CROSS-REFERENCE
This application claims the benefit of U.S. Provisional Application No. 63/213,054 filed Jun. 21, 2021, which is incorporated by reference herein in its entirety
BACKGROUND OF THE INVENTION
Alopecia (hair loss) is ever abundant, and affects many people. Improved therapeutics are needed for treating hair loss.
SUMMARY OF THE INVENTION
Described herein are compositions comprising an oligonucleotide that targets dickkopf WNT signaling pathway inhibitor 2 (DKK2) and when administered to a subject in an effective amount reduces a DKK2 mRNA or protein level. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a hair count in the subject. In some embodiments, the hair count is increased by about 10% or more, as compared to prior to administration. In some embodiments, the hair count includes a vellus hair count, a non-vellus hair count, or a total hair count. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a hair thickness measurement in the subject. In some embodiments, the hair thickness measurement is increased by about 10% or more, as compared to prior to administration. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a hair density measurement in the subject. In some embodiments, the hair density measurement is increased by about 10% or more, as compared to prior to administration. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a number of hair follicles in the subject. In some embodiments, the number of hair follicles is increased by about 10% or more, as compared to prior to administration. In some embodiments, the number of hair follicles includes a number of terminal hair follicles, a number of anagen hair follicles, a number of telogen hair follicles, a number of catagen hair follicles, a number of vellus-like miniaturized hair follicles, a number of indeterminate hair follicles, or a total number of hair follicles. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount changes a hair loss assessment score in the subject. In some embodiments, the hair loss assessment score is changed by about 10% or more, as compared to prior to administration. Described herein, in some embodiments, are compositions comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount changes a protein or mRNA level of β-catenin, α-SMA, collagen I, or collagen III, in the subject. In some embodiments, the protein or mRNA level of β-catenin, α-SMA, collagen I, or collagen III is changed by about 10% or more, as compared to prior to administration. Described herein, in some embodiments, is a composition comprising an oligonucleotide that targets DKK2 and when administered to the skin of a subject in an effective amount decreases a level of DKK2 mRNA or DKK2 protein. In some embodiments, the skin comprises scalp skin. In some embodiments, the level of DKK2 mRNA or DKK2 protein decreased by about 10% or more, as compared to prior to administration. In some embodiments, the oligonucleotide comprises a modified internucleoside linkage. In some embodiments, the modified internucleoside linkage comprises alkylphosphonate, phosphorothioate, methylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester, or a combination thereof. In some embodiments, the modified internucleoside linkage comprises one or more phosphorothioate linkages. In some embodiments, the oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 modified internucleoside linkages. In some embodiments, the oligonucleotide comprises 2 or more modified internucleoside linkages, 3 or more modified internucleoside linkages, 4 or more modified internucleoside linkages, 5 or more modified internucleoside linkages, 6 or more modified internucleoside linkages, 7 or more modified internucleoside linkages, 8 or more modified internucleoside linkages, 9 or more modified internucleoside linkages, 10 or more modified internucleoside linkages, 11 or more modified internucleoside linkages, 12 or more modified internucleoside linkages, 13 or more modified internucleoside linkages, 14 or more modified internucleoside linkages, 15 or more modified internucleoside linkages, 16 or more modified internucleoside linkages, 17 or more modified internucleoside linkages, 18 or more modified internucleoside linkages, 19 or more modified internucleoside linkages, or 20 or more modified internucleoside linkages. In some embodiments, the oligonucleotide comprises a modified nucleoside. In some embodiments, the modified nucleoside comprises a locked nucleic acid (LNA), hexitol nucleic acid (HLA), cyclohexene nucleic acid (CeNA), 2′-methoxyethyl, 2′-O-alkyl, 2′-O-allyl, 2′-O-allyl, 2′-fluoro, or 2′-deoxy, or a combination thereof. In some embodiments, the modified nucleoside comprises a LNA. In some embodiments, the modified nucleoside comprises a 2′,4′ constrained ethyl nucleic acid. In some embodiments, the modified nucleoside comprises a 2′-O-methyl nucleoside, 2′-deoxyfluoro nucleoside, 2′-O—N-methylacetamido (2′-O-NMA) nucleoside, a 2′-O-dimethylaminoethoxyethyl (2′-O-DMAEOE) nucleoside, 2′-O-aminopropyl (2′-O-AP) nucleoside, or 2′-ara-F, or a combination thereof. In some embodiments, the modified nucleoside comprises one or more 2′fluoro modified nucleosides. In some embodiments, the modified nucleoside comprises a 2′ O-alkyl modified nucleoside. In some embodiments, the oligonucleotide comprises a lipid attached at a 3′ or 5′ terminus of the oligonucleotide. In some embodiments, the lipid comprises cholesterol, myristoyl, palmitoyl, stearoyl, lithocholoyl, docosanoyl, docosahexaenoyl, myristyl, palmityl, stearyl, or α-tocopherol, or a combination thereof. In some embodiments, the oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 modified nucleosides. In some embodiments, the oligonucleotide comprises 2 or more modified nucleosides, 3 or more modified nucleosides, 4 or more modified nucleosides, 5 or more modified nucleosides, 6 or more modified nucleosides, 7 or more modified nucleosides, 8 or more modified nucleosides, 9 or more modified nucleosides, 10 or more modified nucleosides, 11 or more modified nucleosides, 12 or more modified nucleosides, 13 or more modified nucleosides, 14 or more modified nucleosides, 15 or more modified nucleosides, 16 or more modified nucleosides, 17 or more modified nucleosides, 18 or more modified nucleosides, 19 or more modified nucleosides, 20 or more modified nucleosides, or 21 or more modified nucleosides. In some embodiments, the oligonucleotide comprises a small interfering RNA (siRNA) comprising a sense strand and an antisense strand. In some embodiments, the sense strand is 14-30 nucleosides in length. In some embodiments, the sense strand comprises the sequence of any one of SEQ ID NOs: 1-3636, or a variant thereof (such as a sequence having 1 or 2 substitutions, insertions, or deletions). In some embodiments, any one of the following is true with regard to the sense strand: all purines comprise 2′ fluoro modified purines, and all pyrimidines comprise a mixture of 2′ fluoro and 2′ methyl modified pyrimidines; all purines comprise 2′ methyl modified purines, and all pyrimidines comprise a mixture of 2′ fluoro and 2′ methyl modified pyrimidines; all purines comprise 2′ fluoro modified purines, and all pyrimidines comprise 2′ methyl modified pyrimidines; all pyrimidines comprise 2′ fluoro modified pyrimidines, and all purines comprise a mixture of 2′ fluoro and 2′ methyl modified purines; all pyrimidines comprise 2′ methyl modified pyrimidines, and all purines comprise a mixture of 2′ fluoro and 2′ methyl modified purines; or all pyrimidines comprise 2′ fluoro modified pyrimidines, and all purines comprise 2′ methyl modified purines. In some embodiments, the sense strand comprises any one of modification patterns 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S. In some embodiments, the antisense strand is 14-30 nucleosides in length. In some embodiments, the sense strand comprises the sequence of any one of SEQ ID NOs: 3637-7272, or a variant thereof (such as a sequence having 1 or 2 substitutions, insertions, or deletions). In some embodiments, any one of the following is true with regard to the antisense strand: all purines comprise 2′ fluoro modified purines, and all pyrimidines comprise a mixture of 2′ fluoro and 2′ methyl modified pyrimidines; all purines comprise 2′ methyl modified purines, and all pyrimidines comprise a mixture of 2′ fluoro and 2′ methyl modified pyrimidines; all purines comprise 2′ methyl modified purines, and all pyrimidines comprise 2′ fluoro modified pyrimidines; all pyrimidines comprise 2′ fluoro modified pyrimidines, and all purines comprise a mixture of 2′ fluoro and 2′ methyl modified purines; all pyrimidines comprise 2′ methyl modified pyrimidines, and all purines comprise a mixture of 2′ fluoro and 2′ methyl modified purines; or all pyrimidines comprise 2′ methyl modified pyrimidines, and all purines comprise 2′ fluoro modified purines. In some embodiments, the antisense strand comprises any one of modification patterns 1AS, 2AS, 3AS, 4AS, or 5AS. Described herein, in some embodiments, are compositions comprising an oligonucleotide that inhibits the expression of DKK2 wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, each strand is independently about 14-30 nucleosides in length, and at least one of the sense strand and the antisense strand comprises a nucleoside sequence comprising about 14-30 contiguous nucleosides of SEQ ID NO: 7599. Described herein, in some embodiments, are compositions comprising an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, each strand is independently about 14-30 nucleosides in length, and at least one of the sense strand and the antisense strand comprises a nucleoside sequence comprising about 14-30 contiguous nucleosides of a full-length human DKK2 pre-mRNA sequence. Described herein, in some embodiments, are methods of treating hair loss in a subject in need thereof comprising administering to the subject a composition described herein. In some embodiments, the hair loss comprises any one or more of male pattern baldness, alopecia areata, or non-scarring hair loss. In some embodiments, the administration is topical.
DETAILED DESCRIPTION OF THE INVENTION
Large-scale human genetic data can improve the success rate of pharmaceutical discovery and development. A Genome Wide Association Study (GWAS) may detect associations between genetic variants and traits in a population sample. A GWAS may enable better understanding of the biology of disease, and provide applicable treatments. A GWAS can utilize genotyping and/or sequencing data, and often involves an evaluation of millions of genetic variants that are relatively evenly distributed across the genome. The most common GWAS design is the case-control study, which involves comparing variant frequencies in cases versus controls. If a variant has a significantly different frequency in cases versus controls, that variant is said to be associated with disease. Association statistics that may be used in a GWAS are p-values, as a measure of statistical significance; odds ratios (OR), as a measure of effect size; or beta coefficients (beta), as a measure of effect size. Researchers often assume an additive genetic model and calculate an allelic odds ratio, which is the increased (or decreased) risk of disease conferred by each additional copy of an allele (compared to carrying no copies of that allele). An additional concept in design and interpretation of GWAS is that of linkage disequilibrium, which is the non-random association of alleles. The presence of linkage disequilibrium can obfuscate which variant is “causal.”
Functional annotation of variants and/or wet lab experimentation can identify the causal genetic variant identified via GWAS, and in many cases may lead to the identification of disease-causing genes. In particular, understanding the functional effect of a causal genetic variant (for example, loss of protein function, gain of protein function, increase in gene expression, or decrease in gene expression) may allow that variant to be used as a proxy for therapeutic modulation of the target gene, or to gain insight into potential therapeutic efficacy and safety of a therapeutic that modulates that target.
Identification of such gene-disease associations has provided insights into disease biology and may be used to identify novel therapeutic targets for the pharmaceutical industry. In order to translate the therapeutic insights derived from human genetics, disease biology in patients may be exogenously ‘programmed’ into replicating the observation from human genetics. There are several potential options for therapeutic modalities that may be brought to bear in translating therapeutic targets identified via human genetics into novel medicines. These may include well established therapeutic modalities such as small molecules and monoclonal antibodies, maturing modalities such as oligonucleotides, and emerging modalities such as gene therapy and gene editing. The choice of therapeutic modality can depend on several factors including the location of a target (for example, intracellular, extracellular, or secreted), a relevant tissue (for example, skin) and a relevant indication.
Hair loss is a common problem, particularly among men, but is also common among women. It may be affected by any of several factors, including heredity, hormones, thyroid disorders, nutritional status, environmental factors, physical stress, or emotional stress. Hair loss may include, among other things, androgenetic alopecia (male pattern baldness), alopecia areata, or non-scarring hair loss. The DKK2 gene is located on chromosome 4 and encodes dickkopf WNT signaling pathway inhibitor 2 (DKK2), a member of the dickkopf family. A non-limiting example of a DKK2 gene is included on GenBank under NCBI reference sequence NM_014421.3 (May 9, 2020). DKK2 proteins may be secreted, include two cysteine rich regions, and be involved in embryonic development through interactions with the Wnt signaling pathway. DKK2 can act as either an agonist or antagonist of Wnt/beta-catenin signaling, depending on the cellular context and the presence of the co-factor kremen 2. Activity of DKK2 may also be modulated by binding to the Wnt co-receptor LDL-receptor related protein 6 (LRP6). In some cases, DKK2 protein is intracellular. In some cases, DKK2 protein is secreted. The secreted DKK2 protein may be locally secreted. Here, it is shown that genetic variants that cause inactivation of the DKK2 gene in humans are associated with decreased risk of male pattern baldness. Therefore, inhibition of DKK2 serve as a therapeutic strategy for treatment of hair loss such as male pattern baldness, alopecia areata, or non-scarring hair loss.
Disclosed herein are compositions comprising an oligonucleotide that targets DKK2. The oligonucleotide may include a small interfering RNA (siRNA) or an antisense oligonucleotide (ASO). Also provided herein are methods of treating hair loss by providing an oligonucleotide that targets DKK2 to a subject in need thereof.
