Oligonucleotide-mediated knockdown of ACVR2b
Patent Information
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- SOUFFLÉ THERAPEUTICS INC
- Filing Date
- 2025-12-03
- Publication Date
- 2026-07-09
AI Technical Summary
Current weight loss treatments, including pharmacological interventions and surgical procedures, fail to maintain significant weight reduction over the long term due to muscle mass loss, leading to weight regain and associated health risks.
Inhibition of Activin receptor 2B (ACVR2B) expression using oligonucleotides, such as RNAi agents, to preserve and increase muscle mass during weight loss, combining with GLP-1 receptor agonism to enhance fat loss and maintain lean tissue.
This approach promotes sustainable weight management by preserving muscle mass and reducing fat mass, improving metabolic and musculoskeletal health, and reducing the risk of weight regain.
Abstract
Description
OLIGONUCLEOTIDE-MEDIATED KNOCKDOWN OF ACVR2BCROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63 / 727,473 filed on December 3, 2024, the entirety of which is incorporated herein by reference.INCORPORATION BY REFERENCE OF SEQUENCE LISTING
[0002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled 360770-000 l_SeqList_ST26.xml, created December 02, 2025, which is 39,031,861 bytes in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety.BACKGROUND
[0003] Obesity is a complex, long-term condition projected to affect over 25% of the global population by 2035. While lifestyle interventions like diet and increased physical activity can help, they often fail to achieve substantial, long-lasting weight loss. Historically, surgical procedures have been the most effective method for significant weight reduction, with pharmacological treatments yielding only modest results. However, even those who experience considerable weight loss must contend with biological mechanisms that promote weight regain, creating an ongoing challenge in maintaining reduced body weight.
[0004] The discovery of incretin hormones, such as glucagon-like peptide 1 (GLP-1), has shed light on the neural and hormonal pathways involved in energy balance and metabolism. The approval of semaglutide, a potent GLP-1 receptor agonist, marked a breakthrough in obesity treatment, with clinical studies showing an average weight loss of about 14.9% over 68 weeks. Further research on combining hormone therapies has led to the development of drugs like tirzepatide and retatrutide, which have shown even more promising results in reducing body weight.
[0005] Although these treatments offer significant benefits, maintaining weight loss over the long term remains challenging. For example, a study on semaglutide found that individuals regained roughly two-thirds of the lost weight within a year after stopping treatment. This pattern is common across various weight loss methods, with the loss typically involving reductions in both lean and fat mass. Since skeletal muscle plays a crucial role in energy expenditure and insulin sensitivity, losing muscle mass during weight loss can lead to decreased energy expenditure andDocket No.: SOUF-001-02WO contribute to weight regain. Moreover, low muscle mass is associated with higher mortality risks from cardiovascular and other causes, highlighting the need for weight loss strategies that preserve and increase lean tissue.
[0006] Research into inhibitors of TGF0-related ligands, such as myostatin and Activin A, which regulate muscle mass, has shown potential in this regard. These ligands act through activin type II receptors (ActRIIA / B), and blocking these receptors — whether through genetic means or pharmacological interventions — has led to significant increases in muscle mass. Recent studies with bimagrumab, an antibody targeting both ActRIIA and ActRIIB, demonstrated a 3.6% increase in lean mass and a 20.5% reduction in fat mass in overweight and obese individuals, resulting in a 6.5% overall weight loss. Importantly, the loss of fat mass was maintained 12 weeks after treatment ended, a contrast to the typical weight regains observed with treatments like semaglutide.
[0007] The combination of ActRII inhibition with GLP-1 receptor agonism holds potential for not only reducing fat mass but also preserving muscle, potentially leading to better long-term weight management. Mechanistically, ActRII inhibition promotes muscle growth by reducing Smad2 / 3 activity and increasing Akt signaling, which drives protein synthesis and muscle hypertrophy. While previous studies have shown that certain components of the Akt pathway are not essential for muscle growth, more recent research suggests that a minimal level of Akt signaling is required to maintain muscle mass.
[0008] In conclusion, GLP-1 receptor agonists are highly effective in promoting weight loss and improving metabolic health. To optimize these outcomes, preserving and increasing muscle mass during weight loss, potentially through ActRIIB or ActRIIA inhibition, represents a promising therapeutic approach. By enhancing fat loss and maintaining and increasing lean tissue, this strategy could lead to more sustainable weight management and improvements in both metabolic and musculoskeletal health.SUMMARY
[0009] In some embodiments, the present disclosure provides an oligonucleotide for inhibiting expression of Activin receptor 2B (ACVR2B). In some embodiments, the present disclosure provides an oligonucleotide for inhibiting expression of ACVR2B, wherein the oligonucleotide comprises an antisense strand comprising at least 14 contiguous nucleotides substantially complementary to a sequence of nucleotides encoding ACVR2B, with no more than 4 mismatched nucleotides.Docket No.: SOUF-001-02WO
[0010] In some embodiments, the present disclosure provides a pharmaceutical composition comprising an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or excipient.
[0011] In some embodiments, the present disclosure provides methods of using provided oligonucleotides. In some embodiments, the present disclosure provides a method for inhibiting ACVR2B expression or treating an ACVR2B related disorder in a subject, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0012] In some embodiments, the present disclosure provides a method of treating obesity in a subject in need thereof, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0013] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for weight loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0014] In some embodiments, the present disclosure provides a method of preserving muscle mass in a subject in need of treatment for weight loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0015] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for reduction of excess body weight or for maintenance of weight reduction, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0016] In some embodiments, the present disclosure provides a method of preserving muscle mass in a subject in need of treatment for reduction of excess body weight or for maintenance of weight reduction, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.Docket No.: SOUF-001-02WO
[0017] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for a reduction of major adverse cardiovascular events (e.g., cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke), the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmacal composition comprising an oligonucleotide described herein to the subject.
[0018] In some embodiments, the present disclosure provides a method of preserving muscle mass in a subject in need of treatment for a reduction of major adverse cardiovascular events (e.g., cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke), the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0019] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for type 2 diabetes, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0020] In some embodiments, the present disclosure provides a method of preserving muscle mass in a subject in need of treatment for type 2 diabetes, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0021] In some embodiments, the present disclosure provides a method of inhibiting ActRII (e.g., through inhibition of ACVR2B expression) in a subject experiencing weight loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.DETAILED DESCRIPTION
[0022] Provided herein are oligonucleotides for inhibiting the expression of Activin receptor 2B (“ACVR2B”). In some embodiments, the oligonucleotide comprises an antisense strand substantially complementary to a sequence encoding ACVR2B. In some embodiments, the antisense strand comprises at least 14 contiguous nucleotides (for example, 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 contiguousDocket No.: SOUF-001-02WO nucleotides) substantially complementary to the sequence of nucleotides encoding ACVR2B, with no more than 4 mismatched nucleotides.
[0023] The term “antisense strand” refers to an oligonucleotide having a nucleotide sequence substantially complementary to a target sequence in a transcript, e.g., an mRNA encoding ACVR2B. In embodiments wherein the oligonucleotide is an RNAi agent, the term antisense strand may be used interchangeably with the term “guide strand”. In some embodiments, an antisense strand disclosed herein is 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
[0024] The term “sense strand” refers to an oligonucleotide having a nucleotide sequence substantially complementary to an antisense strand, e.g., the antisense strand of an RNAi agent herein. The term “sense strand” may be used interchangeably with the term “passenger strand.” In some embodiments, a sense strand disclosed herein is 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. For example, each of the sense strands in Tables 1A-1C is 19 nucleotides in length and substantially complementary to the corresponding antisense strand shown in the same row.
[0025] As used herein, and unless otherwise indicated, the term “complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. In some embodiments, a duplex structure disclosed herein is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 base pairs in length.
[0026] The tenns “complementary”, “completely complementary” and “substantially complementary” herein can be used with respect to the base matching between the antisense strand of an oligonucleotide, e.g., an RNAi agent, and a target sequence, or between the sense strand and the antisense strand of an RNAi agent, as will be understood from the context of their use. Complementary sequences, e.g., between an antisense strand and a target sequence in a target transcript, or between the sense and antisense strand of an siRNA, include base-pairing of the oligonucleotide or polynucleotide comprising a first nucleotide sequence to an oligonucleotide or polynucleotide comprising a second nucleotide sequence over the entire length of one or both nucleotide sequences. Such sequences can be referred to as “completely complementary” with respect to each other when there are 0 mismatched base pairs upon hybridization of the two sequences. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be completely complementary, or theyDocket No.: SOUF-001-02WO can form one or more, but generally not more than 5, 4, 3, 2, or 1 mismatched base pairs upon hybridization for a duplex up to 30 base pairs, while retaining the ability to hybridize under the conditions most relevant to their ultimate application, e.g., inhibition of gene expression via a RNA-induced silencing complex (RISC) pathway. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, an siRNA comprising one oligonucleotide 21 nucleotides in length and another oligonucleotide 19 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 19 nucleotides that is fully complementary to the shorter oligonucleotide, can yet be referred to as “completely complementary” for the purposes described herein.
[0027] “Complementary” sequences, as used herein, can also include, or be formed entirely from, non-Watson-Crick base pairs or base pairs formed from non-natural and modified nucleotides, in so far as the above requirements with respect to their ability to hybridize are fulfilled. Such non- Watson-Crick base pairs include, but are not limited to, G:U Wobble or Hoogsteen base pairing.
[0028] If an RNA strand contains one or more thymidines (“T”s) in the sequence, the thymidines (“T”s) represent uridines (“U”s). For example, the nucleotide “T”, as used in the unmodified siRNAs sense and antisense strands in Table 1A, for example, SEQ ID NOS 494- 1227, 1297-1322, 1420-1520, 1522-1563, 1565-1599, 1721-1752, 1754-2065, 2068-2098, 2103- 2196, and 2198-2454, represents RNA uridine, and the corresponding RNA sense and antisense strands are listed in Table 1C.
[0029] In some embodiments, the present disclosure provides an oligonucleotide or RNAi agent, as described herein, or a pharmaceutically acceptable salt thereof. As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in, J. PHARMACEUTICAL SCIENCES, 1977, (66); 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the nucleic acids and analogues thereof of this disclosure include those derived from suitable inorganic and organic acids and bases. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(Ci-4alkyl)4 salts. In some embodiments, a pharmaceutically acceptable salt is the sodium salt. In some embodiments, a pharmaceutically acceptable salt is the potassium salt.Docket No.: SOUF-001-02WO
[0030] In some embodiments, the oligonucleotide comprises an antisense strand comprising at least 14 contiguous nucleotides (for example, 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 contiguous nucleotides) substantially complementary to a sequence of nucleotides within a transcript encoding ACVR2B. In some embodiments, the antisense strand has no more than 5 mismatched nucleotides to the sequence of nucleotides within the transcript encoding ACVR2B. In some embodiments, the antisense strand has no more than 4 mismatched nucleotides to the sequence of nucleotides within the transcript encoding ACVR2B. In some embodiments, the antisense strand has no more than 3 mismatched nucleotides to the sequence of nucleotides within the transcript encoding ACVR2B. In some embodiments, the antisense strand has no more than 2 mismatched nucleotides to the sequence of nucleotides within the transcript encoding ACVR2B. In some embodiments, the antisense strand has no more than 1 mismatched nucleotides to the sequence of nucleotides within the transcript encoding ACVR2B. In some embodiments, the antisense strand is completely complementary to the sequence of nucleotides within the transcript encoding ACVR2B (e.g., 0 mismatches).
[0031] ACVR2B is a single protein. Exemplary sequences encoding ACVR2B may be found, for example, at NCBI RefSeq ID NM_001106.4 (SEQ ID NO: 4932). In some embodiments, ACVR2B is encoded by a nucleotide sequence corresponding to the transcript having the NCBI RefSeq ID NM_001106.4 (SEQ ID NO: 4932).
[0032] In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 75% nucleotide sequence identity to SEQ ID NO: 4932. In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 80% nucleotide sequence identity to SEQ ID NO: 4932. In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 85% nucleotide sequence identity to SEQ ID NO: 4932. In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 90% nucleotide sequence identity to SEQ ID NO: 4932. In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 95% nucleotide sequence identity to SEQ ID NO: 4932. In some embodiments, the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 99% nucleotide sequence identity to SEQ ID NO: 4932.
[0033] In some embodiments, the antisense strand is substantially complementary to a sequence of nucleotides corresponding to an untranslated region of the ACVR2B transcript. In some embodiments, the antisense strand is substantially complementary to the sequence ofDocket No.: SOUF-001-02WO nucleotides corresponding to an untranslated region of the ACVR2B transcript with no more than 5, 4, 3, 2, 1 , or 0 mismatches. In some embodiments, the antisense strand is completely complementary to the sequence of nucleotides corresponding to an untranslated region of the ACVR2B transcript.RNAi Agents
[0034] In some embodiments, the oligonucleotide is an RNAi agent or RNAi trigger for inhibiting expression of ACVR2B. As used herein, an “RNAi agent” or “RNAi trigger” refers to an oligonucleotide molecule capable of inducing RNA interference (RNAi), which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. The RNAi agents disclosed herein include but are not limited to: short (or small) interfering RNAs (siRNAs), double stranded RNAs (dsRNA), micro RNAs (miRNAs), short hairpin RNAs (shRNA), and dicer substrates (e.g., DsiRNAs).
[0035] In some embodiments, the RNAi agent is a double stranded RNA molecule comprising an antisense strand and a sense strand that are complementary to one another and hybridize to form a duplex or double stranded region. One strand of the RNAi agent, the antisense strand or guide strand, includes a region of complementarity to a target sequence in ACVR2B. The other strand, the sense strand or passenger strand, includes a region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. In some embodiments, the double stranded RNA molecule may be formed by base pairing between two separate molecules of RNA (e.g., an antisense strand and a sense strand). In some embodiments, the double stranded RNA molecule is a self-complementary molecule formed by intramolecular base pairing between two separate regions of a single RNA molecule (e.g., an antisense region linked to a sense strand through an unpaired RNA linker forming a loop or hairpin loop).
[0036] Where the two strands are part of a self-complementary molecule, the connecting RNA chain is referred to as a “hairpin loop.” A hairpin loop can comprise at least one unpaired nucleotide. In some embodiments, the hairpin loop can comprise at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 23 or more unpaired nucleotides or nucleotides not directed to the target site of the dsRNA. In some embodiments, the haiipin loop can be 10 or fewer nucleotides. In some embodiments, the hairpin loop can be 8 or fewer unpaired nucleotides. In some embodiments, the hairpin loop can be 4-10 unpaired nucleotides. In some embodiments, the hairpin loop can be 4-8 nucleotides. In some embodiments, the hairpin loop canDocket No.: SOUF-001-02WO contain 1-4 oligoethyne glycols, including ethylene glycol, di ethylene glycol, triethylene glycol, tetraethylene glycol, hexaethylene glycol, or any combination thereof.
[0037] Where the two substantially complementary strands of a double stranded RNA molecule comprise separate RNA molecules, those molecules need not, but can be covalently connected. In certain embodiments, where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3 ’-end of one strand and the 5 ’-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker” (though it is noted that certain other structures defined elsewhere herein can also be referred to as a “linker”). The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the double stranded RNA molecule minus any overhangs that are present in the duplex.
[0038] In some embodiments, the RNAi agent is an siRNA.
[0039] In some embodiments, the RNAi agent is a shRNA.
[0040] In some embodiments, the RNAi agent is a dicer substrate (e.g., a Dicer-substrate siRNA).
[0041] In some embodiments, the sense and antisense strands of the dsRNA are each independently about 15 to about 30 nucleotides in length, or about 25 to about 30 nucleotides in length, e.g., each strand is independently between 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, 18-22, 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.
[0042] In some embodiments, the duplex structure is between 15 and 30 base pairs in length, e.g., between, 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, 18-22, 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 base pairs in length.
[0043] An RNAi agent as described herein can further include one or more single-stranded nucleotide overhangs, e.g., an overhang of 1, 2, 3, or 4 nucleotides. RNAi agent having at least one nucleotide overhang can have unexpectedly superior inhibitory properties relative to their blunt-ended counterparts. A nucleotide overhang can comprise or consist of a nucleotide / nucleoside analog, including a deoxynucleotide, an inverted deoxynucleotide or an inverted abasic nucleotide. The overhang(s) can be on the sense strand, the antisense strand or anyDocket No.: SOUF-001-02WO combination thereof. Furthermore, the nucleotide(s) of an overhang can be present on the 5'-end, 3’-end or both ends of either an antisense or sense strand of the RNAi agent. In certain embodiments, longer, extended overhangs are possible.
[0044] In some embodiments, the antisense strand is 21 nucleotides in length, and the sense strand is 19 nucleotides in length. In some embodiments, the antisense strand is 19 nucleotides in length, and the sense strand is 19 nucleotides in length.
[0045] The oligonucleotides disclosed herein may be unmodified or modified (e.g., chemically modified or conjugated). A modified oligonucleotide as disclosed herein comprises an identical nucleobase sequence as compared to a corresponding unmodified oligonucleotide, but further comprises one or more modifications as disclosed herein.
