Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
  • C12N15/1135—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against oncogenes or tumor suppressor genes
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
  • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/10—Type of nucleic acid
  • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]

Definitions

• the present application relates to oligonucleotides and uses thereof, particularly uses relating to the treatment of conditions relating to bile duct paucity.
• cholestasis is a common liver disease, particularly in neonates, which results in diminished bile flow and excretion, and prolonged conjugated hyperbilirubinemia.
• paucity of intrahepatic bile ducts is associated with various disorders and anomalies, including the familial syndrome, referred to as Alagille syndrome (AGS), which involves chronic cholestasis, cardiac anomalies, musculoskeletal abnormalities, ocular anomalies, and dysmorphic faces.
• AGS Alagille syndrome
• paucity of bile ducts is associated with rapidly progressive liver disease.
• Biliary Atresia is another progressive, fibro-obliterative disorder of the intra- and extra- hepatic bile ducts in infancy. Suitable methods for treating such patients, including methods for improving bile duct paucity, are lacking.
• aspects of the disclosure relate to methods for treating bile duct paucity and related conditions in a subject.
• the disclosure relates to the discovery that selectively inhibiting CTNNB 1 expression in a subject is useful for increasing bile duct capacity (e.g., for stimulating new bile duct formation) of the subject.
• methods provided herein utilize RNAi oligonucleotides for reducing b-catenin activity in a subject, and thereby increasing bile duct capacity (e.g., promoting regeneration of bile ducts) of the subject.
• a consequence of the increased bile duct capacity produced by methods provided herein is an improvement in bile flow (e.g., increased bile acid uptake) and a corresponding decrease in circulating bile acid (see, e.g., Example 4, which shows that administration of CTNNB 1 RNAi oligonucleotides reduced bile acid levels in an animal model of bile duct damage).
• reduction of b-catenin activity decreases bile acid synthesis in hepatocytes, which can prevent bile acid- induced acute toxicity due to bile duct paucity in a subject.
• methods provided herein are useful for treating bile duct paucity-associated conditions, such as Alagille syndrome and Biliary Atresia through regeneration of new bile ducts and reduction of bile acid synthesis.
• One aspect of the present disclosure provides oligonucleotides for reducing expression of CTNNB 1, in which the oligonucleotides comprise an antisense strand of 15 to 30 nucleotides in length.
• the region of complementarity is at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, or at least 22 contiguous nucleotides in length.
• the region of complementarity is fully complementary to the target sequence of CTNNB 1.
• the region of complementarity to CTNNB 1 is at least 19 contiguous nucleotides in length.
• the antisense strand is 19 to 27 nucleotides in length.
• the antisense strand is 21 to 27 nucleotides in length.
• the oligonucleotide further comprises a sense strand of 15 to 40 nucleotides in length, in which the sense strand forms a duplex region with the antisense strand.
• the sense strand is 19 to 40 nucleotides in length.
• the antisense strand is 27 nucleotides in length and the sense strand is 25 nucleotides in length.
• the duplex region is at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 nucleotides in length.
• an oligonucleotide further comprises a 3 '-overhang sequence on the antisense strand of two nucleotides in length.
• an oligonucleotide comprises an antisense strand and a sense strand that are each in a range of 21 to 23 nucleotides in length.
• an oligonucleotide comprises a duplex structure in a range of 19 to 21 nucleotides in length.
• an oligonucleotide comprises a duplex structure in a range of 19 to 21 nucleotides in length.
• oligonucleotide comprises a 3 '-overhang sequence of one or more nucleotides in length, in which the 3 '-overhang sequence is present on the antisense strand, the sense strand, or the antisense strand and sense strand.
• an oligonucleotide comprises a 3 '- overhang sequence of two nucleotides in length, in which the 3 '-overhang sequence is present on the antisense strand, and in which the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length, such that the sense strand and antisense strand form a duplex of 21 nucleotides in length.
• the region of complementarity to CTNNB 1 is at least
• the sense strand comprises at its 3 '-end a stem-loop set forth as: S1-L-S2, in which Sl is complementary to S2, and in which L forms a loop between S 1 and S2 of 3 to 5 nucleotides in length.
• Another aspect of the present disclosure provides an oligonucleotide for reducing expression of CTNNB 1, the oligonucleotide comprising an antisense strand and a sense strand, in which the antisense strand is 21 to 27 nucleotides in length and has a region of complementarity to CTNNB 1 , in which the sense strand comprises at its 3 '-end a stem-loop set forth as: S 1-L-S2, in which S 1 is complementary to S2, and in which L forms a loop between S 1 and S2 of 3 to 5 nucleotides in length, and in which the antisense strand and the sense strand form a duplex structure of at least 19 nucleotides in length but are not covalently linked.
• the region of complementarity is fully complementary to at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 contiguous nucleotides of CTNNB 1 mRNA.
• L is a tetraloop. In some embodiments, L is 4 nucleotides in length. In some embodiments, L comprises a sequence set forth as GAAA.
• an oligonucleotide comprises at least one modified nucleotide.
• the modified nucleotide comprises a 2'-modification.
• the 2'-modification is a modification selected from: 2'-aminoethyl, 2'- fluoro, 2'-0-methyl, 2'-0-methoxyethyl, and 2'-deoxy-2'-lluoro-[3-d-arabinonucleic acid.
• all of the nucleotides of an oligonucleotide are modified.
• an oligonucleotide comprises at least one modified intemucleotide linkage.
• the at least one modified internucleotide linkage is a phosphorothioate linkage.
• the 4 '-carbon of the sugar of the 5 '-nucleotide of the antisense strand comprises a phosphate analog.
• the phosphate analog is oxymethylphosphonate, vinylphosphonate, or malonylphosphonate.
• At least one nucleotide of an oligonucleotide is conjugated to one or more targeting ligands.
• each targeting ligand comprises a carbohydrate, amino sugar, cholesterol, polypeptide or lipid.
• each targeting ligand comprises a N-acetylgalactosamine (GalNAc) moiety.
• the GalNac moiety is a monovalent GalNAc moiety, a bivalent GalNAc moiety, a trivalent GalNAc moiety, or a tetravalent GalNAc moiety.
• up to 4 nucleotides of L of the stem- loop are each conjugated to a monovalent GalNAc moiety.
• the targeting ligand comprises an aptamer.
• Another aspect of the present disclosure provides a composition comprising an oligonucleotide of the present disclosure and an excipient.
• Another aspect of the present disclosure provides a method comprising administering a composition of the present disclosure to a subject.
• the method results in decreased bile duct paucity in a subject.
• the method results in an increase in bile duct formation, and thus an increase in bile duct capacity, in a subject.
• the subject to be treated suffers from Alagille syndrome.
• the subject to be treated suffers from Biliary Atresia.
• Another aspect of the present disclosure provides an oligonucleotide for reducing expression of CTNNB1, the oligonucleotide comprising a sense strand of 15 to 40 nucleotides in length and an antisense strand of 15 to 30 nucleotides in length, in which the sense strand forms a duplex region with the antisense strand, and the antisense strand comprises a complementary sequence.
• the oligonucleotide comprises a pair of sense and antisense strands selected from a row of the table set forth in Appendix A.
• FIG. 1 is a series of photographs showing immunohistochemistry staining for CK19 in liver sections from mice fed with 0.1% 3,5-diethoxycarbonyl-l,4-dihydrocollidine (DDC) and treated with PBS (first three panels) and from mice fed with 0.1% DDC and treated with CTNNB 1 RNAi oligonucleotide (last three panels).
• CK19 is a ductal epithelial marker.
• the CTNNB 1 RNAi oligonucleotide is provided that comprises a sense strand having a sequence as set forth SEQ ID NO: 1 and an antisense strand having a sequence as set forth SEQ ID NO: 2.
• FIG. 2 includes a series of photographs showing immunohistochemistry staining for CK19 in liver sections from mice fed 0.1% DDC and treated with PBS or
• the top row of photographs show results with PBS treatment and the bottom row of photographs shows results with CTNNB 1 RNAi oligonucleotide.
• the treatment day is shown on the bottom with two immunohistochemistry stains for each day.
• Results for mice on a normal diet (mice not fed 0.1% DDC) for each treatment are shown on the far right.
• FIG. 3 is a series of photographs showing immunohistochemistry staining for CK19 in liver sections from Mdr2 +/ mice treated with PBS (first panel at left), from Mdr mice treated with PBS (second and third panels from left), and from Mdr A mice treated with CTNNB 1 RNAi oligonucleotide (final three panels shown at right). The gender of each mouse is indicated below the relevant panel.
• FIG. 4 is a series of photographs showing immunohistochemistry staining for CK19 in liver sections from each individual wildtype animal treated with PBS (first three panels starting at left), 5 mg/kg CTNNB 1 RNAi oligonucleotide (fourth panel from left) and 100 mg/kg CTNNB 1 RNAi oligonucleotide, Q1W x 6 (last three panels shown at right).
• FIG. 5 is a series of photographs showing ductule architecture using resin casting in two DDC-fed animals (Animal 1 and Animal 2) treated with PBS (top two panels) or with CTNNB 1 RNAi oligonucleotide (bottom two panels).
• the images for Animal 1 are with 2X magnification with the scale bars indicating 500 pm and the images for Animal 2 are with 4X magnification with the scale bars indicating 100pm.
• FIG. 6 is a photograph showing ductule architecture by ink injection in a single DDC-fed animal treated with CTNNB 1 RNAi oligonucleotide. The images are with 10X magnification with the scale bars indicating 50 pm.
