a peptide, e.g., a molecule with specific affinity for a co-ligand, or an antibody, e.g., an antibody that binds to a particular cell type, such as a hepatocyte. Ligands may include hormones and hormone receptors. They may include non-peptide species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent galactose, N-acetyl-galactosamine, N-acetyl-glucosamine, multivalent mannose, or multivalent fucose.

[0212] A ligand can be a substance, e.g., a drug, that can increase uptake of an oligonucleotide agent into a cell, e.g., by disrupting the cytoskeleton of the cell, e.g., by disrupting the microtubules, microfilaments, and / or intermediate filaments of the cell. The drug can be, for example, taxon, vincristine, vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.

[0213] In some embodiments, the ligand attached to the oligonucleotide as described herein functions as a pharmacokinetic modulator (PK modulator). PK modulators include lipophilic substances, bile acids, steroids, phospholipid analogs, peptides, protein binders, PEG, vitamins, and the like. Exemplary PK modulators include, but are not limited to, cholesterol, fatty acids, cholic acid, lithocholic acid, dialkyl glycerides, diacyl glycerides, phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin, and the like. Oligonucleotides containing multiple phosphorothioate bonds are also known to bind to serum proteins, and therefore short oligonucleotides, for example, about 5-base, 10-base, 15-base, or 20-base oligonucleotides, containing multiple phosphorothioate bonds in the backbone, are also suitable as ligands (e.g., as PK-modulating ligands). In addition, aptamers that bind serum components (e.g., serum proteins) are also suitable for use as PK-modulating ligands in the embodiments described herein.

[0214] Ligand-conjugated oligonucleotides can be synthesized by using oligonucleotides that have pendant reactive functional groups, such as those resulting from the attachment of a linking molecule onto an oligonucleotide (described below). The reactive oligonucleotides can be reacted directly with commercially available ligands, with synthesized ligands that have any of a variety of protecting groups, or with ligands that have a linking moiety attached to the ligand.

[0215] The oligonucleotides used in the conjugates can be conveniently and routinely produced by the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several suppliers, including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art can additionally or alternatively be used. It is also known to use similar techniques to prepare other oligonucleotides, such as phosphorothioates and alkylated derivatives.

[0216] For ligand-conjugated oligonucleotides, such as ligand molecules having sequence-specific linked nucleosides, oligonucleotides and oligonucleosides can be assembled on a suitable DNA synthesizer using standard nucleotide or nucleoside precursors, or nucleotide or nucleoside conjugate precursors that already have a linking moiety, ligand-nucleotide or nucleoside conjugate precursors that already have a ligand molecule, or non-nucleoside ligand-bearing components.

[0217] When using a conjugate precursor that already has a linking moiety, synthesis of the sequence-specific linked nucleoside is typically completed and then the ligand molecule is reacted with the linking moiety to form the ligand-conjugated oligonucleotide. In some embodiments, the oligonucleotide or linked nucleoside is synthesized by an automated synthesizer using phosphoramidites derived from the ligand-nucleoside conjugates, in addition to standard and non-standard phosphoramidites that are commercially available and routinely used in oligonucleotide synthesis.

[0218] i. Lipid complex In one embodiment, the ligand or complex is lipid or lipid-based molecule.Such lipid or lipid-based molecule can bind to serum protein, for example, human serum albumin (HSA).HSA binding ligand allows the distribution of complex to target tissue, for example, non-renal target tissue in the body.Lipid or lipid-based ligand can (a) increase the degradation resistance of complex, (b) increase targeting or transport to target cell or cell membrane, and / or (c) be used to adjust the binding to serum protein, for example, HSA.

[0219] In another embodiment, the ligand is a moiety, e.g., a vitamin, which is taken up by a target cell, e.g., a proliferative cell. Exemplary vitamins include vitamins A, E, and K.

[0220] ii. Cell-penetrating agents In another embodiment, the ligand is a cell-penetrating agent, such as a helical cell-penetrating agent. In one embodiment, the agent is amphipathic. An exemplary agent is a peptide, such as tat or antennapedia. If the agent is a peptide, it can be modified, including peptidyl mimetics, invertomers, non-peptide or pseudopeptide bonds, and the use of D-amino acids. In one embodiment, the helical agent is an alpha-helical agent, which can have a lipophilic and lipophobic phase.

[0221] The ligand can be a peptide or peptidomimetic. Peptidomimetics (also referred to herein as oligopeptidomimetics) are molecules that can fold into defined three-dimensional structures similar to natural peptides. Attachment of peptides and peptidomimetics to oligonucleotide agents can affect the pharmacokinetic distribution of the oligonucleotide, such as by enhancing cellular recognition and uptake. The peptide or peptidomimetic moiety can be about 5-50 amino acids in length, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length.

[0222] The peptide or peptidomimetic can be, for example, a cell penetrating peptide, a cationic peptide, an amphipathic peptide, or a hydrophobic peptide (e.g., composed mainly of Tyr, Trp, or Phe). The peptide moiety can be a dendrimeric peptide, a constrained peptide, or a cross-linked peptide. In another alternative, the peptide moiety can include a hydrophobic membrane translocation sequence (MTS). An exemplary hydrophobic MTS-containing peptide is RFGF, which has the amino acid sequence AAVALLPAVLLALLAP. RFGF analogs containing hydrophobic MTS (e.g., the amino acid sequence AALLPVLLAAP) can be targeting moieties. The peptide moiety can be a "delivery" peptide, which can carry large polar molecules, including peptides, oligonucleotides, and proteins, across cell membranes. For example, it has been found that sequences derived from the HIV Tat protein (GRKKRRQRRRPPQ) and the Drosophila antennapedia protein (RQIKIWFQNRRMKWKK) can function as delivery peptides. The peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identified from a phage display library, or a one bead one compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-84, 1991). An example of a peptide or peptidomimetic tethered to an oligonucleotide agent by a monomer unit incorporated for cell targeting purposes is an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. The peptide portion can range in length from about 5 amino acids to about 40 amino acids. The peptide portion can have structural modifications, such as to increase stability or induce conformational properties. Any of the structural modifications described below can be utilized.