[0046] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) differing by no more than 4 nucleotides from any one of the antisense strands of Tables 1A-1C. In some embodiments, the antisense strand differs by no more than 3 nucleotides from any one of the antisense strands of Tables 1A-1C. In some embodiments, the antisense strand differs by no more than 2 nucleotides from any one of the antisense strands of Tables 1A-1C. In some embodiments, the antisense strand differs by no more than 1 nucleotide from any one of the antisense strands of Tables 1 A-1C. In some embodiments, the antisense strand comprises any one of the antisense strands of Tables 1A-1C. In some embodiments, the antisense strand consists of any one of the antisense strands of Tables 1A-1C.
[0047] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) differing by no more than 4 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand differs by no more than 3 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand differs by no more than 2 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand differs by no more than 1 nucleotide from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand consists of the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0048] In some embodiments, the antisense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%,Docket No.: SOUF-001-02WO96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the antisense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682- 4931.
[0049] In some embodiments, the antisense strand consists of a nucleotide sequence having the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0050] In some embodiments, the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) differing by no more than 4 nucleotides from any one of the sense strands of Tables 1A-1C. In some embodiments, the sense strand differs by no more than 3 nucleotides from any one of the sense strands of Tables 1A-1C. In some embodiments, the sense strand differs by no more than 2 nucleotides from any one of the sense strands of Tables 1 A-1C. In some embodiments, the sense strand differs by no more than 1 nucleotide from any one of the sense strands of Tables 1 A-1C. In some embodiments, the sense strand comprises any one of the sense strands of Tables 1 A-1C. In some embodiments, the sense strand consists of any one of the sense strands of Tables 1A-1C.
[0051] In some embodiments, the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the sense strand differs by no more than 3 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the sense strand differs by no more than 2 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the sense strand differs by no more than 1 nucleotide from the nucleotide sequence of any one of 1-1227 or 2455-3681. In some embodiments, the sense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the sense strand consists of the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0052] In some embodiments, the sense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the sense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (forDocket No.: SOUF-001-02WO example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0053] In some embodiments, the sense strand consists of a nucleotide sequence having the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0054] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides differing (for example, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) by no more than 4 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand comprises a nucleotide sequence at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides from the nucleotide sequence of any one of SEQ ID Nos: 1-1227 or 2455-3681.
[0055] In some embodiments, the antisense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0056] In some embodiments, the antisense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand comprises a nucleotide sequence having at least 90% nucleotide sequence identity (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide sequence identity) to the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0057] In some embodiments, the antisense strand consists of a nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand consists of a nucleotide sequence of any one of SEQ ID Nos: 1-1227 or 2455-3681.
[0058] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1237, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 10. In someDocket No.: SOUF-001-02WO embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1 , 2, 3, or 4 nucleotides) from SEQ ID NO: 1237, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 10. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1237, and the sense strand comprises the nucleotide sequence SEQ ID NO: 10. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1237, and the sense strand consists of the nucleotide sequence SEQ ID NO: 10.
[0059] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1339, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 112. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1339, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 112. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1339, and the sense strand comprises the nucleotide sequence SEQ ID NO: 112. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1339, and the sense strand consists of the nucleotide sequence SEQ ID NO: 112.
[0060] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1373, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 146. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1373, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 146. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1373, and the sense strand comprises the nucleotide sequence SEQ ID NO: 146. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1373, and the sense strand consists of the nucleotide sequence SEQ ID NO: 146.Docket No.: SOUF-001-02WO
[0061] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1454, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 227. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1454, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 227. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1454, and the sense strand comprises the nucleotide sequence SEQ ID NO: 227. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1454, and the sense strand consists of the nucleotide sequence SEQ ID NO: 227.
[0062] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1455, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 228. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1455, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 228. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1455, and the sense strand comprises the nucleotide sequence SEQ ID NO: 228. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1455, and the sense strand consists of the nucleotide sequence SEQ ID NO: 228.
[0063] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1456, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 229. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1456, and the sense strandDocket No.: SOUF-001-02WO comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 229. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1456, and the sense strand comprises the nucleotide sequence SEQ ID NO: 229. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1456, and the sense strand consists of the nucleotide sequence SEQ ID NO: 229.
[0064] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1458, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 231. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1458, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 231. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1458, and the sense strand comprises the nucleotide sequence SEQ ID NO: 231. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1458, and the sense strand consists of the nucleotide sequence SEQ ID NO: 231.
[0065] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1600, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 373. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1600, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 373. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1600, and the sense strand comprises the nucleotide sequence SEQ ID NO: 373. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1600, and the sense strand consists of the nucleotide sequence SEQ ID NO: 373.
[0066] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) fromDocket No.: SOUF-001-02WOSEQ ID NO: 1605, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 378. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1605, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 378. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1605, and the sense strand comprises the nucleotide sequence SEQ ID NO: 378. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1605, and the sense strand consists of the nucleotide sequence SEQ ID NO: 378.
[0067] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1613, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 386. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1613, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 386. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1613, and the sense strand comprises the nucleotide sequence SEQ ID NO: 386. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1613, and the sense strand consists of the nucleotide sequence SEQ ID NO: 386.
[0068] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1617, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 390. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1617, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 390. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1617, and the sense strand comprises the nucleotide sequenceDocket No.: SOUF-001-02WOSEQ ID NO: 390. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1617, and the sense strand consists of the nucleotide sequence SEQ ID NO: 390.
[0069] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1618, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 391. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1618, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 391. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1618, and the sense strand comprises the nucleotide sequence SEQ ID NO: 391. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1618, and the sense strand consists of the nucleotide sequence SEQ ID NO: 391.
[0070] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1619, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 392. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1619, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 392. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1619, and the sense strand comprises the nucleotide sequence SEQ ID NO: 392. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1619, and the sense strand consists of the nucleotide sequence SEQ ID NO: 392.
[0071] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1659, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 432. In someDocket No.: SOUF-001-02WO embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1 , 2, 3, or 4 nucleotides) from SEQ ID NO: 1659, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 432. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1659, and the sense strand comprises the nucleotide sequence SEQ ID NO: 432. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1659, and the sense strand consists of the nucleotide sequence SEQ ID NO: 432.
[0072] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1672, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 445. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1672, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 445. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1672, and the sense strand comprises the nucleotide sequence SEQ ID NO: 445. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1672, and the sense strand consists of the nucleotide sequence SEQ ID NO: 445.
[0073] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1673, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 446. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1673, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 446. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1673, and the sense strand comprises the nucleotide sequence SEQ ID NO: 446. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1673, and the sense strand consists of the nucleotide sequence SEQ ID NO: 446.Docket No.: SOUF-001-02WO
[0074] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1675, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 448. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1675, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 448. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1675, and the sense strand comprises the nucleotide sequence SEQ ID NO: 448. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1675, and the sense strand consists of the nucleotide sequence SEQ ID NO: 448.
[0075] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1676, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 449. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1676, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 449. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1676, and the sense strand comprises the nucleotide sequence SEQ ID NO: 449. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1676, and the sense strand consists of the nucleotide sequence SEQ ID NO: 449.
[0076] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1821, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 594. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1821, and the sense strandDocket No.: SOUF-001-02WO comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 594. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1821, and the sense strand comprises the nucleotide sequence SEQ ID NO: 594. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1821, and the sense strand consists of the nucleotide sequence SEQ ID NO: 594.
[0077] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1834, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 607. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1834, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 607. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1834, and the sense strand comprises the nucleotide sequence SEQ ID NO: 607. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1834, and the sense strand consists of the nucleotide sequence SEQ ID NO: 607.
[0078] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1839, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 615. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1839, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 615. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1839, and the sense strand comprises the nucleotide sequence SEQ ID NO: 615. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1839, and the sense strand consists of the nucleotide sequence SEQ ID NO: 615.
[0079] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) fromDocket No.: SOUF-001-02WOSEQ ID NO: 1840, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 616. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1840, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 616. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1840, and the sense strand comprises the nucleotide sequence SEQ ID NO: 616. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1840, and the sense strand consists of the nucleotide sequence SEQ ID NO: 616.
[0080] In some embodiments, the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1841, and the sense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, or 19 contiguous nucleotides) differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 617. In some embodiments, the antisense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 1841, and the sense strand comprises a nucleotide sequence differing by no more than 4 nucleotides (for example, 1, 2, 3, or 4 nucleotides) from SEQ ID NO: 617. In some embodiments, the antisense strand comprises the nucleotide sequence SEQ ID NO: 1841, and the sense strand comprises the nucleotide sequence SEQ ID NO: 617. In some embodiments, the antisense strand consists of the nucleotide sequence SEQ ID NO: 1841, and the sense strand consists of the nucleotide sequence SEQ ID NO: 617.
[0081] An ACVR2B RNAi agent described herein can contain one or more mismatches to the target sequence (e.g., a sequence of between 15 and 30 nucleotides in length). In some embodiment, an ACVR2B RNAi agent as described herein contains no more than 4 mismatches (e.g., no more than 4, 3, 2, 1, or 0 mismatches to the target sequence). If the antisense strand of the RNAi agent contains mismatches to a target sequence, it may be preferable that the area of mismatch is not located in the center of the region of complementarity. If the antisense strand of the RNAi agent contains mismatches to the target sequence, it may be preferable that the mismatch be restricted to be within the last 5 nucleotides from either the 5’- or 3 ’-end of the region of complementarity. For example, for a 21 nucleotide RNAi agent, the strand, which is complementary to a region of, e.g., ACVR2B, generally does not contain any mismatch within the central 11 nucleotides. The methods described herein or methods known in the art can be used toDocket No.: SOUF-001-02WO determine whether an RNAi agent containing a mismatch to a target sequence is effective in inhibiting the expression of ACVR2B. Consideration of the efficacy of RNAi agents with mismatches in inhibiting expression of a target gene is important, especially if the particular region of complementarity in a target gene is known to have polymorphic sequence variation within the population.
[0082] In some embodiments, any one of the RNAi agents described herein can reduce expression levels of ACVR2B. In some embodiments, reduction in expression levels is assayed using an RT-qPCR assay to perform relative quantification of ACVR2B mRNA in HEK-293 cell line. The skilled artisan will appreciate that various approaches to quantify knockdown of ACVR2B expression for assessing RNAi agent activity may be used in the art, including commercially available kits, e.g., from Thermo. In some embodiments, any one of the RNAi agents described herein can reduce expression levels of an ACVR2B mRNA when assayed in cultured cells. Any suitable cells known in the art may be used to assess the RNAi agents. In some embodiments, the cultured cells are HEK-293 cells. In some embodiments, administration of any one of the RNAi agents disclosed herein to a cultured cell results in a reduction in expression level of an ACVR2B. In some embodiments, administration of the RNAi agent results in at least a 55% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 60% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 65% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 70% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 75% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least an 80% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least an 85% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 90% reduction in expression levels of the ACVR2B mRNA. In some embodiments, administration of the RNAi agent results in at least a 95% reduction in expression levels of the ACVR2B mRNA.Single-stranded antisense oligonucleotides
[0083] In some embodiments, the oligonucleotide is a single-stranded antisense oligonucleotide, or “ASO.” ASOs comprise an antisense strand with at least partial complementary to a target sequence in an RNA. Upon binding to a target sequence, downregulation of the RNADocket No.: SOUF-001-02WO may be achieved through various mechanisms, including, but not limited to, sterically blocking translation or recruitment of RNase H.
[0084] In some embodiments, the ASO comprises a nucleic acid sequence of at least 14 contiguous nucleotides (for example, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) that differ by no more than 1, 2, 3, or 4 nucleotides from any one of SEQ ID NOs: 1228-2454 or 3682- 4931. In some embodiments, the ASO comprises a nucleic acid sequence of at least 14 contiguous nucleotides that differ by no more than 1, 2, 3, or 4 nucleotides from any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the ASO comprises a nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0085] In some embodiments, the ASO comprises 2'-deoxy ribonucleotides and phosphorothioate intemucleoside linkages.
[0086] In some embodiments, the ASO is a “gapmer” ASO comprising a 2'-deoxy "gap" region flanked by "wings" having nucleotides with 2'-modified ribonucleotides. In some embodiments, the ASO is an "MOE gapmer" in which the 2'-modified ribonucleotide is a 2'-O- methoxyethyl (2’-M0E or simply MOE) modification, and each of the internucleoside linkages is a phosphorothioate.Modified Nucleotides
[0087] The oligonucleotides disclosed herein may be modified or unmodified. In some embodiments, any one of the oligonucleotides contain one or more modifications. As used herein, a modification to a nucleotide or “modified nucleotide” refers to any nucleotide other than the canonical ribonucleotides adenine, guanine, cytosine, and uracil.
[0088] In some embodiments, the oligonucleotide comprises one or more modified nucleotides. In some embodiments, no more than 1, 2, 3, 4, or 5 of the nucleotides of the oligonucleotide are unmodified nucleotides. In some embodiments, all nucleotides of the oligonucleotide are modified nucleotides.
[0089] In some embodiments, wherein the oligonucleotide is an RNAi agent, the antisense strand comprises one or more modified nucleotides. In some embodiments, no more than 1, 2, 3, 4, or 5 of the nucleotides of the antisense strand are unmodified nucleotides. In some embodiments, all nucleotides of the antisense strand are modified nucleotides.
[0090] In some embodiments, wherein the oligonucleotide is an RNAi agent, the sense strand comprises one or more modified nucleotides. In some embodiments, no more than I, 2, 3, 4, or 5 of the nucleotides of the sense strand are unmodified nucleotides. In some embodiments, all nucleotides of the sense strand are modified nucleotides.Docket No.: SOUF-001-02WO
[0091] Modified nucleotides include, but are not limited to 2'-modified nucleotides, 3' to 3’ linkages (inverted) nucleotides, bridged nucleotides, 2',3'-seco nucleotide mimics (e.g., unlocked nucleobase analogues (UNAs), locked nucleotides (LNAs), 5'-(S)-methyl-2’-deoxy-2’- fluoronucleotide (5’Me-Nf), vinyl phosphonate deoxyribonucleotides, vinyl phosphonate nucleotides, a nucleotide comprising a 5'-phosphorothioate group, a nucleotide comprising a 5'- methylphosphonate group, a nucleotide comprising a 5’ phosphate or 5’ phosphate mimic and N- (methane sulfonyl) phosphoramidate group. In some embodiments, 2'-modified nucleotides (e.g., a nucleotide with a group other than a hydroxyl group at the 2' position of the five-membered sugar ring) include, but are not limited to, 2'-O-methyl nucleotides (represented herein as a lower case letter n in a nucleotide sequence), 2'-deoxy-2'-fluoro nucleotides (represented herein as Nf, also represented herein as 2'-fluoro nucleotide). In some embodiments, a modified nucleotide is a nucleotide comprising a 5'-methylphosphate group.
[0092] In some embodiments, modified nucleotides include, but are not limited to, deoxyribonucleotides, nucleotide mimics, abasic nucleotides, 5' to 5' linkages (inverted) nucleotides, non-natural base-comprising nucleotides, peptide nucleic acids (PNAs), 3'-O- methoxy (2’ intemucleoside linked) nucleotides, 2’-deoxy-2’-fluoro-arabino nucleotides, cyclopropyl phosphonate nucleotides (cPrpN), vinyl phosphonate 2’ -(methoxyethyl) unlocked nucleotides, a nucleotide comprising 2-hydroxymethyl-tetrahydrofurane-5-phosphate, 2'-deoxy nucleotides (represented herein as dN), 2'-methoxy ethyloxy (2'-O-(2-methoxylethyl)) nucleotides, 2’-amino nucleotides, and 2'-alkyl nucleotides. It is not necessary for all positions in a given compound to be uniformly modified. Conversely, more than one modification may be incorporated in a single oligonucleotide. Modification at one nucleotide is independent of modification at another nucleotide.
[0093] In some embodiments, the nucleotide modification comprises a deoxyribonucleotide, a 3 ’-terminal deoxythymidine (dT) nucleotide, an abasic nucleotide, a 2'- modified nucleotide, a 3' to 3' linkages (inverted) nucleotide, a 5' to 5' linkages (inverted) nucleotide, a non-natural base-comprising nucleotide, a nucleotide comprising a 5'- phosphorothioate group, a nucleotide comprising a 5'-methylphosphonate group, a nucleotide comprising a 5’ phosphate or 5’ phosphate mimic, a nucleotide comprising 2-hydroxymethyl- tetrahydrofurane-5-phosphate, or a nucleotide comprising a N-( methane sulfonyl) phosphoramidate group. In some embodiments, the nucleotide modification comprises a nucleotide comprising a 5'-methylphosphate group.
[0094] In some embodiments, the one or more modifications are selected from a ribose modification, a backbone modification, a nucleobase modification, or a combination thereof. InDocket No.: SOUF-001-02WO some embodiments, the one or more modifications is a combination of a ribose modification, a backbone modification, and / or a nucleobase modification.