I. Compositions
Disclosed herein, in some embodiments, are compositions comprising an oligonucleotide. In some embodiments, the composition comprises an oligonucleotide that targets dickkopf WNT signaling pathway inhibitor 2 (DKK2). In some embodiments, the composition consists of an oligonucleotide that targets DKK2. In some embodiments, the oligonucleotide reduces DKK2 mRNA expression in the subject. In some embodiments, the oligonucleotide reduces DKK2 protein expression in the subject. The oligonucleotide may include a small interfering RNA (siRNA) described herein. The oligonucleotide may include an antisense oligonucleotide (ASO) described herein. In some embodiments, a composition described herein is used in a method of treating a disorder in a subject in need thereof. Some embodiments relate to a composition comprising an oligonucleotide for use in a method of treating a disorder as described herein. Some embodiments relate to use of a composition comprising an oligonucleotide, in a method of treating a disorder as described herein.
Some embodiments include a composition comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount decreases DKK2 mRNA or protein levels in a cell, fluid or tissue. Some embodiments include a composition comprising an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount decreases DKK2 mRNA levels in a cell or tissue. In some embodiments, the cell is a skin cell. In some embodiments, the tissue is skin (e.g. scalp dermis). In some embodiments, the DKK2 mRNA levels are decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by about 10% or more, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100%, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by no more than about 10%, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the DKK2 mRNA levels are decreased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount decreases DKK2 protein levels in a cell, fluid or tissue. In some embodiments, the cell is a skin cell. In some embodiments, the fluid is a blood, serum, or plasma. In some cases, the administration of the oligonucleotide decreases circulatingDKK2 protein levels. In some embodiments, the tissue is skin (e.g. scalp dermis). In some embodiments, the DKK2 protein levels are decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by about 10% or more, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100%, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by no more than about 10%, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the DKK2 protein levels are decreased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount decreases hair loss (e.g. male pattern baldness, alopecia areata, or non-scarring hair loss) or a symptom of hair loss. In some embodiments, the hair loss or symptom of hair loss is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by about 10% or more, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100%, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by no more than about 10%, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the hair loss or symptom of hair loss is decreased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the hair loss or symptom of hair loss is assessed by phototrichogram. In some embodiments, the hair loss or symptom of hair loss is assessed by a macrophotography analysis.
In some embodiments, the hair loss or symptom of hair loss is assessed by a questionnaire such as a Men's Hair Growth Questionnaire (MHGQ) or a Kingsley Alopecia Profile (KAP) questionnaire. In some embodiments, the hair loss or symptom of hair loss is assessed by a scalp biopsy. In some embodiments, the decrease in hair loss or symptom of hair loss is determined as a change in a hair loss hair loss assessment score. For example, the change in the hair loss assessment score may be an increase in the hair loss assessment score. In some embodiments, the change in the hair loss assessment score is a decrease in the hair loss assessment score. In some embodiments, the hair loss assessment score is obtained as part of an assessment that includes the questionnaire. In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount results in a change in an hair loss assessment score. In some embodiments, the hair loss assessment score is changed by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by about 10% or more, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by no more than about 10%, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the hair loss assessment score is changed by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a total hair count (e.g. a vellus and non-vellus hair count). In some embodiments, the total hair count is determined in an area of skin. In some embodiments, the total hair count is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the total hair count is increased by about 10% or more, as compared to prior to administration. In some embodiments, the total hair count is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the total hair count is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the total hair count is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the total hair count is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the total hair count is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the total hair count is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the total hair count is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the total hair count is assessed by phototrichogram. In some embodiments, the total hair count is assessed by a macrophotography analysis.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a vellus hair count. In some embodiments, the vellus hair count is determined in an area of skin. In some embodiments, the vellus hair count is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the vellus hair count is increased by about 10% or more, as compared to prior to administration. In some embodiments, the vellus hair count is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the vellus hair count is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the vellus hair count is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the vellus hair count is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the vellus hair count is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the vellus hair count is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the vellus hair count is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the vellus hair count is assessed by phototrichogram. In some embodiments, the vellus hair count is assessed by a macrophotography analysis.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a non-vellus hair count. In some embodiments, the non-vellus hair count is determined in an area of skin. In some embodiments, the non-vellus hair count is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by about 10% or more, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the non-vellus hair count is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the non-vellus hair count is assessed by phototrichogram. In some embodiments, the non-vellus hair count is assessed by a macrophotography analysis.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases hair thickness. In some embodiments, the thicknesses (e.g. widths) of individual hairs are increased. In some embodiments, the hair thickness is determined in an area of skin. The increased hair thickness may include an increased vellus hair thickness. The increased hair thickness may include an increased non-vellus hair thickness. In some embodiments, the hair thickness is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the hair thickness is increased by about 10% or more, as compared to prior to administration. In some embodiments, the hair thickness is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the hair thickness is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the hair thickness is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the hair thickness is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the hair thickness is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the hair thickness is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the hair thickness is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the hair thickness is assessed by phototrichogram. In some embodiments, the hair thickness is assessed by a macrophotography analysis.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases hair density. In some embodiments, the hair density is determined in an area of skin. In some embodiments, the hair density comprises a number of hairs per an area of skin. The increased hair density may include an increased vellus hair density. The increased hair density may include an increased non-vellus hair density. In some embodiments, the hair density is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the hair density is increased by about 10% or more, as compared to prior to administration. In some embodiments, the hair density is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the hair density is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the hair density is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the hair density is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the hair density is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the hair density is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the hair density is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the hair density is assessed by phototrichogram. In some embodiments, the hair density is assessed by a macrophotography analysis.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a number of hair follicles. In some embodiments, the number of hair follicles is determined in an area of skin. The hair follicles may include terminal hair follicles, anagen hair follicles, telogen hair follicles, catagen hair follicles, vellus or vellus-like miniaturized hair follicles, or indeterminate hair follicles. In some embodiments, the hair follicles include terminal hair follicles. In some embodiments, the hair follicles include anagen hair follicles. In some embodiments, the hair follicles include telogen hair follicles. In some embodiments, the hair follicles include catagen hair follicles. In some embodiments, the hair follicles include vellus or vellus-like miniaturized hair follicles. In some embodiments, the hair follicles include indeterminate hair follicles. In some embodiments, the number of hair follicles is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by about 10% or more, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the number of hair follicles is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the number of hair follicles is assessed in a scalp biopsy.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount increases a hair color measurement. In some embodiments, the hair color measurement is determined on an area of skin. In some embodiments, the hair color measurement is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the hair color measurement is increased by about 10% or more, as compared to prior to administration. In some embodiments, the hair color measurement is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the hair color measurement is increased by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the hair color measurement is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the hair color measurement is increased by no more than about 10%, as compared to prior to administration. In some embodiments, the hair color measurement is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the hair color measurement is increased by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the hair color measurement is increased by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition comprises an oligonucleotide that targets DKK2 and when administered to a subject in an effective amount results in a change in expression of a gene or protein. The gene or protein may include a β-catenin gene. The gene or protein may include a β-catenin protein. The gene or protein may include an α-SMA gene. The gene or protein may include an α-SMA protein. The gene or protein may include a collagen I gene. The gene or protein may include a collagen I protein. The gene or protein may include a collagen III gene. The gene or protein may include a collagen III protein. In some embodiments, the change in expression is determined in a tissue (e.g. skin), cell, or fluid sample. In some embodiments, the expression is changed by about 2.5% or more, about 5% or more, or about 7.5% or more, as compared to prior to administration. In some embodiments, the expression is changed by about 10% or more, as compared to prior to administration. In some embodiments, the expression is changed by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, or about 100% or more, as compared to prior to administration. In some embodiments, the expression is changed by about 200% or more, about 300% or more, about 400% or more, about 500% or more, about 600% or more, about 700% or more, about 800% or more, about 900% or more, or about 1000% or more, as compared to prior to administration. In some embodiments, the expression is changed by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, as compared to prior to administration. In some embodiments, the expression is changed by no more than about 10%, as compared to prior to administration. In some embodiments, the expression is changed by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100%, as compared to prior to administration. In some embodiments, the expression is changed by no more than about 200%, no more than about 300%, no more than about 400%, no more than about 500%, no more than about 600%, no more than about 700%, no more than about 800%, no more than about 900%, or no more than about 1000%, as compared to prior to administration. In some embodiments, the expression is changed by 2.5%, 5%, 7.5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000%, or by a range defined by any of the two aforementioned percentages.
A. siRNAs
In some embodiments, the composition comprises an oligonucleotide that targets DKK2, wherein the oligonucleotide comprises a small interfering RNA (siRNA). In some embodiments, the composition comprises an oligonucleotide that targets DKK2, wherein the oligonucleotide comprises a small interfering RNA (siRNA) comprising a sense strand and an antisense strand.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand is 14-30 nucleosides in length. In some embodiments, the composition comprises a sense strange that is at least about 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleosides in length, or a range defined by any of the two aforementioned numbers. In some embodiments, the composition comprises an antisense strand is 14-30 nucleosides in length. In some embodiments, the composition comprises an antisense strange that is at least about 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleosides in length, or a range defined by any of the two aforementioned numbers.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, each strand is independently about 14-30 nucleosides in length, and at least one of the sense strand and the antisense strand comprises a nucleoside sequence comprising about 14-30 contiguous nucleosides of a full-length human DKK2 pre-mRNA sequence. In some embodiments, at least one of the sense strand and the antisense strand comprise a nucleoside sequence comprising at least about 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more contiguous nucleosides of the pre-mRNA sequence.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, each strand is independently about 14-30 nucleosides in length, and at least one of the sense strand and the antisense strand comprises a nucleoside sequence comprising about 14-30 contiguous nucleosides of a full-length human DKK2 mRNA sequence such as SEQ ID NO: 7599. In some embodiments, at least one of the sense strand and the antisense strand comprise a nucleoside sequence comprising at least about 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more contiguous nucleosides of one of SEQ ID NO: 7599.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand and the antisense strand form a double-stranded RNA duplex. In some embodiments, the first base pair of the double-stranded RNA duplex is an AU base pair.
In some embodiments, the sense strand further comprises a 3′ overhang. In some embodiments, the 3′ overhang comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleosides, or a range of nucleotides defined by any two of the aforementioned numbers. In some embodiments, the 3′ overhang comprises 1, 2, or more nucleosides. In some embodiments, the 3′ overhang comprises 2 nucleosides. In some embodiments, the sense strand further comprises a 5′ overhang. In some embodiments, the 5′ overhang comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleosides, or a range of nucleotides defined by any two of the aforementioned numbers. In some embodiments, the 5′ overhang comprises 1, 2, or more nucleosides. In some embodiments, the 5′ overhang comprises 2 nucleosides.