• FIG. 7 A is a graph comparing the total bile acid concentration from bile samples collected by gravity flow from mice on a control diet treated with PBS, fed 0.1% DDC and treated with PBS, and from mice fed 0.1% DDC while being treated with four weekly doses of CTNNB 1 RNAi oligonucleotide. Swiss Webster female mice were used.
• FIG. 7B is a graph comparing the bile flow rate for mice on a control diet treated with PBS, for mice fed 0.1% DDC treated with PBS and for mice fed 0.1% DDC treated QW x 4 with CTNNB 1 RNAi oligonucleotide. Swiss Webster female mice were used.
• FIG. 7C is a series of graphs comparing expression of CTNNB 1, Cyp27al, Cyp7al, Cyp8Bl and Shp in DDC-fed mice treated with PBS (light gray bars) and in mice treated QW x 4 with CTNNB 1 RNAi oligonucleotide (dark gray bars). Swiss Webster female mice were used.
• the disclosure provides methods utilizing oligonucleotides targeting CTNNB1 mRNA that are effective for reducing CTNNB 1 expression in cells, particularly liver cells (e.g., hepatocytes) for the treatment of bile duct paucity. Accordingly, in related aspects, the disclosure provided methods of treating bile duct paucity that involve selectively reducing CTNNB 1 gene expression in liver.
• CTNNB 1 targeting oligonucleotides provided herein are designed for delivery to selected cells of target tissues (e.g., liver hepatocytes) to treat bile duct paucity in a subject.
• Administering As used herein, the terms“administering” or
• “administration” means to provide a substance (e.g., an oligonucleotide) to a subject in a manner that is pharmacologically useful (e.g., to treat a condition in the subject).
• a substance e.g., an oligonucleotide
• the term“approximately” or“about,” as applied to one or more values of interest, refers to a value that is similar to a stated reference value.
• the term“approximately” or“about” refers to a range of values that fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).
• Alagille syndrome refers to an disorder characterized by a narrowing, malformation, and/or paucity of bile ducts in the liver.
• Alagille syndrome impaired differentiation of intrahepatic bile ducts can lead to narrowing, malformation, and paucity of bile ducts.
• Such bile duct abnormalities reduce bile flow
• Asialoglycoprotein receptor As used herein, the term
• ASGPR Asialoglycoprotein receptor or“ASGPR” refers to a bipartite C-type lectin formed by a major 48 kDa (ASGPR-l) and minor 40 kDa subunit (ASGPR-2). ASGPR is primarily expressed on the sinusoidal surface of hepatocyte cells and has a major role in binding, internalization, and subsequent clearance of circulating glycoproteins that contain terminal galactose or N-acetylgalactosamine residues (asialoglycoproteins).
• CTNNB1 As used herein, CTNNB1 is a gene that encodes b-catenin protein.
• CTNNB1 encodes at least four transcripts, namely NMJ301904.3 (variant 1), NM_001098209.1 (variant 2), NM_001098210.1 (variant 3), and NM_00l330729.l (variant 4).
• Variants 1, 2, and 3 encode the same isoform (NP_00l091680.l, isoform 1).
• Variant 4 encodes isoform 2 (NPJ301317658.1), which has a shorter N-terminus compared to isoform 1.
• CTNNB 1 encodes at least two transcripts, namely NM_0076l4.3 (variant 1) and NM_00l 165902.1 (variant 2). Both transcripts encode the same protein (see, e.g., sequences provided in NP_00l 159374.1 and NP 031640.1 ).
• Bile duct paucity refers to a diminished bile duct function resulting from an absence of bile ducts, a reduction in the number and/or size of bile ducts, or a blockage of bile ducts in a subject.
• bile duct paucity is associated with an absence or reduced number of intrahepatic ducts.
• bile duct paucity is associated with absence or reduced number of extrahepatic ducts.
• bile duct paucity is associated with blockage of intrahepatic or extrahepatic ducts.
• paucity of interlobular bile ducts may be calculated by determining the ratio of portal tracts lacking a bile duct compared to the total number of portal tracts (see, e.g., Hadchouel Paucity of interlobular bile ducts. Semin Diagn Pathol. 1992 Feb;9(l):24-30, which is hereby incorporated by reference in its entirety for this purpose).
• Bile duct paucity-associated condition refers to a condition in a subject resulting in or associated with a reduction in the number or size of functional bile ducts in a subject compared with a normal control subject who does not have the condition.
• a subject having a BDP-associated conditions has a reduction in the number and/or size of a functional bile ducts.
• the defective biliary system in the subject occurs in intrahepatic bile ducts.
• the intrahepatic ducts with impaired function are selected from the group consisting of: periportal bile ductules (canals of Hering), and intralobular bile ductules (cholangioles).
• the bile ducts with impaired function in the subject are extrahepatic bile ducts.
• the extrahepatic ducts with impaired function are selected from the group consisting of: the left hepatic duct, the right hepatic duct, and the common hepatic duct.
• the BDP-associated condition is Alagille syndrome.
• the BDP-associated condition is Biliary Atresia.
• Biliary Atresia As used herein,“Biliary Atresia (BA)” refers to a disease, particularly in infants, in which destruction or obliteration of bile ducts obstructs bile flow.
• nucleotides e.g., two nucleotide on opposing nucleic acids or on opposing regions of a single nucleic acid strand
• nucleotides e.g., two nucleotide on opposing nucleic acids or on opposing regions of a single nucleic acid strand
• a purine nucleotide of one nucleic acid that is complementary to a pyrimidine nucleotide of an opposing nucleic acid may base pair together by forming hydrogen bonds with one another.
• complementary nucleotides can base pair in the Watson-Crick manner or in any other manner that allows for the formation of stable duplexes.
• two nucleic acids may have nucleotide sequences that are complementary to each other so as to form regions of complementarity, as described herein.
• deoxyribonucleotide refers to a nucleotide having a hydrogen at the 2' position of its pentose sugar as compared with a ribonucleotide.
• a modified deoxyribonucleotide is a deoxyribonucleotide having one or more modifications or substitutions of atoms other than at the 2' position, including modifications or substitutions in or of the sugar, phosphate group or base.
• Double-stranded oligonucleotide refers to an oligonucleotide that is substantially in a duplex form.
• complementary base-pairing of duplex region(s) of a double- stranded oligonucleotide is formed between antiparallel sequences of nucleotides of covalently separate nucleic acid strands.
• complementary base-pairing of duplex region(s) of a double- stranded oligonucleotide is formed between antiparallel sequences of nucleotides of nucleic acid strands that are covalently linked.
• complementary base pairing of duplex region(s) of a double- stranded oligonucleotide is formed from a single nucleic acid strand that is folded (e.g., via a hairpin) to provide complementary antiparallel sequences of nucleotides that base pair together.
• a double-stranded oligonucleotide comprises two covalently separate nucleic acid strands that are fully duplexed with one another.
• a double- stranded oligonucleotide comprises two covalently separate nucleic acid strands that are partially duplexed, e.g., having overhangs at one or both ends.
• a double-stranded oligonucleotide comprises antiparallel sequences of nucleotides that are partially complementary, and thus, may have one or more mismatches, which may include internal mismatches or end
• duplex in reference to nucleic acids (e.g., oligonucleotides), refers to a structure formed through complementary base-pairing of two antiparallel sequences of nucleotides.
• Excipient refers to a non-therapeutic agent that may be included in a composition, for example, to provide or contribute to a desired consistency or stabilizing effect.
• Hepatocyte As used herein, the term“hepatocyte” or“hepatocytes” refers to cells of the parenchymal tissues of the liver. These cells make up approximately 70-85% of the liver’s mass and manufacture serum albumin, fibrinogen, and the prothrombin group of clotting factors (except for Factors 3 and 4). Markers for hepatocyte lineage cells may include, but are not limited to: transthyretin (Ttr), glutamine synthetase (Glul), hepatocyte nuclear factor la (Hnfla), and hepatocyte nuclear factor 4a (Hnf4a).
• Ttr transthyretin
• Glul glutamine synthetase
• Hnfla hepatocyte nuclear factor la
• Hnf4a hepatocyte nuclear factor 4a
• Markers for mature hepatocytes may include, but are not limited to: cytochrome P450 (Cyp3al 1), fumarylacetoacetate hydrolase (Fah), glucose 6-phosphate (G6p), albumin (Alb), and OC2-2F8. See, e.g., Huch et ah, (2013), Nature, 494(7436): 247-250, the contents of which relating to hepatocyte markers is incorporated herein by reference.
• loop refers to an unpaired region of a nucleic acid (e.g. , oligonucleotide) that is flanked by two antiparallel regions of the nucleic acid that are sufficiently complementary to one another, such that under appropriate hybridization conditions (e.g., in a phosphate buffer, in a cells), the two antiparallel regions, which flank the unpaired region, hybridize to form a duplex (referred to as a“stem”).
• a“stem a duplex
• Modified Internucleotide Linkage refers to an internucleotide linkage having one or more chemical modifications compared with a reference intemucleotide linkage comprising a phosphodiester bond.
• a modified nucleotide is a non-naturally occurring linkage.
• a modified intemucleotide linkage confers one or more desirable properties to a nucleic acid in which the modified intemucleotide linkage is present.
• a modified nucleotide may improve thermal stability, resistance to degradation, nuclease resistance, solubility, bioavailability, bioactivity, reduced immunogenicity, etc.
• Modified nucleotide refers to a nucleotide having one or more chemical modifications compared with a corresponding reference nucleotide selected from: adenine ribonucleotide, guanine ribonucleotide, cytosine ribonucleotide, uracil ribonucleotide, adenine deoxyribonucleotide, guanine
• a modified nucleotide is a non-naturally occurring nucleotide.