[0223] RGD peptides for use in the compositions and methods can be linear or cyclic, and can be modified, for example, glycosylated or methylated, to facilitate targeting to a particular tissue(s).RGD-containing peptides and peptidomimetics can include synthetic RGD mimetics in addition to D-amino acids.In addition to RGD, other moieties can be used that target integrin ligands.Some complexes of this ligand target PECAM-1 or VEGF.

[0224] The cell-penetrating peptide can penetrate cells, such as microbial cells, such as bacterial or fungal cells, or mammalian cells, such as human cells. The microbial cell-penetrating peptide can be, for example, an α-helical linear peptide (e.g., LL-37 or cecropin P1), a disulfide bond-containing peptide (e.g., α-defensin, β-defensin, or bactenecin), or a peptide containing only one or two key amino acids (e.g., PR-39 or indolicidin). The cell-penetrating peptide can include a nuclear localization signal (NLS). For example, the cell-penetrating peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res. 31:2717-2724, 2003).

[0225] iii. Carbohydrate Complex In some embodiments of the compositions and methods described herein, the oligonucleotide further comprises a carbohydrate. Carbohydrate-conjugated oligonucleotides are advantageous in compositions suitable for in vivo therapeutic applications in addition to in vivo delivery of nucleic acids, as described herein. As used herein, "carbohydrate" refers to either a compound that is a carbohydrate itself, composed of one or more monosaccharide units having at least six carbon atoms (which may be linear, branched or cyclic) with an oxygen, nitrogen or sulfur atom bonded to each carbon atom, or a compound that has as part of it a carbohydrate moiety, each of which is composed of one or more monosaccharide units having at least six carbon atoms (which may be linear, branched or cyclic) with an oxygen, nitrogen or sulfur atom bonded to each carbon atom. Representative carbohydrates include sugars (monosaccharides, disaccharides, trisaccharides and oligosaccharides containing about 4, 5, 6, 7, 8 or 9 monosaccharide units), as well as polysaccharides, such as starch, glycogen, cellulose and polysaccharide gums. Particular monosaccharides include sugars of C5 or higher (e.g., C5, C6, C7, or C8), and disaccharides and trisaccharides include sugars having two or three monosaccharide units (e.g., C5, C6, C7, or C8).

[0226] In one aspect, a complex carbohydrate for use in the compositions and methods described herein is a monosaccharide.

[0227] In some embodiments, the carbohydrate conjugate further comprises one or more additional ligands as described above, such as, but not limited to, a PK modulator and / or a cell penetrating peptide.

[0228] Additional carbohydrate conjugates (and linkers) suitable for use include those described in PCT Publication Nos. WO2014 / 179620 and WO2014 / 179627, the contents of each of which are incorporated herein by reference in their entirety.

[0229] iv. Linker In some aspects, the conjugates or ligands described herein may be attached to the oligonucleotide using a variety of linkers, which may be cleavable or non-cleavable.

[0230] The linker is typically a direct bond or an atom, such as oxygen or sulfur, or a unit, such as NR 8 , C(O), C(O)NH, SO, SO 2 , S.O. 2 NH, or a chain of atoms, for example, but not limited to, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, aryl alkyl, aryl alkenyl, aryl alkynyl, heteroaryl alkyl, heteroaryl alkenyl, heteroaryl alkynyl, heterocyclyl alkyl, heterocyclyl alkenyl, heterocyclyl alkynyl, aryl, heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylaryl alkyl, alkylaryl alkenyl, alkylaryl alkynyl, alkenylaryl alkyl, alkenylaryl alkenyl, alkenylaryl alkynyl, alkynylaryl alkyl, alkynylaryl alkenyl, alkynylaryl alkynyl, alkylheteroaryl alkyl, alkylheteroaryl alkenyl, alkylheteroarylalkynyl, alkenylheteroarylalkyl, alkenylheteroarylalkenyl, alkenylheteroarylalkynyl, alkynylheteroarylalkyl, alkynylheteroarylalkenyl, alkynylheteroarylalkynyl, alkylheterocyclylalkyl, alkylheterocyclylalkenyl, alkylheterocyclylalkynyl, alkenylheterocyclylalkyl, alkenylheterocyclylalkenyl, alkenylheterocyclylalkynyl, alkynylheterocyclylalkyl, alkynylheterocyclylalkenyl, alkynylheterocyclylalkynyl, alkylaryl, alkenylaryl, alkynylaryl, alkylheteroaryl, alkenylheteroaryl, alkynylheteroaryl, and the like, wherein one or more methylenes are selected from the group consisting of O, S, S(O), SO 2 , N(R 8), C(O), substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocyclic (wherein R 8 is hydrogen, acyl, aliphatic or substituted aliphatic). In one embodiment, the linker is about 1-24, 2-24, 3-24, 4-24, 5-24, 6-24, 6-18, 7-18, 8-18, 7-17, 8-17, 6-16, 7-17, 8-16 or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 21, 22, 23, or 24 atoms.

[0231] A cleavable linking group is one that is sufficiently stable outside a cell, but that upon entry into a target cell is cleaved to release the two moieties that the linker is holding together. In some embodiments, the cleavable linking group is cleaved at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or more, or at least 100 times faster in the target cell or under a first reference condition (which may be selected, for example, to mimic or represent intracellular conditions) than in the subject's blood or under a second reference condition (which may be selected, for example, to mimic or represent conditions found in blood or serum).

[0232] Cleavable linking groups are susceptible to cleaving agents, such as pH, redox potential, or the presence of degradable molecules. Generally, cleaving agents are more prevalent or found at higher levels or activity inside cells than in serum or blood. Examples of such degrading agents include redox agents that are selective for a particular substrate or have no substrate specificity at all, such as oxidizing or reducing enzymes, or reducing agents, such as mercaptans present in cells, that can degrade redox-cleavable linking groups by reduction, esterases, endosomes or agents that can cause an acidic environment, such as those that cause a pH of 5 or less, general acids, peptidases (which can be substrate specific), and enzymes that can function as phosphatases to hydrolyze or degrade acid-cleavable linking groups.