In some embodiments, the antisense strand further comprises a 3′ overhang. In some embodiments, the 3′ overhang comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleosides, or a range of nucleotides defined by any two of the aforementioned numbers. In some embodiments, the 3′ overhang comprises 1, 2, or more nucleosides. In some embodiments, the 3′ overhang comprises 2 nucleosides. In some embodiments, the antisense strand further comprises a 5′ overhang. In some embodiments, the 5′ overhang comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleosides, or a range of nucleotides defined by any two of the aforementioned numbers. In some embodiments, the 5′ overhang comprises 1, 2, or more nucleosides. In some embodiments, the 5′ overhang comprises 2 nucleosides.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the siRNA binds with a 19mer in a human DKK2 mRNA. In some embodiments, the siRNA binds with a 12mer, a 13mer, a 14mer, a 15mer, a 16mer, a 17mer, a 18mer, a 19mer, a 20mer, a 21mer, a 22mer, a 23mer, a 24mer, or a 25mer in a human DKK2 mRNA.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the siRNA binds with a 17mer in a non-human primate DKK2 mRNA. In some embodiments, the siRNA binds with a 12mer, a 13mer, a 14mer, a 15mer, a 16mer, a 17mer, a 18mer, a 19mer, a 20mer, a 21mer, a 22mer, a 23mer, a 24mer, or a 25mer in a non-human primate DKK2 mRNA.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the siRNA binds with a 19mer in a human DKK2 mRNA, or a combination thereof. In some embodiments, the siRNA binds with a 12mer, a 13mer, a 14mer, a 15mer, a 16mer, a 17mer, and 18mer, a 19mer, a 20mer, a 21mer, a 22mer, a 23mer, a 24mer, or a 25mer in a human DKK2 mRNA.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the siRNA binds with a human DKK2 mRNA and less than or equal to 20 human off-targets, with no more than 2 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 10 human off-targets, with no more than 2 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 30 human off-targets, with no more than 2 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 40 human off-targets, with no more than 2 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 50 human off-targets, with no more than 2 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 10 human off-targets, with no more than 3 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 20 human off-targets, with no more than 3 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 30 human off-targets, with no more than 3 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 40 human off-targets, with no more than 3 mismatches in the antisense strand. In some embodiments, the siRNA binds with a human DKK2 mRNA and less than or equal to 50 human off-targets, with no more than 3 mismatches in the antisense strand.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, siRNA binds with a human DKK2 mRNA target site that does not harbor an SNP, with a minor allele frequency (MAF) greater or equal to 1% (pos. 2-18). In some embodiments, the MAF is greater or equal to about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, or about 20%.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA in Table 2B. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence in Table 2B. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 2B, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 2B, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence in Table 2B. The sense strand or antisense strand may comprise an overhang. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with a base sequence of an siRNA in any of Table 4-6. In some embodiments, the sense strand or antisense strand sequence comprises or consists of sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical to a base sequence of an siRNA in any of Table 4-6. In some embodiments, the sense strand or antisense strand sequence comprises or consists of the sequence of a base sequence of an siRNA in any of Table 4-6, or a sense strand or antisense strand sequence thereof having 1, 2, 3, or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand sequence comprises or consists of the sequence of a base sequence of an siRNA in any of Table 4-6, or a sense strand or antisense strand sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand sequence comprises or consists of a sequence 100% identical to a base sequence of an siRNA in any of Table 4-6. The sense strand or antisense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand may comprise a modification pattern described herein. The sense strand or antisense strand may comprise, or may lack an overhang. The sense strand or antisense strand may comprise a lipid moiety. The sense strand or antisense strand may comprise a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand having a sequence in accordance with any of SEQ ID NOs: 1-3636. In some embodiments, the sense strand sequence comprises or consists of sequence at least 75% identical to any one of SEQ ID NOs: 1-3636, at least 80% identical to any one of SEQ ID NOs: 1-3636, at least 85% identical to of any one of SEQ ID NOs: 1-3636, at least 90% identical to any one of SEQ ID NOs: 1-3636, or at least 95% identical to any one of SEQ ID NOs: 1-3636. In some embodiments, the sense strand sequence comprises or consists of the sequence of any one of SEQ ID NOs: 1-3636, or a sense strand sequence thereof having 1, 2, 3, or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand sequence comprises or consists of the sequence of any one of SEQ ID NOs: 1-3636, or a sense strand sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand sequence comprises or consists of a sequence 100% identical to SEQ ID NOs: 1-3636. The sense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand may comprise a modification pattern described herein. The sense strand may comprise an overhang. The sense strand may comprise a lipid moiety. The sense strand may comprise a GalNAc moiety.
In some embodiments, the siRNA comprises an antisense strand having a sequence in accordance with any of SEQ ID NOs: 3637-7272. In some embodiments, the antisense strand sequence comprises or consists of sequence at least 75% identical to any one of SEQ ID NOs: 3637-7272, at least 80% identical to any one of SEQ ID NOs: 3637-7272, at least 85% identical to of any one of SEQ ID NOs: 5491-10980, at least 90% identical to any one of SEQ ID NOs: 3637-7272, or at least 95% identical to any one of SEQ ID NOs: 3637-7272. In some embodiments, the antisense strand sequence comprises or consists of the sequence of any one of SEQ ID NOs: 3637-7272, or an antisense strand sequence thereof having 1, 2, 3, or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the antisense strand sequence comprises or consists of the sequence of any one of SEQ ID NOs: 3637-7272, or an antisense strand sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the antisense strand sequence comprises or consists of a sequence 100% identical to SEQ ID NOs: 3637-7272. The antisense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The antisense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The antisense strand may comprise an overhang. The antisense strand may comprise a modification pattern described herein. The antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset A. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset A. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset A, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset A, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset A. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset B. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset B. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset B, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset B, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset B. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset C. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset C. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset C, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset C, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset C. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset D. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset D. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset D, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset D, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset D. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset E. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset E. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset E, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset E, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset E. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence of an siRNA of subset F. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence of subset F. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset F, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand of subset F, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence of subset F. The sense strand or antisense strand may comprise any modifications described herein. The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
B. ASOs
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an antisense oligonucleotide (ASO). In some embodiments, the ASO is 12-30 nucleosides in length. In some embodiments, the ASO is 14-30 nucleosides in length. In some embodiments, the ASO is at least about 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleosides in length, or a range defined by any of the two aforementioned numbers. In some embodiments, the ASO is 15-25 nucleosides in length. In some embodiments, the ASO is 20 nucleosides in length.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an ASO about 12-30 nucleosides in length and comprising a nucleoside sequence comprising about 12-30 contiguous nucleosides of a full-length human DKK2 pre-mRNA sequence; wherein (i) the oligonucleotide comprises a modification comprising a modified nucleoside and/or a modified internucleoside linkage, and/or (ii) the composition comprises a pharmaceutically acceptable carrier.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an ASO about 12-30 nucleosides in length and comprising a nucleoside sequence comprising about 12-30 contiguous nucleosides of a full-length human DKK2 mRNA sequence such as SEQ ID NO: 7599; wherein (i) the oligonucleotide comprises a modification comprising a modified nucleoside and/or a modified internucleoside linkage, and/or (ii) the composition comprises a pharmaceutically acceptable carrier.
C. Modification Patterns
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a modification comprising a modified nucleoside and/or a modified internucleoside linkage, and/or (ii) the composition comprises a pharmaceutically acceptable carrier. In some embodiments, the oligonucleotide comprises a modification comprising a modified nucleoside and/or a modified internucleoside linkage. In some embodiments, the oligonucleotide comprises a modified internucleoside linkage. In some embodiments, the modified internucleoside linkage comprises alkylphosphonate, phosphorothioate, methylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester, or a combination thereof. In some embodiments, the modified internucleoside linkage comprises one or more phosphorothioate linkages. Benefits of the modified internucleoside linkage may include decreased toxicity or improved pharmaco*kinetics.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a modified internucleoside linkage, wherein the oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 modified internucleoside linkages, or a range of modified internucleoside linkages defined by any two of the aforementioned numbers. In some embodiments, the oligonucleotide comprises no more than 18 modified internucleoside linkages. In some embodiments, the oligonucleotide comprises no more than 20 modified internucleoside linkages. In some embodiments, the oligonucleotide comprises 2 or more modified internucleoside linkages, 3 or more modified internucleoside linkages, 4 or more modified internucleoside linkages, 5 or more modified internucleoside linkages, 6 or more modified internucleoside linkages, 7 or more modified internucleoside linkages, 8 or more modified internucleoside linkages, 9 or more modified internucleoside linkages, 10 or more modified internucleoside linkages, 11 or more modified internucleoside linkages, 12 or more modified internucleoside linkages, 13 or more modified internucleoside linkages, 14 or more modified internucleoside linkages, 15 or more modified internucleoside linkages, 16 or more modified internucleoside linkages, 17 or more modified internucleoside linkages, 18 or more modified internucleoside linkages, 19 or more modified internucleoside linkages, or 20 or more modified internucleoside linkages.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises the modified nucleoside. In some embodiments, the modified nucleoside comprises a locked nucleic acid (LNA), hexitol nucleic acid (HLA), cyclohexene nucleic acid (CeNA), 2′-methoxyethyl, 2′-O-alkyl, 2′-O-allyl, 2′-fluoro, or 2′-deoxy, or a combination thereof. In some embodiments, the modified nucleoside comprises a LNA. In some embodiments, the modified nucleoside comprises a 2′,4′ constrained ethyl nucleic acid. In some embodiments, the modified nucleoside comprises HLA. In some embodiments, the modified nucleoside comprises CeNA. In some embodiments, the modified nucleoside comprises a 2′-methoxyethyl group. In some embodiments, the modified nucleoside comprises a 2′-O-alkyl group. In some embodiments, the modified nucleoside comprises a 2′-O-allyl group. In some embodiments, the modified nucleoside comprises a 2′-fluoro group. In some embodiments, the modified nucleoside comprises a 2′-deoxy group. In some embodiments, the modified nucleoside comprises a 2′-O-methyl nucleoside, 2′-deoxyfluoro nucleoside, 2′-O—N-methylacetamido (2′-O-NMA) nucleoside, a 2′-O-dimethylaminoethoxyethyl (2′-O-DMAEOE) nucleoside, 2′-O-aminopropyl (2′-O-AP) nucleoside, or 2′-ara-F, or a combination thereof. In some embodiments, the modified nucleoside comprises a 2′-O-methyl nucleoside. In some embodiments, the modified nucleoside comprises a 2′-deoxyfluoro nucleoside. In some embodiments, the modified nucleoside comprises a 2′-O-NMA nucleoside. In some embodiments, the modified nucleoside comprises a 2′-O-DMAEOE nucleoside. In some embodiments, the modified nucleoside comprises a 2′-O-aminopropyl (2′-O-AP) nucleoside. In some embodiments, the modified nucleoside comprises 2′-ara-F. In some embodiments, the modified nucleoside comprises one or more 2′fluoro modified nucleosides. In some embodiments, the modified nucleoside comprises a 2′ O-alkyl modified nucleoside. Benefits of the modified nucleoside may include decreased toxicity or improved pharmaco*kinetics.
In some embodiments, the oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 modified nucleosides, or a range of nucleosides defined by any two of the aforementioned numbers. In some embodiments, the oligonucleotide comprises no more than 19 modified nucleosides. In some embodiments, the oligonucleotide comprises no more than 21 modified nucleosides. In some embodiments, the oligonucleotide comprises 2 or more modified nucleosides, 3 or more modified nucleosides, 4 or more modified nucleosides, 5 or more modified nucleosides, 6 or more modified nucleosides, 7 or more modified nucleosides, 8 or more modified nucleosides, 9 or more modified nucleosides, 10 or more modified nucleosides, 11 or more modified nucleosides, 12 or more modified nucleosides, 13 or more modified nucleosides, 14 or more modified nucleosides, 15 or more modified nucleosides, 16 or more modified nucleosides, 17 or more modified nucleosides, 18 or more modified nucleosides, 19 or more modified nucleosides, 20 or more modified nucleosides, or 21 or more modified nucleosides.
The oligonucleotide may include purines. Examples of purines include adenine (A) or guanine (G), or modified versions thereof. The oligonucleotide may include pyrimidines. Examples of pyrimidines include cytosine (C), thymine (T), or uracil (U), or modified versions thereof.
In some embodiments, purines of the oligonucleotide comprise 2′ fluoro modified purines. In some embodiments, purines of the oligonucleotide comprise 2′-O-methyl modified purines. In some embodiments, purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all purines of the oligonucleotide comprise 2′ fluoro modified purines. In some embodiments, all purines of the oligonucleotide comprise 2′-O-methyl modified purines. In some embodiments, all purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. 2′-O-methyl may include 2′ O-methyl.
In some embodiments, pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines. In some embodiments, pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines.
In some embodiments, purines of the oligonucleotide comprise 2′ fluoro modified purines, and pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the oligonucleotide comprise 2′-O-methyl modified purines, and pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the oligonucleotide comprise 2′ fluoro modified purines, and pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines. In some embodiments, purines of the oligonucleotide comprise 2′-O-methyl modified purines, and pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines, and purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines, and purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines, and purines of the oligonucleotide comprise 2′-O-methyl modified purines. In some embodiments, pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines, and purines of the oligonucleotide comprise 2′ fluoro modified purines.
In some embodiments, all purines of the oligonucleotide comprise 2′ fluoro modified purines, and all pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the oligonucleotide comprise 2′-O-methyl modified purines, and all pyrimidines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the oligonucleotide comprise 2′ fluoro modified purines, and all pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the oligonucleotide comprise 2′-O-methyl modified purines, and all pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines, and all purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines, and all purines of the oligonucleotide comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′ fluoro modified pyrimidines, and all purines of the oligonucleotide comprise 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the oligonucleotide comprise 2′-O-methyl modified pyrimidines, and all purines of the oligonucleotide comprise 2′ fluoro modified purines.
In some cases, the oligonucleotide comprises a particular modification pattern. In some embodiments, position 9 counting from the 5′ end of the of a strand of the oligonucleotide may have a 2′F modification. In some embodiments, when position 9 of a strand of the oligonucleotide is a pyrimidine, then all purines in a strand of the oligonucleotide have a 2′OMe modification. In some embodiments, when position 9 is the only pyrimidine between positions 5 and 11 of the sense stand, then position 9 is the only position with a 2′F modification in a strand of the oligonucleotide. In some embodiments, when position 9 and only one other base between positions 5 and 11 of a strand of the oligonucleotide are pyrimidines, then both of these pyrimidines are the only two positions with a 2′F modification in a strand of the oligonucleotide. In some embodiments, when position 9 and only two other bases between positions 5 and 11 of a strand of the oligonucleotide are pyrimidines, and those two other pyrimidines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. In some embodiments, when there are more than 2 pyrimidines between positions 5 and 11 of a strand of the oligonucleotide, then all combinations of pyrimidines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that a strand of the oligonucleotide does not have three 2′F modifications in a row. In some cases, a strand of the oligonucleotide of any of the siRNAs comprises a modification pattern which conforms to any or all of these a strand of the oligonucleotide rules.