[0095] In some embodiments, the oligonucleotide comprises one or more nucleobase modifications. Nucleobase modifications include, for example, synthetic and natural nucleobases, such as 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, (e.g., 2-aminopropyladenine, 5-propynyluracil, or 5-propynylcytosine), 5-methylcytosine (5-me- C), 5 -hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-alkyl (e.g., 6-methyl,6-ethyl, 6-isopropyl, or 6-n-butyl) derivatives of adenine and guanine, 2-alkyl (e.g., 2-methyl, 2- ethyl, 2-isopropyl, or 2-n-butyl) and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine, 2-thiocytosine, 5-halouracil, cytosine, 5-propynyl uracil, 5-propynyl cytosine, 6- azo uracil, 6-azo cytosine, 6-azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-sulfhydryl, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo (e.g., 5-bromo), 5 -trifluoromethyl, and other 5-substituted uracils and cytosines, 7-methylguanine and7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine, 7 -deazaadenine, 3- deazaguanine, and 3 -deazaadenine, or combinations thereof.
[0096] In some embodiments, the oligonucleotide comprises one or more backbone modification or non-standard linkages (e.g., modified internucleoside linkages). In some embodiments, a backbone modification is a non-phosphate-containing covalent intemucleoside linkage. Modified intemucleoside linkages or backbones include, but are not limited to, 5’- phosphorothioate groups (represented herein as a lower case “s”), chiral phosphorothioates, thiophosphates, phosphorodithioates, phosphotriesters, aminoalkyl-phosphotriesters, alkyl phosphonates (e.g., methyl phosphonates or 3'-alkylene phosphonates), chiral phosphonates, phosphinates, phosphoramidates (e.g., 3'-amino phosphoramidate, aminoalky Iphosphoramidates, or thionophosphoramidates), thionoalkyl-phosphonates, thionoalkylphosphotriesters, morpholino linkages, boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of boranophosphates, or boranophosphates having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2' -5' to 5'-2'. In some embodiments, a modified backbone or modified intemucleoside linkage lacks a phosphorus atom. Modified intemucleoside linkages lacking a phosphorus atom include, but are not limited to, short chain alkyl or cycloalkyl intersugar linkages, mixed heteroatom and alkyl or cycloalkyl inter-sugar linkages, or one or more short chain heteroatomic or heterocyclic inter-sugar linkages. In some embodiments, modified intemucleoside backbones include, but are not limited to, siloxane backbones, sulfide backbones, sulfoxide backbones, sulfone backbones, formacetyl and thioformacetyl backbones, methylene formacetyl and thioform acetyl backbones, alkene-containing backbones, sulfamate backbones,Docket No.: SOUF-001-02WO methyieneimino and methylenehydrazino backbones, sulfonate and sulfonamide backbones, amide backbones, and other backbones having mixed N, O, S, and CH2 components.
[0097] In some embodiments, the backbone modification comprises phosphorothioate.
[0098] In some embodiments, any one of the oligonucleotides disclosed herein further comprise a sequence of 3 ’-terminal deoxythymidine (dT) nucleotides. In some embodiments, any one of the antisense strands described herein further comprises at least one terminal dT nucleotide. In some embodiments, any one of the antisense strands described herein further comprises 2 or more terminal dT nucleotides, e.g., 2, 3, 4, or more terminal dT nucleotides. In some embodiments, wherein the oligonucleotide is an RNAi agent, any one of the sense strands described herein further comprises at least one terminal dT nucleotide. In some embodiments, any one of the sense strands described herein further comprises 2 or more terminal dT nucleotides, e.g. , 2, 3, 4, or more terminal dT nucleotides. In some embodiments, the antisense and sense strand of an RNAi agent herein each contain one or more terminal dT nucleotides.
[0099] In some embodiments, any one of the oligonucleotides disclosed herein further comprises at least one phosphorothioate internucleoside or phosphorodithioate intemucleoside linkage. In some embodiments, any one of the oligonucleotides disclosed herein further comprises at least one phosphorothioate internucleoside linkage. In some embodiments, at least one phosphorothioate intemucleoside linkage is at the 5’ end of the antisense strand. In some embodiments, the oligonucleotide comprises at least 2 phosphorothioate intemucleoside linkages at the 5’ end of the antisense strand. In some embodiments, at least one phosphorothioate intemucleoside linkage is at the 3’ end of the antisense strand. In some embodiments, the oligonucleotide comprises at least 2 phosphorothioate intemucleoside linkages at the 3’ end of the antisense strand. In some embodiments, wherein the oligonucleotide is an RNAi agent, the at least one phosphorothioate intemucleoside linkage is at the 5’ end of the sense strand. In some embodiments, the oligonucleotide comprises at least 2 phosphorothioate intemucleoside linkages at the 5’ end of the sense strand. In some embodiments, the at least one phosphorothioate intemucleoside linkage is at the 3’ end of the sense strand. In some embodiments, the oligonucleotide comprises at least 2 phosphorothioate intemucleoside linkages at the 3’ end of the sense strand.
[0100] In some embodiments, any one of the oligonucleotides disclosed herein further comprises a terminal, chiral modification. In some embodiments, the terminal chiral modification is at the first intemucleoside linkage at the 3’ end of the sense and / or antisense strand. In some embodiments, the terminal chiral modification is at the first and second intemucleoside linkage at the 3’ end of the sense and / or antisense strand. In some embodiments, the chiral modificationDocket No.: SOUF-001-02WO comprises a phosphorus atom of the intemucleoside linkage being in either Rp or Sp configuration. In some embodiments, the siRNA agent further comprises a terminal, chiral modification occurring at the first intemucleoside linkage at the 3’ end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the sense strand, having the linkage phosphoms atom in either Rp configuration or Sp configuration. In some embodiments, the siRNA agent further comprises a terminal, chiral modification occurring at the first and second intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphoms atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the antisense strand, having the linkage phosphoms atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5' end of the sense strand, having the linkage phosphoms atom in either Rp or Sp configuration. In some embodiments, the siRNA agent further comprises a terminal, chiral modification occurring at the first, second, and third intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphoms atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the antisense strand, having the linkage phosphoms atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the sense strand, having the linkage phosphoms atom in either Rp or Sp configuration. In some embodiments, the siRNA agent further comprises a terminal, chiral modification occurring at the first and second intemucleoside linkages at the 3" end of the antisense strand, having the linkage phosphoms atom in Sp configuration, a terminal, chiral modification occurring at the third intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphoms atom in Rp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the antisense strand, having the linkage phosphoms atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ end of the sense strand, having the linkage phosphoms atom in either Rp or Sp configuration. In some embodiments, the siRNA agent further comprises a terminal, chiral modification occurring at the first and second intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphoms atom in Sp configuration, a terminal, chiral modification occurring at the first and second intemucleoside linkages at the 5’ end of the antisense strand, having the linkage phosphoms atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleosideDocket No.: SOUF-001-02WO linkage at the 5’ end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
[0101] In some embodiments, any one of the oligonucleotides disclosed herein further comprises a phosphate or phosphate mimic at the 5’-end of the antisense strand. In some embodiments, a phosphate or phosphate mimic at the 5 ’-end of the antisense strand is a 5 ’-vinyl phosphonate (VP).RNAi Agent Modification Motifs
[0102] In some embodiments, any one of the antisense or sense strands disclosed herein are modified according to a modification motif or pattern.
[0103] In some embodiments, an antisense strand disclosed herein comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2'-O-methyl- nucleoside-3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0104] In some embodiments, an antisense strand disclosed herein comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'- vinylphosphonate-2'-O-methyl-uridine-3’-phosphorothioate; ns is a 2'-O-methyl-nucleoside-3'- phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl- nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0105] In some embodiments, a sense strand disclosed herein comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, wherein ns is a 2'-O-methyl-nucleoside-3'- phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro- nucleoside-3'-phosphate.
[0106] In some embodiments, a sense strand disclosed herein comprises a modification pattern NfsnsNfnNfnNfnNfnNfnNfnNfnNfnNf, wherein ns is a 2'-O-methyl-nucleoside-3'- phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl- nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0107] In some embodiments, an RNAi agent disclosed herein comprises a sense strand and an antisense strand, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2'-O-methyl-nucleoside-3'- phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl- nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3’-phosphate.Docket No.: SOUF-001-02WO
[0108] In some embodiments, an RNAi agent disclosed herein comprises a sense strand and an antisense strand, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'-vinylphosphonate-2'-O-methyl- uridine-3’-phosphorothioate; ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; Nfs is a 2'- deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl-nucleoside-3’-phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0109] In some embodiments, a strand of an RNAi agent comprises a modification pattern according to Nfsa(nNf)bnscn, wherein n is a 2'-O-methyl-nucleoside-3’ -phosphate; Nfs is a 2'- deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphate; and ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; and wherein a is at least 1, b is 5-10, and c is at least 1. In some embodiments, a is at least 2, b is at least 8, and c is at least 2. In some embodiments, a is 2, b is 8, and c is 2. In some embodiments, the strand of the RNAi agent comprises the modification pattern NfsNfsnNfnNfnNfnNfnNfnNfnNfnNfnsnsn. In some embodiments, the strand is the antisense strand. In some embodiments, the antisense strand comprises the sequence of any one of SEQ ID Nos: 1228-2454 or 3682-4931. In some embodiments, the strand is the sense strand. In some embodiments, the sense strand comprises the sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0110] In some embodiments, a strand of an RNAi agent comprises a modification pattern according to nSd(Nfn)eNf, wherein n is a 2'-O-methyl-nucleoside-3’ -phosphate; Nf is a 2'-deoxy- 2'-fhioro-nucleoside-3'-phosphate; and ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; and wherein d is at least 1, and e is 5-10. In some embodiments, d is at least 2 and e is at least 8. In some embodiments, the RNAi agent comprises the modification pattern nsnsNfnNfnNfnNfnNfnNfnNfnNfnNf. In some embodiments, the strand is the sense strand. In some embodiments, the sense strand comprises the sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681. In some embodiments, the RNAi agent comprises the modification pattern nsnsNfnNfnNfnNfnNfnNfnNfnNfnNfnsn. In some embodiments, the strand is the antisense strand. In some embodiments, the antisense strand comprises the sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0111] In some embodiments, the antisense strand comprises a modification pattern according to Nfsa(nNf)bnscn, wherein n is a 2'-O-methyl-nucleoside-3’ -phosphate; Nfs is a 2'- deoxy-2'-fhioro-nucleoside-3'-phosphorothioate; Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphate; and ns is a 2’-O-methyl-nucleoside-3'-phosphorothioate; and wherein a is at least 1 , b is 5-10, and c is at least 1, and the sense strand comprises a modification pattern according toDocket No.: SOUF-001-02WO nsd(Nfn)eNf, wherein n is a 2'-O-methyl-nucleoside-3’ -phosphate; Nf is a 2'-deoxy-2'-fluoro- nucleoside-3’-phosphate; and ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; and wherein d is at least 1, and e is 5-10. In some embodiments, the antisense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 1228-2454 or 3682-4931. In some embodiments, the sense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0112] In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4909, and the sense strand comprises or consists of SEQ ID NO: 2464. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4910, and the sense strand comprises or consists of SEQ ID NO: 2566. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4911, and the sense strand comprises or consists of SEQ ID NO: 2600. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4912, and the sense strand comprises or consists of SEQ ID NO: 2681. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4913, and the sense strand comprises or consists of SEQ ID NO: 2682. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4914, and the sense strand comprises or consists of SEQ ID NO: 2683. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4915, and the sense strand comprises or consists of SEQ ID NO: 2685. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4916, and the sense strand comprises or consists of SEQ ID NO: 2827. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4917, and the sense strand comprises or consists of SEQ ID NO: 2832. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4918, and the sense strand comprises or consists of SEQ ID NO: 2840. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4919, and the sense strand comprises or consists of SEQ ID NO: 2844. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4920, and the sense strand comprises or consists of SEQ ID NO: 2845. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4921, and the sense strand comprises or consists of SEQ ID NO: 2846. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4922, and the sense strand comprises or consists of SEQ ID NO: 2886. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4923, and the sense strand comprises or consists of SEQ ID NO: 2899. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4924, and the sense strand comprises or consists of SEQ ID NO: 2900. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4925, and the sense strand comprises or consists of SEQ ID NO: 2902. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4926, and the sense strandDocket No.: SOUF-001-02WO comprises or consists of SEQ ID NO: 2903. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4927, and the sense strand comprises or consists of SEQ ID NO: 3048. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4928, and the sense strand comprises or consists of SEQ ID NO: 3061. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4929, and the sense strand comprises or consists of SEQ ID NO: 3066. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4930, and the sense strand comprises or consists of SEQ ID NO: 3067. In some embodiments, the antisense strand comprises or consists of SEQ ID NO: 4931, and the sense strand comprises or consists of SEQ ID NO: 3068.
[0113] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand comprises the motif F(SF)nSnn, wherein n is from 2 to about 20, nn is 0 or 1, one of F and S is a 2'-deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O-methyl modified nucleoside. In some embodiments, each of the antisense and the sense strand is 17-23 nucleotides in length. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0114] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand comprises the chemical modification pattern of nNfnnnNfnNfNfnnnnNfnNfnnnnn and the sense strand comprises the chemical modification nnnnnnNfnNfNfNfnnnnnnnn, wherein n is a 2’-O-methyl-nucleoside and Nf is a 2’-deoxy-2’- fluoro-nucleoside. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence of any one according to SEQ ID NOs: 1-1227.
[0115] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand comprises a region having the formula XI -Y- X2, wherein Y is a subregion of from about 5 to about 12 linked nucleosides and each of XI subregion and X2 subregion is, independently, a plurality of linked nucleosides having the formula FSFS, where one of F and S is a 2'-deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O-methyl modified nucleoside; and each intemucleoside linkage of said XI subregion and X2 subregion is, independently, a phosphodiester or a phosphorothioate intemucleoside linkage. In some embodiments, each of the antisense and the sense strand is 20-23 nucleotides in length. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequenceDocket No.: SOUF-001-02WO according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0116] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand comprises a contiguous sequence of linked nucleosides that define an alternating motif of the formula: 5'-Q(-L-Z-L-Q)n(-L-Z)nn-3', wherein: each L is an intemucleoside linking group; either each Q is a 2'-deoxy-2’ -fluoro nucleoside and each Z is a 2'-O-methyl nucleoside; or each Q is a 2'-O-methyl nucleoside and each Z is a 2'- deoxy-2’ -fluoro nucleoside; and n is from 8 to 14 and nn is 0 or 1. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454.
[0117] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand is represented by the formula:wherein, B l', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA; Tl', T2', and T3' each independently represent a nucleotide comprising a chemical modification selected from the group consisting of DNA, RNA, LNA, 2’ -deoxy-2’ -fluoronucleotide, and 5'-(S)-methyl-2’ -deoxy-2’ -fluoronucleotide; ql is 4 to 15 nucleotides in length; q3 or q7 is independently 1-6 nucleotide(s) in length; q2 or q6 is independently 1-3 nucleotide(s) in length; q4 is 0-3 nucleotide(s) in length; and q5 is 0-10 nucleotide(s) in length; and wherein the antisense strand has 2’ -deoxy-2’ -fluoro modifications, and wherein the 2’ -deoxy-2’ -fluoro modifications on the antisense strand consist of four, and only four, 2’ -deoxy-2’ -fluoro modifications, or six, and only six, 2’ -deoxy-2’ -fluoro modifications. In some embodiments, the antisense strand is 19-25 nucleotides in length. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0118] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand and the sense strand are represented by the formula:Docket No.: SOUF-001-02WO riwherein Bl, Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA; Cl is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugar modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand; IT, T2', and T3' each independently represent a nucleotide comprising a modification providing the nucleotide a steric bulk that is less than or equal to the steric bulk of a 2'-0Me modification, wherein the modification is at the 2'-position of a ribose sugar of the nucleotide or at a position of a non-ribose nucleotide similar to the 2'- position of a ribose sugar; each nl, and ql is independently 4 to 15 nucleotides in length; each q3, and q7 is independently 1-6 nucleotide(s) in length; each q2 and q6 is independently 1-3 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4, and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length, and T1 each are 2’-deoxy-2’- fluoronucleotides; n3 is 7 nucleotides in length, and B2 each are 2'-0Me nucleotides; and n5 is 3 nucleotides in length, and B3 each are 2'-0Me nucleotides. In some embodiments, wherein the antisense strand and sense strand are each 14 to 40 nucleotides. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0119] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand is represented by the formula:Docket No.: SOUF-001-02WO(Is)wherein: B l, B2, and B3 each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'-substituted alkyl, 2'- halo, ENA, and BNA / LNA; Cl is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugar modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand; T1 represents a nucleotide comprising a 2’ -deoxy-2’ -fluoro modification; nl or n3 is independently 4 to 15 nucleotides in length; n5 is 1-6 nucleotide(s) in length; n2 is 3; n4 is 0-3 nucleotide(s) in length; and wherein the sense strand has 2’ -deoxy-2’ -fluoro modifications, and wherein the 2’-deoxy-2’-fluoro modifications on the sense strand consist of four, and only four, 2’ -deoxy-2’ -fluoro modifications, wherein the four 2’ -deoxy-2’ -fluoro modifications are at positions 7 and 9-11 from the 5'-end of the sense strand. In some embodiments, wherein the antisense strand and sense strand are each 19-25 nucleotides. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0120] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand is complementary to at least one portion of a mRNA of the target gene (e.g., ACVR2B), wherein the oligonucleotide is represented by the formula:wherein: Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-0 -methyl and 2’ -deoxy-2’ -fluoro; each Bl, B2, and B3 is 2'-0Me; Cl is glycerol nucleic acid (GNA) placed at a site opposite to the seed region (positions 2-8) of the antisense strand; Tl', T2', and T3' are each 2’-deoxy-2’-Docket No.: SOUF-001-02WO fluoronucleotides, wherein: IT is at position 14 from the 5' end of the antisense strand, and q2 is 1 ; and T3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1 ; each nl , n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length, and T1 each are 2’ -deoxy-2’ -fluoro nucleotides, and wherein (a) the oligonucleotide is covalently conjugated to at least one ligand; and (b) one of the Tl nucleotides is at position 11 from the 5' end of the sense strand. In some embodiments, the sense strand comprises 19-22 nucleotides and the antisense strand comprises 19-25 nucleotides. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0121] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the oligonucleotide is represented by the formula:(I)wherein B l', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-methyl and 2’ -deoxy-2’ -fluoro; each Bl, B2, and B3 is 2'-0me nucleotides; Cl is glycerol nucleic acid (GNA) placed at a site opposite to the seed region (positions 2-8) of the antisense strand; IT, T2', and T3' are each 2’-deoxy-2’- fluoro nucleotides, wherein: Tl' is at position 14 from the 5' end of the antisense strand, and q2 is 1; and T3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1; each nl, n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length, and Tl each are 2’ -deoxy-2’ -fluoro nucleotides, and wherein (a) the oligonucleotide is covalently conjugated to at least one ligand: and (b) one of the Tl nucleotides is at a position in the sense strand that is opposite to position 11 from the 5' end of the antisense strand; and (c) the oligonucleotide comprises at least one phosphorothioate intemucleoside linkage. In some embodiments, the sense strand comprises 19-Docket No.: SOUF-001-02WO22 nucleotides and the antisense strand comprises 19-25 nucleotides. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.