• a modified nucleotide has one or more chemical modifications in its sugar, nucleobase and/or phosphate group.
• a modified nucleotide has one or more chemical moieties conjugated to a corresponding reference nucleotide.
• a modified nucleotide confers one or more desirable properties to a nucleic acid in which the modified nucleotide is present.
• a modified nucleotide may improve thermal stability, resistance to degradation, nuclease resistance, solubility, bioavailability, bioactivity, reduced immunogenicity, etc.
• a modified nucleotide comprises a 2’- O-methyl or a 2’-F substitution at the 2’ position of the ribose ring.
• A“nicked tetraloop structure” is a structure of a RNAi oligonucleotide characterized by the presence of separate sense (passenger) and antisense (guide) strands, in which the sense strand has a region of complementarity to the antisense strand such that the two strands form a duplex, and in which at least one of the strands, generally the sense strand, extends from the duplex in which the extension contains a tetraloop and two self-complementary sequences forming a stem region adjacent to the tetraloop, in which the tetraloop is configured to stabilize the adjacent stem region formed by the self-complementary sequences of the at least one strand.
• oligonucleotide refers to a short nucleic acid, e.g., of less than 100 nucleotides in length.
• An oligonucleotide can comprise ribonucleotides, deoxyribonucleotides, and/or modified nucleotides including, for example, modified ribonucleotides.
• An oligonucleotide may be single-stranded or double-stranded.
• An oligonucleotide may or may not have duplex regions.
• an oligonucleotide may be, but is not limited to, a small interfering RNA (siRNA), microRNA (miRNA), short hairpin RNA (shRNA), dicer substrate interfering RNA (dsiRNA), antisense oligonucleotide, short siRNA, or single-stranded siRNA.
• a double- stranded oligonucleotide is an RNAi oligonucleotide.
• Overhang refers to terminal non-base- pairing nucleotide(s) resulting from one strand or region extending beyond the terminus of a complementary strand with which the one strand or region forms a duplex.
• an overhang comprises one or more unpaired nucleotides extending from a duplex region at the 5' terminus or 3' terminus of a double- stranded oligonucleotide.
• the overhang is a 3' or 5' overhang on the antisense strand or sense strand of a double-stranded oligonucleotide.
• Phosphate analog refers to a chemical moiety that mimics the electrostatic and/or steric properties of a phosphate group.
• a phosphate analog is positioned at the 5' terminal nucleotide of an oligonucleotide in place of a 5 '-phosphate, which is often susceptible to enzymatic removal.
• a 5' phosphate analog contains a phosphatase-resistant linkage. Examples of phosphate analogs include 5' phosphonates, such as 5' methylenephosphonate (5'-MP) and 5'-(E)-vinylphosphonate (5'- VP).
• an oligonucleotide has a phosphate analog at a 4 '-carbon position of the sugar (referred to as a“4 '-phosphate analog”) at a 5'- terminal nucleotide.
• a 4 '-phosphate analog is oxymethylphosphonate, in which the oxygen atom of the oxymethyl group is bound to the sugar moiety (e.g., at its 4'-carbon) or analog thereof. See, for example, International Patent Application PCT/US2017/049909, filed on September 1, 2017, U.S.
• Reduced expression As used herein, the term“reduced expression” of a gene refers to a decrease in the amount of RNA transcript or protein encoded by the gene and/or a decrease in the amount of activity of the gene in a cell or subject, as compared to an appropriate reference cell or subject.
• the act of treating a cell with a double- stranded oligonucleotide may result in a decrease in the amount of RNA transcript, protein and/or enzymatic activity (e.g., encoded by the CTNNB 1 gene) compared to a cell that is not treated with the double- stranded oligonucleotide.
• “reducing expression” as used herein refers to an act that results in reduced expression of a gene (e.g ., CTNNB 1).
• Region of Complementarity refers to a sequence of nucleotides of a nucleic acid (e.g. , a double-stranded oligonucleotide) that is sufficiently complementary to an antiparallel sequence of nucleotides (e.g., a target nucleotide sequence within an mRNA) to permit hybridization between the two sequences of nucleotides under appropriate hybridization conditions, e.g., in a phosphate buffer, in a cell, etc.
• a region of complementarity may be fully complementary to a nucleotide sequence (e.g., a target nucleotide sequence present within an mRNA or portion thereof).
• a region of complementary that is fully complementary to a nucleotide sequence present in an mRNA has a contiguous sequence of nucleotides that is complementary, without any mismatches or gaps, to a corresponding sequence in the mRNA.
• a region of complementarity may be partially complementary to a nucleotide sequence (e.g., a nucleotide sequence present in an mRNA or portion thereof).
• a region of complementary that is partially complementary to a nucleotide sequence present in an mRNA has a contiguous sequence of nucleotides that is complementary to a corresponding sequence in the mRNA but that contains one or more mismatches or gaps (e.g., 1, 2, 3, or more mismatches or gaps) compared with the corresponding sequence in the mRNA, provided that the region of complementarity remains capable of hybridizing with the mRNA under appropriate hybridization conditions.
• mismatches or gaps e.g., 1, 2, 3, or more mismatches or gaps
• Ribonucleotide refers to a nucleotide having a ribose as its pentose sugar, which contains a hydroxyl group at its 2' position.
• a modified ribonucleotide is a ribonucleotide having one or more modifications or substitutions of atoms other than at the 2' position, including modifications or substitutions in or of the ribose, phosphate group or base.
• RNAi Oligonucleotide refers to either (a) a double stranded oligonucleotide having a sense strand (passenger) and antisense strand (guide), in which the antisense strand or part of the antisense strand is used by the Argonaute 2 (Ago2) endonuclease in the cleavage of a target mRNA or (b) a single stranded oligonucleotide having a single antisense strand, where that antisense strand (or part of that antisense strand) is used by the Ago2 endonuclease in the cleavage of a target mRNA.
• Ago2 Argonaute 2
• Strand refers to a single contiguous sequence of nucleotides linked together through intemucleotide linkages (e.g., phosphodiester linkages, phosphorothioate linkages). In some embodiments, a strand has two free ends, e.g., a 5 '-end and a 3 '-end.
• the term“subject” means any mammal, including mice, rabbits, and humans.
• the subject is a human or non-human primate.
• the terms“individual” or“patient” may be used interchangeably with“subject.”
• the subject is an adolescent human subject (e.g., less than 18 years of age, less than 12 years of age, less than 6 years of age, less than 3 years of age).
• the subject is an adult human subject (e.g., of 18 or more years or age).
• Synthetic refers to a nucleic acid or other molecule that is artificially synthesized (e.g., using a machine (e.g., a solid state nucleic acid synthesizer)) or that is otherwise not derived from a natural source (e.g., a cell or organism) that normally produces the molecule.
• a machine e.g., a solid state nucleic acid synthesizer
• a natural source e.g., a cell or organism
• Targeting ligand refers to a molecule (e.g., a carbohydrate, amino sugar, cholesterol, polypeptide or lipid) that selectively binds to a cognate molecule (e.g., a receptor) of a tissue or cell of interest and that is conjugatable to another substance for purposes of targeting the other substance to the tissue or cell of interest.
• a targeting ligand may be conjugated to an oligonucleotide for purposes of targeting the oligonucleotide to a specific tissue or cell of interest.
• a targeting ligand selectively binds to a cell surface receptor.
• a targeting ligand when conjugated to an oligonucleotide facilitates delivery of the oligonucleotide into a particular cell through selective binding to a receptor expressed on the surface of the cell and endosomal internalization by the cell of the complex comprising the oligonucleotide, targeting ligand and receptor.
• a targeting ligand is conjugated to an oligonucleotide via a linker that is cleaved following or during cellular internalization such that the oligonucleotide is released from the targeting ligand in the cell.
• Tetraloop refers to a loop that increases stability of an adjacent duplex formed by hybridization of flanking sequences of nucleotides.
• the increase in stability is detectable as an increase in melting temperature (T m ) of an adjacent stem duplex that is higher than the T m of the adjacent stem duplex expected, on average, from a set of loops of comparable length consisting of randomly selected sequences of nucleotides.
• a tetraloop can confer a melting temperature of at least 50 °C, at least 55 °C., at least 56 °C, at least 58 °C, at least 60 °C, at least 65 °C or at least 75 °C in 10 mM NaHP0 4 to a hairpin comprising a duplex of at least 2 base pairs in length.
• a tetraloop may stabilize a base pair in an adjacent stem duplex by stacking interactions.
• interactions among the nucleotides in a tetraloop include but are not limited to non- Watson-Crick base-pairing, stacking interactions, hydrogen bonding, and contact interactions (Cheong et al., Nature 1990 Aug.
• a tetraloop comprises or consists of 3 to 6 nucleotides, and is typically 4 to 5 nucleotides. In certain embodiments, a tetraloop comprises or consists of three, four, five, or six nucleotides, which may or may not be modified (e.g., which may or may not be conjugated to a targeting moiety). In one embodiment, a tetraloop consists of four nucleotides.
• nucleotide may be used in the tetraloop and standard IUPAC-IUB symbols for such nucleotides may be used as described in Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.
• the letter“N” may be used to mean that any base may be in that position
• the letter“R” may be used to show that A (adenine) or G (guanine) may be in that position
• “B” may be used to show that C (cytosine), G (guanine), or T (thymine) may be in that position.