[0233] Cleavable linking groups, such as disulfide bonds, may be sensitive to pH. While the pH of human serum is 7.4, the average intracellular pH is slightly lower, ranging from about 7.1 to 7.3. Endosomes have a more acidic pH, ranging from 5.5 to 6.0, and lysosomes have an even more acidic pH of approximately 5.0. Some linkers have cleavable linking groups that are cleaved at a preferred pH, releasing the cationic lipid from the ligand inside the cell or into a desired compartment of the cell.

[0234] The linker may include a cleavable linking group that can be cleaved by a specific enzyme. The type of cleavable linking group incorporated into the linker may depend on the cell to be targeted. For example, a ligand that targets the liver may be linked to a cationic lipid via a linker that includes an ester group. Because liver cells are rich in esterase, the linker will be cleaved more efficiently in liver cells than in cell types that are not rich in esterase. Other cell types that are rich in esterase include lung, renal cortex, and testis cells.

[0235] Linkers containing peptide bonds may be used when targeting cell types that are rich in peptidases, such as liver cells and synovial cells.

[0236] In general, the suitability of a candidate cleavable linking group can be evaluated by testing the ability (or conditions) of a degrading agent to cleave the candidate linking group. It may also be desirable to test the candidate cleavable linking group for its ability to resist cleavage in blood or when in contact with other non-target tissues. Thus, the relative susceptibility to cleavage can be determined between at least two conditions, where at least one condition is selected to indicate cleavage in target cells and another condition is selected to indicate cleavage in other tissues or biological fluids, such as blood or serum. Evaluation can be performed in a cell-free system, in cells, in cell culture, in organ or tissue culture, or in whole animals. It may be useful to perform initial evaluation in a cell-free or culture conditions and confirm by further evaluation in whole animals. In some embodiments, useful candidate compounds are cleaved at least 2-fold, 4-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, or 100-fold faster in cells (or under in vitro conditions selected to mimic intracellular conditions) when compared to blood or serum (or under in vitro conditions selected to mimic extracellular conditions).

[0237] a. Redox-cleavable linking group In one embodiment, the cleavable linking group is a redox cleavable linking group that is cleaved upon reduction or oxidation. An example of a reductively cleavable linking group is a disulfide linking group (--S--S--). The methods described herein can be used to determine whether a candidate cleavable linking group is a suitable "reductively cleavable linking group" or is suitable for use with, for example, a particular oligonucleotide moiety and a particular targeting agent. For example, the candidate can be evaluated by incubation with dithiothreitol (DTT) or other reducing agents using reagents known in the art that mimic the cleavage rate that would be observed in cells, for example, target cells. The candidate can be evaluated under conditions selected to mimic blood or serum conditions. In one embodiment, the candidate compound is cleaved at most about 10% in blood. In other embodiments, useful candidate compounds are degraded at least 2, 4, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 times faster in cells (or under in vitro conditions selected to mimic intracellular conditions) when compared to blood (or under in vitro conditions selected to mimic extracellular conditions). The cleavage rate of the candidate compound can be determined using standard enzyme kinetics assays under conditions selected to mimic the intracellular medium and compared to conditions selected to mimic the extracellular medium.

[0238] b. Phosphate-based cleavable linkers In another embodiment, the cleavable linker comprises a phosphate-based cleavable linking group. The phosphate-based cleavable linking group is cleaved by an agent that degrades or hydrolyzes the phosphate group. An example of an agent that cleaves a phosphate group in a cell is an enzyme such as a phosphatase in the cell. An example of a phosphate-based linking group is -OP(O)(OR k )-O-, -OP(S)(OR k )-O-, -OP(S)(SR k )-O-, -SP(O)(OR k )-O-, -OP(O)(OR k )-S-, -SP(O)(OR k )-S-, -OP(S)(ORk )-S-, -SP(S)(OR k )-O-, -OP(O)(R k )-O-, -OP(S)(R k )-O-, -SP(O)(R k )-O-, -SP(S)(R k )-O-, -SP(O)(R k )-S-, -OP(S)(R k )-S-. These candidates can be evaluated using methods similar to those described above.

[0239] c. acid-cleavable linking group In another embodiment, the cleavable linker comprises an acid-cleavable linking group. An acid-cleavable linking group is a linking group that is cleaved under acidic conditions. In some embodiments, the acid-cleavable linking group is cleaved in an acidic environment having a pH of about 6.5 or less (e.g., about 6.0, 5.75, 5.5, 5.25, 5.0, or less) or by an agent such as an enzyme that can function as a general acid. In cells, certain low pH organelles, such as endosomes and lysosomes, can provide a cleavage environment for the acid-cleavable linking group. Examples of acid-cleavable linking groups include, but are not limited to, hydrazones, esters, and esters of amino acids. Acid-cleavable groups can have the general formula -C=NN--, C(O)O, or -OC(O). In one embodiment, the carbon attached to the oxygen of the ester (alkoxy group) is an aryl group, a substituted alkyl group, or a tertiary alkyl group, such as dimethylpentyl or t-butyl. These candidates can be evaluated using methods similar to those described above.

[0240] d. Ester-based linking groups In another embodiment, the cleavable linker comprises an ester-based cleavable linking group. The ester-based cleavable linking group is cleaved by enzymes such as esterases and amidases in cells. Examples of ester-based cleavable linking groups include, but are not limited to, esters of alkylene, alkenylene and alkynylene groups. Ester cleavable linking groups have the general formula --C(O)O--, or --OC(O)--. These candidates can be evaluated using methods similar to those described above.

[0241] e. Peptide-Based Cleavage Groups In yet another embodiment, the cleavable linker comprises a peptide-based cleavable linking group. The peptide-based cleavable linking group is cleaved by enzymes, such as peptidases and proteases, in cells. A peptide-based cleavable linking group is a peptide bond formed between amino acids to generate oligopeptides (e.g., dipeptides, tripeptides, etc.) and polypeptides. A peptide-based cleavable group does not include amide groups (-C(O)NH-). An amide group can be formed between any alkylene, alkenylene, or alkynylene. A peptide bond is a special type of amide bond formed between amino acids to generate peptides and proteins. A peptide-based cleaving group is generally limited to peptide bonds (i.e., amide bonds) formed between amino acids to generate peptides and proteins, and does not include the entire amide functionality. A peptide-based cleavable linking group has the general formula -NHCHR A C(O)NHCHR B C(O)—, where R A and R B are the R groups of two adjacent amino acids. These candidates can be evaluated using methods similar to those described above.