[0122] In some embodiments, any one of the RNAi agents disclosed herein comprises a modification pattern wherein the antisense strand has sufficient complementarity to a target sequence to mediate RNA interference, wherein said sense strand comprises at least one thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5' region of the antisense strand or a precursor thereof, wherein the antisense strand further comprises one or both of the following characteristics: (i) 2, 3, 4, 5 or 6 2'-deoxy-2'-fluoro modifications: and (ii) 1, 2, 3, 4 or 5 phosphorothioate intemucleoside linkages; and said sense strand comprises one or both of the following characteristics: (iii) 2, 3, 4, or 5 2'-deoxy-2'-fluoro modifications; and (iv) 1, 2, 3, 4 or 5 phosphorothioate internucleoside linkages. In some embodiments, the antisense strand and sense strand are each 14 to 40 nucleotides. In some embodiments, the antisense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1228-2454. In some embodiments, the sense strand corresponds to the unmodified nucleobase sequence according to any one of SEQ ID NOs: 1-1227.Pharmaceutical Compositions
[0123] The present disclosure also includes pharmaceutical compositions and formulations comprising the oligonucleotides (e.g., an RNAi agent or ASO) described herein, or a pharmaceutically acceptable salt thereof. In one embodiment, provided herein are pharmaceutical compositions comprising an oligonucleotide (e.g., an RNAi agent or ASO), as described herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or excipient. The pharmaceutical compositions comprising the oligonucleotides described herein are useful for treating or preventing a condition or symptoms associated with ACVR2B expression. Such pharmaceutical compositions are formulated based on the mode of delivery. One example is compositions that are formulated for systemic administration via parenteral delivery, e.g., by subcutaneous (SC), intramuscular (IM), or intravenous (IV) delivery. In some embodiments, an oligonucleotide is formulated in buffer solutions such as phosphate-buffered saline solutions, liposomes, micellar structures, and capsids. In some embodiments, naked oligonucleotides or conjugates thereof are formulated in water or in an aqueous solution (e.g., water with pH adjustments). In some embodiments, naked oligonucleotides or conjugates thereof are formulatedDocket No.: SOUF-001-02WO in basic buffered aqueous solutions (e.g., PBS). The pharmaceutical compositions of the invention may be administered in dosages sufficient to inhibit expression of the target gene.
[0124] A “pharmaceutically acceptable carrier or excipient” is a pharmaceutically acceptable solvent, suspending agent, or any other pharmacologically inert vehicle for delivering one or more oligonucleotides to a subject. The excipient can be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with the oligonucleotide and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, com starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).
[0125] In some embodiments, the present disclosure also includes a pharmaceutical composition suitable for injectable use, which comprises sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. For intravenous or subcutaneous administration, suitable carriers include physiological saline, bacteriostatic water, CREMOPHOR EL® (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. In many cases, it will be preferable to include 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.
[0126] Formulations for topical administration of oligonucleotides can include sterile and non- sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the oligonucleotides in liquid or solid oil bases. The solutions can also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present disclosure. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethyleneDocket No.: SOUF-001-02WO glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.
[0127] In some embodiments, the oligonucleotides herein are conjugated to one or more non- nucleotide groups including, but not limited to, a targeting group / targeting moiety, linking group, delivery polymer, or a delivery vehicle. The non-nucleotide group can enhance targeting, delivery, or attachment of the oligonucleotide.
[0128] In some embodiments, at least one nucleotide of the oligonucleotide herein is conjugated to one or more targeting ligands, such as a carbohydrate, amino sugar, cholesterol, polypeptide, or lipid. Exemplary targeting ligands include, but are not limited to, thyrotropin, melanotropin, lectin, a glycoprotein, surfactant protein A, mucin carbohydrate, a multivalent lactose moiety, a multivalent galactose moiety, a N-acetylgalactosamine (GalNAc) moiety, a N- acetyl-glucosamine moiety, a multivalent mannose moiety, a multivalent fucose moiety, a glycosylated polypeptide, transferrin or an antibody, antibody fragment, protein, peptide, or aptamer capable of binding the transferrin receptor, bisphosphonate, polyglutamate, polyaspartate, cholesterol, bile acid, folate, vitamin B 12, biotin, an RGD peptide, or an RGD peptide mimetic. In some embodiments, the targeting ligand comprises a N-acetylgalactosamine (GalNAc) moiety. In some embodiments, the GalNAc moiety comprises a monovalent GalNAc moiety, a bivalent GalNAc moiety, a trivalent GalNAc moiety, or a tetravalent GalNAc moiety.
[0129] The non-nucleotide group can be covalently linked to the 3' and / or 5' end of either the antisense strand and / or the sense strand, when present. In some embodiments, when the oligonucleotide is an RNAi agent, the RNAi agent contains a non-nucleotide group linked to the 3' and / or 5' end of the sense strand. In some embodiments, a non-nucleotide group is linked to the 5' end of an ACVR2B RNAi agent sense strand. A non-nucleotide group may be linked directly or indirectly to the oligonucleotide via a linker / linking group. In some embodiments, a non- nucleotide group is linked to the oligonucleotide via a labile, cleavable, or reversible bond or linker.
[0130] In some embodiments, the targeting moiety is a targeting ligand. In some embodiments, the targeting ligand is small molecule-based, sugar-based (e.g., saccharide-based), fatty acid-based, protein-based, or nucleic acid-based targeting ligand. In some embodiments, the targeting moiety is a protein-based targeting ligand. In some embodiments, the protein-based targeting ligand is an antibody, nanobody, affibody, a peptibody, or a peptide. In some embodiments, the protein-based targeting ligand is an antibody, a fragment thereof, or an antigenbinding fragment thereof.Docket No.: SOUF-001-02WO
[0131] Various formulations have been developed to facilitate oligonucleotide use. For example, 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. In some embodiments, an oligonucleotide herein is fonuulated in buffer solutions such as phosphate buffered saline solutions, liposomes, micellar structures and capsids. Formulations of oligonucleotides with cationic lipids can be used to facilitate transfection of the oligonucleotides into cells. For example, 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. Accordingly, in some embodiments, a formulation herein comprises a lipid nanoparticle. In some embodiments, 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). In some embodiments, the formulations herein comprise an excipient. In some embodiments, an excipient confers to a composition improved stability, improved absorption, improved solubility and / or therapeutic enhancement of the active ingredient. In some embodiments, 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). In some embodiments, an oligonucleotide is lyophilized for extending its shelf-life and then made into a solution before use (e.g., administration to a subject). Accordingly, an excipient in a composition comprising any one of the oligonucleotides described herein may be a lyoprotectant (e.g., mannitol, lactose, polyethylene glycol or polyvinylpyrrolidone) or a collapse temperature modifier (e.g., dextran, Ficoll® or gelatin).Methods of Treatment
[0132] The present disclosure also provides methods of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt, to reduce or inhibit ACVR2B expression in a subject. The methods include contacting one or more cells in a subject with an oligonucleotide of the disclosure, or a pharmaceutically acceptable salt, thereby inhibiting expression of ACVR2B in the cells. The present disclosure also provides use of any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt, in the manufacture of aDocket No.: SOUF-001-02WO medicament for reducing or inhibiting ACVR2B expression in a subject, or for preventing or treating an ACVR2B related disorder in a subject.
[0133] Reduction in ACVR2B expression can be assessed by any methods known in the art. For example, a reduction in the expression of ACVR2B may be determined by determining the mRNA expression level of ACVR2B using methods routine to one of ordinary skill in the art, e.g., northern blotting, qRT-PCR; by determining the protein level of ACVR2B using methods routine to one of ordinary skill in the art, such as western blotting, immunological techniques. In some embodiments, the reduction of ACVR2B expression is determined by measuring ACVR2B expression in a population of cardiomyocytes or muscle cells derived from the subject. In some embodiments, the reduction of ACVR2B expression is determined by measuring ACVR2B expression in a tissue (e.g., myocardium tissue or skeletal muscle tissue) derived from the subject. In some embodiments, the reduction of ACVR2B expression is determined by measuring ACVR2B expression in serum derived from the subject. In some embodiments, the reduction of ACVR2B expression is determined by measuring expression of ACVR2B biomarkers in serum derived from the subject.
[0134] The present disclosure further provides methods of treatment of a subject in need thereof. The methods of treatment include administering an oligonucleotide of the disclosure to a subject, e.g., a subject that would benefit from inhibition of ACVR2B expression, in a therapeutically effective amount of an oligonucleotide targeting an ACVR2B gene or a pharmaceutical composition comprising an oligonucleotide targeting an ACVR2B gene.
[0135] In some embodiments, the present disclosure provides a method of treating obesity in a subject in need thereof, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0136] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for weight loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0137] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for reduction of excess body weight or for maintenance of weight reduction, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.Docket No.: SOUF-001-02WO
[0138] In some embodiments, the present disclosure provides a method of preserving or increasing muscle mass in a subject in need of treatment for type 2 diabetes, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0139] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject experiencing weight loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0140] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with spinal muscular atrophy (SMA), the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a phanuaceutical composition comprising an oligonucleotide described herein to the subject.
[0141] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with obesity, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0142] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with cachexia, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0143] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with muscle wasting, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0144] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with antiandrogen induced muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a phanuaceutical composition comprising an oligonucleotide described herein to the subject.Docket No.: SOUF-001-02WO
[0145] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with glucocorticoid-induced muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0146] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with chronic kidney disease-associated muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0147] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with cast- or immobilization-associated muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0148] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with cancer-associated muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0149] In some embodiments, the present disclosure provides a method of inhibiting ACVR2B expression in a subject with heart failure-associated muscle loss, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0150] In some embodiments, the present disclosure provides a method of preserving muscle mass in a subject in need thereof, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0151] In some embodiments, the present disclosure provides a method of increasing muscle mass in a subject in need thereof, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.Docket No.: SOUF-001-02WO
[0152] In some embodiments, the present disclosure provides a method of increasing muscle strength in a subject in need thereof, the method comprising administering an effective amount of an oligonucleotide described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising an oligonucleotide described herein to the subject.
[0153] The in vivo methods of the disclosure may include administering to a subject a composition containing an oligonucleotide disclosed herein, or a pharmaceutically acceptable salt thereof, wherein the oligonucleotide includes a nucleotide sequence that is complementary to at least a part of a sequence of nucleotides encoding ACVR2B of the subject to be treated.
[0154] The oligonucleotide can be administered by any means known in the art including, but not limited to oral, intraperitoneal, or parenteral routes, including intracranial (e.g., intraventricular, intraparenchymal, and intrathecal), intravenous, intramuscular, intravitreal, subcutaneous, transdermal, airway (aerosol), nasal, rectal, and topical (including buccal and sublingual) administration. In certain embodiments, the compositions are administered by intravenous infusion or injection. In certain embodiments, the compositions are administered by subcutaneous injection. In certain embodiments, the compositions are administered by intrathecal injection. The administration of the oligonucleotide may be repeated over a period of time. The administration may be repeated on a regular basis. In some embodiments, after an initial treatment regimen, the treatments can be administered on a less frequent basis. A repeat-dose regimen may include administration of a therapeutic amount of an oligonucleotide on a regular basis.
[0155] An oligonucleotide of the disclosure may be administered as a “free oligonucleotide.” A free oligonucleotide is administered in the absence of a pharmaceutical composition. The naked oligonucleotide may be in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In one embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the oligonucleotide can be adjusted such that it is suitable for administering to a subject. Alternatively, an RNAi agent of the disclosure may be administered as a pharmaceutical composition, such as a dsRNA liposomal formulation.
[0156] The present disclosure also provides methods of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent an ACVR2B related disorder in a subject. Non-limiting examples of ACVR2B related disorders include obesity, including sarcopenic obesity; sarcopenia; and muscle wasting diseases, such as cachexia. In some embodiments, an ACVR2B related disorder is a muscle wasting disorder associated with cancer or chronic illnesses. In some embodiments, an ACVR2B related disorder is selected from the group consisting of type 2 diabetes; Fibrodysplasia Ossificans Progressiva;Docket No.: SOUF-001-02WO muscular dystrophy; muscle atrophy; spinal muscular atrophy (SMA); amyotrophic lateral sclerosis (ALS); sporadic inclusion body myositis; and muscle loss, such as antiandrogen induced muscle loss, glucocorticoid induced muscle loss, chronic kidney disease associated muscle loss, cast associated muscle loss, cancer associated muscle loss, immobilization associated muscle loss, and heart failure associated muscle loss.
[0157] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent obesity.
[0158] In some embodiments, an ACVR2B related disorder is a muscle wasting disease. Non-limiting examples of a muscle wasting disease include muscular dystrophy, amyotrophic lateral sclerosis (ALS), and cachexia (muscle wasting disorder associated with cancer or chronic illnesses). In some embodiments, a muscle wasting disease is muscle atrophy, or spinal muscular atrophy (SMA).
[0159] In some embodiments, an oligonucleotide disclosed herein, or a pharmaceutically acceptable salt, promotes muscle growth and prevents atrophy. In some embodiments, an oligonucleotide disclosed herein, or a pharmaceutically acceptable salt, slows or reverses muscle degeneration. In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent muscle atrophy, e.g., while wearing an orthopedic cast.
[0160] In some embodiments, cachexia is a complex metabolic syndrome characterized by severe muscle wasting and weight loss. In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent cachexia in a subject.
[0161] In some embodiments, sarcopenia is an age-related loss of muscle mass and function. In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent sarcopenia.
[0162] In some embodiments, an ACVR2B related disorder is Fibrodysplasia Ossificans Progressiva. In some embodiments, an ACVR2B related disorder is heterotaxy.
[0163] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent sarcopenic obesity.Docket No.: SOUF-001-02WO
[0164] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent muscle waste-associated disorders.
[0165] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent sporadic inclusion body myositis.
[0166] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent cachexia.
[0167] In some embodiments, the present disclosure provides a method of using any one of the oligonucleotides disclosed herein, or a pharmaceutically acceptable salt thereof, to treat or prevent muscle waste, e.g., after a broken hip.
[0168] In some embodiments, the methods herein may further comprise administering to the subject an additional agent or therapy suitable for treatment or prevention of an ACVR2B related disorder. Non-limiting examples of an additional agent or therapy include anti-ACVR2B antibodies. In some embodiments, an additional agent or therapy is selected from the group consisting of anti-ACVR2A antibodies, anti-Myostatin antibodies, and anti-Activin A antibodies.Exemplary Embodiments:
[0169] Embodiment 1 : An oligonucleotide for inhibiting expression of Activin receptor 2B (ACVR2B), wherein the oligonucleotide comprises an antisense strand comprising at least 14 contiguous nucleotides substantially complementary to a sequence of nucleotides encoding ACVR2B, with no more than 4 mismatched nucleotides.
[0170] Embodiment 2: The oligonucleotide of Embodiment 1, wherein the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 90% nucleotide sequence identity to SEQ ID NO: 4932.
[0171] Embodiment 3: The oligonucleotide of Embodiment 1 or 2, wherein the oligonucleotide targets a sequence of nucleotides corresponding to positions of SEQ ID NO: 4932 (NM_001106.4) selected from Table 4.