• tetraloops include the UNCG family of tetraloops (e.g., UUCG), the GNRA family of tetraloops (e.g., GAAA), and the CUUG tetraloop (Woese et al., Proc Natl Acad Sci USA. 1990 November; 87(2l):8467-7l; Antao et al., Nucleic Acids Res. 1991 Nov. 11; l9(21):5901-5).
• UUCG UUCG
• GNRA GNRA family of tetraloops
• CUUG tetraloop Wiese et al., Proc Natl Acad Sci USA. 1990 November; 87(2l):8467-7l; Antao et al., Nucleic Acids Res. 1991 Nov. 11; l9(21):5901-5).
• DNA tetraloops include the d(GNNA) family of tetraloops (e.g., d(GTTA)), the d(GNRA) family of tetraloops, the d(GNAB) family of tetraloops, the d(CNNG) family of tetraloops, and the d(TNCG) family of tetraloops (e.g., d(TTCG)).
• d(GNNA) family of tetraloops e.g., d(GTTA)
• d(GNRA) family of tetraloops
• the d(GNAB) family of tetraloops e.g., d(GNAB) family of tetraloops
• d(CNNG) family of tetraloops e.g., d(TTCG)
• Treat refers to the act of providing care to a subject in need thereof, e.g., through the administration a therapeutic agent (e.g., an oligonucleotide) to the subject, for purposes of improving the health and/or well-being of the subject with respect to an existing condition (e.g. , a disease, disorder) or to prevent or decrease the likelihood of the occurrence of a condition.
• a therapeutic agent e.g., an oligonucleotide
• treatment involves reducing the frequency or severity of at least one sign, symptom or contributing factor of a condition (e.g., disease, disorder) experienced by a subject.
• CTNNB 1 targeting oligonucleotides can be used to achieve therapeutic benefit for subjects with bile duct paucity by reducing b-catenin activity, and consequently, by increasing bile duct formation and inhibiting bile acid synthesis.
• oligonucleotides are hereby incorporated by reference in their entireties for this purpose.
• Targeting sequences can be put into multiple different oligonucleotide structures (or formats) as described herein.
• oligonucleotides provided herein are designed so as to have regions of complementarity to CTNNB 1 mRNA for purposes of targeting the mRNA in cells and inhibiting its expression.
• the region of complementarity is generally of a suitable length and base content to enable annealing of the oligonucleotide (or a strand thereof) to CTNNB 1 mRNA for purposes of inhibiting its expression.
• an oligonucleotide disclosed herein comprises a region of complementarity (e.g., on an antisense strand of a double-stranded oligonucleotide) that is at least partially complementary along its length to a sequence as set forth in SEQ ID NO: 3. In some embodiments, an oligonucleotide disclosed herein comprises a region of
• complementarity e.g., on an antisense strand of a double- stranded oligonucleotide
• a region of complementarity of an oligonucleotide that is complementary to contiguous nucleotides of a sequence as set forth in SEQ ID NO: 3 spans the entire length of an antisense strand.
• a region of complementarity of an oligonucleotide that is complementary to contiguous nucleotides of a sequence as set forth in any one of SEQ ID NO: 3 spans a portion of the entire length of an antisense strand (e.g., all but two nucleotides at the 3’ end of the antisense strand).
• the region of complementarity is at least 12, at least
• an oligonucleotide provided herein has a region of complementarity to CTNNB 1 that is in the range of 12 to 30 (e.g., 12 to 30, 12 to 22, 15 to 25, 17 to 21, 18 to 27, 19 to 27, or 15 to 30) nucleotides in length. In some embodiments, an oligonucleotide provided herein has a region of complementarity to CTNNB 1 that is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length.
• a region of complementarity to CTNNB 1 may have one or more mismatches compared with a corresponding sequence of CTNNB 1 mRNA.
• a region of complementarity on an oligonucleotide may have up to 1, up to 2, up to 3, up to 4, up to 5, etc. mismatches provided that it maintains the ability to form complementary base pairs with CTNNB 1 mRNA under appropriate hybridization conditions.
• a region of complementarity on an oligonucleotide may have no more than 1, no more than 2, no more than 3, no more than 4, or no more than 5 mismatches provided that it maintains the ability to form complementary base pairs with CTNNB 1 mRNA under appropriate hybridization conditions.
• oligonucleotide Structures if there are more than one mismatches in a region of complementarity, they may be positioned consecutively (e.g ., 2, 3, 4, or more in a row), or interspersed throughout the region of complementarity provided that the oligonucleotide maintains the ability to form complementary base pairs with CTNNB 1 mRNA under appropriate hybridization conditions. ii. Oligonucleotide Structures
• oligonucleotides that are useful for targeting CTNNB 1 mRNA in the methods of the present disclosure, including RNAi, miRNA, etc. Any of the structures described herein or elsewhere may be used as a framework to target CTNNB 1 mRNA.
• Double-stranded oligonucleotides for targeting CTNNB 1 expression (e.g., via the RNAi pathway) generally have a sense strand and an antisense strand that form a duplex with one another.
• the sense and antisense strands are not covalently linked. However, in some embodiments, the sense and antisense strands are covalently linked.
• double-stranded oligonucleotides for reducing expression of CTNNB 1 engage RNA interference (RNAi).
• RNAi RNA interference
• oligonucleotides have been developed with each strand having sizes of 19-25 nucleotides with at least one 3’ overhang of 1 to 5 nucleotides (see, e.g., U.S. Patent No. 8,372,968). Longer oligonucleotides have also been developed that are processed by Dicer to generate active RNAi products (see, e.g., U.S. Patent No. 8,883,996). Further work produced extended double- stranded oligonucleotides where at least one end of at least one strand is extended beyond a duplex targeting region, including structures where one of the strands includes a
• thermodynamically- stabilizing tetraloop structure see, e.g., U.S. Patent Nos. 8,513,207 and 8,927,705, as well as W02010033225, which are incorporated by reference herein for their disclosure of these oligonucleotides.
• Such stractures may include single-stranded extensions (on one or both sides of the molecule) as well as double-stranded extensions.
• sequences described herein can be incorporated into, or targeted using, oligonucleotides that comprise sense and antisense strands that are both in the range of 17 to 36 nucleotides in length.
• oligonucleotides incorporating such sequences are provided that have a tetraloop structure within a 3’ extension of their sense strand, and two terminal overhang nucleotides at the 3’ end of its antisense strand.
• the two terminal overhang nucleotides are GG.
• one or both of the two terminal GG nucleotides of the antisense strand is or are not complementary to the target.
• oligonucleotides incorporating such sequences are provided that have sense and antisense strands that are both in the range of 21 to 23 nucleotides in length.
• a 3’ overhang is provided on the sense, antisense, or both sense and antisense strands that is 1 or 2 nucleotides in length.
• an oligonucleotide has a guide strand of 23 nucleotides and a passenger strand of 21 nucleotides, in which the 3 '-end of passenger strand and 5 '-end of guide strand form a blunt end and where the guide strand has a two nucleotide 3' overhang.
• oligonucleotides may be in the range of 21 to 23 nucleotides in length.
• oligonucleotides may have an overhang (e.g., of 1, 2, or 3 nucleotides in length) in the 3’ end of the sense and/or antisense strands.
• oligonucleotides e.g., siRNAs
• an oligonucleotide of the invention has a 36 nucleotide sense strand that comprises an region extending beyond the antisense-sense duplex, where the extension region has a stem-tetraloop structure where the stem is a six base pair duplex and where the tetraloop has four nucleotides.
• three or four of the tetraloop nucleotides are each conjugated to a monovalent GalNac ligand.
• an oligonucleotide of the invention comprises a 25 nucleotide sense strand and a 27 nucleotide antisense strand that when acted upon by a dicer enzyme results in an antisense strand that is incorporated into the mature RISC.
• Other oligonucleotides designs for use with the compositions and methods disclosed herein include: l6-mer siRNAs (see, e.g., Nucleic Acids in Chemistry and Biology.
• shRNAs e.g., having 19 bp or shorter stems; see, e.g., Moore et al. Methods Mol. Biol. 2010; 629: 141-158
• blunt siRNAs e.g., of 19 bps in length; see: e.g. , Kraynack and Baker, RNA Vol. 12, r163-176 (2006)
• siRNA asymmetrical siRNAs
• asymmetrical siRNAs see, e.g., Sun et al, Nat. Biotechnol. 26, 1379-1382 (2008)
• asymmetric shorter-duplex siRNA see, e.g., Chang et al, Mol Ther. 2009 Apr; 17(4): 725-32
• fork siRNAs see, e.g., Hohjoh, FEBS Letters, Vol 557, issues 1-3; Jan 2004, p 193-198
• single-stranded siRNAs (Eisner; Nature Biotechnology 30, 1063 (2012))
• dumbbell- shaped circular siRNAs see, e.g., Abe et al.
• oligonucleotide structures that may be used in some embodiments to reduce or inhibit the expression of CTNNB 1 are microRNA (miRNA), short hairpin RNA (shRNA), and short siRNA (see, e.g., Hamilton et al., Embo J., 2002, 21(17): 4671-4679; see also U.S. Application No. 20090099115).
• miRNA microRNA
• shRNA short hairpin RNA
• siRNA see, e.g., Hamilton et al., Embo J., 2002, 21(17): 4671-4679; see also U.S. Application No. 20090099115.
• a double-stranded oligonucleotide may have an antisense strand of up to 40 nucleotides in length (e.g., up to 40, up to 35, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17, or up to 12 nucleotides in length).
• an oligonucleotide may have an antisense strand of at least 12 nucleotides in length (e.g., at least 12, at least 15, at least 19, at least 21, at least 22, at least 25, at least 27, at least 30, at least 35, or at least 38 nucleotides in length).