In some embodiments, when position 9 of a strand of the oligonucleotide is a purine, then all purines in a strand of the oligonucleotide have a 2′OMe modification. In some embodiments, when position 9 is the only purine between positions 5 and 11 of the sense stand, then position 9 is the only position with a 2′F modification in a strand of the oligonucleotide. In some embodiments, when position 9 and only one other base between positions 5 and 11 of a strand of the oligonucleotide are purines, then both of these purines are the only two positions with a 2′F modification in a strand of the oligonucleotide. In some embodiments, when position 9 and only two other bases between positions 5 and 11 of a strand of the oligonucleotide are purines, and those two other purines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. In some embodiments, when there are more than 2 purines between positions 5 and 11 of a strand of the oligonucleotide, then all combinations of purines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that a strand of the oligonucleotide does not have three 2′F modifications in a row. In some cases, a strand of the oligonucleotide of any of the siRNAs comprises a modification pattern which conforms to any or all of these a strand of the oligonucleotide rules.
In some cases, position 9 of a strand of the oligonucleotide can be a 2′deoxy. In these cases, 2′F and 2′OMe modifications may occur at the other positions of a strand of the oligonucleotide. In some cases, a strand of the oligonucleotide of any of the siRNAs comprises a modification pattern which conforms to these a strand of the oligonucleotide rules.
In some embodiments, position nine of the sense strand comprises a 2′ fluoro-modified pyrimidine. In some embodiments, all purines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, 1, 2, 3, 4, or 5 pyrimidines between positions 5 and 11 comprise a 2′flouro-modified pyrimidine, provided there are not three 2′ fluoro-modified pyrimidines in a row. In some embodiments, the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotide. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides, 2′-O-methyl modified nucleotides and unmodified deoxyribonucleotide. In some embodiments, position nine of the sense strand comprises a 2′ fluoro-modified pyrimidine; all purines of the sense strand comprises 2′-O-methyl modified purines; 1, 2, 3, 4, or 5 pyrimidines between positions 5 and 11 comprise a 2′flouro-modified pyrimidine, provided there are not three 2′ fluoro-modified pyrimidines in a row; the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides; and the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotides.
In some embodiments, position nine of the sense strand comprises a 2′ fluoro-modified purine. In some embodiments, all pyrimidines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, 1, 2, 3, 4, or 5 purines between positions 5 and 11 comprise a 2′flouro-modified purine, provided there are not three 2′ fluoro-modified purine in a row. In some embodiments, the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotide. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides, 2′-O-methyl modified nucleotides and unmodified deoxyribonucleotide. In some embodiments, position nine of the sense strand comprises a 2′ fluoro-modified purine; all pyrimidine of the sense strand comprises 2′-O-methyl modified pyrimidines; 1, 2, 3, 4, or 5 purines between positions 5 and 11 comprise a 2′flouro-modified purines, provided there are not three 2′ fluoro-modified purines in a row; the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides; and the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotides. In some embodiments, there are not three 2′ fluoro-modified purines in a row. In some embodiments, there are not three 2′ fluoro-modified pyrimidines in a row.
In some embodiments, position nine of the sense strand comprises an unmodified deoxyribonucleotide. In some embodiments, positions 5, 7, and 8 of the sense strand comprise 2′fluoro-modified nucleotides. In some embodiments, all pyrimidines in positions 10 to 21 of the sense strand comprise 2′-O-methyl modified pyrimidines and all purines in positions 10 to 21 of the comprise 2′-O-methyl modified purines or 2′fluoro-modified purines. In some embodiments, the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides, 2′-O-methyl modified nucleotides and unmodified deoxyribonucleotides. In some embodiments, position nine of the sense strand comprises an unmodified deoxyribonucleotide; positions 5, 7, and 8 of the sense strand comprise 2′fluoro-modified nucleotides; all pyrimidines in positions 10 to 21 of the sense strand comprise 2′-O-methyl modified pyrimidines and all purines in positions 10 to 21 of the comprise 2′-O-methyl modified purines or 2′fluoro-modified purines; the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides; and the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotides.
In some embodiments, position nine of the sense strand comprises an unmodified deoxyribonucleotide. In some embodiments, positions 5, 7, and 8 of the sense strand comprise 2′fluoro-modified nucleotides. In some embodiments, all purines in positions 10 to 21 of the sense strand comprise 2′-O-methyl modified purines and all pyrimidines in positions 10 to 21 of the comprise 2′-O-methyl modified pyrimidines or 2′fluoro-modified pyrimidines. In some embodiments, the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotides. In some embodiments, the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides, 2′-O-methyl modified nucleotides and unmodified deoxyribonucleotides. In some embodiments, position nine of the sense strand comprises an unmodified deoxyribonucleotide; positions 5, 7, and 8 of the sense strand comprise 2′fluoro-modified nucleotides; all purines in positions 10 to 21 of the sense strand comprise 2′-O-methyl modified purines and all pyrimidines in positions 10 to 21 of the comprise 2′-O-methyl modified pyrimidines or 2′fluoro-modified pyrimidines; the odd-numbered positions of the antisense strand comprise 2′-O-methyl modified nucleotides; and the even-numbered positions of the antisense strand comprise 2′flouro-modified nucleotides and unmodified deoxyribonucleotide.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a targeting ligand.
In some embodiments, the moiety includes a negatively charged group attached at a 5′ end of the oligonucleotide. This may be referred to as a 5′-end group. In some embodiments, the negatively charged group is attached at a 5′ end of an antisense strand of an siRNA disclosed herein. The 5′-end group may be or include a 5′-end phosphorothioate, 5′-end phosphorodithioate, 5′-end vinylphosphonate (5′-VP), 5′-end methylphosphonate, 5′-end cyclopropyl phosphonate, or a 5′-deoxy-5′-C-malonyl. The 5′-end group may comprise 5′-VP. In some embodiments, the 5′-VP comprises a trans-vinylphosphate or cis-vinylphosphate. The 5′-end group may include an extra 5′ phosphate. A combination of 5′-end groups may be used.
In some embodiments, the oligonucleotide includes a negatively charged group. The negatively charged group may aid in cell or tissue penetration. The negatively charged group may be attached at a 5′ or 3′ end (e.g. a 5′ end) of the oligonucleotide. This may be referred to as an end group. The end group may be or include a phosphorothioate, phosphorodithioate, vinylphosphonate, methylphosphonate, cyclopropyl phosphonate, or a deoxy-C-malonyl. The end group may include an extra 5′ phosphate such as an extra 5′ phosphate. A combination of end groups may be used.
In some embodiments, the oligonucleotide includes a phosphate mimic. In some embodiments, the phosphate mimic comprises vinyl phosphonate. In some embodiments, the vinyl phosphonate comprises a trans-vinylphosphate. In some embodiments, the vinyl phosphonate comprises a cis-vinylphosphate. An example of a nucleotide that includes a vinyl phosphonate is shown below.
In some embodiments, the vinyl phosphonate increases the stability of the oligonucleotide. In some embodiments, the vinyl phosphonate increases the accumulation of the oligonucleotide in tissues. In some embodiments, the vinyl phosphonate protects the oligonucleotide from an exonuclease or a phosphatase. In some embodiments, the vinyl phosphonate improves the binding affinity of the oligonucleotide with the siRNA processing machinery.
In some embodiments, the oligonucleotide includes 1 vinyl phosphonate. In some embodiments, the oligonucleotide includes 2 vinyl phosphonates. In some embodiments, the oligonucleotide includes 3 vinyl phosphonates. In some embodiments, the oligonucleotide includes 4 vinyl phosphonates. In some embodiments, the antisense strand of the oligonucleotide comprises a vinyl phosphonate at the 5′ end. In some embodiments, the antisense strand of the oligonucleotide comprises a vinyl phosphonate at the 3′ end. In some embodiments, the sense strand of the oligonucleotide comprises a vinyl phosphonate at the 5′ end. In some embodiments, the sense strand of the oligonucleotide comprises a vinyl phosphonate at the 3′ end.
1. Hydrophobic Moieties
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a hydrophobic moiety. The hydrophobic moiety may be attached at a 3′ or 5′ terminus of the oligonucleotide. The hydrophobic moiety may include a lipid such as a fatty acid. The hydrophobic moiety may include a hydrocarbon. The hydrocarbon may be linear. The hydrocarbon may be non-linear. The hydrophobic moiety may include a lipid moiety or a cholesterol moiety, or a combination thereof.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a lipid attached at a 3′ or 5′ terminus of the oligonucleotide. In some embodiments, the lipid comprises cholesterol, myristoyl, palmitoyl, stearoyl, lithocholoyl, docosanoyl, docosahexaenoyl, myristyl, palmityl, stearyl, or α-tocopherol, or a combination thereof.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a hydrophobic ligand or moiety. In some embodiments, the hydrophobic ligand or moiety comprises cholesterol. In some embodiments, the hydrophobic ligand or moiety comprises a cholesterol derivative. In some embodiments, the hydrophobic ligand or moiety is attached at a 3′ terminus of the oligonucleotide. In some embodiments, the hydrophobic ligand or moiety s attached at a 5′ terminus of the oligonucleotide. In some embodiments, the composition comprises a sense strand, and the hydrophobic ligand or moiety is attached to the sense strand (e.g. attached to a 5′ end of the sense strand, or attached to a 3′ end of the sense strand). In some embodiments, the composition comprises an antisense strand, and the hydrophobic ligand or moiety is attached to the antisense strand (e.g. attached to a 5′ end of the antisense strand, or attached to a 3′ end of the antisense strand). In some embodiments, the composition comprises a hydrophobic ligand or moiety attached at a 3′ or 5′ terminus of the oligonucleotide.
In some embodiments, a hydrophobic moiety is attached to the oligonucleotide (e.g. a sense strand and/or an antisense strand of a siRNA). In some embodiments, a hydrophobic moiety is attached at a 3′ terminus of the oligonucleotide. In some embodiments, a hydrophobic moiety is attached at a 5′ terminus of the oligonucleotide. In some embodiments, the hydrophobic moiety comprises cholesterol. In some embodiments, the hydrophobic moiety includes a cyclohexanyl.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a lipid attached at a 3′ or 5′ terminus of the oligonucleotide. In some embodiments, a lipid is attached at a 3′ terminus of the oligonucleotide. In some embodiments, a lipid is attached at a 5′ terminus of the oligonucleotide. In some embodiments, the lipid comprises cholesterol, myristoyl, palmitoyl, stearoyl, lithocholoyl, docosanoyl, docosahexaenoyl, myristyl, palmityl, stearyl, or α-tocopherol, or a combination thereof. In some embodiments, the lipid comprises stearyl, lithocholyl, docosanyl, docosahexaenyl, or myristyl. In some embodiments, the lipid comprises cholesterol. In some embodiments, the lipid includes a sterol such as cholesterol. In some embodiments, the lipid comprises stearyl, t-butylphenol, n-butylphenol, octylphenol, dodecylphenol, phenyl n-dodecyl, octadecylbenzamide, hexadecylbenzamide, or octadecylcyclohexyl. In some embodiments, the lipid comprises phenyl para C12.
In some embodiments, the oligonucleotide comprises any aspect of the following structure:
In some embodiments, the oligonucleotide comprises any aspect of the following structure:
In some embodiments, the oligonucleotide comprises any aspect of the following structure:
In some embodiments, the oligonucleotide comprises any aspect of the following structure: The aspect included in the oligonucleotide may include the entire structure, or may include the lipid moiety, of any of the structures shown. In some embodiments, n is 1-3. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, R is an alkyl group. In some embodiments, the alkyl group contains 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbons. In some embodiments, the alkyl group contains 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 carbons, or a range defined by any two of the aforementioned numbers of carbons. In some embodiments, the alkyl group contains 4-18 carbons. In some embodiments, the lipid moiety comprises an alcohol or ether.
In some embodiments, the lipid includes a fatty acid. In some embodiments, the lipid comprises a lipid depicted in Table 1. The example lipid moieties in Table 1 are shown attached at a 5′ end of an oligonucleotide, in which the 5′ terminal phosphate of the oligonucleotide is shown with the lipid moiety. In some embodiments, a lipid moiety in Table 1 may be attached at a different point of attachment than shown. For example, the point of attachment of any of the lipid moieties in the table may be at a 3′ oligonucleotide end. In some embodiments, the lipid is used for targeting the oligonucleotide to a non-hepatic cell or tissue.