[0172] Embodiment 4: The oligonucleotide of any one of Embodiments 1-3, wherein the antisense strand is substantially or completely complementary to a sequence of nucleotides corresponding to an untranslated region of the ACVR2B transcript.
[0173] Embodiment 5: The oligonucleotide of any one of Embodiments 1-4, wherein the oligonucleotide is an RNAi agent.Docket No.: SOUF-001-02WO
[0174] Embodiment 6: The oligonucleotide of Embodiment 5, wherein the RNAi agent is a double stranded small interfering RNA (siRNA), a short hairpin RNA, or a Dicer-substrate siRNA (DsiRNA).
[0175] Embodiment 7 : The oligonucleotide of Embodiment 6, wherein the oligonucleotide is a double-stranded small interfering RNA (siRNA) further comprising a sense strand, wherein the sense strand and antisense strand form a double stranded region.
[0176] Embodiment 8: The oligonucleotide of any one of Embodiments 1-7, wherein the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) differing by no more than 4, 3, 2, or 1 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682- 4931, or a nucleotide sequence having at least 90% nucleotide sequence identity to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0177] Embodiment 9: The oligonucleotide of any one of Embodiments 1-8, wherein the antisense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
[0178] Embodiment 10: The oligonucleotide of any one of Embodiments 7-9, wherein the sense strand comprises a nucleotide sequence differing by no more than 4, 3, 2, or 1 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681, or a nucleotide sequence having at least 90% nucleotide sequence identity to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
[0179] Embodiment 11: The oligonucleotide of any one of Embodiments 7-10, wherein the sense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455- 3681.
[0180] Embodiment 12: The oligonucleotide of any one of Embodiments 7-11, wherein the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand comprises a nucleotide sequence of any one of SEQ ID Nos: 1- 1227 or 2455-3681.
[0181] Embodiment 13: The oligonucleotide of any one of Embodiments 7-12, wherein each strand is no more than 30 nucleotides in length, or 19-30 nucleotides in length, or 19-23 nucleotides in length, or 19-21 nucleotides in length.
[0182] Embodiment 14: The oligonucleotide of any one of Embodiments 7-13, wherein at least one strand comprises a 3’ overhang of at least 1 nucleotide or at least 2 nucleotides.
[0183] Embodiment 15: The oligonucleotide of any one of Embodiments 7-14, wherein at least one strand comprises a 5’ overhang of at least 1 nucleotide, or at least 2 nucleotides.Docket No.: SOUF-001-02WO
[0184] Embodiment 16: The oligonucleotide of any one of Embodiments 7-15, wherein the double stranded region is 15-30 nucleotide pairs in length, or 15-23 nucleotide pairs in length, or 17-25 nucleotide pairs in length, or 19-23 nucleotide pairs in length, or 19-21 nucleotide pairs in length.
[0185] Embodiment 17: The oligonucleotide of any one of Embodiments 7-16, wherein the antisense is 21 nucleotides in length and the sense strand is 19 nucleotides in length.
[0186] Embodiment 18: The oligonucleotide of any one of Embodiments 1-4, wherein the oligonucleotide is a single-stranded antisense oligonucleotide (ASO).
[0187] Embodiment 19: The oligonucleotide of Embodiment 18, wherein the ASO comprises a nucleic acid sequence comprising at least 14 contiguous nucleotides (for example, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) that differ by no more than 1, 2, 3, or 4 nucleotides from any one of SEQ ID NOs: 1228-2454.
[0188] Embodiment 20: The oligonucleotide of Embodiment 18 or 19, wherein the ASO comprises a nucleic acid sequence comprising at least 14 contiguous nucleotides (for example, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) that differ by no more than 1, 2, 3 or 4 nucleotides from any one of SEQ ID NOs: 3682-4931.
[0189] Embodiment 21: The oligonucleotide of any one of Embodiments 1-20, wherein the oligonucleotide comprises one or more modifications.
[0190] Embodiment 22: The oligonucleotide of Embodiment 21, wherein the one or more modifications is selected from a ribose modification, a backbone modification, a nucleobase modification, or a combination thereof.
[0191] Embodiment 23: The oligonucleotide of Embodiment 22, wherein the ribose modification comprises a locked nucleic acid (LNA), a tricyclo-DNA (tcDNA), 2'-deoxy-2'- fluoro, 2'-O-methyl, 2'-methoxyethyl (2'-MOE), 2'-deoxy-2’-arabino-fluoro, 2'-O-benzyl, 2'-O- methyl-4-pyridine, 2’ cyclic ethyl (cET), phosphorodiamidate morpholino (PMO), glycol nucleic acid (GNA), unlocked nucleic acid (UNA), or a combination thereof.
[0192] Embodiment 24: The oligonucleotide of Embodiment 23, wherein the ribose modification comprises a 2’-deoxy-2'-fluoro, 2’-O-methyl, glycol nucleic acid (GNA), unlocked nucleic acid (UNA), a threose nucleic acid (TNA), or a combination thereof.
[0193] Embodiment 25: The oligonucleotide of Embodiment 23 or 24, wherein the ribose modification is a 2'-deoxy-2'-fluoro, 2'-O-methyl modification, or a combination thereof.
[0194] Embodiment 26: The oligonucleotide of any one of Embodiments 22-25, wherein the backbone modification comprises phosphorothioate, phosphorodithioate, methylphosphonate,Docket No.: SOUF-001-02WO methyoxypropyl-phosphonate, 5'-(E)-vinylphosphonate, 5'-methyl phosphonate, 5'- phosphorothioate, peptide nucleic acid (PNA), or a combination thereof.
[0195] Embodiment 27: The oligonucleotide of Embodiment 26, wherein the backbone modification comprises a phosphorothioate.
[0196] Embodiment 28: The oligonucleotide of any one of Embodiments 22-27, wherein the backbone modification comprises a phosphorothioate modification.
[0197] Embodiment 29: The oligonucleotide of any one of Embodiments 22-28, wherein the nucleobase modification comprises 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, 5-methylcytosine (5-Me-C), 5 -hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, N6-alkyl derivatives, N2-alkyl, 2-thiouracil, 2-thiothymine, 2- thiocytosine, 5-halouracil, cytosine, 5-propynyl uracil, 5-propynyl cytosine, 6-azo uracil, 6-azo cytosine, 6-azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-sulfhydryl, 8- thioalkyl, 8-hydroxy, 5-halo, 5-trifluoromethyl, N7-methylguanine, N7-methyladenine, 8- azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3 -deazaguanine, 3-deazaadenine, or any combination thereof.
[0198] Embodiment 30: The oligonucleotide of Embodiment 29, wherein the oligonucleotide comprises at least one modified nucleotide selected from the group consisting of a deoxy nucleotide, a 3 ’-terminal deoxy thymidine (dT) nucleotide, a 2'-O-methyl modified nucleotide, a 2'-deoxy-2'-fluoro modified nucleotide, a 2'-deoxy-modified nucleotide, a 2’-5’- linked ribonucleotide (3’-RNA), a locked nucleotide, an unlocked nucleotide, a conformationally restricted nucleotide, a constrained ethyl nucleotide, an abasic nucleotide, a 2’-amino-modified nucleotide, a 2'-O-allyl-modified nucleotide, 2' -C-alkyl-modified nucleotide, 2’ -hydroxylmodified nucleotide, a 2’-O-(methoxy ethyl) modified nucleotide, a 2’ -O-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate morpholino, a non-natural base comprising nucleotide, a tetrahydropyran modified nucleotide, a 1,5-anhydrohexitol modified nucleotide, a cyclohexenyl modified nucleotide, a nucleotide comprising a 5'-phosphorothioate group, a nucleotide comprising a 5'-methylphosphonate group, a nucleotide comprising a 5'- methylphosphate group, a nucleotide comprising a 5’ phosphate or 5’ phosphate mimic, a nucleotide comprising vinyl phosphonate, a glycol nucleic acid (GNA), a glycol nucleic acid S- Isomer (S-GNA), a nucleotide comprising 2-hydroxymethyl-tetrahydrofurane-5-phosphate, a nucleotide comprising 2’ -deoxy thymidine-3’ phosphate, a nucleotide comprising 2’- deoxy guanosine-3’ -phosphate: a cytidine-2'-phosphate, a guanosine-2'-phosphate, a uridine-2'- phosphate, an adenosine-2'-phosphate, a 2'-O-hexadecyl-adenosine-3’-phosphate, a 2'-O- hexadecyl-cytidine-3'-phosphate, a 2'-O-hexadecyl-guanosine-3'-phosphate, and a 2'-O-Docket No.: SOUF-001-02WO hexadecyl-uridine-3'-phosphate, a 3'-3' inverted nucleotide linkage, a 5’-5’ inverted nucleotide linkage, TNA, and combinations thereof.
[0199] Embodiment 31: The oligonucleotide of Embodiment 30, wherein the oligonucleotide comprises a modified nucleotide selected from the group consisting of a deoxy nucleotide, a 3’-terminal deoxythymidine (dT) nucleotide, a 3'-3' inverted nucleotide linkage, a 5’- 5’ inverted nucleotide linkage, a 5'-(E)-vinylphosphonate-2’-O-methyluridine-3’-phosphate, and a combination thereof.
[0200] Embodiment 32: The oligonucleotide of Embodiment 30 or 31, wherein the oligonucleotide comprises 5'-(E)-vinylphosphonate-2’-O-methyluridine-3’ -phosphate.
[0201] Embodiment 33: The oligonucleotide of Embodiment 21, wherein at least one of the modifications is a thermally destabilizing nucleotide modification.
[0202] Embodiment 34: The oligonucleotide of Embodiment 33, wherein the thermally destabilizing nucleotide modification is selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; destabilizing sugar modification; a 2’-deoxy modification; an acyclic nucleotide, an unlocked nucleic acids (UNA); a glycerol nucleic acid (GNA), and a combination thereof.
[0203] Embodiment 35: The oligonucleotide of Embodiment 31, wherein the modification comprises a short sequence of 3’ -terminal deoxythymidine nucleotide (dT).
[0204] Embodiment 36: The oligonucleotide of any one of Embodiments 21-35, wherein the modifications on the nucleotides are 2’-O-methyl and 2’deoxy-2’-fluoro modifications.
[0205] Embodiment 37: The oligonucleotide of any one of Embodiments 21-36, wherein the oligonucleotide comprises at least one phosphorothioate intemucleoside or phosphorodithioate intemucleoside linkage.
[0206] Embodiment 38: The oligonucleotide of Embodiment 37, wherein the oligonucleotide comprises 6-8 phosphorothioate intemucleoside linkages.
[0207] Embodiment 39: The oligonucleotide of Embodiment 37 or 38, wherein the oligonucleotide comprises at least 1, or at least 2, phosphorothioate intemucleoside linkage at a 5’ end of the sense strand.
[0208] Embodiment 40: The oligonucleotide of any one of Embodiments 37-39, wherein the oligonucleotide comprises at least 1 phosphorothioate intemucleoside linkage at a 3’ end of the sense strand.
[0209] Embodiment 41: The oligonucleotide of any one of Embodiments 37-40, wherein the oligonucleotide comprises at least 1 , or at least 2, phosphorothioate intemucleoside linkage at a 5’ end of the antisense strand.Docket No.: SOUF-001-02WO
[0210] Embodiment 42: The oligonucleotide of any one of Embodiments 37-41, wherein the oligonucleotide comprises at least 1 phosphorothioate intemucleoside linkage at a 3’ end of the antisense strand.
[0211] Embodiment 43: The oligonucleotide of any one of Embodiments 37-42, wherein no more than five of the nucleotides of the antisense strand are unmodified nucleotides.
[0212] Embodiment 44: The oligonucleotide of any one of Embodiments 37-43, wherein all the nucleotides of the antisense strand are modified nucleotides.
[0213] Embodiment 45: The oligonucleotide of any one of Embodiments 37-44, wherein no more than five of the nucleotides of the sense strand are unmodified nucleotides.
[0214] Embodiment 46: The oligonucleotide of any one of Embodiments 37-45, wherein all the nucleotides of the sense strand are modified nucleotides.
[0215] Embodiment 47: The oligonucleotide of any one of Embodiments 7-46, wherein the antisense strand comprises a chemical modification pattern according to (Nfs)a(nNf)b(ns)cn, wherein: n is a 2’-O-methyl-nucleoside-3’ -phosphate;Nfs is a 2'-deoxy-2’-fhioro-nucleoside-3'-phosphorothioate;Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate; ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; a is at least 1; b is 5-10; and c is at least 1.
[0216] Embodiment 48: The oligonucleotide of Embodiment 47, wherein the antisense strand comprises a chemical modification pattern NfsNfsnNfnNfnNfnNfnNfnNfnNfnNfnsnsn.
[0217] Embodiment 49: The oligonucleotide of any one of Embodiments 7-48, wherein the sense strand comprises a chemical modification pattern according to (ns)d(Nfn)eNf, wherein: n is a 2’-O-methyl-nucleoside-3’ -phosphate;Nf is a 2’ -deoxy-2'-fhioro-nucleoside-3’ -phosphate; ns is a 2 ’-O-methyl-nucleoside-3’ -phosphorothioate; d is at least 1 ; and e is 5-10.
[0218] Embodiment 50: The oligonucleotide of Embodiment 49, wherein the sense strand comprises a chemical modification pattern nsnsNfnNfnNfnNfnNfnNfnNfnNfnNf.
[0219] Embodiment 51 : The oligonucleotide of any one of Embodiments 7-50, wherein each of the antisense and the sense strand is independently 17-23 nucleotides in length, whereinDocket No.: SOUF-001-02WO the antisense strand comprises the motif F(SF)nSnn, wherein n is from 2 to about 20, nn is 0 or 1 , one of F and S is a 2'-deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O- methyl modified nucleoside.
[0220] Embodiment 52: The oligonucleotide of any one of Embodiments 7-51, wherein the antisense strand comprises the chemical modification pattern of nNfnnnNfnNfNfnnnnNfnNfnnnnn and the sense strand comprises the chemical modification nnnnnnNfnNfNfNfnnnnnnnn, wherein n is a 2’ -O-methyl -nucleoside and Nf is a 2’-deoxy-2’- fluoro-nucleoside.
[0221] Embodiment 53: The oligonucleotide of any one of Embodiments 7-52, wherein each of the antisense and the sense strand is independently 20-23 nucleotides in length, wherein the antisense strand comprises a region having the formula X1-Y-X2, wherein Y is a subregion of from about 5 to about 12 linked nucleosides and each of XI subregion and X2 subregion is, independently, a plurality of linked nucleosides having the formula FSFS, where one of F and S is a 2'-deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O-methyl modified nucleoside; and each internucleoside linkage of said XI subregion and X2 subregion is, independently, a phosphodiester or a phosphorothioate internucleoside linkage.
[0222] Embodiment 54: The oligonucleotide of any one of Embodiments 7-53, wherein each of the antisense and the sense strand is independently 17-23 nucleotides in length, wherein the antisense strand comprises a contiguous sequence of linked nucleosides that define an alternating motif of the formula:5 '-Q(-L-Z-L-Q)n(-L-Z)nn-3' wherein: each L is an intemucleoside linking group: either each Q is a 2'-deoxy-2’ -fluoro-nucleoside and each Z is a 2'-O-methyl nucleoside, or each Q is a 2'-O-methyl nucleoside and each Z is a 2'-deoxy-2’ -fluoro nucleoside; n is from 8 to 14; and nn is 0 or 1.
[0223] Embodiment 55: The oligonucleotide of any one of Embodiments 7-54, wherein the antisense strand is 19-25 nucleotides in length and is represented by the formula:wherein:Docket No.: SOUF-001-02WOB l', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA;IT, T2', and T3' each independently represent a nucleotide comprising a chemical modification selected from the group consisting of DNA, RNA, LNA, 2'-deoxy-2’ -fluoro, and 5'-methyl-2'-deoxy-2’ -fluoro nucleotides; ql is 4 to 15 nucleotides in length; q3 or q7 is independently 1-6 nucleotide(s) in length; q2 or q6 is independently 1-3 nucleotide(s) in length; q4 is 0-3 nucleotide(s) in length; and q5 is 0-10 nucleotide(s) in length; wherein: the antisense strand has 2'-deoxy-2’ -fluoro modifications, and wherein the 2'-deoxy-2’- fluoro modifications on the antisense strand consist of four, and only four, 2'-deoxy-2’ -fluoro modifications, or six, and only six, 2'-deoxy-2’ -fluoro modifications.
[0224] Embodiment 56: The oligonucleotide of any one of Embodiments 7-55, wherein the antisense strand and sense strand are each 14 to 40 nucleotides, and are represented by the formula:wherein:B l, BT, B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA;Cl is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugarDocket No.: SOUF-001-02WO modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand;Tl', T2', and T3' each independently represent a nucleotide comprising a modification providing the nucleotide a steric bulk that is less than or equal to the steric bulk of a 2'-0Me modification, wherein the modification is at the 2'-position of a ribose sugar of the nucleotide or at a position of a non-ribose nucleotide similar to the 2'- position of a ribose sugar; each nl, and ql is independently 4 to 15 nucleotides in length; each q3, and q7 is independently 1-6 nucleotide(s) in length; each q2 and q6 is independently 1-3 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4, and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length, and T1 each are 2'-deoxy-2’ -fluoro nucleotides; n3 is 7 nucleotides in length, and B2 each are 2'-0Me nucleotides: and n5 is 3 nucleotides in length, and B3 each are 2'-0Me nucleotides.