• an oligonucleotide may have an antisense strand in a range of 12 to 40 (e.g., 12 to 40, 12 to 36, 12 to 32, 12 to 28, 15 to 40, 15 to 36, 15 to 32, 15 to 28, 17 to 21, 17 to 25, 19 to 27, 19 to 30, 20 to 40, 22 to 40, 25 to 40, or 32 to 40) nucleotides in length.
• an oligonucleotide may have an antisense strand of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleotides in length.
• an antisense strand of an oligonucleotide may be referred to as a“guide strand.”
• a“guide strand” For example, if an antisense strand can engage with RNA- induced silencing complex (RISC) and bind to an Argonaut protein, or engage with or bind to one or more similar factors, and direct silencing of a target gene, it may be referred to as a guide strand.
• RISC RNA- induced silencing complex
• a sense strand complementary to a guide strand may be referred to as a“passenger strand.”
• an oligonucleotide may have a sense strand (or passenger strand) of up to 40 nucleotides in length (e.g., up to 40, up to 36, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17, or up to 12 nucleotides in length).
• a sense strand or passenger strand of up to 40 nucleotides in length (e.g., up to 40, up to 36, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17, or up to 12 nucleotides in length).
• an oligonucleotide may have a sense strand of at least 12 nucleotides in length (e.g., at least 12, at least 15, at least 19, at least 21, at least 25, at least 27, at least 30, at least 36, or at least 38 nucleotides in length).
• an oligonucleotide may have a sense strand in a range of 12 to 40 (e.g., 12 to 40, 12 to 36, 12 to 32, 12 to 28, 15 to 40, 15 to 36, 15 to 32, 15 to 28, 17 to 21, 17 to 25, 19 to 27, 19 to 30, 20 to 40, 22 to 40, 25 to 40, or 32 to 40) nucleotides in length.
• an oligonucleotide may have a sense strand of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleotides in length.
• a sense strand comprises a stem-loop structure at its 3'- end. In some embodiments, a sense strand comprises a stem-loop structure at its 5 -end. In some embodiments, a stem is a duplex of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 base pairs in length. In some embodiments, a stem-loop provides the molecule better protection against degradation (e.g., enzymatic degradation) and facilitates targeting characteristics for delivery to a target cell. For example, in some embodiments, a loop provides added nucleotides on which modification can be made without substantially affecting the gene expression inhibition activity of an oligonucleotide.
• an oligonucleotide in which the sense strand comprises (e.g., at its 3 '-end) a stem-loop set forth as: S1-L-S2, in which Si is complementary to S 2 , and in which L forms a loop between Si and S2 of up to 10 nucleotides in length (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length).
• a loop (L) of a stem- loop is a tetraloop (e.g., within a nicked tetraloop structure).
• a tetraloop may contain ribonucleotides, deoxyribonucleotides, modified nucleotides, and combinations thereof. Typically, a tetraloop has 4 to 5 nucleotides.
• a duplex formed between a sense and antisense strand is at least 12 (e.g., at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21) nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length). In some embodiments, a duplex formed between a sense and antisense strand is 12,
• a duplex formed between a sense and antisense strand does not span the entire length of the sense strand and/or antisense strand. In some embodiments, a duplex between a sense and antisense strand spans the entire length of either the sense or antisense strands. In certain embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. d. Oligonucleotide Ends
• an oligonucleotide provided herein comprises sense and antisense strands, such that there is a 3’-overhang on either the sense strand or the antisense strand, or both the sense and antisense strand.
• oligonucleotides provided herein have one 5’end that is thermodynamically less stable compared to the other 5’ end.
• an asymmetric oligonucleotide is provided that includes a blunt end at the 3’ end of a sense strand and an overhang at the 3’ end of an antisense strand.
• a 3’ overhang on an antisense strand is 1-8 nucleotides in length (e.g., 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides in length).
• an oligonucleotide for RNAi has a two nucleotide overhang on the
• an overhang is a 3' overhang comprising a length of between one and six nucleotides, optionally one to five, one to four, one to three, one to two, two to six, two to five, two to four, two to three, three to six, three to five, three to four, four to six, four to five, five to six nucleotides, or one, two, three, four, five or six nucleotides.
• the overhang is a 5' overhang comprising a length of between one and six nucleotides, optionally one to five, one to four, one to three, one to two, two to six, two to five, two to four, two to three, three to six, three to five, three to four, four to six, four to five, five to six nucleotides, or one, two, three, four, five or six nucleotides.
• 3’ end or 5’ end of a sense and/or antisense strand are modified.
• one or two terminal nucleotides of the 3’ end of an antisense strand are modified.
• the last nucleotide at the 3' end of an antisense strand is modified, e.g., comprises 2’-modification, e.g., a 2’-0-methoxyethyl.
• the last one or two terminal nucleotides at the 3’ end of an antisense strand are complementary to the target.
• the last one or two nucleotides at the 3’ end of the antisense strand are not complementary to the target.
• the 5’ end and/or the 3’ end of a sense or antisense strand has an inverted cap nucleotide. e. Mismatches
• the 3’- terminus of the sense strand contains one or more mismatches. In one embodiment, two mismatches are incorporated at the 3’ terminus of the sense strand.
• base mismatches or destabilization of segments at the 3’-end of the sense strand of the oligonucleotide improved the potency of synthetic duplexes in RNAi, possibly through facilitating processing by Dicer.
• an oligonucleotide for reducing CTNNB1 expression as described herein is single- stranded.
• Such structures may include, but are not limited to single-stranded RNAi oligonucleotides.
• RNAi oligonucleotides Recent efforts have demonstrated the activity of single-stranded RNAi oligonucleotides (see, e.g., Matsui et al. (May 2016), Molecular Therapy, Vol. 24(5), 946-955).
• oligonucleotides provided herein are antisense oligonucleotides (ASOs).
• An antisense oligonucleotide is a single- stranded oligonucleotide that has a nucleobase sequence which, when written in the 5' to 3' direction, comprises the reverse complement of a targeted segment of a particular nucleic acid and is suitably modified (e.g., as a gapmer) so as to induce RNaseH mediated cleavage of its target RNA in cells or (e.g., as a mixmer) so as to inhibit translation of the target mRNA in cells.
• Antisense oligonucleotides for use in the instant disclosure may be modified in any suitable manner known in the art including, for example, as shown in U.S. Patent No.
• antisense oligonucleotides including, e.g., length, sugar moieties of the nucleobase (pyrimidine, purine), and alterations of the heterocyclic portion of the nucleobase.
• antisense molecules have been used for decades to reduce expression of specific target genes (see, e.g., Bennett et al. Pharmacology of Antisense Drugs, Annual Review of Pharmacology and Toxicology, Vol. 57: 81-105).
• Oligonucleotides may be modified in various ways to improve or control specificity, stability, delivery, bioavailability, resistance from nuclease degradation, immunogenicity, base-paring properties, RNA distribution and cellular uptake and other features relevant to therapeutic or research use. See, e.g., Bramsen et al., Nucleic Acids Res., 2009, 37, 2867-2881; Bramsen and Kjems (Frontiers in Genetics, 3 (2012): 1-22).
• oligonucleotides of the present disclosure may include one or more suitable modifications.
• a modified nucleotide has a modification in its base (or nucleobase), the sugar (e.g., ribose, deoxyribose), or the phosphate group.
• oligonucleotides may be delivered in vivo by conjugating them to or encompassing them in a lipid nanoparticle (LNP) or similar carrier.
• LNP lipid nanoparticle
• an oligonucleotide is not protected by an LNP or similar carrier (e.g.,“naked delivery”), it may be advantageous for at least some of the its nucleotides to be modified. Accordingly, in certain embodiments of any of the oligonucleotides provided herein, all or substantially all of the nucleotides of an LNP or similar carrier.
• oligonucleotide are modified. In certain embodiments, more than half of the nucleotides are modified. In certain embodiments, less than half of the nucleotides are modified. Typically, with naked delivery, every nucleotide is modified at the 2'-position of the sugar group of that nucleotide. These modifications may be reversible or irreversible. Typically, the 2'-position modification is 2'-fluoro, 2'-0-methyl, etc. In some embodiments, an oligonucleotide as disclosed herein has a number and type of modified nucleotides sufficient to cause the desired characteristic (e.g., protection from enzymatic degradation, capacity to target a desired cell after in vivo administration, and/or thermodynamic stability). a. Sugar Modifications
• a modified sugar (also referred to herein as a sugar analog) includes a modified deoxyribose or ribose moiety, e.g., in which one or more modifications occur at the 2', 3', 4', and/or 5' carbon position of the sugar.
• a modified sugar may also include non-natural alternative carbon structures such as those present in locked nucleic acids (“LNA”) (see, e.g., Koshkin et al. (1998), Tetrahedron 54, 3607-3630), unlocked nucleic acids (“UNA”) (see, e.g., Snead et al.
• LNA locked nucleic acids
• NAA unlocked nucleic acids
• a nucleotide modification in a sugar comprises a 2'- modification.
• the 2 '-modification may be 2'-aminoethyl, 2'-fluoro, 2'- O-methyl, 2'-0-methoxyethyl, or 2'-dcoxy-2'-fluoro-p-d-arabinonuclcic acid.
• the modification is 2'-fluoro, 2'-0-methyl, or 2'-0-methoxyethyl.
• 2' position modifications that have been developed for use in oligonucleotides can be employed in oligonucleotides disclosed herein.