[0242] In one embodiment, the oligonucleotide is conjugated to the carbohydrate via a linker. The linker includes bivalent and trivalent branched linker groups. The linker of the oligonucleotide carbohydrate conjugate includes, but is not limited to, those described in formulas 24-35 of PCT Publication No. WO2018 / 195165.

[0243] Representative U.S. patents which teach the preparation of oligonucleotide conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979, 4,948,882, 5,218,105, 5,525,465, 5,541,313, 5,545,730, 5,552,538, 5,578,717, 5,580,731, 5,591,584, 5,109,124, 5,118,802, 5,138,045, 5,414,077, 5,486,603, No. 5,512,439, No. 5,578,718, No. 5,608,046, No. 4,587,044, No. 4,605,735, No. 4,667,025, No. 4,762,779, No. 4,789,737, No. 4,824,941 , No. 4,835,263, No. 4,876,335, No. 4,904,582, No. 4,958,013, No. 5,0 No. 82,830, No. 5,112,963, No. 5,214,136, No. 5,082,830, No. 5,112,963 No. 5,214,136, No. 5,245,022, No. 5,254,469, No. 5,258,506, No. 5, No. 262,536, No. 5,272,250, No. 5,292,873, No. 5,317,098, No. 5,371,24 No. 1, No. 5,391,723, No. 5,416,203, No. 5,451,463, No. 5,510,475, No. 5 ,512,667, 5,514,785, 5,565,552, 5,567,810, 5,574,1 42, 5,585,481, 5,587,371, 5,595,726, 5,597,696, 5,599,923, 5,599,928, and 5,688,941, 6,294,664, 6,320,017, 6,576,752, 6,783,931, 6,900,297, 7,037,646, and 8,106,022, the contents of each of which are incorporated herein by reference in their entirety.

[0244] Not all positions in a given compound need be uniformly modified, and in fact more than one of the above modifications may be incorporated into a single compound, or even into a single nucleoside within an oligonucleotide. Oligonucleotide compounds that are chimeric compounds are also contemplated. Chimeric oligonucleotides usually contain at least one region in which the RNA is modified to confer increased resistance to nuclease degradation, increased cellular uptake, and / or increased binding affinity to the target nucleic acid to the oligonucleotide. Additional regions of the oligonucleotide may serve as substrates for enzymes capable of cleaving RNA:DNA. As an example, RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. Thus, activation of RNase H results in cleavage of the RNA target, thereby greatly improving the efficiency of oligonucleotide inhibition of gene expression. As a result, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, optionally, associated nucleic acid hybridization techniques known in the art.

[0245] In certain cases, the nucleotides of the oligonucleotide may be modified by non-ligand groups. Numerous non-ligand molecules have been conjugated to oligonucleotides to enhance the activity, cellular distribution, or cellular uptake of the oligonucleotide, and procedures for carrying out such conjugation are available in the scientific literature. Such non-ligand moieties include lipid moieties, such as cholesterol (Kubo, T. et al., Biochem. Biophys. Res. Comm, 2007, 365(1):54-61; Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86:6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4:1053), thioethers, such as hexyl-S-tritylthiol (Manoharan et al., Ann. NY Acad. Sci., 1992, 660:306; Manoharan et al., Bioorg. Med. Chem. Lett., 1993, 3:2765), thiocholesterol (Oberhauser et al., Nucl. Acids, 1997, 1:131-132), and the like. Res., 1992, 20:533), aliphatic chains, e.g., dodecanediol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10:111; Kabanov et al., FEBS Lett., 1990, 259:327; Svinarchuk et al., Biochimie, 1993, 75:49), phospholipids, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36:3651; Shea et al., Nucl. Acids Res., 1990, 18:3777), polyamines or polyethylene glycol chains (Manoharan et al., al., Nucleosides & Nucleotides, 1995, 14:969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651), palmityl moieties (Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or octadecylamine or hexylamino-carbonyl-oxycholesterol moieties (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277:923). Representative U.S. patents teaching the preparation of such oligonucleotide conjugates are listed above. A typical conjugation protocol involves the synthesis of an oligonucleotide bearing an amino linker at one or more positions in the sequence. The amino group is then reacted with the molecule being conjugated using an appropriate coupling or activating reagent. The conjugation reaction can be carried out either with the oligonucleotide still attached to the solid support or in solution phase after oligonucleotide cleavage. Purification of the oligonucleotide conjugate by HPLC usually provides a pure conjugate.

[0246] IV.Medicinal Uses The oligonucleotides, or pharma- ceutically acceptable salts thereof, compositions described herein are useful in the methods described herein and, without wishing to be bound by theory, are believed to exert their desired effects by their ability to modulate the levels, state, and / or activity of the MutSβ heterodimer comprising MSH3, for example, by inhibiting the activity or levels of MSH3 protein in mammalian cells.

[0247] One embodiment relates to a method of treating a disorder associated with DNA mismatch repair, such as a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder) in a subject in need of such treatment. Another embodiment includes decreasing the level of MSH3 in a cell of a subject identified as having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder). Additionally, another embodiment includes a method of inhibiting expression of MSH3 in a cell of a subject. A further embodiment includes a method of decreasing a nucleotide repeat expansion in a cell. The method includes contacting a cell with an oligonucleotide, or a pharma- ceutically acceptable salt thereof, in an amount effective to inhibit expression of MSH3 in the cell, thereby inhibiting expression of MSH3 in the cell.

[0248] Based on the above method, the oligonucleotide, or a pharma- ceutically acceptable salt thereof, or a composition comprising such an oligonucleotide, or a pharma- ceutically acceptable salt thereof, is intended for use in therapy, or for use as a medicine, or for use in treating a disorder associated with DNA mismatch repair, such as a repeat expansion disorder, in a subject in need of such treatment, or for use in reducing the level of MSH3 in a cell of a subject identified as having a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), or for use in inhibiting the expression of MSH3 in a cell of a subject, or for use in reducing a nucleotide repeat expansion (e.g., a trinucleotide repeat expansion) in a cell. The use includes contacting a cell with the oligonucleotide, or a pharma- ceutically acceptable salt thereof, in an amount effective to inhibit the expression of MSH3 in the cell, thereby inhibiting the expression of MSH3 in the cell. The embodiments described below that relate to the methods described herein are also applicable to these further embodiments.