[0225] Embodiment 57: The oligonucleotide of any one of Embodiments 7-56, wherein the antisense strand and sense strand are each 19-25 nucleotides in length, wherein the antisense strand is represented by the formula:(Is)wherein:Bl, B2, and B3 each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'-substituted alkyl, 2'- halo, ENA, and BNA / LNA;Cl is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugar modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand;T1 represents a nucleotide comprising a 2'-deoxy-2’ -fluoro modification; nl or n3 is independently 4 to 15 nucleotides in length; n5 is 1-6 nucleotide(s) in length; n2 is 3;Docket No.: SOUF-001-02WO n4 is 0-3 nucleotide(s) in length; and wherein the sense strand has 2'-deoxy-2’-fluoro modifications, and wherein the 2'-deoxy- 2’ -fluoro modifications on the sense strand consist of four, and only four, 2'-deoxy-2’ -fluoro modifications, wherein the four 2'-deoxy-2’ -fluoro modifications are at positions 7 and 9-11 from the 5'-end of the sense strand.
[0226] Embodiment 58: The oligonucleotide of any one of Embodiments 7-57, wherein the antisense strand is complementary to at least one portion of a mRNA of the target gene (e.g., ACVR2B), wherein: the sense strand comprises 19-22 nucleotides, the antisense strand comprises 19-25 nucleotides; and the oligonucleotide is represented by the formula:wherein:Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-methyl and 2'-deoxy-2’ -fluoro; each B l, B2, and B3 is 2'-O-methyl nucleotide;Cl is glycerol nucleic acid (GNA) placed at a site opposite to the seed region (positions 2-8) of the antisense strand;Tl', T2', and T3' are each 2'-F, wherein:Tl' is at position 14 from the 5' end of the antisense strand, and q2 is 1 ; andT3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1 ; each nl, n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length;Docket No.: SOUF-001-02WO n2 is 3 nucleotides in length; andT1 each are 2'-deoxy-2’ -fluoro nucleotides, wherein(a) the oligonucleotide is covalently conjugated to at least one ligand; and(b) one of the T1 nucleotides is at position 11 from the 5' end of the sense strand.
[0227] Embodiment 59: The oligonucleotide of any one of Embodiments 7-58, wherein the sense strand comprises 19-22 nucleotides, the antisense strand comprises 19-25 nucleotides; and the oligonucleotide is represented by the formula:(Iwherein:Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-methyl and 2'-deoxy-2’ -fluoro; each Bl, B2, and B3 is 2'-OMe;Cl is glycerol nucleic acid (GN A) placed at a site opposite to the seed region (positions 2-8) of the antisense strand;TT, T2', and T3' are each 2'-deoxy-2’ -fluoro, wherein:T1 ' is at position 14 from the 5' end of the antisense strand, and q2 is 1 ; andT3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1; each nl, n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length; andT1 each are 2'-deoxy-2’ -fluoro, andDocket No.: SOUF-001-02WO wherein(a) the oligonucleotide is covalently conjugated to at least one ligand;(b) one of the T1 nucleotides is at a position in the sense strand that is opposite to position 11 from the 5' end of the antisense strand; and(c) the oligonucleotide comprises at least one phosphorothioate internucleoside linkage.
[0228] Embodiment 60: The oligonucleotide of any one of Embodiments 7-59, wherein the antisense strand and sense strand are each 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to a target sequence to mediate RNA interference, wherein said sense strand comprises at least one thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5' region of the antisense strand or a precursor thereof, wherein the antisense strand further comprises one or both of the following characteristics:(i) 2, 3, 4, 5 or 6 2'-deoxy-2’ -fluoro modifications; and(ii) 1, 2, 3, 4 or 5 phosphorothioate internucleoside linkages; and said sense strand comprises one or both of the following characteristics:(iii) 2, 3, 4, or 5 2'-deoxy-2’ -fluoro modifications; and(iv) 1, 2, 3, 4 or 5 phosphorothioate internucleoside linkages.
[0229] Embodiment 61 : The oligonucleotide of any one of Embodiments 7-46, wherein the antisense strand comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2’-O-methyl-nucleoside-3’-phosphorothioate; Nfs is a 2’-deoxy-2’-fluoro- nucleoside-3’-phosphorothioate; n is a 2’-O-methyl-nucleoside-3’-phosphate; and Nf is a 2’-deoxy- 2'-fluoro-nucleoside-3’-phosphate.
[0230] Embodiment 62: The oligonucleotide of any one of Embodiments 7-46, wherein the antisense strand disclosed herein comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'-vinylphosphonate-2'-O-methyl- uridine-3’ -phosphorothioate; ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; Nfs is a 2'- deoxy-2'-fhioro-nucleoside-3'-phosphorothioate: n is a 2'-O-methyl-nucleoside-3’-phosphate; and Nf is a 2’-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0231] Embodiment 63: The oligonucleotide of any one of Embodiments 7-46, wherein the sense strand disclosed herein comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, wherein ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl-nucleoside-3'- phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0232] Embodiment 64: The oligonucleotide of any one of Embodiments 7-46, wherein the sense strand disclosed herein comprises a modification patternDocket No.: SOUF-001-02WONfsnsNfnNfnNfnNfnNfnNfnNfnNfnNf, wherein ns is a 2'-O-methyl-nucleoside-3'- phosphorothioate; Nfs is a 2’-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate; n is a 2'-0-methyl- nucleoside-3’-phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
[0233] Embodiment 65: The oligonucleotide of any one of Embodiments 7-46, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro- nucleoside-3'-phosphate.
[0234] Embodiment 66: The oligonucleotide of any one of Embodiments 7-46, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'-vinylphosphonate-2'-O-methyl-uridine-3'-phosphorothioate; ns is a 2'-O- methyl-nucleoside-3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro- nucleoside-3 ' -phosphate .
[0235] Embodiment 67: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 3682- 4931.
[0236] Embodiment 68: The oligonucleotide of Embodiment 67, wherein the sense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 2455-3681.
[0237] Embodiment 69: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4909, and the sense strand comprises SEQ ID NO: 2464.
[0238] Embodiment 70: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4910, and the sense strand comprises SEQ ID NO: 2566.
[0239] Embodiment 71: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4911, and the sense strand comprises SEQ ID NO: 2600.
[0240] Embodiment 72: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4912, and the sense strand comprises SEQ ID NO: 2681.Docket No.: SOUF-001-02WO
[0241] Embodiment 73: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 491 , and the sense strand comprises SEQ ID NO:2682.
[0242] Embodiment 74: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4914, and the sense strand comprises SEQ ID NO:2683.
[0243] Embodiment 75: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4915, and the sense strand comprises SEQ ID NO: 2685.
[0244] Embodiment 76: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4916, and the sense strand comprises SEQ ID NO: 2827.
[0245] Embodiment 77: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4917, and the sense strand comprises SEQ ID NO: 2832.
[0246] Embodiment 78: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4918, and the sense strand comprises SEQ ID NO: 2840.
[0247] Embodiment 79: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4919, and the sense strand comprises SEQ ID NO:2844.
[0248] Embodiment 80: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4920, and the sense strand comprises SEQ ID NO:2845.
[0249] Embodiment 81: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4921, and the sense strand comprises SEQ ID NO:2846.
[0250] Embodiment 82: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4922, and the sense strand comprises SEQ ID NO: 2886.
[0251] Embodiment 83: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4923, and the sense strand comprises SEQ ID NO: 2899.Docket No.: SOUF-001-02WO
[0252] Embodiment 84: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4924, and the sense strand comprises SEQ ID NO: 2900.
[0253] Embodiment 85: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4925, and the sense strand comprises SEQ ID NO:2902.
[0254] Embodiment 86: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4926, and the sense strand comprises SEQ ID NO:2903.
[0255] Embodiment 87: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4927, and the sense strand comprises SEQ ID NO: 3048.
[0256] Embodiment 88: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4928, and the sense strand comprises SEQ ID NO: 3061.
[0257] Embodiment 89: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4929, and the sense strand comprises SEQ ID NO:3066.
[0258] Embodiment 90: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4930, and the sense strand comprises SEQ ID NO:3067.
[0259] Embodiment 91: The oligonucleotide of any one of Embodiments 7-66, wherein the antisense strand comprises SEQ ID NO: 4931, and the sense strand comprises SEQ ID NO:3068.
[0260] Embodiment 92: The oligonucleotide of any one of Embodiments 7-91, further comprising a terminal, chiral modification occurring at the first internucleoside linkage at the 3’- end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5 ’-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’-end of the sense strand, having the linkage phosphorus atom in either Rp configuration or Sp configuration.
[0261] Embodiment 93: The oligonucleotide of any one of Embodiments 7-92, further comprising a terminal, chiral modification occurring at the first and second intemucleoside linkages at the 3’-end of the antisense strand, having the linkage phosphorus atom in SpDocket No.: SOUF-001-02WO configuration, a terminal, chiral modification occurring at the first internucleoside linkage at the 5’ -end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first internucleoside linkage at the 5 ’-end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
[0262] Embodiment 94: The oligonucleotide of any one of Embodiments 7-93, further comprising a terminal, chiral modification occurring at the first, second and third internucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5 '-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
[0263] Embodiment 95: The oligonucleotide of any one of Embodiments 7-94, further comprising a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the third intemucleoside linkages at the 3 ’-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5 ’-end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
[0264] Embodiment 96: The oligonucleotide of any one of Embodiments 7-95, further comprising a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 3’-end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 5 ’-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5 ’-end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
[0265] Embodiment 97: The oligonucleotide of any one of Embodiments 1-96, further comprising a phosphate or phosphate mimic at the 5’ -end of the antisense strand.
[0266] Embodiment 98: The oligonucleotide of Embodiment 97, wherein the phosphate mimic is a 5’ -vinyl phosphonate (VP).
[0267] Embodiment 99: The oligonucleotide of any one of Embodiments 1 -98, further comprising a targeting ligand.Docket No.: SOUF-001-02WO
[0268] Embodiment 100: The oligonucleotide of Embodiment 99, wherein the targeting ligand is a small molecule-based, sugar-based (e.g., saccharide -based), fatty acid-based, proteinbased, or nucleic acid-based targeting ligand.
[0269] Embodiment 101: The oligonucleotide of Embodiment 100, wherein the proteinbased targeting ligand is an antibody, nanobody, affibody, peptibody, or a peptide.
[0270] Embodiment 102: An oligonucleotide selected from the sense strands, antisense strands, and RNAi agents as listed in Tables 1A and IB, or a pharmaceutically acceptable salt thereof.
[0271] Embodiment 103: A pharmaceutical composition comprising the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or excipient.
[0272] Embodiment 104: A method for inhibiting ACVR2B expression or treating an ACVR2B related disorder in a subject, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0273] Embodiment 105: The method of Embodiment 104, wherein the subject is a human.
[0274] Embodiment 106: The method of Embodiment 104 or 105, wherein the reduction of ACVR2B mRNA or protein expression levels is measured in a population of myocytes or cardiomyocytes derived from the subject.
[0275] Embodiment 107: The method of any one of Embodiments 104-106, wherein the reduction of ACVR2B mRNA or protein expression levels is measured in tissues derived from the subject.
[0276] Embodiment 108: The method of any one of Embodiments 104-107, further comprising administering to the subject an additional agent or a therapy suitable for treatment or prevention of an ACVR2B related disorder.
[0277] Embodiment 109: A method of treating obesity in a subject in need thereof, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0278] Embodiment 110: A method of preserving or increasing muscle mass in a subject in need of treatment for weight loss, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.Docket No.: SOUF-001-02WO
[0279] Embodiment 111 : A method of preserving or increasing muscle mass in a subject in need of treatment for reduction of excess body weight or for maintenance of weight reduction, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0280] Embodiment 112: A method of preserving or increasing muscle mass in a subject in need of treatment for a reduction of major adverse cardiovascular events (e.g., cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke), the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0281] Embodiment 113: A method of preserving or increasing muscle mass in a subject in need of treatment for type 2 diabetes, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0282] Embodiment 114: A method of inhibiting ActRII (e.g., through inhibition of ACVR2B expression) in a subject experiencing weight loss, the method comprising administering an effective amount of the oligonucleotide of any one of Embodiments 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of Embodiment 103 to the subject.
[0283] Embodiment 115: The method of any one of Embodiments 104-114, wherein the subject is receiving or has received a GLP-1 receptor agonist (e.g., semaglutide, dulaglutide, liraglutide, exenatide, tirzepatide).
[0284] The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se.
[0285] As used herein, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. For example, “a” or “an” means “at least one” or “one or more.”
[0286] Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein are intended to have the same meaning as is commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In someDocket No.: SOUF-001-02WO cases, terms with commonly understood meanings are defined herein for clarity and / or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. All publications, including patent documents, scientific articles and databases, referred to in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication were individually incorporated by reference. If a definition set forth herein is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the definition set forth herein prevails over the definition that is incorporated herein by reference.
[0287] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.EXAMPLES
[0288] The following examples are provided to further illustrate some embodiments of the present disclosure, but are not intended to limit the scope of the disclosure; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.Example 1: ACVR2B siRNA Design and Evaluation
[0289] A set of siRNAs were designed to target sequences encoding human Activin receptor 2B (ACVR2B) (shown here as SEQ ID NO: 4932). A detailed list of the unmodified siRNA sense and antisense strand sequences is shown in Tables 1A and 1C below. A detailed list of modified siRNAs is shown in Table IB below. Table 2 provides names for the nucleotide abbreviations used in the nucleic acid sequences herein. Oligonucleotides were chemically synthesized using phosphorami dite approach and after quality control using UV- and massspectroscopy sense and antisense strands were annealed to perform screening. Table 3 provides exemplary sequences of ACVR2B mRNA transcripts.
[0290] HEK293 cells (ATCC, CRL-1573) cells were maintained by biweekly passing in DMEM supplemented with 10% FBS, 20 mM L-glutamine, 10 mM HEPES pH 7.2, 1 mM sodium pyruvate, lx MEM non-essential amino acids, and lx Pen / Strep (DMEM complete). HEK293 cells were purchased and cultured as described to produce frozen stocks in 10% DMSO in complete media. Briefly, each vial of cells was thawed in 37 °C water bath and transferred to a 50 mL centrifuge tube filled with complete DMEM. The tube was then centrifuged at 200g for 5 minutes, the media aspirated, and the cells resuspended to appropriate density and seeded for continuous culture.Docket No.: SOUF-001-02WO
[0291] On the day of transfection, HEK293 cells were dissociated and seeded into 96 well plates at 10,000 cells / well in 80 pL of complete media. Transfection mixes were prepared by adding 5 pL of 5 pM siRNA to 45 pL of fresh OptiMEM media (ThermoFisher, 31985062) in a v-bottom polypropylene 96 well plate (USA Scientific, 1833-9610). A master mix of Lipofectamine RNAiMax (ThermoFisher, 13778150) and OptiMEM media was created at a ratio of 0.3 pL RNAiMax and 10 pL of OptiMEM per reaction. 50 pL of RNAiMax master mix was added to each 50 pL of siRNA / OptiMEM and the plate was sealed with sterile plate tape (USA Scientific, 2920-0010). Each transfection mix plate was then rotated at 400 rpm for 5 minutes, then removed and allowed to sit at room temperature in the tissue culture hood for 15 minutes. Following incubation, 20 pL of each siRNA / RNAiMax was added to respective wells of the HEK293 cells, in triplicate. This created a final concentration of 50 nM siRNA per well. At 48 hours post transfection, 50 pL of fresh complete media was added to the cells for feeding. Transfections were allowed to incubate for 72 hours prior to harvest and RNA isolation.
[0292] Multiple dose validation screens were performed just as the initial screens with small changes to preparation and final siRNA dosing. Individual siRNA at 5 pM were diluted appropriately into OptiMEM media to make a highest dose. Serial dilutions 10, 3.33, 1, 0.33, 0.1, 0.033, 0.01, 0.0033, 0.001, 0.00033, 0.0001, O.OOOO33 nM were prepared in separate plates using fresh OptiMEM. Just as with the single dose screens, 50 pL of RNAiMax master mix (0.3 pL RNAiMax to 10 pL OptiMEM) was added to each diluted siRNA. Each plate was then taped, rotated at 400 rpm for 5 minutes, and allowed to incubate at room temperature for 15 minutes. 20 pL of each siRNA reaction was then added to pre -plated HEK293 cells. Transfections were allowed to incubate for 72h prior to harvest and RNA isolation.