• a modification in a sugar comprises a modification of the sugar ring, which may comprise modification of one or more carbons of the sugar ring.
• a modification of a sugar of a nucleotide may comprise a linkage between the - carbon and a 1 '-carbon or 4 '-carbon of the sugar.
• the linkage may comprise an ethylene or methylene bridge.
• a modified nucleotide has an acyclic sugar that lacks a 2'-carbon to 3 '-carbon bond.
• a modified nucleotide has a thiol group, e.g., in the 4' position of the sugar.
• the terminal 3 '-end group (e.g., a 3 '-hydroxyl) is a phosphate group or other group, which can be used, for example, to attach linkers, adapters or labels or for the direct ligation of an oligonucleotide to another nucleic acid.
• a 3 '-end group e.g., a 3 '-hydroxyl
• the terminal 3 '-end group is a phosphate group or other group, which can be used, for example, to attach linkers, adapters or labels or for the direct ligation of an oligonucleotide to another nucleic acid.
• 5' -terminal phosphate groups of oligonucleotides may or in some
• oligonucleotides comprising a 5 '-phosphate group may be susceptible to degradation via phosphatases or other enzymes, which can limit their bioavailability in vivo.
• oligonucleotides include analogs of 5' phosphates that are resistant to such degradation.
• a phosphate analog may be oxymethylphosphonate, vinylphosphonate, or malonylphosphonate.
• the 5' end of an oligonucleotide strand is attached to a chemical moiety that mimics the electrostatic and steric properties of a natural 5 '-phosphate group (“phosphate mimic”) (see, e.g., Prakash et al. (2015), Nucleic Acids Res., Nucleic Acids Res. 2015 Mar 31; 43(6): 2993-3011, the contents of which relating to phosphate analogs are incorporated herein by reference). Many phosphate mimics have been developed that can be attached to the 5' end (see, e.g., U.S. Patent No. 8,927,513, the contents of which relating to phosphate analogs are incorporated herein by reference).
• a hydroxyl group is attached to the 5' end of the oligonucleotide.
• an oligonucleotide has a phosphate analog at a 4'- carbon position of the sugar (referred to as a“4 '-phosphate analog”). See, for example, International Patent Application PCT/US2017/049909, filed on September 1, 2017, U.S.
• an oligonucleotide provided herein comprises a 4'-phosphate analog at a 5 '-terminal nucleotide.
• a phosphate analog is an
• a 4'-phosphate analog is a thiomethylphosphonate or an aminomethylphosphonate, in which the sulfur atom of the thiomethyl group or the nitrogen atom of the aminomethyl group is bound to the 4 '-carbon of the sugar moiety or analog thereof.
• a 4'-phosphate analog is an oxymethylphosphonate.
• an oxymethylphosphonate is represented by the formula -0-CH 2- P0(0H) 2 or -O-C H 2— PO ( O R ) 2 , in which R is independently selected from H, CH 3 , an alkyl group, CH2CH2CN, CH 2 OCOC(CH 3 ) 3 , CH 2 OCH2CH 2 Si(CH 3 ) 3 , or a protecting group.
• the alkyl group is CthCtb. More typically, R is independently selected from H, CH 3 , or CH2CH 3 .
• the oligonucleotide may comprise a modified intemucleoside linkage.
• phosphate modifications or substitutions may result in an oligonucleotide that comprises at least one (e.g., at least 1, at least 2, at least 3 or at least 5) modified intemucleotide linkage.
• oligonucleotides disclosed herein comprises 1 to 10 (e.g., 1 to 10, 2 to 8, 4 to 6, 3 to 10, 5 to 10, 1 to 5, 1 to 3 or 1 to 2) modified intemucleotide linkages.
• any one of the oligonucleotides disclosed herein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 modified intemucleotide linkages.
• a modified intemucleotide linkage may be a phosphorodithioate linkage, a phosphorothioate linkage, a phosphotriester linkage, a thionoalkylphosphonate linkage, a thionoalkylphosphotriester linkage, a phosphoramidite linkage, a phosphonate linkage or a boranophosphate linkage.
• at least one modified intemucleotide linkage of any one of the oligonucleotides as disclosed herein is a phosphorothioate linkage.
• oligonucleotides provided herein have one or more modified nucleobases.
• modified nucleobases also referred to herein as base analogs
• base analogs are linked at the G position of a nucleotide sugar moiety.
• a modified nucleobase is a nitrogenous base. In certain embodiments, a modified nucleobase does not contain a nitrogen atom. See e.g., U.S. Published Patent Application No. 20080274462. In some embodiments, a modified nucleotide comprises a universal base. However, in certain embodiments, a modified nucleotide does not contain a nucleobase (abasic).
• a universal base is a heterocyclic moiety located at the
• nucleotide sugar moiety in a modified nucleotide or the equivalent position in a nucleotide sugar moiety substitution that, when present in a duplex, can be positioned opposite more than one type of base without substantially altering the structure of the duplex.
• a reference single-stranded nucleic acid e.g., a reference single-stranded nucleic acid
• a single- stranded nucleic acid containing a universal base forms a duplex with the target nucleic acid that has a lower T m than a duplex formed with the complementary nucleic acid.
• the single-stranded nucleic acid containing the universal base forms a duplex with the target nucleic acid that has a higher T m than a duplex formed with the nucleic acid comprising the mismatched base.
• Non-limiting examples of universal-binding nucleotides include inosine, 1-b-
• a reversibly modified nucleotide comprises a glutathione-sensitive moiety.
• nucleic acid molecules have been chemically modified with cyclic disulfide moieties to mask the negative charge created by the
• such a reversible modification allows protection during in vivo administration (e.g., transit through the blood and/or lysosomal/endosomal
• oligonucleotide will be exposed to nucleases and other harsh environmental conditions (e.g., pH).
• nucleases and other harsh environmental conditions e.g., pH
• glutathione When released into the cytosol of a cell where the levels of glutathione are higher compared to extracellular space, the modification is reversed and the result is a cleaved oligonucleotide.
• glutathione sensitive moieties it is possible to introduce sterically larger chemical groups into the oligonucleotide of interest as compared to the options available using irreversible chemical modifications. This is because these larger chemical groups will be removed in the cytosol and, therefore, should not interfere with the biological activity of the oligonucleotides inside the cytosol of a cell.
• these larger chemical groups can be engineered to confer various advantages to the nucleotide or oligonucleotide, such as nuclease resistance, lipophilicity, charge, thermal stability, specificity, and reduced immunogenicity.
• the structure of the glutathione-sensitive moiety can be engineered to modify the kinetics of its release.
• a glutathione-sensitive moiety is attached to the sugar of the nucleotide. In some embodiments, a glutathione-sensitive moiety is attached to the 2'- carbon of the sugar of a modified nucleotide. In some embodiments, the glutathione-sensitive moiety is located at the 5 '-carbon of a sugar, particularly when the modified nucleotide is the 5 '-terminal nucleotide of the oligonucleotide. In some embodiments, the glutathione-sensitive moiety is located at the 3 '-carbon of a sugar, particularly when the modified nucleotide is the 3 '-terminal nucleotide of the oligonucleotide.
• the glutathione-sensitive moiety comprises a sulfonyl group.
• a sulfonyl group See, e.g., International Patent Application Publication WO 2018/039364, which was published on March 1, 2018, and U.S. Prov. Appl. No. 62/378,635, entitled Compositions Comprising Reversibly Modified Oligonucleotides and Uses Thereof, which was filed on August 23, 2016, the contents of which are incorporated by reference herein for its relevant disclosures.
• oligonucleotides of the disclosure may be desirable to target the oligonucleotides of the disclosure to one or more cells or one or more organs. Such a strategy may help to avoid undesirable effects in other organs, or may avoid undue loss of the oligonucleotide to cells, tissue or organs that would not benefit for the oligonucleotide. Accordingly, in some embodiments, oligonucleotides disclosed herein may be modified to facilitate targeting of a particular tissue, cell or organ , e.g., to facilitate delivery of the oligonucleotide to the liver. In certain embodiments, oligonucleotides disclosed herein may be modified to facilitate delivery of the oligonucleotide to the hepatocytes of the liver. In some embodiments, an
• oligonucleotide comprises a nucleotide that is conjugated to one or more targeting ligands.
• a targeting ligand may comprise a carbohydrate, amino sugar, cholesterol, peptide, polypeptide, protein or part of a protein (e.g., an antibody or antibody fragment) or lipid.
• a targeting ligand is an aptamer.
• a targeting ligand may be an RGD peptide that is used to target tumor vasculature or glioma cells, CREKA peptide to target tumor vasculature or stoma, transferrin, lactoferrin, or an aptamer to target transferrin receptors expressed on CNS vasculature, or an anti-EGFR antibody to target EGFR on glioma cells.
• the targeting ligand is one or more GalNAc moieties.
• nucleotides of an oligonucleotide are each conjugated to a separate targeting ligand. In some embodiments, 2 to 4 nucleotides of an oligonucleotide are each conjugated to a separate targeting ligand.
• targeting ligands are conjugated to 2 to 4 nucleotides at either ends of the sense or antisense strand (e.g ., ligands are conjugated to a 2 to 4 nucleotide overhang or extension on the 5' or 3' end of the sense or antisense strand) such that the targeting ligands resemble bristles of a toothbrush and the oligonucleotide resembles a toothbrush.
• an antisense strand e.g ., ligands are conjugated to a 2 to 4 nucleotide overhang or extension on the 5' or 3' end of the sense or antisense strand
• oligonucleotide may comprise a stem- loop at either the 5' or 3' end of the sense strand and 1, 2, 3 or 4 nucleotides of the loop of the stem may be individually conjugated to a targeting ligand, as described, for example, in International Patent Application Publication WO 2016/100401, which was published on lune 23, 2016, the relevant contents of which are incorporated herein by reference.