In some embodiments, the lipid or lipid moiety includes 16 to 18 carbons. In some embodiments, the lipid includes 16 carbons. In some embodiments, the lipid includes 17 carbons. In some embodiments, the lipid includes 18 carbons. In some embodiments, the lipid moiety includes 16 carbons. In some embodiments, the lipid moiety includes 17 carbons. In some embodiments, the lipid moiety includes 18 carbons.
The hydrophobic moiety may include a linker that comprises a carbocycle. The carbocycle may be six-membered. Some examples of a carbocycle include phenyl or cyclohexyl. The linker may include a phenyl. The linker may include a cyclohexyl. The lipid may be attached to the carbocycle, which may in turn be attached at a phosphate (e.g. 5′ or 3′ phosphate) of the oligonucleotide. In some embodiments, the lipid or hydrocarbon, and the end of the sense are connected to the phenyl or cyclohexyl linker in the 1,4; 1,3; or 1,2 substitution pattern (e.g. the para, meta, or ortho phenyl configuration). In some embodiments, the lipid or hydrocarbon, and the end of the sense are connected to the phenyl or cyclohexyl linker in the 1,4 substitution pattern (e.g. the para phenyl configuration). The lipid may be attached to the carbocycle in the 1,4 substitution pattern relative to the oligonucleotide. The lipid may be attached to the carbocycle in the 1,3 substitution pattern relative to the oligonucleotide. The lipid may be attached to the carbocycle in the 1,2 substitution pattern relative to the oligonucleotide. The lipid may be attached to the carbocycle in the ortho orientation relative to the oligonucleotide. The lipid may be attached to the carbocycle in the para orientation relative to the oligonucleotide. The lipid may be attached to the carbocycle in the meta orientation relative to the oligonucleotide.
The lipid moiety may comprise or consist of the following structure
In some embodiments, the lipid moiety comprises or consists of the following structure:
In some embodiments, the lipid moiety comprises the following structure:
In some embodiments, the lipid moiety comprises or consist of the following structure:
In some embodiments, the dotted line indicates a covalent connection. The covalent connection may between an end of the sense or antisense strand. For example, the connection may be to the 5′ end of the sense strand. In some embodiments, n is 0-3. In some embodiments, n is 1-3. In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, n is 5. In some embodiments, n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, R is an alkyl group. In some embodiments, the alkyl group contains 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbons. In some embodiments, the alkyl group contains 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 carbons, or a range defined by any two of the aforementioned numbers of carbons. In some embodiments, R comprises or consists of an alkyl group containing 4-18 carbons.
The lipid moiety may be attached at a 5′ end of the oligonucleotide. The 5′ end may have one phosphate linking the lipid moiety to a 5′ carbon of a sugar of the oligonucleotide. The 5′ end may have two phosphates linking the lipid moiety to a 5′ carbon of a sugar of the oligonucleotide. The 5′ end may have three phosphates linking the lipid moiety to a 5′ carbon of a sugar of the oligonucleotide. The 5′ end may have one phosphate connected to the 5′ carbon of a sugar of the oligonucleotide, where the one phosphate is connected to the lipid moiety. The 5′ end may have two phosphates connected to the 5′ carbon of a sugar of the oligonucleotide, where the one of the two phosphates is connected to the lipid moiety. The 5′ end may have three phosphates connected to the 5′ carbon of a sugar of the oligonucleotide, where the one of the three phosphates is connected to the lipid moiety. The sugar may include a ribose. The sugar may include a deoxyribose. The sugar may be modified a such as a 2′ modified sugar (e.g. a 2′ O-methyl or 2′ fluoro ribose). A phosphate of the 5′ end may include a modification such as a sulfur in place of an oxygen. Two phosphates of the 5′ end may include a modification such as a sulfur in place of an oxygen. Three phosphates of the 5′ end may include a modification such as a sulfur in place of an oxygen.
In some embodiments, the oligonucleotide includes 1 lipid moiety. In some embodiments, the oligonucleotide includes 2 lipid moieties. In some embodiments, the oligonucleotide includes 3 lipid moieties. In some embodiments, the oligonucleotide includes 4 lipid moieties.
Some embodiments relate to a method of making an oligonucleotide comprising a hydrophobic conjugate. A strategy for making hydrophobic conjugates may include use of a phosphoramidite reagent based upon a 6-membered ring alcohol such as a phenol or cyclohexanol. The phosphoramidite may be reacted to a nucleotide to connect the nucleotide to the hydrophobic moiety, and thereby produce the hydrophobic conjugate. Some examples of phosphoramidite reagents that may be used to produce a hydrophobic conjugate are provided as follows:
In some embodiments, n is 1-3. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, R is an alkyl group. In some embodiments, the alkyl group contains 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbons. In some embodiments, the alkyl group contains 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 carbons, or a range defined by any two of the aforementioned numbers of carbons. In some embodiments, R comprises or consists of an alkyl group containing 4-18 carbons. Any one of the phosphoramidite reagents may be reacted to a 5′ end of an oligonucleotide to produce an oligonucleotide comprising a hydrophobic moiety. In some embodiments, the phosphoramidite reagents is reacted to a 5′ end of a sense strand of an siRNA. The sense strand may then be hybridized to an antisense strand to form a duplex. The hybridization may be performed by incubating the sense and antisense strands in solution at a given temperature. The temperature may be gradually reduced. The temperature may comprise or include a temperature comprising an annealing temperature for the sense and antisense strands. The temperature may be below or include a temperature below the annealing temperature for the sense and antisense strands. The temperature may be below a melting temperature of the sense and antisense strands.
The lipid may be attached to the oligonucleotide by a linker. The linker may include a polyethyleneglycol (e.g. tetraethyleneglycol).
The modifications described herein may be useful for delivery to a cell or tissue, for example, extrahepatic delivery or targeting of an oligonucleotide composition. The modifications described herein may be useful for targeting an oligonucleotide composition to a cell or tissue.
ETL2 may be conjugated to an oligonucleotide using the following reagent:
2. Sugar Moieties
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a sugar moiety. The sugar moiety may include an N-acetyl galactose moiety (e.g. an N-acetylgalactosamine (GalNAc) moiety), an N-acetyl glucose moiety (e.g. an N-acetylglucosamine (GlcNAc) moiety), a fucose moiety, or a mannose moiety. The sugar moiety may include 1, 2, 3, or more sugar molecules. The sugar moiety may be attached at a 3′ or 5′ terminus of the oligonucleotide. The sugar moiety may include an N-acetyl galactose moiety. The sugar moiety may include an N-acetylgalactosamine (GalNAc) moiety. The sugar moiety may include an N-acetyl glucose moiety. The sugar moiety may include N-acetylglucosamine (GlcNAc) moiety. The sugar moiety may include a fucose moiety. The sugar moiety may include a mannose moiety. N-acetyl glucose, GlcNAc, fucose, or mannose may be useful for targeting macrophages when they target or bind a mannose receptor such as CD206. The sugar moiety may be useful for binding or targeting an asialoglycoprotein receptor such as an asialoglycoprotein receptor of a hepatocyte. The GalNAc moiety may bind to an asialoglycoprotein receptor. The GalNAc moiety may target a hepatocyte.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an N-acetylgalactosamine (GalNAc) moiety. GalNAc may be useful for hepatocyte targeting. The GalNAc moiety may include a bivalent or trivalent branched linker. The oligo may be attached to 1, 2 or 3 GalNAcs through a bivalent or trivalent branched linker. The GalNAc moiety may include 1, 2, 3, or more GalNAc molecules. The GalNAc moiety may be attached at a 3′ or 5′ terminus of the oligonucleotide.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an N-acetylgalactosamine (GalNAc) ligand for hepatocyte targeting. In some embodiments, the composition comprises GalNAc. In some embodiments, the composition comprises a GalNAc derivative. In some embodiments, the GalNAc ligand is attached at a 3′ terminus of the oligonucleotide. In some embodiments, the GalNAc ligand is attached at a 5′ terminus of the oligonucleotide. In some embodiments, the composition comprises a sense strand, and the GalNAc ligand is attached to the sense strand (e.g. attached to a 5′ end of the sense strand, or attached to a 3′ end of the sense strand). In some embodiments, the composition comprises an antisense strand, and the GalNAc ligand is attached to the antisense strand (e.g. attached to a 5′ end of the antisense strand, or attached to a 3′ end of the antisense strand). In some embodiments, the composition comprises a GalNAc ligand attached at a 3′ or 5′ terminus of the oligonucleotide.
Disclosed herein, in some embodiments, are compositions comprising an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises a GalNAc moiety. The GalNAc moiety may be included in any formula, structure, or GalNAc moiety shown below. In some embodiments, described herein is a compound (e.g. oligonucleotide) represented by Formula (I) or (II):
or a salt thereof, wherein
-
- J is an oligonucleotide;
- each w is independently selected from any value from 1 to 20;
- each v is independently selected from any value from 1 to 20;
- n is selected from any value from 1 to 20;
- m is selected from any value from 1 to 20;
- z is selected from any value from 1 to 3, wherein
- if z is 3, Y is C
- if z is 2, Y is CR6, or
- if z is 1, Y is C(R6)2;
- Q is selected from:
- C3-10 carbocycle optionally substituted with one or more substituents independently selected from halogen, —CN, —NO2, —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, —S(O)R7, and C1-6 alkyl, wherein the C1-6 alkyl, is optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, and —NH2;
- R1 is a linker selected from:
- —O—, —S—, —N(R7)—, —C(O)—, —C(O)N(R7)—, —N(R7)C(O)—, —N(R7)C(O)N(R7)—, —OC(O)N(R7)—, —N(R7)C(O)O—, —C(O)O—, —OC(O)—, —S(O)—, —S(O)2—, —OS(O)2—, —OP(O)(OR7)O—, —SP(O)(OR7)O—, —OP(S)(OR7)O—, —OP(O)(SR7)O—, —OP(O)(OR7)S—, —OP(O)(O−)O—, —SP(O)(O−)O—, —OP(S)(O−)O—, —OP(O)(S−)O—, —OP(O)(O−)S—, —OP(O)(OR7)NR7—, —OP(O)(N(R7)2)NR7—, —OP(OR7)O—, —OP(N(R7)2)O—, —OP(OR7)N(R7)—, and —OPN(R7)2NR7—;
- each R2 is independently selected from:
- C1-6 alkyl optionally substituted with one or more substituents independently selected from halogen, —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, and —S(O)R7;
- R3 and R4 are each independently selected from:
- —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, and —S(O)R7;
- each R5 is independently selected from:
- —OC(O)R7, —OC(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —N(R7)C(O)OR7, —C(O)R7, —C(O)OR7, and —C(O)N(R7)2;
- each R6 is independently selected from:
- hydrogen;
- halogen, —CN, —NO2, —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, and —S(O)R7; and
- C1-6 alkyl optionally substituted with one or more substituents independently selected from halogen, —CN, —NO2, —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, and —S(O)R7;
- each R7 is independently selected from:
- hydrogen;
- C1-6 alkyl, C2-6 alkenyl, and C2-6 alkynyl, each of which is optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, —NH2, ═O, ═S, —O—C1-6 alkyl, —S—C1-6 alkyl, —N(C1-6 alkyl)2, —NH(C1-6 alkyl), C3-10 carbocycle, and 3- to 10-membered heterocycle; and
- C3-10 carbocycle, and 3- to 10-membered heterocycle, each of which is optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, —NH2, ═O, ═S, —O—C1-6 alkyl, —S—C1-6 alkyl, —N(C1-6 alkyl)2, —NH(C1-6 alkyl), C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, C3-10carbocycle, 3- to 10-membered heterocycle, and C1-6haloalkyl.