[0293] 72 hours post transfection, cells were harvested, and RNA isolated using the Quick-RNA 96 Kit (Zymo Research, R1053) according to the manufacturer protocol using vacuum manifolds for washing and eluting via swing bucket centrifuging at 1500g. Harvested RNA was assayed for ACVR2B expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). Untransfected controls from each transfection plate were pooled together and a 1:5 dilution series is produced for each qPCR assay plate for direct normalization. A single qPCR assay was performed for each sample using an ACVR2B Taqman probe set (Hs00609603_ml-FAM) multiplexed with a common GAPDH-VIC probe (ThermoFisher, 4326317E) according to the manufacturer instructions for a combined primer / probe set. Thermocycling and data acquisition was performed with an Applied Biosystems QuantStudio 3 / 5 Real-Time PCR System.Docket No.: SOUF-001-02WO
[0294] Quantification of Target mRNA Levels and Knockdown Efficiency: The mRNA levels of the target gene and the efficiency of siRNA-mediated knockdown (shown as %KD in Table IB) were assessed using relative quantification. Cq values for both the target and reference (housekeeping) genes were obtained via quantitative PCR (qPCR) for each sample. The relative expression of the target gene (as shown Table IB) was calculated using the 2A(-AACq) method, where ACq represents the difference between the Cq values of the target and reference genes and AACq refers to the difference between the ACq values for treatment samples and only lipofectamine treated control samples.
[0295] IC50 Determination: IC50 values for siRNAs (as shown in Table IB) were determined by plotting the percentage of target gene depletion against the logarithm of siRNA concentrations. A sigmoidal dose-response (variable slope) curve was fitted to the data using the Curve Fitting function in GraphPad Prism (version 7.0). The IC50 value was defined as the siRNA concentration resulting in 50% gene knockdown.
[0296] Table 1A provides exemplary siRNAs with the sequences of the sense strand and the antisense strand. Column 1 shows the beginning position of the target sequence in ACVR2B_human #NM_001106.4 (SEQ ID NO: 4932). The target sequence is 19 nucleotide long starting from the beginning position. For example, row 1 shows that the beginning position of the target sequence is 516, which means that the target sequence is the sequence corresponding to positions 516-534 of ACVR2B_human #NM_001106.4 (SEQ ID NO: 4932). The sequences of the sense strands and antisense strands are shown from the 5’ end to the 3’ end.Table 1ADocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WO
[0297] Table IB provides exemplary IC50, Knockdown, and Species Selectivity data for certain siRNAs comprising modified sense strand and modified antisense strand. Column 1 shows the beginning position of the target sequence in ACVR2B_human_# NM_001106.4 (SEQ ID NO: 4932). The target sequence is 19 nucleotide long starting from the beginning position. For example, row 1 shows that the beginning position of the target sequence is 516, which means that the target sequence is the sequence corresponding to positions 516-534 of ACVR2B_human_#NM_001106.4 (SEQ ID NO: 4932). In Table IB, the sequences are shownDocket No.: SOUF-001-02WO from the 5’ end to the 3’ end. The modified sense strands each have 19 nucleotides, and the modified antisense strands each have 21 nucleotides. The Species Selectivity was determined based on homology of the ACVR2B genes in human, cynomolgus monkey (shown as “cyno” in Table IB), and mouse. The knockdown (“KD") results are shown as % KD at 10 nM dosage.Table IBDocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WOTable 1C provides exemplary unmodified siRNAs with the sequences of the sense strand and the antisense strand. Column 1 shows the beginning position of the target sequence in ACVR2B_human #NM_001106.4 (SEQ ID NO: 4932). The target sequence is 19 nucleotide long starting from the beginning position. For example, row 1 shows that the beginning position of the target sequence is 9764, which means that the target sequence is the sequence corresponding to positions 9764-9782 of ACVR2B_human #NM_001106.4 (SEQ ID NO: 4932). In Table 1C, the sequences are shown from the 5’ end to the 3’ end. As the nucleotide “T” in the unmodified siRNAs in Table 1A represents RNA uridine (“U”), the siRNAs in Table 1C may be used interchangeably with the siRNAs in Table 1A targeting the same positions.Docket No.: SOUF-001-02WOTable 1CDocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WOTable 2: List of abbreviations of modified nucleotides in the nucleic acid sequences disclosed herein, e.g., in Table IBDocket No.: SOUF-001-02WOTable 3: Exemplary sequences of ACVR2B mRNA transcriptDocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WO
[0298] Table 4 provides targeting positions within SEQ ID NO: 4932 (NM_001106.4) for an oligonucleotide of the present disclosure. In some embodiments, an oligonucleotide targets a sequence corresponding to positions selected from Table 4.Table 4.Docket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WODocket No.: SOUF-001-02WO
[0299] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the present disclosure may be employed in practicing the present disclosure. It is intended that the following claims define the scope of the present disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Claims
Docket No.: SOUF-001-02WOCLAIMSWhat is claimed is:
1. An oligonucleotide for inhibiting expression of Activin receptor 2B (ACVR2B), wherein the oligonucleotide comprises an antisense strand comprising at least 14 contiguous nucleotides substantially complementary to a sequence of nucleotides encoding ACVR2B, with no more than 4 mismatched nucleotides.
2. The oligonucleotide of claim 1, wherein the sequence of nucleotides encoding ACVR2B comprises a nucleotide sequence having at least 90% nucleotide sequence identity to SEQ ID NO: 4932.
3. The oligonucleotide of claim 1 or 2, wherein the oligonucleotide targets a sequence of nucleotides corresponding to positions of SEQ ID NO: 4932 (NM_001106.4) selected from Table 4.
4. The oligonucleotide of any one of claims 1-3, wherein the antisense strand is substantially or completely complementary to a sequence of nucleotides corresponding to an untranslated region of the ACVR2B transcript.
5. The oligonucleotide of any one of claims 1-4, wherein the oligonucleotide is an RNAi agent.
6. The oligonucleotide of claim 5, wherein the RNAi agent is a double stranded small interfering RNA (siRNA), a short hairpin RNA, or a Dicer-substrate siRNA (DsiRNA).
7. The oligonucleotide of claim 6, wherein the oligonucleotide is a double-stranded small interfering RNA (siRNA) further comprising a sense strand, wherein the sense strand and antisense strand form a double stranded region.
8. The oligonucleotide of any one of claims 1-7, wherein the antisense strand comprises a nucleotide sequence comprising at least 15 contiguous nucleotides (for example, 15. 16, 17, 18, 19, 20, or 21 contiguous nucleotides) differing by no more than 4, 3, 2, or 1 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, or a nucleotide sequence having at least 90% nucleotide sequence identity to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.Docket No.: SOUF-001-02WO9. The oligonucleotide of any one of claims 1-8, wherein the antisense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931.
10. The oligonucleotide of any one of claims 7-9, wherein the sense strand comprises a nucleotide sequence differing by no more than 4, 3, 2, or 1 nucleotides from the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681, or a nucleotide sequence having at least 90% nucleotide sequence identity to a portion of the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
11. The oligonucleotide of any one of claims 7-10, wherein the sense strand comprises the nucleotide sequence of any one of SEQ ID NOs: 1-1227 or 2455-3681.
12. The oligonucleotide of any one of claims 7-11, wherein the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 1228-2454 or 3682-4931, and the sense strand comprises a nucleotide sequence of any one of SEQ ID Nos: 1-1227 or 2455-3681.
13. The oligonucleotide of any one of claims 7-12, wherein each strand is no more than 30 nucleotides in length, or 19-30 nucleotides in length, or 19-23 nucleotides in length, or 19-21 nucleotides in length.
14. The oligonucleotide of any one of claims 7-13, wherein at least one strand comprises a 3' overhang of at least 1 nucleotide or at least 2 nucleotides.
15. The oligonucleotide of any one of claims 7-14, wherein at least one strand comprises a 5’ overhang of at least 1 nucleotide, or at least 2 nucleotides.
16. The oligonucleotide of any one of claims 7-15, wherein the double stranded region is 15-30 nucleotide pairs in length, or 15-23 nucleotide pairs in length, or 17-25 nucleotide pairs in length, or 19-23 nucleotide pairs in length, or 19-21 nucleotide pairs in length.
17. The oligonucleotide of any one of claims 7-16, wherein the antisense is 21 nucleotides in length and the sense strand is 19 nucleotides in length.
18. The oligonucleotide of any one of claims 1-4, wherein the oligonucleotide is a singlestranded antisense oligonucleotide (ASO).Docket No.: SOUF-001-Q2WO19. The oligonucleotide of claim 18, wherein the ASO comprises a nucleic acid sequence comprising at least 14 contiguous nucleotides (for example, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) that differ by no more than 1, 2, 3, or 4 nucleotides from any one of SEQ ID NOs: 1228-2454.
20. The oligonucleotide of claim 18 or 19, wherein the ASO comprises a nucleic acid sequence comprising at least 14 contiguous nucleotides (for example, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides) that differ by no more than 1, 2, 3 or 4 nucleotides from any one of SEQ ID NOs: 3682-4931.
21. The oligonucleotide of any one of claims 1-20, wherein the oligonucleotide comprises one or more modifications.
22. The oligonucleotide of claim 21, wherein the one or more modifications is selected from a ribose modification, a backbone modification, a nucleobase modification, or a combination thereof.
23. The oligonucleotide of claim 22, wherein the ribose modification comprises a locked nucleic acid (LNA), a tricyclo-DNA (tcDNA), 2'-deoxy-2'-fluoro, 2'-O-methyl, 2'-methoxyethyl (2 - MOE), 2'-deoxy-2'-arabino-fluoro, 2'-O-benzyl, 2'-O-methyl-4-pyridine, 2' cyclic ethyl (cET), phosphorodiamidate morpholino (PMO), glycol nucleic acid (GNA), unlocked nucleic acid (UNA), or a combination thereof.
24. The oligonucleotide of claim 23, wherein the ribose modification comprises a 2'-deoxy-2'- fluoro, 2'-O-methyl, glycol nucleic acid (GNA), unlocked nucleic acid (UNA), a threose nucleic acid (TNA), or a combination thereof.
25. The oligonucleotide of claim 23 or 24, wherein the ribose modification is a 2'-deoxy-2’- fluoro, 2'-O-methyl modification, or a combination thereof.
26. The oligonucleotide of any one of claims 22-25, wherein the backbone modification comprises phosphorothioate, phosphorodithioate, methylphosphonate, methyoxypropyl- phosphonate, 5'-(E)-vinylphosphonate, 5’-methyl phosphonate, 5'-methylphosphate, 5'- phosphorothioate, peptide nucleic acid (PNA), or a combination thereof.Docket No.: SOUF-001-02WO27. The oligonucleotide of claim 26, wherein the backbone modification comprises a phosphorothioate.
28. The oligonucleotide of any one of claims 22-27, wherein the backbone modification comprises a phosphorothioate modification.
29. The oligonucleotide of any one of claims 22-28, wherein the nucleobase modification comprises 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, 5-methylcytosine (5-Me-C), 5 -hydroxymethyl cytosine, xanthine, hypoxanthine, 2- aminoadenine, N6-alkyl derivatives, N2-alkyl, 2-thiouracil, 2-thiothymine, 2-thiocytosine, 5- halouracil, cytosine, 5-propynyl uracil, 5-propynyl cytosine, 6-azo uracil, 6-azo cytosine, 6- azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-sulfhydryl, 8-thioalkyl, 8-hydroxy, 5-halo, 5-trifluoromethyl, N7-methylguanine, N7-methyladenine, 8-azaguanine, 8- azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, or any combination thereof.
30. The oligonucleotide of claim 29, wherein the oligonucleotide comprises at least one modified nucleotide selected from the group consisting of a deoxy nucleotide, a 3 ’-terminal deoxythymidine (dT) nucleotide, a 2'-O-methyl modified nucleotide, a 2'-deoxy-2'-fluoro modified nucleotide, a 2'-deoxy-modified nucleotide, a 2’-5’-linked ribonucleotide (3’-RNA), a locked nucleotide, an unlocked nucleotide, a conformationally restricted nucleotide, a constrained ethyl nucleotide, an abasic nucleotide, a 2’-amino-modified nucleotide, a 2’-O- allyl -modified nucleotide, 2’ -C-alkyl -modified nucleotide, 2’ -hydroxyl-modified nucleotide, a 2’ -O-(methoxy ethyl) modified nucleotide, a 2’-O-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate morpholino, a non-natural base comprising nucleotide, a tetrahydropyran modified nucleotide, a 1,5-anhydrohexitol modified nucleotide, a cyclohexenyl modified nucleotide, a nucleotide comprising a 5'-phosphorothioate group, a nucleotide comprising a 5'-methylphosphonate group, a nucleotide comprising a 5'- methylphosphate group, a nucleotide comprising a 5' phosphate or 5’ phosphate mimic, a nucleotide comprising vinyl phosphonate, a glycol nucleic acid (GNA), a glycol nucleic acid S-Isomer (S-GNA), a nucleotide comprising 2-hydroxymethyl-tetrahydrofurane-5-phosphate, a nucleotide comprising 2’-deoxythymidine-3’phosphate, a nucleotide comprising 2’- deoxy guanosine-3’ -phosphate; a cytidine-2'-phosphate, a guanosine-2'-phosphate, a uridine-Docket No.: SOUF-001-02WO2'-phosphate, an adenosine-2'-phosphate, a 2'-O-hexadecyl-adenosine-3'-phosphate, a 2'-0- hexadecyl-cytidine-3'-phosphate, a 2'-O-hexadecyl-guanosine-3'-phosphate, and a 2'-0- hexadecyl-uridine-3'-phosphate, a 3'-3' inverted nucleotide linkage, a 5’-5’ inverted nucleotide linkage, TNA, and combinations thereof.
31. The oligonucleotide of claim 30, wherein the oligonucleotide comprises a modified nucleotide selected from the group consisting of a deoxy nucleotide, a 3 ’-terminal deoxythymidine (dT) nucleotide, a 3'-3' inverted nucleotide linkage, a 5’-5’ inverted nucleotide linkage, a 5'-(E)-vinylphosphonate-2’-O-methyluridine-3' -phosphate, and a combination thereof.
32. The oligonucleotide of claim 30 or 31, wherein the oligonucleotide comprises 5'-(E)- vinylphosphonate-2’-O-methyluridine-3’ -phosphate.
33. The oligonucleotide of claim 21, wherein at least one of the modifications is a thermally destabilizing nucleotide modification.
34. The oligonucleotide of claim 33, wherein the thermally destabilizing nucleotide modification is selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; destabilizing sugar modification; a 2’-deoxy modification; an acyclic nucleotide, an unlocked nucleic acids (UNA); a glycerol nucleic acid (GNA), and a combination thereof.
35. The oligonucleotide of claim 31, wherein the modification comprises a short sequence of 3’- terminal deoxythymidine nucleotide (dT).
36. The oligonucleotide of any one of claims 21-35, wherein the modifications on the nucleotides are 2’-O-methyl and 2’deoxy-2’ -fluoro modifications.
37. The oligonucleotide of any one of claims 21-36, wherein the oligonucleotide comprises at least one phosphorothioate internucleoside or phosphorodithioate internucleoside linkage.
38. The oligonucleotide of claim 37, wherein the oligonucleotide comprises 6-8 phosphorothioate internucleoside linkages.Docket No.: SOUF-001-02WO39. The oligonucleotide of claim 37 or 38, wherein the oligonucleotide comprises at least 1 , or at least 2, phosphorothioate intemucleoside linkage at a 5’ end of the sense strand.
40. The oligonucleotide of any one of claims 37-39, wherein the oligonucleotide comprises at least 1 phosphorothioate intemucleoside linkage at a 3’ end of the sense strand.
41. The oligonucleotide of any one of claims 37-40, wherein the oligonucleotide comprises at least 1, or at least 2, phosphorothioate intemucleoside linkage at a 5’ end of the antisense strand.
42. The oligonucleotide of any one of claims 37-41, wherein the oligonucleotide comprises at least 1 phosphorothioate intemucleoside linkage at a 3’ end of the antisense strand.
43. The oligonucleotide of any one of claims 37-42, wherein no more than five of the nucleotides of the antisense strand are unmodified nucleotides.
44. The oligonucleotide of any one of claims 37-43, wherein all the nucleotides of the antisense strand are modified nucleotides.
45. The oligonucleotide of any one of claims 37-44, wherein no more than five of the nucleotides of the sense strand are unmodified nucleotides.
46. The oligonucleotide of any one of claims 37-45, wherein all the nucleotides of the sense strand are modified nucleotides.
47. The oligonucleotide of any one of claims 7-46, wherein the antisense strand comprises a chemical modification pattern according to (Nfs)a(nNf)b(ns)cn, wherein: n is a 2’-O-methyl-nucleoside-3’ -phosphate;Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphorothioate;Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate; ns is a 2'-O-methyl-nucleoside-3'-phosphorothioate; a is at least 1; b is 5-10; and c is at least 1.Docket No.: SOUF-001-02WO48. The oligonucleotide of claim 47, wherein the antisense strand comprises a chemical modification pattern NfsNfsnNfnNfnNfnNfnNfnNfnNfnNfnsnsn.