• oligonucleotide that reduces the expression of CTNNB1 to the hepatocytes of the liver of a subject.
• Any suitable hepatocyte targeting moiety may be used for this purpose.
• GalNAc is a high affinity ligand for asialoglycoprotein receptor (ASGPR), which is primarily expressed on the sinusoidal surface of hepatocyte cells and has a major role in binding, internalization, and subsequent clearance of circulating glycoproteins that contain terminal galactose or N-acetylgalactosamine residues (asialoglycoproteins).
• Conjugation (either indirect or direct) of GalNAc moieties to oligonucleotides of the instant disclosure may be used to target these oligonucleotides to the ASGPR expressed on these hepatocyte cells.
• an oligonucleotide of the instant disclosure is conjugated directly or indirectly to a monovalent GalNAc.
• the oligonucleotide is conjugated directly or indirectly to more than one monovalent GalNAc (i.e., is conjugated to 2, 3, or 4 monovalent GalNAc moieties, and is typically conjugated to 3 or 4 monovalent GalNAc moieties).
• an oligonucleotide of the instant disclosure is conjugated to one or more bivalent GalNAc, trivalent GalNAc, or tetravalent GalNAc moieties.
• nucleotides of an oligonucleotide are each conjugated to a GalNAc moiety.
• 2 to 4 nucleotides of the loop (L) of the stem-loop are each conjugated to a separate GalNAc.
• targeting ligands are conjugated to 2 to 4 nucleotides at either ends of the sense or antisense strand (e.g., ligands are conjugated to a 2 to 4 nucleotide overhang or extension on the 5 ' or 3 ' end of the sense or antisense strand) such that the GalNAc moieties resemble bristles of a toothbrush and the oligonucleotide resembles a toothbrush.
• an oligonucleotide may comprise a stem- loop at either the 5' or 3' end of the sense strand and 1, 2, 3 or 4 nucleotides of the loop of the stem may be individually conjugated to a GalNAc moiety.
• GalNAc moieties are conjugated to a nucleotide of the sense strand.
• four GalNAc moieties can be conjugated to nucleotides in the tetraloop of the sense strand, where each GalNAc moiety is conjugated to one nucleotide.
• a targeting ligand is conjugated to a nucleotide using a click linker.
• an acetal-based linker is used to conjugate a targeting ligand to a nucleotide of any one of the oligonucleotides described herein.
• Acetal-based linkers are disclosed, for example, in International Patent Application Publication Number W02016100401 Al, which published on lune 23, 2016, and the contents of which relating to such linkers are incorporated herein by reference.
• the linker is a labile linker.
• the linker is fairly stable.
• a duplex extension (up to 3, 4, 5, or 6 base pairs in length) is provided between a targeting ligand (e.g., a GalNAc moiety) and a double- stranded oligonucleotide.
• oligonucleotides can be delivered to a subject or a cellular environment using a formulation that minimizes degradation, facilitates delivery and/or uptake, or provides another beneficial property to the oligonucleotides in the formulation.
• compositions comprising oligonucleotides (e.g., single- stranded or double- stranded oligonucleotides) to reduce the expression of CTNNB1.
• Such compositions can be suitably formulated such that when administered to a subject, either into the i mediate environment of a target cell or systemically, a sufficient portion of the oligonucleotides enter the cell to reduce CTNNB 1 expression.
• an oligonucleotide is formulated in buffer solutions such as phosphate-buffered saline solutions, liposomes, micellar structures, and capsids.
• buffer solutions such as phosphate-buffered saline solutions, liposomes, micellar structures, and capsids.
• naked oligonucleotides or conjugates thereof are formulated in water or in an aqueous solution (e.g., water with pH adjustments).
• naked oligonucleotides or conjugates thereof are formulated in basic buffered aqueous solutions (e.g., PBS)
• Formulations of oligonucleotides with cationic lipids can be used to facilitate transfection of the oligonucleotides into cells.
• cationic lipids such as lipofectin, cationic glycerol derivatives, and polycationic molecules ( e.g ., polylysine) can be used.
• Suitable lipids include Oligofectamine, Lipofectamine (Life Technologies), NC388 (Ribozyme Pharmaceuticals, Inc., Boulder, Colo.), or FuGene 6 (Roche) all of which can be used according to the manufacturer’s instructions.
• a formulation comprises a lipid nanoparticle.
• an excipient comprises a liposome, a lipid, a lipid complex, a microsphere, a microparticle, a nanosphere, or a nanoparticle, or may be otherwise formulated for administration to the cells, tissues, organs, or body of a subject in need thereof (see, e.g., Remington: The Science and Practice of Pharmacy, 22nd edition, Pharmaceutical Press, 2013).
• formulations as disclosed herein comprise an excipient.
• an excipient confers to a composition improved stability, improved absorption, improved solubility and/or therapeutic enhancement of the active ingredient.
• an excipient is a buffering agent (e.g., sodium citrate, sodium phosphate, a tris base, or sodium hydroxide) or a vehicle (e.g., a buffered solution, petrolatum, dimethyl sulfoxide, or mineral oil).
• a buffering agent e.g., sodium citrate, sodium phosphate, a tris base, or sodium hydroxide
• a vehicle e.g., a buffered solution, petrolatum, dimethyl sulfoxide, or mineral oil.
• an oligonucleotide is lyophilized for extending its shelf-life and then made into a solution before use (e.g. , administration to a subject).
• an excipient in a composition comprising any one of the oligonucleotides described herein may be a lyoprotectant (e.g., mannitol, lactose, polyethylene glycol, or polyvinyl pyrolidone), or a collapse temperature modifier (e.g., dextran, ficoll, or gelatin).
• a lyoprotectant e.g., mannitol, lactose, polyethylene glycol, or polyvinyl pyrolidone
• a collapse temperature modifier e.g., dextran, ficoll, or gelatin
• a pharmaceutical composition is formulated to be compatible with its intended route of administration.
• routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.
• the route of administration is intravenous or subcutaneous.
• compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the
• suitable carriers include physiological saline, bacteriostatic water, Cremophor EL.TM. (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS).
• the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
• isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride in the composition.
• Sterile injectable solutions can be prepared by incorporating the oligonucleotides in a required amount in a selected solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
• a composition may contain at least about 0.1% of the therapeutic agent (e.g., an oligonucleotide for reducing CTNNB1 expression) or more, although the percentage of the active ingredient(s) may be between about 1% and about 80% or more of the weight or volume of the total composition.
• the therapeutic agent e.g., an oligonucleotide for reducing CTNNB1 expression
• the percentage of the active ingredient(s) may be between about 1% and about 80% or more of the weight or volume of the total composition.
• Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.
• a cell is any cell that expresses CTNNB 1 (e.g . , hepatocytes, macrophages, monocyte-derived cells, prostate cancer cells, cells of the brain, endocrine tissue, bone marrow, lymph nodes, lung, gall bladder, liver, duodenum, small intestine, pancreas, kidney, gastrointestinal tract, bladder, adipose and soft tissue and skin).
• CTNNB 1 e.g . , hepatocytes, macrophages, monocyte-derived cells, prostate cancer cells, cells of the brain, endocrine tissue, bone marrow, lymph nodes, lung, gall bladder, liver, duodenum, small intestine, pancreas, kidney, gastrointestinal tract, bladder, adipose and soft tissue and skin.
• the cell is a primary cell that has been obtained from a subject and that may have undergone a limited number of a passages, such that the cell substantially maintains its natural phenotypic properties.
• a cell to which the oligonucleotide is delivered is ex vivo or in vitro (i.e., can be delivered to a cell in culture or to an organism in which the cell resides).
• methods are provided for delivering to a cell an effective amount any one of the oligonucleotides disclosed herein for purposes of reducing expression of CTNNB 1 solely in hepatocytes.
• oligonucleotides disclosed herein can be introduced using appropriate nucleic acid delivery methods including injection of a solution containing the oligonucleotides, bombardment by particles covered by the oligonucleotides, exposing the cell or organism to a solution containing the oligonucleotides, or electroporation of cell membranes in the presence of the oligonucleotides.
• appropriate nucleic acid delivery methods including injection of a solution containing the oligonucleotides, bombardment by particles covered by the oligonucleotides, exposing the cell or organism to a solution containing the oligonucleotides, or electroporation of cell membranes in the presence of the oligonucleotides.
• Other appropriate methods for delivering including injection of a solution containing the oligonucleotides, bombardment by particles covered by the oligonucleotides, exposing the cell or organism to a solution containing the oligonucleotides, or
• oligonucleotides to cells may be used, such as lipid-mediated carrier transport, chemical- mediated transport, and cationic liposome transfection such as calcium phosphate, and others.
• an appropriate assay to evaluate one or more properties of a cell or subject or by biochemical techniques that evaluate molecules indicative of CTNNB 1 expression (e.g., RNA, protein).
• the extent to which an oligonucleotide provided herein reduces levels of expression of CTNNB 1 is evaluated by comparing expression levels (e.g., mRNA or protein levels of CTNNB 1 to an appropriate control (e.g., a level of CTNNB 1 expression in a cell or population of cells to which an oligonucleotide has not been delivered or to which a negative control has been delivered).
• an appropriate control level of CTNNB 1 expression may be a predetermined level or value, such that a control level need not be measured every time.
• the predetermined level or value can take a variety of forms.