[0249] Contacting a cell with the oligonucleotide, or a pharma- ceutically acceptable salt thereof, can be performed in vitro or in vivo. Contacting a cell with the oligonucleotide, or a pharma- ceutically acceptable salt thereof, in vivo includes contacting a cell or a group of cells in a subject, e.g., a human subject, with the oligonucleotide, or a pharma- ceutically acceptable salt thereof. A combination of in vitro and in vivo methods of contacting a cell is also possible. As noted above, contacting a cell can be direct or indirect. Furthermore, contacting a cell can be achieved via a targeting ligand, including any ligand described herein or known in the art. In some embodiments, the targeting ligand is a carbohydrate moiety, e.g., GalNAc ... 3 The ligand may be a ligand, or any other ligand that directs the oligonucleotide to a site of interest. The cells may include cells of the central nervous system, or muscle cells.

[0250] Inhibition of expression of the MSH3 gene includes any level of inhibition of the MSH3 gene, such as at least partial suppression of MSH3 gene expression, such as at least 20% inhibition, etc. In some embodiments, inhibition is at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%.

[0251] Expression of the MSH3 gene can be assessed based on the level of any variable associated with MSH3 gene expression, for example, MSH3 mRNA levels or MSH3 protein levels.

[0252] Inhibition can be assessed by a decrease in the absolute or relative level of one or more of these variables compared to a control level, which can be any type of control level used in the art, such as a pre-dose baseline level or a level determined from a similar subject, cell, or sample that is untreated or treated with a control, such as a buffer-only control or an inactive agent control.

[0253] In some embodiments, surrogate markers may be used to detect inhibition of MSH3. For example, effective treatment of a nucleotide repeat expansion disorder (e.g., a trinucleotide repeat expansion disorder), as demonstrated by accepted diagnostic and monitoring criteria, with an agent that reduces MSH3 expression may be taken to indicate a clinically relevant reduction in MSH3.

[0254] In some embodiments of the method, expression of the MSH3 gene is inhibited to at least 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% or less of the detection level of the assay. In some embodiments, the method includes a clinically relevant inhibition of MSH3 expression, e.g., as demonstrated by a clinically relevant outcome following treatment of a subject with an agent to reduce expression of MSH3.

[0255] Inhibition of expression of the MSH3 gene may be manifested by a decrease in the amount of mRNA expressed by a first cell or population of cells (such cells may be present, for example, in a sample derived from a subject) in which the MSH3 gene is transcribed and the cell(s) have been treated (e.g., by contacting the cell(s) with an oligonucleotide, or a pharma- ceutically acceptable salt thereof, or by administering an oligonucleotide, or a pharma- ceutically acceptable salt thereof, to a subject in which the cells are or were present) such that expression of the MSH3 gene is inhibited when compared to a second cell or population of cells substantially identical to the first cell or population of cells, but in which the cell(s) have not been so treated (a control cell(s) that have not been treated with the oligonucleotide, or a pharma- ceutically acceptable salt thereof, or that have not been treated with an oligonucleotide targeted to the gene of interest, or a pharma- ceutically acceptable salt thereof). The degree of inhibition may be represented by the following:

[0256]

number

[0257] In other aspects, inhibition of expression of the MSH3 gene may be assessed in terms of a parameter functionally related to MSH3 gene expression, such as a reduction in MSH3 protein expression or the MSH3 signaling pathway. MSH3 gene silencing may be determined in any cell expressing MSH3, either endogenously or heterologously from an expression construct, and by any assay known in the art.

[0258] Inhibition of expression of MSH3 protein may be manifested by a decrease in the level of MSH3 protein expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject). As explained above, for the purpose of assessing mRNA suppression, inhibition of protein expression levels in treated cells or groups of cells may similarly be expressed as a percentage of protein levels in control cells or groups of cells.

[0259] The control cell or cell group that can be used to evaluate the inhibition of expression of the MSH3 gene includes a cell or cell group that has not yet been contacted with the oligonucleotide. For example, the control cell or cell group can be derived from an individual subject (e.g., a human or animal subject) before the subject is treated with the oligonucleotide.

[0260] The level of MSH3 mRNA expressed by a cell or group of cells can be determined using any method known in the art for assessing mRNA expression. In one embodiment, the expression level of MSH3 in a sample is determined by detecting a transcribed polynucleotide, or a portion thereof, such as the mRNA of the MSH3 gene. RNA can be extracted from cells using RNA extraction techniques, including, for example, using acid phenol / guanidine isothiocyanate extraction (RNAzol B, Biogenesis), RNEASY™ RNA preparation kit (Qiagen) or PAXgene (PreAnalytix, Switzerland). Exemplary assay formats utilizing ribonucleic acid hybridization include nuclear run-on assays, RT-PCR, RNase protection assays, northern blotting, in situ hybridization, and microarray analysis. Circulating MSH3 mRNA can be detected using the methods described in PCT Publication No. WO2012 / 177906, the entire contents of which are incorporated herein by reference. In some embodiments, the expression level of MSH3 is determined using a nucleic acid probe. The term "probe" as used herein refers to any molecule that can selectively bind to a particular MSH3 sequence, for example, to an mRNA or polypeptide. Probes can be synthesized by one skilled in the art or obtained from appropriate biological preparations. Probes can be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.

[0261] The isolated mRNA may be used in hybridization or amplification assays, including, but not limited to, Southern or Northern analysis, polymerase chain reaction (PCR) analysis, and probe arrays. One method of determining mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to MSH3 mRNA. In one embodiment, the mRNA is immobilized on a solid surface and contacted with the probe, for example, by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an AFFYMETRIX gene chip array. One skilled in the art can easily adapt known mRNA detection methods for use in determining MSH3 mRNA levels.

[0262] Alternative methods for determining the expression level of MSH3 in a sample include processes such as nucleic acid amplification of mRNA and / or reverse transcriptase (to prepare cDNA) in the sample, for example by means of RT-PCR (experimental aspects described in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self-sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcription amplification systems (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-beta replicase (Lizardi et al. (1988) Bio / Technology 6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are particularly useful for detection of nucleic acid molecules when such molecules are present in very low numbers. In some embodiments, the expression level of MSH3 is determined by quantitative fluorogenic RT-PCR (i.e., the TAQMAN™ system) or DUAL-GLO® luciferase assay.