49. The oligonucleotide of any one of claims 7-48, wherein the sense strand comprises a chemical modification pattern according to (ns)d(Nfn)eNf, wherein: n is a 2’ -O-methyl-nucleoside-3’ -phosphate;Nf is a 2’ -deoxy-2'-fluoro-nucleoside-3’ -phosphate; ns is a 2’-O-methyl-nucleoside-3’-phosphorothioate; d is at least 1 ; and e is 5-10.
50. The oligonucleotide of claim 49, wherein the sense strand comprises a chemical modification pattern nsnsNfnNfnNfnNfnNfnNfnNfnNfnNf.
51. The oligonucleotide of any one of claims 7-50, wherein each of the antisense and the sense strand is independently 17-23 nucleotides in length, wherein the antisense strand comprises the motif F(SF)nSnn, wherein n is from 2 to about 20, nn is 0 or 1, one of F and S is a 2'- deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O-methyl modified nucleoside.
52. The oligonucleotide of any one of claims 7-51, wherein the antisense strand comprises the chemical modification pattern of nNfnnnNfnNfNfnnnnNfnNfnnnnn and the sense strand comprises the chemical modification nnnnnnNfnNfNfNfnnnnnnnn, wherein n is a 2’ -O- methyl-nucleoside and Nf is a 2’-deoxy-2’-fluoro-nucleoside.
53. The oligonucleotide of any one of claims 7-52, wherein each of the antisense and the sense strand is independently 20-23 nucleotides in length, wherein the antisense strand comprises a region having the formula X1-Y-X2, wherein Y is a subregion of from about 5 to about 12 linked nucleosides and each of XI subregion and X2 subregion is, independently, a plurality of linked nucleosides having the formula FSFS, where one of F and S is a 2'-deoxy-2’ -fluoro modified nucleoside and the other of F and S is a 2'-O-methyl modified nucleoside; and each intemucleoside linkage of said XI subregion and X2 subregion is, independently, a phosphodiester or a phosphorothioate intemucleoside linkage.
54. The oligonucleotide of any one of claims 7-53, wherein each of the antisense and the sense strand is independently 17-23 nucleotides in length, wherein the antisense strand comprises a contiguous sequence of linked nucleosides that define an alternating motif of the formula:Docket No.: SOUF-001-02WO5 '-Q(-L-Z-L-Q)n(-L-Z)nn-3' wherein: each L is an intemucleoside linking group; either each Q is a 2'-deoxy-2" -fluoro-nucleoside and each Z is a 2'-O-methyl nucleoside, or each Q is a 2'-O-methyl nucleoside and each Z is a 2'-deoxy-2’ -fluoro nucleoside; n is from 8 to 14; and nn is 0 or 1.
55. The oligonucleotide of any one of claims 7-54, wherein the antisense strand is 19-25 nucleotides in length and is represented by the formula:wherein:BT, B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA;TT, T2', and T3' each independently represent a nucleotide comprising a chemical modification selected from the group consisting of DNA, RNA, LNA, 2'-deoxy-2’ -fluoro, and 5'-methyl-2'-deoxy-2’ -fluoro nucleotides; ql is 4 to 15 nucleotides in length; q3 or q7 is independently 1-6 nucleotide(s) in length; q2 or q6 is independently 1-3 nucleotide(s) in length; q4 is 0-3 nucleotide(s) in length; and q5 is 0-10 nucleotide(s) in length; wherein: the antisense strand has 2'-deoxy-2’ -fluoro modifications, and wherein the 2'-deoxy-2’- fluoro modifications on the antisense strand consist of four, and only four, 2'-deoxy-2’ -fluoro modifications, or six, and only six, 2'-deoxy-2’ -fluoro modifications.
56. The oligonucleotide of any one of claims 7-55, wherein the antisense strand and sense strand are each 14 to 40 nucleotides, and are represented by the formula:Docket No.: SOUF-001-02WOwherein:B l, Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'- substituted alkyl, 2'-halo, ENA, and BNA / LNA;Cl is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugar modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand;IT, T2', and T3' each independently represent a nucleotide comprising a modification providing the nucleotide a steric bulk that is less than or equal to the steric bulk of a 2'-0Me modification, wherein the modification is at the 2'-position of a ribose sugar of the nucleotide or at a position of a non-ribose nucleotide similar to the 2'- position of a ribose sugar; each nl, and ql is independently 4 to 15 nucleotides in length; each q3, and q7 is independently 1-6 nucleotide(s) in length; each q2 and q6 is independently 1-3 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4. and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length, and T1 each are 2'-deoxy-2’ -fluoro nucleotides; n3 is 7 nucleotides in length, and B2 each are 2'-0Me nucleotides; and n5 is 3 nucleotides in length, and B3 each are 2'-0Me nucleotides.Docket No.: SOUF-001-02WO57. The oligonucleotide of any one of claims 7-56, wherein the antisense strand and sense strand are each 19-25 nucleotides in length, wherein the antisense strand is represented by the formula:(Is)wherein:Bl, B2, and B3 each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-alkyl, 2'-substituted alkoxy, 2'-substituted alkyl, 2'- halo, ENA, and BNA / LNA;C 1 is a thermally destabilizing nucleotide, selected from the group consisting of i) a nucleotide that forms a mismatch pair with the opposing nucleotide in the antisense strand, ii) a nucleotide having an abasic modification, and iii) a nucleotide having a sugar modification, and placed at a site opposite to the seed region (positions 2-8) of the antisense strand:T1 represents a nucleotide comprising a 2'-deoxy-2’ -fluoro modification; nl or n3 is independently 4 to 15 nucleotides in length; n5 is 1-6 nucleotide(s) in length; n2 is 3; n4 is 0-3 nucleotide(s) in length; and wherein the sense strand has 2'-deoxy-2’-fluoro modifications, and wherein the 2'-deoxy- 2’ -fluoro modifications on the sense strand consist of four, and only four, 2’-deoxy-2’ -fluoro modifications, wherein the four 2'-deoxy-2’ -fluoro modifications are at positions 7 and 9-11 from the 5'-end of the sense strand.
58. The oligonucleotide of any one of claims 7-57, wherein the antisense strand is complementary to at least one portion of a mRNA of the target gene (e.g., ACVR2B), wherein: the sense strand comprises 19-22 nucleotides, the antisense strand comprises 19-25 nucleotides; and the oligonucleotide is represented by the formula:Docket No.: SOUF-001-02WO(Twherein:Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-methyl and 2'-deoxy-2’ -fluoro; each Bl, B2, and B3 is 2'-O-methyl nucleotide;Cl is glycerol nucleic acid (GNA) placed at a site opposite to the seed region (positions 2-8) of the antisense strand;Tl', T2', and T3' are each 2'-F, wherein:Tl' is at position 14 from the 5' end of the antisense strand, and q2 is 1 ; andT3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1 ; each nl, n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length; andTl each are 2'-deoxy-2' -fluoro nucleotides, wherein(a) the oligonucleotide is covalently conjugated to at least one ligand; and(b) one of the Tl nucleotides is at position 11 from the 5' end of the sense strand.
59. The oligonucleotide of any one of claims 7-58, wherein the sense strand comprises 19-22 nucleotides, the antisense strand comprises 19-25 nucleotides; and the oligonucleotide is represented by the formula:Docket No.: SOUF-001-02WO(Dwherein:Bl', B2', B3', and B4' each independently represent a nucleotide containing a modification selected from the group consisting of 2'-O-methyl and 2'-deoxy-2' -fluoro; each Bl, B2, and B3 is 2'-0Me;C l is glycerol nucleic acid (GNA) placed at a site opposite to the seed region (positions 2-8) of the antisense strand;Tl', T2', and T3' are each 2'-deoxy-2’ -fluoro, wherein:Tl' is at position 14 from the 5' end of the antisense strand, and q2 is 1; andT3' is at position 2 from the 5' end of the antisense strand, and q6 and q7 are 1; each nl, n3, and ql is independently 4 to 15 nucleotides in length; each n5 and q3 is independently 1-6 nucleotide(s) in length; q5 is 0-10 nucleotide(s) in length; each n4 and q4 is independently 0-3 nucleotide(s) in length; n2 is 3 nucleotides in length; andTl each are 2'-deoxy-2' -fluoro, and wherein(a) the oligonucleotide is covalently conjugated to at least one ligand;(b) one of the Tl nucleotides is at a position in the sense strand that is opposite to position 11 from the 5' end of the antisense strand; and(c) the oligonucleotide comprises at least one phosphorothioate internucleoside linkage.
60. The oligonucleotide of any one of claims 7-59, wherein the antisense strand and sense strand are each 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity toDocket No.: SOUF-001-02WO a target sequence to mediate RNA interference, wherein said sense strand comprises at least one thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5' region of the antisense strand or a precursor thereof, wherein the antisense strand further comprises one or both of the following characteristics:(i) 2, 3, 4, 5 or 6 2'-deoxy-2’ -fluoro modifications: and(ii) 1, 2, 3, 4 or 5 phosphorothioate internucleoside linkages; and said sense strand comprises one or both of the following characteristics:(iii) 2, 3, 4, or 5 2'-deoxy-2’ -fluoro modifications; and(iv) 1, 2, 3, 4 or 5 phosphorothioate internucleoside linkages.
61. The oligonucleotide of any one of claims 7-46, wherein the antisense strand comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2'-O-methyl- nucleoside-3 '-phosphorothioate; Nfs is a 2'-deoxy-2'-fhroro-nucleoside-3'-phosphorothioate: n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphate.
62. The oligonucleotide of any one of claims 7-46, wherein the antisense strand disclosed herein comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'-vinylphosphonate-2'-O-methyl-uridine-3’ -phosphorothioate; ns is a 2'-0-methyl- nucleoside-3 '-phosphorothioate; Nfs is a 2'-deoxy-2'-fhroro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphate.
63. The oligonucleotide of any one of claims 7-46, wherein the sense strand disclosed herein comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, wherein ns is a 2'-O- methyl-nucleoside-3 '-phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3 '-phosphate.
64. The oligonucleotide of any one of claims 7-46, wherein the sense strand disclosed herein comprises a modification pattern NfsnsNfnNfnNfnNfnNfnNfnNfnNfnNf, wherein ns is a 2'- O-methyl-nucleoside-3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fluoro-nucleoside-3'- phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro- nucleoside-3'-phosphate.Docket No.: SOUF-001-02WO65. The oligonucleotide of any one of claims 7-46, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein ns is a 2'-O-methyl- nucleoside-3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fhioro-nucleoside-3'-phosphorothioate; n is a 2'-O-methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fhioro-nucleoside-3'- phosphate.
66. The oligonucleotide of any one of claims 7-46, wherein the sense strand comprises a modification pattern nsnsnnNfnNfNfNfnnnnnnnnnn, and the antisense strand comprises a modification pattern vpUsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn, wherein vpUs is a 5'- vinylphosphonate-2'-O-methyl-uridine-3’-phosphorothioate; ns is a 2'-O-methyl-nucleoside- 3'-phosphorothioate; Nfs is a 2'-deoxy-2'-fhioro-nucleoside-3'-phosphorothioate; n is a 2'-O- methyl-nucleoside-3’ -phosphate; and Nf is a 2'-deoxy-2'-fluoro-nucleoside-3'-phosphate.
67. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 3682-4931.
68. The oligonucleotide of claim 67, wherein the sense strand comprises a nucleotide sequence according to any one of SEQ ID NOs: 2455-3681.
69. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4909, and the sense strand comprises SEQ ID NO: 2464.
70. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4910, and the sense strand comprises SEQ ID NO: 2566.
71. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4911, and the sense strand comprises SEQ ID NO: 2600.
72. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4912, and the sense strand comprises SEQ ID NO: 2681.
73. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4913, and the sense strand comprises SEQ ID NO: 2682.Docket No.: SOUF-001-02WO74. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4914, and the sense strand comprises SEQ ID NO: 2683.
75. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4915, and the sense strand comprises SEQ ID NO: 2685.
76. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4916, and the sense strand comprises SEQ ID NO: 2827.
77. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4917, and the sense strand comprises SEQ ID NO: 2832.
78. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4918, and the sense strand comprises SEQ ID NO: 2840.
79. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4919, and the sense strand comprises SEQ ID NO: 2844.
80. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4920, and the sense strand comprises SEQ ID NO: 2845.
81. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4921, and the sense strand comprises SEQ ID NO: 2846.
82. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4922, and the sense strand comprises SEQ ID NO: 2886.
83. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4923, and the sense strand comprises SEQ ID NO: 2899.
84. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4924, and the sense strand comprises SEQ ID NO: 2900.Docket No.: SOUF-001-02WO85. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4925, and the sense strand comprises SEQ ID NO: 2902.
86. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4926, and the sense strand comprises SEQ ID NO: 2903.
87. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4927, and the sense strand comprises SEQ ID NO: 3048.
88. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4928, and the sense strand comprises SEQ ID NO: 3061.
89. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4929, and the sense strand comprises SEQ ID NO: 3066.
90. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4930, and the sense strand comprises SEQ ID NO: 3067.
91. The oligonucleotide of any one of claims 7-66, wherein the antisense strand comprises SEQ ID NO: 4931, and the sense strand comprises SEQ ID NO: 3068.
92. The oligonucleotide of any one of claims 7-91, further comprising a terminal, chiral modification occurring at the first intemucleoside linkage at the 3 ’-end of the antisense strand, having the linkage phosphoms atom in Sp configuration, a terminal, chiral modification occurring at the first internucleoside linkage at the 5 ’-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first internucleoside linkage at the 5 ’-end of the sense strand, having the linkage phosphorus atom in either Rp configuration or Sp configuration.
93. The oligonucleotide of any one of claims 7-92, further comprising a terminal, chiral modification occurring at the first and second internucleoside linkages at the 3 ’-end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the antisense strand, having the linkage phosphoms atom in Rp configuration, and a terminal, chiral modificationDocket No.: SOUF-001-02WO occurring at the first internucleoside linkage at the 5’ -end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
94. The oligonucleotide of any one of claims 7-93, further comprising a terminal, chiral modification occurring at the first, second and third intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
95. The oligonucleotide of any one of claims 7-94, further comprising a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 3’ end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the third intemucleoside linkages at the 3 ’-end of the antisense strand, having the linkage phosphorus atom in Rp configuration, a terminal, chiral modification occurring at the first intemucleoside linkage at the 5’ -end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5 ’-end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
96. The oligonucleotide of any one of claims 7-95, further comprising a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 3 ’-end of the antisense strand, having the linkage phosphorus atom in Sp configuration, a terminal, chiral modification occurring at the first, and second intemucleoside linkages at the 5’ -end of the antisense strand, having the linkage phosphorus atom in Rp configuration, and a terminal, chiral modification occurring at the first intemucleoside linkage at the 5' -end of the sense strand, having the linkage phosphorus atom in either Rp or Sp configuration.
97. The oligonucleotide of any one of claims 1-96, further comprising a phosphate or phosphate mimic at the 5 ’-end of the antisense strand.
98. The oligonucleotide of claim 97, wherein the phosphate mimic is a 5’-vinyl phosphonate (VP).
99. The oligonucleotide of any one of claims 1-98, further comprising a targeting ligand.Docket No.: SOUF-001-02WO100. The oligonucleotide of claim 99, wherein the targeting ligand is a small molecule-based, sugar-based (e.g., saccharide-based), fatty acid-based, protein-based, or nucleic acid-based targeting ligand.
101. The oligonucleotide of claim 100, wherein the protein-based targeting ligand is an antibody, nanobody, affibody, peptibody, or a peptide.
102. An oligonucleotide selected from the sense strands, antisense strands, and RNAi agents as listed in Tables 1A, IB, and 1C, or a pharmaceutically acceptable salt thereof.
103. A pharmaceutical composition comprising the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or excipient.
104. A method for inhibiting ACVR2B expression or treating an ACVR2B related disorder in a subject, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
105. The method of claim 104, wherein the subject is a human.
106. The method of claim 104 or 105, wherein the reduction of ACVR2B mRNA or protein expression levels is measured in a population of myocytes or cardiomyocytes derived from the subject.
107. The method of any one of claims 104-106, wherein the reduction of ACVR2B mRNA or protein expression levels is measured in tissues derived from the subject.
108. The method of any one of claims 104-107, further comprising administering to the subject an additional agent or a therapy suitable for treatment or prevention of an ACVR2B related disorder.
109. A method of treating obesity in a subject in need thereof, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or aDocket No.: SOUF-001-02WO pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
110. A method of preserving or increasing muscle mass in a subject in need of treatment for weight loss, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
111. A method of preserving or increasing muscle mass in a subject in need of treatment for reduction of excess body weight or for maintenance of weight reduction, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1 - 102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
112. A method of preserving or increasing muscle mass in a subject in need of treatment for a reduction of major adverse cardiovascular events (e.g., cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke), the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
113. A method of preserving or increasing muscle mass in a subject in need of treatment for type 2 diabetes, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
114. A method of inhibiting ActRII (e.g., through inhibition of ACVR2B expression) in a subject experiencing weight loss, the method comprising administering an effective amount of the oligonucleotide of any one of claims 1-102, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 103 to the subject.
115. The method of any one of claims 104-114, wherein the subject is receiving or has received a GLP-1 receptor agonist (e.g., semaglutide, dulaglutide, liraglutide, exenatide, tirzepatide).