In some embodiments, each w is independently selected from any value from 1 to 10. In some embodiments, each w is independently selected from any value from 1 to 5. In some embodiments, each w is 1. In some embodiments, each v is independently selected from any value from 1 to 10. In some embodiments, each v is independently selected from any value from 1 to 5. In some embodiments, each v is 1. In some embodiments, n is selected from any value from 1 to 10. In some embodiments, n is selected from any value from 1 to 5. In some embodiments, n is 2. In some embodiments, m is selected from any value from 1 to 10. In some embodiments, m is selected from any value from 1 to 5. In some embodiments, m is selected from 1 and 2. In some embodiments, z is 3 and Y is C. In some embodiments, Q is selected from C5-6 carbocycle optionally substituted with one or more substituents independently selected from halogen, —CN, —NO2, —OR7, —SR7, —N(R7)2, —C(O)R7, —C(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, —OC(O)N(R7)2, —N(R7)C(O)OR7, —C(O)OR7, —OC(O)R7, and —S(O)R7. In some embodiments, Q is selected from C5-6 carbocycle optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, and —NH2. In some embodiments, Q is selected from phenyl and cyclohexyl, each of which is optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, and —NH2. In some embodiments, Q is selected from phenyl. In some embodiments, Q is selected from cyclohexyl. In some embodiments, R1 is selected from —OP(O)(OR7)O—, —SP(O)(OR7)O—, —OP(S)(OR7)O—, —OP(O)(SR7)O—, —OP(O)(OR7)S—, —OP(O)(O−)O—, —SP(O)(O−)O—, —OP(S)(O−)O—, —OP(O)(S−)O—, —OP(O)(O−)S—, —OP(O)(OR7)NR7—, —OP(O)(N(R7)2)NR7—, —OP(OR7)O—, —OP(N(R7)2)O—, —OP(OR7)N(R7)—, and —OPN(R7)2NR7. In some embodiments, R1 is selected from —OP(O)(OR7)O—, —SP(O)(OR7)O—, —OP(S)(OR7)O—, —OP(O)(SR7)O—, —OP(O)(OR7)S—, —OP(O)(O−)O—, —SP(O)(O−)O—, —OP(S)(O−)O—, —OP(O)(S−)O—, —OP(O)(O−)S—, and —OP(OR7)O—. In some embodiments, R1 is selected from —OP(O)(OR7)O—, —OP(S)(OR7)O—, —OP(O)(O−)O—, —OP(S)(O−)O—, —OP(O)(S−)O—, and —OP(OR7)O—. In some embodiments, R1 is selected from —OP(O)(OR7)O— and —OP(OR7)O—. In some embodiments, R2 is selected from C1-3 alkyl substituted with one or more substituents independently selected from halogen, —OR7, —OC(O)R7, —SR7, —N(R7)2, —C(O)R7, and —S(O)R7. In some embodiments, R2 is selected from C1-3 alkyl substituted with one or more substituents independently selected from —OR7, —OC(O)R7, —SR7, and —N(R7)2. In some embodiments, R2 is selected from C1-3 alkyl substituted with one or more substituents independently selected from —OR7 and —OC(O)R7. In some embodiments, R3 is selected from halogen, —OR7, —SR7, —N(R7)2, —C(O)R7, —OC(O)R7, and —S(O)R7. In some embodiments, R3 is selected from —OR7, —SR7, —OC(O)R7, and —N(R7)2. In some embodiments, R3 is selected from —OR7— and —OC(O)R7. In some embodiments, R4 is selected from halogen, —OR7, —SR7, —N(R7)2, —C(O)R7, —OC(O)R7, and —S(O)R7. In some embodiments, R4 is selected from —OR7—SR7, —OC(O)R7, and —N(R7)2. In some embodiments, R4 is selected from —OR7— and —OC(O)R7. In some embodiments, R5 is selected from —OC(O)R7, —OC(O)N(R7)2, —N(R7)C(O)R7, —N(R7)C(O)N(R7)2, and —N(R7)C(O)OR7. In some embodiments, R5 is selected from —OC(O)R7 and —N(R7)C(O)R7. In some embodiments, each R7 is independently selected from: hydrogen; and C1-6 alkyl optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, —NH2, ═O, ═S, —O—C1-6 alkyl, —S—C1-6 alkyl, —N(C1-6 alkyl)2, —NH(C1-6 alkyl), C3-10 carbocycle, or 3- to 10-membered heterocycle. In some embodiments, each R7 is independently selected from C1-6 alkyl optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, —NH2, ═O, ═S, —O—C1-6 alkyl, —S—C1-6 alkyl, —N(C1-6 alkyl)2, and —NH(C1-6 alkyl). In some embodiments, each R7 is independently selected from C1-6 alkyl optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, and —SH. In some embodiments, w is 1; v is 1; n is 2; m is 1 or 2; z is 3 and Y is C; Q is phenyl or cyclohexyl, each of which is optionally substituted with one or more substituents independently selected from halogen, —CN, —OH, —SH, —NO2, —NH2, and C1-3 alkyl; R1 is selected from —OP(O)(OR7)O—, —OP(S)(OR7)O—, —OP(O)(O—)O—, —OP(S)(O—)O—, —OP(O)(S−)O—, and —OP(OR7)O—; R2 is C1 alkyl substituted with —OH or —OC(O)CH3;
- R3 is —OH or —OC(O)CH3; R4 is —OH or —OC(O)CH3; and Rt is —NH(O)CH3. In some embodiments, the compound comprises:
In some embodiments, the oligonucleotide (J) is attached at a 5′ end or a 3′ end of the oligonucleotide. In some embodiments, the oligonucleotide comprises DNA. In some embodiments, the oligonucleotide comprises RNA. In some embodiments, the oligonucleotide comprises one or more modified internucleoside linkages. In some embodiments, the one or more modified internucleoside linkages comprise alkylphosphonate, phosphorothioate, methylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester, or a combination thereof. In some embodiments, the oligonucleotide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 modified internucleoside linkages. In some embodiments, the compound binds to an asialoglycoprotein receptor. In some embodiments, the compound targets a hepatocyte.
Some embodiments include the following, where J is the oligonucleotide:
J may include one or more additional phosphates, or one or more phosphorothioates linking to the oligonucleotide. J may include one or more additional phosphates linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide.
Some embodiments include the following, where J is the oligonucleotide:
J may include one or more additional phosphates, or one or more phosphorothioates linking to the oligonucleotide. J may include one or more additional phosphates linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide.
Some embodiments include the following, where J is the oligonucleotide:
J may include one or more phosphates or phosphorothioates linking to the oligonucleotide. J may include one or more phosphates linking to the oligonucleotide. J may include a phosphate linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide. J may include a phosphorothioate linking to the oligonucleotide.
Some embodiments include the following, where J is the oligonucleotide:
The structure in this compound attached to the oligonucleotide (J) may be referred to as “ETL17,” and is an example of a GalNAc moiety. J may include one or more phosphates or phosphorothioates linking to the oligonucleotide. J may include one or more phosphates linking to the oligonucleotide. J may include a phosphate linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide. J may include a phosphorothioate linking to the oligonucleotide.
Some embodiments include the following, where the phosphate or “5′” indicates a connection to the oligonucleotide:
Some embodiments include the following, where the phosphate or “5′” indicates a connection to the oligonucleotide:
Some embodiments include the following, where J is the oligonucleotide:
include one or more phosphates or phosphorothioates linking to the oligonucleotide. J may include one or more phosphates linking to the oligonucleotide. J may include a phosphate linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide. J may include a phosphorothioate linking to the oligonucleotide.
Some embodiments include the following, where J is the oligonucleotide:
The structure in this compound attached to the oligonucleotide (J) may be referred to as “ETL1,” and is an example of a GalNAc moiety. J may include one or more phosphates or phosphorothioates linking to the oligonucleotide. J may include one or more phosphates linking to the oligonucleotide. J may include a phosphate linking to the oligonucleotide. J may include one or more phosphorothioates linking to the oligonucleotide. J may include a phosphorothioate linking to the oligonucleotide.
3. siRNA Modification Patterns
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2 wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the sense strand comprises modification pattern 1S: 5′-NfsnsNfnNfnNfNfNfnNfnNfnNfnNfnNfsnsn-3′ (SEQ ID NO: 7600), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the sense strand comprises modification pattern 2S: 5′-nsnsnnNfnNfNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7601), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the sense strand comprises modification pattern 3S: 5′-nsnsnnNfnNfnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7602), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the sense strand comprises modification pattern 4S: 5′-NfsnsNfnNfnNfNfNfnNfnNfnNfnNfnNfsnsnN-moiety-3′ (SEQ ID NO: 7603), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 5S: 5′-nsnsnnNfnNfNfNfnnnnnnnnnnsnsnN-moiety-3′ (SEQ ID NO: 7604), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. The moiety may include any moiety such as a lipid moiety. In some embodiments, the sense strand comprises modification pattern 6S: 5′-nnnnNfNfnnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7605), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 7S: 5′-nnnnnnNfNfNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7606), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 8S: 5′-nnnnnNfNfNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7607), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 9S: 5′-nnnnnnNfnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7608), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 10S: 5′-nnnnnnnNfNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7609), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 11S: 5′-nnnnnNfnnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7610), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 12S: 5′-nnnnNfNfnNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7611), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 13S: 5′-nnnnNfnnnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7612), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 14S: 5′-nnnnNfnnNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7613), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 15S: 5′-nnnnnNfNfNfNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7614), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 16S: 5′-nnnnNfNfnnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7615), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 17S: 5′-nnnnnNfNfnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7616), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 18S: 5′-nnnnNfnNfnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7617), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 19S: 5′-nnnnNfnNfnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7618), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 20S: 5′-nnnnnnnnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7619), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 21S: 5′-nnnnNfnnNfNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7620), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 22S: 5′-nnnnNfnnnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7621), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 23S: 5′-nnnnnNfnNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7622), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 24S: 5′-nnnnnnNfnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7623), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 25S: 5′-nnnnnNfnNfNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7624), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 26S: 5′-nnnnnnnnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7625), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 27S: 5′-nnnnNfnNfnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7626), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 28S: 5′-nnnnnNfnnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7627), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 29S: 5′-nnnnnNfnnNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7628), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 30S: 5′-nnnnNfNfnnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7629), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 31S: 5′-nnnnnNfNfnNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7630), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 32S: 5′-nnnnnNfNfnNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7631), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 33S: 5′-nnnnnnnNfNfNfNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7632), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 34S: 5′-nnnnnnNfNfNfNfNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7633), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 35S: 5′-nnnnnNfnNfNfNfNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7634), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 36S: 5′-nnnnnNfNfNfNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7635), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 37S: 5′-nnnnNfnnNfNfNfNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7636), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 38S: 5′-nnnnNfnNfNfNfNfnnnnnnnnnsnsn-3′ (SEQ ID NO: 7637), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 39S: 5′-nnnnNfNfnNfNfnNfnnnnnnnnsnsn-3′ (SEQ ID NO: 7638), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 40S: 5′-nnnnNfNfNfNfNfnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7639), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 41S: 5′-nnnnNfnNfNfdNnnnnnnnnnnsnsn-3′ (SEQ ID NO: 7640), wherein “Nf” is a 2′ fluoro-modified nucleoside, “dN” is a 2′ deoxy-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides. In some embodiments, the sense strand comprises modification pattern 42S: 5′-NfsnsNfnNfnNfnNfnNfnNfnNfnNfnNfsnsn-3′ (SEQ ID NO: 7641), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, “s” is a phosphorothioate linkage, and N comprises one or more nucleosides.
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2 wherein the oligonucleotide comprises an siRNA comprising a sense strand and an antisense strand, wherein the antisense strand comprises modification pattern 1AS: 5′-nsNfsnNfnNfnNfnNfnnnNfnNfnNfnsnsn-3′ (SEQ ID NO: 7642), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the antisense strand comprises modification pattern 2AS: 5′-nsNfsnnnNfnNfNfnnnnNfnNfnnnsnsn-3′ (SEQ ID NO: 7643), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the antisense strand comprises modification pattern 3AS: 5′-nsNfsnnnNfnnnnnnnNfnNfnnnsnsn-3′ (SEQ ID NO: 7644), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the antisense strand comprises modification pattern 4AS: 5′-nsNfsnNfnNfnnnnnnnNfnNfnnnsnsn-3′ (SEQ ID NO: 7645), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the antisense strand comprises modification pattern 5AS: 5′-nsNfsnNfnNfnNfnNfnNfnNfnNfnNfnsnsn-3′ (SEQ ID NO: 7646), wherein “Nf” is a 2′ fluoro-modified nucleoside, “n” is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage.
In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 1S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S, and the antisense strand comprises pattern 1AS. In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S, and the antisense strand comprises pattern 2AS. In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S, and the antisense strand comprises pattern 3AS. In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S, and the antisense strand comprises pattern 4AS. In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S, and the antisense strand comprises pattern 5AS.
In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 11S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S. In some embodiments, the sense strand comprises pattern 1S, 2S, 3S, 4S, or 5S. In some embodiments, the sense strand comprises modification pattern 1AS, 2AS, 3AS, 4AS, or 5AS. In some embodiments, the antisense strand comprises modification pattern 1AS, 2AS, 3AS, 4AS, or 5AS. In some embodiments, the antisense strand comprises modification pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 1S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, or 42S. In some embodiments, the sense strand or the antisense strand comprises modification pattern ASO1.
In some embodiments, purines of the sense strand comprise 2′ fluoro modified purines. In some embodiments, purines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all purines of the sense strand comprise 2′ fluoro modified purines. In some embodiments, all purines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, all purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines.
In some embodiments, pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines.
In some embodiments, purines of the sense strand comprise 2′ fluoro modified purines, and pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the sense strand comprise 2′-O-methyl modified purines, and pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the sense strand comprise 2′ fluoro modified purines, and pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, purines of the sense strand comprise 2′-O-methyl modified purines, and pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines, and purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines, and purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines, and purines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines, and purines of the sense strand comprise 2′ fluoro modified purines.