[0263] The expression level of MSH3 mRNA can be monitored using membrane blots (such as those used in hybridization analyses such as Northern, Southern, dot, etc.), or microwells, sample tubes, gels, beads or fibers (or any solid support containing bound nucleic acid). See U.S. Patent Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195, and 5,445,934, which are incorporated herein by reference. Determining the expression level of MSH3 can include using a nucleic acid probe in solution.

[0264] In some embodiments, the level of mRNA expression is assessed using branched DNA (bDNA) ass...

Claims

Claim 1: A single-stranded oligonucleotide having a linked nucleotide length of 15 to 30, wherein the oligonucleotide has at least 95%, 98%, 99% or 100% complementarity with SEQ ID NO: 5151 at positions 876 to 901, 931 to 956, 1310 to 1337, 2141 to 2169, 2267 to 2292, 2543 to 2579, 2620 to 2647, 2685 to 2710, 2769 to 2795, 2798 to 2868, or 2950 to 2975, and contains a region of at least 15 adjacent nucleobases, or a pharmaceutically acceptable salt thereof, where the oligonucleotide is (a) a DNA core sequence containing linked deoxyribonucleosides, (b) a 5' flanking sequence containing linked nucleosides, and (c) a 3' flanking sequence containing linked nucleosides and includes a region of at least 10 adjacent nucleobases where the DNA core is located between the 5' flanking sequence and the 3' flanking sequence, and the 5' flanking sequence and the 3' flanking sequence each contain at least 2 linked nucleosides, and at least 1 nucleoside in each flanking sequence contains an alternative nucleoside. Claim 2: The oligonucleotide according to Claim 1, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide is complementary to at least 17 to 23 adjacent nucleobases at one or more of positions 876 to 901, 931 to 956, 1310 to 1337, 2141 to 2169, 2267 to 2292, 2543 to 2579, 2620 to 2647, 2685 to 2710, 2769 to 2795, 2798 to 2868, or 2950 to 2975 of SEQ ID NO: 5151. Claim 3: The oligonucleotide according to Claim 1, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide is complementary to at least 17 to 20 adjacent nucleobases at one or more of positions 876 to 901, 931 to 956, 1310 to 1337, 2141 to 2169, 2267 to 2292, 2543 to 2579, 2620 to 2647, 2685 to 2710, 2769 to 2795, 2798 to 2868, or 2950 to 2975 of SEQ ID NO: 5151.

4. The 17 to 20 adjacent nucleobases are positions 876, 877, 878, 879, 880, 881, 882, 883, 884, 885, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2151, 2152, 2153, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2274, 2275, 2276, 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2560, 2561, 2562, 2563, 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, 2628, 2629, 2630, 2631, 2685, 2686, 2687, 2688, 2689, 2690, 2691, 2692, 2693, 2694, 2769, 2770, 2771, 2772, 2773, 2774, 2775, 2776, 2777, 2778, 2779, 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, 2825, 2826, 2827, 2828, 2829, 2830, 2831, 2832, 2833, 2834, 2835, 2836, 2837, 2838, 2839, 2840, 2841, 2842, 2843, 2844, 2845, 2846, 2847, 2848, 2849, 2850, 2851, 2852 of SEQ ID NO: 5151.The oligonucleotide according to claim 3, or a pharmaceutically acceptable salt thereof, starting from position 2950, 2951, 2952, 2953, 2954, 2955, 2956, 2957, 2958, or 2959. **Claim 5**: The oligonucleotide according to claim 1, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide is complementary to at least 20 to 23 adjacent nucleobases in one or more of positions 876 to 901, 931 to 956, 1310 to 1337, 2141 to 2169, 2267 to 2292, 2543 to 2579, 2620 to 2647, 2685 to 2710, 2769 to 2795, 2798 to 2868, or 2950 to 2975 of SEQ ID NO: 5151. **Claim 6**: The oligonucleotide according to claim 5, or a pharmaceutically acceptable salt thereof, wherein the 20 to 23 adjacent nucleobases start from position 876, 877, 878, 879, 880, 881, 882, 931, 932, 933, 934, 935, 936, 937, 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 2141, 2142, 2143, 2144, 2145, 2146, 2147, 2148, 2149, 2150, 2267, 2268, 2269, 2270, 2271, 2272, 2273, 2543, 2544, 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2560, 2620, 2621, 2622, 2623, 2624, 2625, 2626, 2627, 2628, 2685, 2686, 2687, 2688, 2689, 2690, 2691, 2769, 2770, 2771, 2772, 2773, 2774, 2775, 2776, 2798, 2799, 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2821, 2822, 2823, 2824, 2825, 2826, 2827, 2828, 2829, 2830, 2831, 2832, 2833, 2834, 2835, 2836, 2837, 2838, 2839, 2840, 2841, 2842, 2843, 2844, 2845, 2846, 2847, 2848, 2849, 2950, 2951, 2952, 2953, 2954, 2955, or 2956 of SEQ ID NO: 5151. **Claim 7** The oligonucleotide according to any one of claims 1 to 6, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide contains at least one alternative nucleoside internucleoside bond. **Claim 8** The oligonucleotide according to claim 7, wherein the at least one alternative internucleoside linkage is a phosphorothioate internucleoside linkage.

9. The oligonucleotide according to claim 7, wherein the at least one alternative internucleoside linkage is a 2'-alkoxy internucleoside linkage.

10. The oligonucleotide according to claim 7, wherein the at least one alternative internucleoside linkage is an alkyl phosphate internucleoside linkage.

11. The oligonucleotide according to claim 1, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide comprises at least one alternative nucleobase.

12. The oligonucleotide according to claim 11, wherein the alternative nucleobase is 5'-methylcytosine, pseudouridine, or 5-methoxyuridine.

13. The oligonucleotide according to claim 1, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide comprises at least one alternative sugar moiety.

14. The oligonucleotide according to claim 13, wherein the alternative sugar moiety is 2'-OMe or a bicyclic nucleic acid.