• a predetermined level or value can take a variety of forms.
• a predetermined level or value can take a variety of forms.
• a predetermined level or value can take a variety of forms.
• predetermined level or value can be single cut-off value, such as a median or mean.
• administration of an oligonucleotide as described herein results in a reduction in the level of CTNNB 1 expression in a cell.
• the reduction in levels of CTNNB 1 expression may be a reduction to 1% or lower, 5% or lower, 10% or lower, 15% or lower, 20% or lower, 25% or lower, 30% or lower, 35% or lower, 40% or lower, 45% or lower, 50% or lower, 55% or lower, 60% or lower, 70% or lower, 80% or lower, or 90% or lower compared with an appropriate control level of CTNNB 1.
• the appropriate control level may be a level of CTNNB 1 expression in a cell or population of cells that has not been contacted with an oligonucleotide as described herein.
• the effect of delivery of an oligonucleotide to a cell according to a method disclosed herein is assessed after a finite period of time.
• levels of CTNNB 1 may be analyzed in a cell at least 8 hours, 12 hours, 18 hours, 24 hours; or at least one, two, three, four, five, six, seven, or fourteen days after introduction of the oligonucleotide into the cell.
• an oligonucleotide is delivered in the form of a transgene that is engineered to express in a cell the oligonucleotides (e.g., its sense and antisense strands).
• an oligonucleotide is delivered using a transgene that is engineered to express any oligonucleotide disclosed herein.
• Transgenes may be delivered using viral vectors (e.g., adenovirus, retrovirus, vaccinia virus, poxvirus, adeno- associated virus or herpes simplex virus) or non- viral vectors (e.g., plasmids or synthetic mRNAs).
• transgenes can be injected directly to a subject. ii. Treatment Methods
• aspects of the disclosure relate to methods for reducing CTNNB1 expression for the treatment of bile duct paucity in a subject.
• the methods may comprise administering to a subject in need thereof an effective amount of any one of the oligonucleotides disclosed herein.
• Such treatments could be used, for example, to promote bile duct and/or regeneration in a subject, thereby promoting draining of bile acid.
• the treatments could also be used, for example, in inhibiting bile acid synthesis in a subject, thereby reducing liver damage.
• the present disclosure provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) bile duct paucity and/or a disease or disorder associated with bile duct paucity (e.g., including Alagille syndrome and Biliary Atresia).
• a disease or disorder associated with bile duct paucity e.g., including Alagille syndrome and Biliary Atresia.
• the disclosure provides a method for preventing in a subject, a disease or disorder as described herein by administering to the subject a therapeutic agent (e.g., an oligonucleotide or vector or transgene encoding same).
• a therapeutic agent e.g., an oligonucleotide or vector or transgene encoding same.
• the subject to be treated is a subject who will benefit therapeutically from a reduction in the amount of b-catenin protein, e.g., in the liver.
• Methods described herein typically involve administering to a subject an effective amount of an oligonucleotide, that is, an amount capable of producing a desirable therapeutic result.
• a therapeutically acceptable amount may be an amount that is capable of treating a disease or disorder.
• the appropriate dosage for any one subject will depend on certain factors, including the subject’s size, body surface area, age, the particular composition to be administered, the active ingredient(s) in the composition, time and route of
• a subject is administered any one of the compositions disclosed herein either enterally (e.g. , orally, by gastric feeding tube, by duodenal feeding tube, via gastrostomy or rectally), parenterally (e.g., subcutaneous injection, intravenous injection or infusion, intra-arterial injection or infusion, intramuscular injection,), topically (e.g., epicutaneous, inhalational, via eye drops, or through a mucous membrane), or by direct injection into a target organ (e.g., the liver of a subject).
• oligonucleotides disclosed herein are administered intravenously or subcutaneously.
• oligonucleotides are administered at a dose in a range of 0.1 mg/kg to 25 mg/kg (e.g., 1 mg/kg to 5mg/kg). In some embodiments, oligonucleotides are administered at a dose in a range of 0.1 mg/kg to 5 mg/kg or in a range of 0.5 mg/kg to 5 mg/kg. [000126] As a non-limiting set of examples, the oligonucleotides of the instant disclosure would typically be administered once per year, twice per year, quarterly (once every three months), bi-monthly (once every two months), monthly, or weekly.
• the subject to be treated is a human or non-human primate or other mammalian subject.
• Other exemplary subjects include domesticated animals such as dogs and cats; livestock such as horses, cattle, pigs, sheep, goats, and chickens; and animals such as mice, rats, guinea pigs, and hamsters.
• Example 1 Evaluation of CTNNB1 RNAi oligonucleotide treatment in a 3, 5 -diethoxy carbonyl- 1,4-dihydrocollidine (DL)C)-fed mouse model of bile duct damage.
• DL 3, 5 -diethoxy carbonyl- 1,4-dihydrocollidine
• RNAi oligonucleotide contained a nicked tetraloop structure, including single monovalent GalNac moieties conjugated at each of four nucleotides of the tetraloop (-GAAA-) on its sense strand and a phosphate analog at the 5’ end of its antisense strand.
• DDC-fed mice were treated with PBS.
• Immunohistochemistry staining was performed on liver sections from DDC-fed mice treated with PBS or CTNNB 1 RNAi oligonucleotide using a rabbit monoclonal antibody (catalog number: ab52625, Abeam, Cambridge, MA) against the ductal epithelial marker CK19 (FIG. 1 and FIG. 2).
• liver sections from mice on a normal diet treated with PBS or CTNNB 1 RNAi oligonucleotides were also evaluated. Mice were dosed weekly (days 0, 7, 14, 21, 28, 35) and sacrificed 3 days post-dose as indicated in FIG. 2. Resin casting was used to visualize ductule architecture in DDC-fed mice treated with control PBS or with CTNNB 1 RNAi oligonucleotide (FIG. 5).
• liver sections from DDC-fed mice treated with CTNNB 1 are shown in FIG. 1 .
• RNAi oligonucleotide having a sense strand sequence as set forth in SEQ ID NO: 1 and an antisense strand sequence as set forth in SEQ ID NO: 2 for 24 days had increased numbers of CK19 positive cells compared to control DDC-mice treated with PBS. Similar results were found in a time course study shown in FIG. 2.
• DDC-feeding results in an increase in the number of CK19 staining that is further increased in liver sections from DCC-fed mice treated with CTNNB 1 RNAi oligonucleotide (having a sense strand sequence as set forth in SEQ ID NO: 1 and an antisense strand sequence as set forth in SEQ ID NO: 2) compared to liver sections from DDC-fed mice treated with PBS 10 days, 24 days and 38 days after the first dose of CTNNB 1 RNAi oligonucleotides (FIG. 2). More small ductules were also observed in DDC-fed mice receiving CTNNB 1 RNAi oligonucleotides compared to mice receiving control PBS (FIG. 5).
• RNAi oligonucleotide targeting of CTNNB 1 mRNA induces bile epithelial cell differentiation and promotes bile duct regeneration in a DDC-fed mouse model of hepatic injury.
• Example 2 Evaluation of CTNNB1 RNAi oligonucleotide treatment in a Mdr2 ' mouse model of bile duct damage.
• CTNNB 1 RNAi oligonucleotides (having a sense strand sequence as set forth in SEQ ID NO: 1 and an antisense strand sequence as set forth in SEQ ID NO: 2) were also tested in another mouse model of biliary damage ( Mdr2 ' mice). Mdr2 ' mice were treated with PBS or CTNNB 1 RNAi oligonucleotides for 66 days. Liver sections from treated mice were stained for the ductal epithelial marker CK19. A liver section from a Mdr2 +l mouse treated with PBS was also analyzed.
• Mdr2 / mice have increased CK19 staining compared to Mdr2 +/ ⁇ mice.
• a further increase in the number of CK19 positive cells was detected in liver sections from Mdr2 ' mice treated with CTNNB 1 RNAi oligonucleotide compared to Mdr2 ' mice treated with PBS. (FIG. 3). Therefore, CTNNB 1 RNAi oligonucleotides also potentially induces bile epithelial cell differentiation in Mdr2 ' mice.
• Example 3 Evaluation of CTNNB 1 RNAi oligonucleotide treatment in wildtype mice fed a normal diets.
• CD-l mice were treated with control PBS, 10 mg/kg CTNNB 1 RNAi oligonucleotide, or 100 mg/kg CTNNB 1 RNAi oligonucleotide once weekly for six weeks (Q1W x 6). Liver sections from treated animals were then stained with an antibody that recognizes the ductal epithelial marker CK19.
• Example 4 Evaluation of CTNNB1 RNAi oligonucleotide treatment on bile synthesis in a DDC-fed mouse model of bile duct damage.
• the total bile acid concentration (FIG. 7A), the bile flow rate (FIG. 7B) and mRNA expression (FIG. 7C) in the liver were evaluated for each treatment group. In particular, the levels of CTNNB 1, Cyp7al, Cyp27a, Cyp8Bl and Shp mRNA were measured (FIG. 1C).
• oligonucleotides reduces bile acid synthesis in a mouse model of bile duct damage.
• sequences presented in the sequence listing may be referred to in describing the structure of an oligonucleotide or other nucleic acid.
• the actual oligonucleotide or other nucleic acid may have one or more alternative nucleotides (e.g., an RNA counterpart of a DNA nucleotide or a DNA counterpart of an RNA nucleotide) and/or one or more modified nucleotides and/or one or more modified intemucleotide linkages and/or one or more other modification compared with the specified sequence while retaining essentially same or similar complementary properties as the specified sequence.

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