In some embodiments, all purines of the sense strand comprise 2′ fluoro modified purines, and all pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the sense strand comprise 2′-O-methyl modified purines, and all pyrimidines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the sense strand comprise 2′ fluoro modified purines, and all pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the sense strand comprise 2′-O-methyl modified purines, and all pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines, and all purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines, and all purines of the sense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the sense strand comprise 2′ fluoro modified pyrimidines, and all purines of the sense strand comprise 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the sense strand comprise 2′-O-methyl modified pyrimidines, and all purines of the sense strand comprise 2′ fluoro modified purines.
In some embodiments, purines of the antisense strand comprise 2′ fluoro modified purines. In some embodiments, purines of the antisense strand comprise 2′-O-methyl modified purines. In some embodiments, purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all purines of the antisense strand comprise 2′ fluoro modified purines. In some embodiments, all purines of the antisense strand comprise 2′-O-methyl modified purines. In some embodiments, all purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines.
In some embodiments, pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, all pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines.
In some embodiments, purines of the antisense strand comprise 2′ fluoro modified purines, and pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the antisense strand comprise 2′-O-methyl modified purines, and pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, purines of the antisense strand comprise 2′ fluoro modified purines, and pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, purines of the antisense strand comprise 2′-O-methyl modified purines, and pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines, and purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines, and purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines, and purines of the antisense strand comprise 2′-O-methyl modified purines. In some embodiments, pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines, and purines of the antisense strand comprise 2′ fluoro modified purines.
In some embodiments, all purines of the antisense strand comprise 2′ fluoro modified purines, and all pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the antisense strand comprise 2′-O-methyl modified purines, and all pyrimidines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the antisense strand comprise 2′ fluoro modified purines, and all pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines. In some embodiments, all purines of the antisense strand comprise 2′-O-methyl modified purines, and all pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines. In some embodiments, all pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines, and all purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines, and all purines of the antisense strand comprise a mixture of 2′ fluoro and 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the antisense strand comprise 2′ fluoro modified pyrimidines, and all purines of the antisense strand comprise 2′-O-methyl modified purines. In some embodiments, all pyrimidines of the antisense strand comprise 2′-O-methyl modified pyrimidines, and all purines of the antisense strand comprise 2′ fluoro modified purines.
Disclosed herein, in some embodiments, are modified oligonucleotides. The modified oligonucleotide may be an siRNA that includes modifications to the ribose rings, and phosphate linkages. The modifications may be in particular patterns that maximize cell delivery, stability, and efficiency. The siRNA may also include a vinyl phosphonate and a hydrophobic group. These modifications may aid in delivery to a cell or tissue within a subject. The modified oligonucleotide may be used in a method such as a treatment method or a method of reducing gene expression.
In some embodiments, the oligonucleotide comprises a duplex consisting of 21 nucleotide single strands with base pairing between 19 of the base pairs. In some embodiments, the duplex comprises single-stranded 2 nucleotide overhangs are at the 3′ ends of each strand. One strand (antisense strand) is complementary to a DKK2 mRNA. Each end of the antisense strand has one to two phosphorothioate bonds. The 5′ end has an optional phosphate mimic such as a vinyl phosphonate. In some embodiments, the oligonucleotide is used to knock down a DKK2 mRNA or a target protein. In some embodiments, the sense strand has the same sequence as the DKK2 mRNA. In some embodiments, there are 1-2 phosphorothioates at the 3′ end. In some embodiments, there are 1 or no phosphorothioates at the 5′ end. In some embodiments, there is a hydrophobic conjugate of 12 to 25 carbons attached at the 5′ end via a phosphodiester bond.
In some cases, the sense strand of any of the siRNAs comprises siRNA with a particular modification pattern. In some embodiments of the modification pattern, position 9 counting from the 5′ end of the sense strand may have a 2′F modification. In some embodiments, when position 9 of the sense strand is a pyrimidine, then all purines in the sense strand have a 2′OMe modification. In some embodiments, when position 9 is the only pyrimidine between positions 5 and 11 of the sense stand, then position 9 is the only position with a 2′F modification in the sense strand. In some embodiments, when position 9 and only one other base between positions 5 and 11 of the sense strand are pyrimidines, then both of these pyrimidines are the only two positions with a 2′F modification in the sense strand. In some embodiments, when position 9 and only two other bases between positions 5 and 11 of the sense strand are pyrimidines, and those two other pyrimidines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. In some embodiments, when there are more than 2 pyrimidines between positions 5 and 11 of the sense strand, then all combinations of pyrimidines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that the sense strand does not have three 2′F modifications in a row. In some cases, the sense strand of any of the siRNAs comprises a modification pattern which conforms to any or all of these sense strand rules.
In some embodiments, when position 9 of the sense strand is a purine, then all purines in the sense strand have a 2′OMe modification. In some embodiments, when position 9 is the only purine between positions 5 and 11 of the sense stand, then position 9 is the only position with a 2′F modification in the sense strand. In some embodiments, when position 9 and only one other base between positions 5 and 11 of the sense strand are purines, then both of these purines are the only two positions with a 2′F modification in the sense strand. In some embodiments, when position 9 and only two other bases between positions 5 and 11 of the sense strand are purines, and those two other purines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. In some embodiments, when there are more than 2 purines between positions 5 and 11 of the sense strand, then all combinations of purines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that the sense strand does not have three 2′F modifications in a row. In some cases, the sense strand of any of the siRNAs comprises a modification pattern which conforms to any or all of these sense strand rules.
In some cases, position 9 of the sense strand can be a 2′deoxy. In these cases, 2′F and 2′OMe modifications may occur at the other positions of the sense strand. In some cases, the sense strand of any of the siRNAs comprises a modification pattern which conforms to these sense strand rules.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence in Table 4. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence in Table 4. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 4, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 4, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence in Table 4. The sense strand or antisense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the first 19 nucleotides of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand may comprise an overhang. The sense strand or antisense strand may comprise any modifications described herein (e.g. a different set of modifications or modification pattern than in Table 4). The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence in Table 5. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence in Table 5. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 5, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 5, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence in Table 5. The sense strand or antisense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the first 19 nucleotides of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand may comprise an overhang. The sense strand or antisense strand may comprise any modifications described herein (e.g. a different set of modifications or modification pattern than in Table 5). The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
In some embodiments, the siRNA comprises a sense strand or antisense strand having a sequence in accordance with the sense strand or antisense strand sequence in Table 6. In some embodiments, the sense strand or antisense strand comprises a sequence at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical, to a sense strand or antisense strand sequence in Table 6. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 6, or a sequence thereof having 3 or 4 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense strand comprises a sequence of a sense or antisense strand in Table 6, or a sequence thereof having 1 or 2 nucleoside substitutions, additions, or deletions. In some embodiments, the sense strand or antisense sequence comprises or consists of a sequence 100% identical to a sense strand or antisense strand sequence in Table 6. The sense strand or antisense strand sequence may include the first 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the first 19 nucleotides of any of the aforementioned sequences. The sense strand or antisense strand sequence may include the last 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 nucleotides (in the 5′ to 3′ direction) of any of the aforementioned sequences. The sense strand or antisense strand may comprise an overhang. The sense strand or antisense strand may comprise any modifications described herein (e.g. a different set of modifications or modification pattern than in Table 6). The sense strand or antisense strand may comprise a lipid moiety or a GalNAc moiety.
4. ASO Modification Patterns
In some embodiments, the composition comprises an oligonucleotide that inhibits the expression of DKK2, wherein the oligonucleotide comprises an antisense oligonucleotide (ASO). In some embodiments, the ASO comprises modification pattern ASO1: 5′-nsnsnsnsnsdNsdNsdNsdNsdNsdNsdNsdNsdNsdNsnsnsnsnsn-3′ (SEQ ID NO: 7647), wherein “dN” is any deoxynucleotide, “n” is a 2′O-methyl or 2′O-methoxyethyl-modified nucleoside, and “s” is a phosphorothioate linkage. In some embodiments, the ASO comprises modification pattern 1S, 2S, 3S, 4S, 5S, 6S, 7S, 8S, 9S, 10S, 1S, 12S, 13S, 14S, 15S, 16S, 17S, 18S, 19S, 20S, 21S, 22S, 23S, 24S, 25S, 26S, 27S, 28S, 29S,30S, 31S, 32S, 33S, 34S, 35S, 36S, 37S, 38S, 39S, 40S, 41S, 42S, 1AS, 2AS, 3AS, 4AS, or 5AS.
D. Formulations
In some embodiments, the composition is a pharmaceutical composition. In some embodiments, the composition is sterile. In some embodiments, the composition further comprises a pharmaceutically acceptable carrier.
In some embodiments, the pharmaceutically acceptable carrier comprises water. In some embodiments, the pharmaceutically acceptable carrier comprises a buffer. In some embodiments, the pharmaceutically acceptable carrier comprises a saline solution. In some embodiments, the pharmaceutically acceptable carrier comprises a cream. In some embodiments, the pharmaceutically acceptable carrier comprises a gel. In some embodiments, the pharmaceutically acceptable carrier comprises water, a buffer, a saline solution, a cream, or a gel. In some embodiments, the pharmaceutically acceptable carrier comprises contains a permeation enhancer. In some embodiments, the formulation contains pharmaceutically acceptable counterions to the oligonucleotides. In some embodiments, the pharmaceutically acceptable counterions increase membrane affinity. In some embodiments, the composition comprises a liposome. In some embodiments, the pharmaceutically acceptable carrier comprises liposomes, lipids, nanoparticles, proteins, protein-antibody complexes, peptides, cellulose, nanogel, or a combination thereof. In some embodiments, the composition is formulated for topical administration.
II. Methods and Uses
Disclosed herein, in some embodiments, are methods of administering a composition described herein to a subject. Some embodiments relate to use a composition described herein, such as administering the composition to a subject.
Some embodiments relate to a method of treating a disorder in a subject in need thereof. Some embodiments relate to use of a composition described herein in the method of treatment. Some embodiments include administering a composition described herein to a subject with the disorder. In some embodiments, the administration treats the disorder in the subject. In some embodiments, the composition treats the disorder in the subject.
In some embodiments, the treatment comprises prevention, inhibition, or reversion of the disorder in the subject. Some embodiments relate to use of a composition described herein in the method of preventing, inhibiting, or reversing the disorder. Some embodiments relate to a method of preventing, inhibiting, or reversing a disorder a disorder in a subject in need thereof. Some embodiments include administering a composition described herein to a subject with the disorder. In some embodiments, the administration prevents, inhibits, or reverses the disorder in the subject. In some embodiments, the composition prevents, inhibits, or reverses the disorder in the subject.
Some embodiments relate to a method of preventing a disorder a disorder in a subject in need thereof. Some embodiments relate to use of a composition described herein in the method of preventing the disorder. Some embodiments include administering a composition described herein to a subject with the disorder. In some embodiments, the administration prevents the disorder in the subject. In some embodiments, the composition prevents the disorder in the subject.
Some embodiments relate to a method of inhibiting a disorder a disorder in a subject in need thereof. Some embodiments relate to use of a composition described herein in the method of inhibiting the disorder. Some embodiments include administering a composition described herein to a subject with the disorder. In some embodiments, the administration inhibits the disorder in the subject. In some embodiments, the composition inhibits the disorder in the subject.
Some embodiments relate to a method of reversing a disorder a disorder in a subject in need thereof. Some embodiments relate to use of a composition described herein in the method of reversing the disorder. Some embodiments include administering a composition described herein to a subject with the disorder. In some embodiments, the administration reverses the disorder in the subject. In some embodiments, the composition reverses the disorder in the subject.
The administration may be topical. For example, a composition or formulation described herein may be administered to a scalp. The topical administration may include rubbing, brushing, swabbing, dabbing, or wiping. The administration may be on a skin area of the subject. The skin area may include hair. The skin area may include hair loss. The skin area may be at risk of hair loss. The skin area may include an area of the head. The skin area may include a scalp. The skin area may include a scalp region. The skin area may include a temporal region. The skin area may include a neck region.
A. Disorders
Some embodiments of the methods described herein include treating a disorder in a subject in need thereof. In some embodiments, the disorder includes hair loss. In some embodiments, the disorder is hair loss. Non-limiting examples of hair loss include androgenetic alopecia (male pattern baldness), alopecia areata, and non-scarring hair loss. In some embodiments, the disorder includes hair discoloration or graying. In some embodiments, the hair loss comprises male pattern baldness. In some embodiments, the hair loss comprises alopecia areata. In some embodiments, the hair loss comprises scarring hair loss. In some embodiments, the hair loss comprises non-scarring hair loss.