15. The oligonucleotide according to claim 1, or a pharmaceutically acceptable salt thereof, further comprising a ligand conjugated to the 5'-end or 3'-end of the oligonucleotide via a monovalent or branched divalent or trivalent linker.

16. The oligonucleotide according to claim 1, or a pharmaceutically acceptable salt thereof, comprising a nucleobase sequence selected from the group consisting of any of SEQ ID NOs: 1 to 5150 and 5152 to 5176.

17. The oligonucleotide according to claim 16, or a pharmaceutically acceptable salt thereof, comprising a nucleobase sequence selected from the group consisting of any one of SEQ ID NOs: 1 to 206 and 5152; 207 to 412 and 5153; 413 to 618 and 5154; 619 to 824 and 5155; 825 to 1030 and 5156; 1031 to 1236 and 5157; 1237 to 1442 and 5158; 1443 to 1648 and 5159; 1649 to 1854 and 5160; 1855 to 2060 and 5161; 2061 to 2266 and 5162; 2267 to 2472 and 5163; 2473 to 2678 and 5164; 2679 to 2884 and 5165; 2885 to 3090 and 5166; 3091 to 3296 and 5167; 3297 to 3502 and 5168; 3503 to 3708 and 5169; 3709 to 3914 and 5170; 3915 to 4120 and 5171; 4121 to 4326 and 5172; 4327 to 4532 and 5173; 4533 to 4738 and 5174; 4739 to 4944 and 5175; or 4945 to 5150 and 5176.

18. The oligonucleotide according to claim 16, or a pharmaceutically acceptable salt thereof, comprising a nucleobase sequence selected from the group consisting of any one of SEQ ID NOs: 1 to 5150.

19. A single-stranded oligonucleotide, wherein the nucleobase sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 5150 and 5152 to 5176, or a pharmaceutically acceptable salt thereof.

20. The nucleobase sequence of the oligonucleotide consists of any one of SEQ ID NOs: 1 to 206 and 5152; 207 to 412 and 5153; 413 to 618 and 5154; 619 to 824 and 5155; 825 to 1030 and 5156; 1031 to 1236 and 5157; 1237 to 1442 and 5158; 1443 to 1648 and 5159; 1649 to 1854 and 5160; 1855 to 2060 and 5161; 2061 to 2266 and 5162; 2267 to 2472 and 5163; 2473 to 2678 and 5164; 2679 to 2884 and 5165; 2885 to 3090 and 5166; 3091 to 3296 and 5167; 3297 to 3502 and 5168; 3503 to 3708 and 5169; 3709 to 3914 and 5170; 3915 to 4120 and 5171; 4121 to 4326 and 5172; 4327 to 4532 and 5173; 4533 to 4738 and 5174; 4739 to 4944 and 5175; or 4945 to 5150 and 5176, the oligonucleotide according to claim 19, or a pharmaceutically acceptable salt thereof.

21. An oligonucleotide selected from the group consisting of antisense oligo numbers 1 to 5150 and 5152 to 5176 in Table 3, or a pharmaceutically acceptable salt thereof.

22. The oligonucleotide according to claim 21, wherein the oligonucleotide is selected from the group consisting of antisense oligo numbers 1 to 5150 in Table 3, or a pharmaceutically acceptable salt thereof.

23. The oligonucleotide is selected from the group consisting of antisense oligo numbers 1 to 206 and 5152; 207 to 412 and 5153; 413 to 618 and 5154; 619 to 824 and 5155; 825 to 1030 and 5156; 1031 to 1236 and 5157; 1237 to 1442 and 5158; 1443 to 1648 and 5159; 1649 to 1854 and 5160; 1855 to 2060 and 5161; 2061 to 2266 and 5162; 2267 to 2472 and 5163; 2473 to 2678 and 5164; 2679 to 2884 and 5165; 2885 to 3090 and 5166; 3091 to 3296 and 5167; 3297 to 3502 and 5168; 3503 to 3708 and 5169; 3709 to 3914 and 5170; 3915 to 4120 and 5171; 4121 to 4326 and 5172; 4327 to 4532 and 5173; 4533 to 4738 and 5174; 4739 to 4944 and 5175; or 4945 to 5150 and 5176 according to claim 21, or a pharmaceutically acceptable salt thereof.

24. The oligonucleotide, or a pharmaceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50%, 60%, 70% or 80% compared to the control at an oligonucleotide concentration of 10 nM, according to claim 1.

25. The oligonucleotide, or a pharmaceutically acceptable salt thereof, reduces MSH3 mRNA expression by at least 50%, 60% or 70% compared to the control at an oligonucleotide concentration of 1 nM, according to claim 1.

26. The oligonucleotide according to claim 24 or 25, wherein the MSH3 mRNA expression is evaluated in vitro.

27. The oligonucleotide according to claim 26, wherein the MSH3 mRNA expression is evaluated in a cell-based assay.

28. The oligonucleotide according to claim 27, wherein the MSH3 mRNA expression is evaluated in HeLa cells.

29. The oligonucleotide according to claim 24 or 25, wherein the decrease in MSH3 mRNA expression is determined by the method of Example 1.

30. The oligonucleotide according to claim 1, wherein the oligonucleotide is a sodium salt.

31. A pharmaceutical composition comprising one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or excipient, said pharmaceutical composition.

32. A composition comprising one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, and lipid nanoparticles, polyplex nanoparticles, lipoplex nanoparticles, or liposomes, said composition.

33. A composition comprising one or more of the oligonucleotides according to claims 1 and 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of inhibiting the transcription of MSH3 in a cell, wherein said method comprises contacting said cell with one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for a time sufficient to obtain degradation of the mRNA transcript of the MSH3 gene, which inhibits the expression of the MSH3 gene in said cell.

34. A composition comprising one or more of the oligonucleotides according to claims 1 and 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of treating, preventing, or delaying the progression of nucleotide repeat expansion disorders, wherein said method comprises administering to a subject in need thereof one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32.

35. A composition comprising one or more of the oligonucleotides according to claims 1 and 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of reducing the level and / or activity of MSH3 in a cell of a subject identified as having a nucleotide repeat expansion disorder, wherein said method comprises contacting said cell with one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32.

36. A composition comprising one or more of the oligonucleotides according to claims 1 and 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of inhibiting the expression of the MSH3 gene in a cell, wherein the method comprises maintaining the cell in contact with one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for a time sufficient to obtain degradation of the mRNA transcript of the MSH3 gene, thereby inhibiting the expression of the MSH3 gene in the cell.

37. A composition comprising one or more of the oligonucleotides according to claims 1 and 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of reducing nucleotide repeat expansion in a cell, wherein the method comprises contacting the cell with one or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32.

38. The composition according to claim 33, wherein the cell is in a subject.

39. The composition according to claim 34, wherein the subject is human.

40. The composition according to claim 38, wherein the cell is a cell of the central nervous system or a muscle cell.

41. The composition according to claim 39, wherein the subject is identified as having a nucleotide repeat expansion disorder.

42. The composition according to claim 41, wherein the nucleotide repeat expansion disorder is spinocerebellar ataxia type 36 or frontotemporal dementia.

43. The composition according to claim 41, wherein the nucleotide repeat expansion disorder is a trinucleotide repeat expansion disorder.

44. The composition according to claim 43, wherein the trinucleotide repeat expansion disorder is a polyglutamine disease.

45. The composition according to claim 44, wherein the polyglutamine disease is selected from the group consisting of dentatorubral-pallidoluysian atrophy, Huntington's disease, spinal bulbar muscular atrophy, spinocerebellar ataxia type 1, spinocerebellar ataxia type 2, spinocerebellar ataxia type 3, spinocerebellar ataxia type 6, spinocerebellar ataxia type 7, spinocerebellar ataxia type 17, and Huntington's disease-like disorder type 2.

46. The composition according to claim 43, wherein the trinucleotide repeat expansion disorder is a non-polyglutamine disease.

47. The composition according to claim 46, wherein the non-polyglutamine disease is selected from the group consisting of fragile X syndrome, fragile X-associated tremor / ataxia syndrome, fragile XE mental retardation, Friedreich's ataxia, myotonic dystrophy type 1, spinocerebellar ataxia type 8, spinocerebellar ataxia type 12, oculopharyngeal muscular dystrophy, fragile X-associated premature ovarian insufficiency, FRA2A syndrome, FRA7A syndrome, and early infantile epileptic encephalopathy.

48. One or more of the oligonucleotides according to claim 1, or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in the prevention or treatment of nucleotide repeat expansion disorders.

49. The oligonucleotide, or a pharmaceutically acceptable salt thereof, pharmaceutical composition, or composition for use according to claim 48, wherein the nucleotide repeat expansion disorder is spinocerebellar ataxia type 36 or frontotemporal dementia.

50. The oligonucleotide, or a pharmaceutically acceptable salt thereof, pharmaceutical composition, or composition for use according to claim 48, wherein the nucleotide repeat expansion disorder is a trinucleotide repeat expansion disorder.

51. The oligonucleotide, or a pharmaceutically acceptable salt thereof, pharmaceutical composition, or composition for use according to claim 50, wherein the trinucleotide repeat expansion disorder is selected from the group consisting of dentatorubral-pallidoluysian atrophy, Huntington's disease, spinal and bulbar muscular atrophy, spinocerebellar ataxia type 1, spinocerebellar ataxia type 2, spinocerebellar ataxia type 3, spinocerebellar ataxia type 6, spinocerebellar ataxia type 7, spinocerebellar ataxia type 17, Huntington's disease-like disorder type 2, fragile X syndrome, fragile X-associated tremor / ataxia syndrome, fragile XE mental retardation, Friedreich's ataxia, myotonic dystrophy type 1, spinocerebellar ataxia type 8, spinocerebellar ataxia type 12, oculopharyngeal muscular dystrophy, fragile X-associated premature ovarian insufficiency, FRA2A syndrome, FRA7A syndrome, and early infantile epileptic encephalopathy.

52. The oligonucleotide, pharmaceutical composition, or composition according to claim 48, wherein the oligonucleotide, or a pharmaceutically acceptable salt thereof, pharmaceutical composition, or composition is administered intrathecally, intraventricularly, into the lateral ventricle, intraocularly, subcutaneously, intravenously, intracisternally, intramuscularly, or orally.

53. A composition comprising one or more of the oligonucleotides according to claim 1 or a pharmaceutically acceptable salt thereof, the pharmaceutical composition according to claim 31, or the composition according to claim 32, for use in a method of preventing or delaying the progression of nucleotide repeat expansion disorder in a subject, comprising administering to the subject an effective amount of one or more of the oligonucleotides according to claim 1 and claim 19, the pharmaceutical composition according to claim 31, or the composition according to claim 32 to delay the progression of the nucleotide repeat expansion disorder in the subject.

54. The composition according to claim 53, wherein the nucleotide repeat expansion disorder is spinocerebellar ataxia type 36 or frontotemporal dementia.

55. The composition according to claim 53, wherein the nucleotide repeat expansion disorder is a trinucleotide repeat expansion disorder.

56. The composition according to claim 55, wherein the trinucleotide repeat expansion disorder is selected from the group consisting of dentatorubral-pallidoluysian atrophy, Huntington's disease, spinal bulbar muscular atrophy, spinocerebellar ataxia type 1, spinocerebellar ataxia type 2, spinocerebellar ataxia type 3, spinocerebellar ataxia type 6, spinocerebellar ataxia type 7, spinocerebellar ataxia type 17, Huntington's disease-like disorder type 2, fragile X syndrome, fragile X-related tremor / ataxia syndrome, fragile XE mental retardation, Friedreich's ataxia, myotonic dystrophy type 1, spinocerebellar ataxia type 8, spinocerebellar ataxia type 12, oculopharyngeal muscular dystrophy, fragile X-related premature ovarian insufficiency, FRA2A syndrome, FRA7A syndrome, and early infantile epileptic encephalopathy.

57. The composition according to claim 53, wherein the method further comprises administering an additional therapeutic agent.

58. The composition according to claim 57, wherein the additional therapeutic agent is an oligonucleotide that hybridizes to mRNA encoding the huntingtin gene.

59. The composition according to claim 53, wherein the progression of the nucleotide repeat expansion disorder is delayed by at least 120 days, such as at least 6 months, at least 12 months, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years or more when compared to the predicted progression.