B. Subjects
Some embodiments of the methods described herein include treatment of a subject. Non-limiting examples of subjects include vertebrates, animals, mammals, dogs, cats, cattle, rodents, mice, rats, primates, monkeys, and humans. In some embodiments, the subject is a vertebrate. In some embodiments, the subject is an animal. In some embodiments, the subject is a mammal. In some embodiments, the subject is a dog. In some embodiments, the subject is a cat. In some embodiments, the subject is a cattle. In some embodiments, the subject is a mouse. In some embodiments, the subject is a rat. In some embodiments, the subject is a primate. In some embodiments, the subject is a monkey. In some embodiments, the subject is an animal, a mammal, a dog, a cat, cattle, a rodent, a mouse, a rat, a primate, or a monkey. In some embodiments, the subject is a human. In some embodiments, the subject is male. In some embodiments, the subject is female.
In some embodiments, the subject has a body mass index (BMI) of 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more, or a range defined by any two of the aforementioned integers. In some embodiments, the subject is overweight. In some embodiments, the subject has a BMI of 25 or more. In some embodiments, the subject has a BMI of 25-29. In some embodiments, the subject is obese. In some embodiments, the subject has a BMI of 30 or more. In some embodiments, the subject has a BMI of 30-39. In some embodiments, the subject has a BMI of 40-50. In some embodiments, the subject has a BMI of 25-50.
In some embodiments, the subject is ≥90 years of age. In some embodiments, the subject is ≥85 years of age. In some embodiments, the subject is ≥80 years of age. In some embodiments, the subject is ≥70 years of age. In some embodiments, the subject is ≥60 years of age. In some embodiments, the subject is ≥50 years of age. In some embodiments, the subject is ≥40 years of age. In some embodiments, the subject is ≥30 years of age. In some embodiments, the subject is ≥20 years of age. In some embodiments, the subject is ≥10 years of age. In some embodiments, the subject is ≥1 years of age. In some embodiments, the subject is ≥0 years of age.
In some embodiments, the subject is ≤100 years of age. In some embodiments, the subject is ≤90 years of age. In some embodiments, the subject is ≤85 years of age. In some embodiments, the subject is ≤80 years of age. In some embodiments, the subject is ≤70 years of age. In some embodiments, the subject is ≤60 years of age. In some embodiments, the subject is ≤50 years of age. In some embodiments, the subject is ≤40 years of age. In some embodiments, the subject is ≤30 years of age. In some embodiments, the subject is ≤20 years of age. In some embodiments, the subject is ≤10 years of age. In some embodiments, the subject is ≤1 years of age.
In some embodiments, the subject is between 0 and 100 years of age. In some embodiments, the subject is between 20 and 90 years of age. In some embodiments, the subject is between 30 and 80 years of age. In some embodiments, the subject is between 40 and 75 years of age. In some embodiments, the subject is between 50 and 70 years of age. In some embodiments, the subject is between 40 and 85 years of age. In some embodiments, the subject is aging. In some embodiments, the subject is an adult.
In some embodiments, the subject has a family history of hair loss. In some embodiments, the subject has hormone levels related to hair loss. In some embodiments, the subject has a thyroid disorder. In some embodiments, the subject is malnourished. In some embodiments, the subject has been subjected to environmental factors affecting hair loss. In some embodiments, the subject has subjected to physical stress. In some embodiments, the subject has subjected to emotional stress.
C. Baseline Measurements
Some embodiments of the methods described herein include obtaining a baseline measurement from a subject. For example, in some embodiments, a baseline measurement is obtained from the subject prior to treating the subject. In some embodiments, the baseline measurement is a baseline hair loss measurement. In some embodiments, the baseline measurement is a baseline measurement of a symptom of hair loss. Non-limiting examples of baseline measurements include a baseline hair loss assessment score, a baseline total hair count, a baseline vellus hair count, a baseline non-vellus hair count, a baseline hair thickness measurement, a baseline hair density measurement, or a baseline number of hair follicles. The baseline measurement may include a baseline hair color measurement. The baseline measurement may include a baseline gene or protein level, a baseline DKK2 mRNA level, or a baseline DKK2 protein level.
In some embodiments, the baseline measurement is obtained non-invasively. In some embodiments, the baseline measurement is obtained directly from the subject. In some embodiments, the baseline measurement is obtained by observation, for example by observation of the subject or of the subject's tissue. In some embodiments, the baseline measurement is obtained noninvasively using an imaging device. In some embodiments, the baseline measurement is obtained using a photograph. In some embodiments, the baseline measurement is obtained using a phototrichogram. In some embodiments, the baseline measurement is obtained using a macrophotography analysis. In some embodiments, the baseline measurement is obtained using a questionnaire.
In some embodiments, the baseline measurement is obtained invasively. In some embodiments, the baseline measurement is obtained in a sample from the subject. In some embodiments, the baseline measurement is obtained in a biopsy such as a scalp biopsy. In some embodiments, the baseline measurement is obtained in one or more histological tissue sections. In some embodiments, the baseline measurement is obtained by performing an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay, on the sample obtained from the subject. In some embodiments, the baseline measurement is obtained by an immunoassay, a colorimetric assay, or a fluorescence assay. In some embodiments, the baseline measurement is obtained by PCR.
In some embodiments, the baseline measurement is a baseline questionnaire result. In some embodiments, the baseline measurement is a baseline hair loss hair loss assessment score. In some embodiments, the baseline questionnaire result comprises a baseline score such as a baseline hair loss assessment score. In some embodiments, the baseline questionnaire result is obtained from a questionnaire. In some embodiments, the baseline questionnaire result is obtained from multiple questionnaires. In some embodiments, the questionnaire is a Men's Hair Growth Questionnaire (MHGQ). In some embodiments, the questionnaire is a Kingsley Alopecia Profile (KAP) questionnaire. The questionnaire may include questions about hair growth that the subject rates. Non-limiting examples of such ratings may include strongly agree, agree, neither agree nor disagree, disagree, and strongly disagree, where each rating is assigned a value. The baseline score may include a sum of each value. In some embodiments, the baseline hair loss assessment score is not based on a questionnaire. In some embodiments, the baseline hair loss assessment score is assessed by a medical practitioner. In some embodiments, the baseline hair loss assessment score includes a semi-quantitative hair visual hair score on a numerical scale such as 1-10.
In some embodiments, the baseline measurement is a baseline hair count. In some embodiments, the baseline hair count is a baseline total hair count. The baseline total hair count may include a baseline vellus hair count and a baseline non-vellus hair count. In some embodiments, the baseline hair count is a baseline vellus hair count. In some embodiments, the baseline hair count is a baseline non-vellus hair count. In some embodiments, the baseline hair count is determined in an area of skin. In some embodiments, the baseline hair count is normalized based on the area of skin. In some embodiments, the baseline hair count is assessed using photography. In some embodiments, the baseline hair count is assessed by phototrichogram. In some embodiments, the baseline hair count is assessed by a macrophotography analysis.
In some embodiments, the baseline measurement is a baseline hair thickness measurement. In some embodiments, the baseline hair thickness measurement is determined in an area of skin. In some embodiments, the baseline hair thickness measurement comprises a width of an individual hair. In some embodiments, the baseline hair thickness measurement comprises widths of multiple individual hairs. In some embodiments, the baseline hair thickness measurement comprises an average of the widths of the multiple individual hairs. In some embodiments, the baseline hair thickness measurement comprises a median of the widths of the multiple individual hairs. The baseline hair thickness measurement may include a baseline vellus hair thickness measurement. The baseline hair thickness measurement may include a baseline non-vellus hair thickness measurement. In some embodiments, the baseline hair thickness measurement is assessed using photography. In some embodiments, the baseline hair thickness measurement is assessed by phototrichogram. In some embodiments, the baseline hair thickness measurement is assessed by a macrophotography analysis.
In some embodiments, the baseline measurement is a baseline hair density measurement. In some embodiments, the baseline hair density measurement is determined in an area of skin. In some embodiments, the baseline hair density measurement comprises a number of hair in the area of skin. In some embodiments, the baseline hair density measurement comprises the number of hair in the area of skin divided by the area of skin. The baseline hair density measurement may include a baseline vellus hair density measurement. The baseline hair density measurement may include a baseline non-vellus hair density measurement. In some embodiments, the baseline hair density measurement is assessed using photography. In some embodiments, the baseline hair density measurement is assessed by phototrichogram. In some embodiments, the baseline hair density measurement is assessed by a macrophotography analysis.
In some embodiments, the baseline measurement is a baseline number of hair follicles. In some embodiments, the baseline number of hair follicles is a baseline total number of hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of terminal hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of anagen hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of telogen hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of catagen hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of miniaturized hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of vellus miniaturized hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of vellus-like miniaturized hair follicles. In some embodiments, the baseline number of hair follicles include a baseline number of indeterminate hair follicles. In some embodiments, the baseline number of hair follicles is determined in an area of skin. In some embodiments, the baseline number of hair follicles is normalized based on the area of skin. In some embodiments, the baseline number of hair follicles is assessed in a biopsy, such as a scalp biopsy. In some embodiments, the baseline number of hair follicles is assessed using photography.
In some embodiments, the baseline measurement is a baseline hair color measurement. In some embodiments, the baseline hair color measurement is determined in an area of skin. In some embodiments, the baseline hair color measurement comprises a color of an individual hair. In some embodiments, the baseline hair color measurement comprises colors of multiple individual hairs. In some embodiments, the baseline hair color measurement comprises an average of the colors of the multiple individual hairs. In some embodiments, the baseline hair color measurement comprises a median of the colors of the multiple individual hairs. The baseline hair color measurement may include a baseline measurement of how gray the har is, or how gray the hairs are. The baseline hair color measurement may include a baseline measurement of how much color is in the hair, or how much color is in the hairs. The baseline hair color measurement may include a baseline measurement of how white the har is, or how white the hairs are. The baseline hair color measurement may include a hair pigmentation measurement. The baseline hair color measurement may include a hair contrast measurement. The baseline hair color measurement may include a baseline vellus hair color measurement. The baseline hair color measurement may include a baseline non-vellus hair color measurement. In some embodiments, the baseline hair color measurement is assessed using photography. In some embodiments, the baseline hair color measurement is assessed by phototrichogram. In some embodiments, the baseline hair color measurement is assessed by a macrophotography analysis. The baseline hair color measurement may be a qualitative measurement. The baseline hair color measurement may be a quantitative measurement. The baseline hair color measurement may be a number, such as an amount of hair color. The baseline hair color measurement may be a rate, such as a rate of hair color loss.
In some embodiments, the baseline measurement is a baseline protein level. In some embodiments, the baseline protein level is a baseline β-catenin protein level. In some embodiments, the baseline protein level is a baseline α-SMA protein level. In some embodiments, the baseline protein level is a baseline collagen protein level. In some embodiments, the collagen of the baseline collagen protein level is collagen I. In some embodiments, the collagen of the baseline collagen protein level is collagen III. In some embodiments, the baseline protein level is assessed in a baseline sample such as a baseline skin sample. In some embodiments, the baseline protein level is indicated as a mass or percentage of protein per sample weight. In some embodiments, the baseline protein level is indicated as a mass or percentage of protein per sample volume. In some embodiments, the baseline protein level is indicated as a mass or percentage of protein per total protein within the sample. In some embodiments, the baseline protein measurement is a baseline circulating protein measurement. In some embodiments, the baseline protein measurement is obtained by an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay.
In some embodiments, the baseline measurement is a baseline mRNA level. In some embodiments, the baseline mRNA level is a baseline β-catenin mRNA level. In some embodiments, the baseline mRNA level is a baseline α-SMA mRNA level. In some embodiments, the baseline mRNA level is a baseline collagen mRNA level. In some embodiments, the collagen of the baseline collagen mRNA level is collagen I. In some embodiments, the collagen of the baseline collagen mRNA level is collagen III. In some embodiments, the baseline mRNA level is assessed in a baseline sample such as a baseline skin sample. In some embodiments, the baseline mRNA level is indicated as a mass or percentage of mRNA per sample weight. In some embodiments, the baseline mRNA level is indicated as a mass or percentage of mRNA per sample volume. In some embodiments, the baseline mRNA level is indicated as a mass or percentage of mRNA per total mRNA within the sample. In some embodiments, the baseline mRNA level is indicated as a mass or percentage of mRNA per total nucleic acids within the sample. In some embodiments, the baseline mRNA level is indicated relative to another mRNA level, such as an mRNA level of a housekeeping gene, within the sample. In some embodiments, the baseline mRNA measurement is obtained by an assay such as a polymerase chain reaction (PCR) assay. In some embodiments, the PCR comprises quantitative PCR (qPCR). In some embodiments, the PCR comprises reverse transcription of the mRNA.
In some embodiments, the baseline measurement is a baseline DKK2 protein measurement. In some embodiments, the baseline DKK2 protein measurement comprises a baseline DKK2 protein level. In some embodiments, the baseline DKK2 protein level is assessed in a baseline sample such as a baseline skin sample or a baseline fluid sample (e.g. blood, serum, or plasma). In some embodiments, the baseline DKK2 protein level is indicated as a mass or percentage of DKK2 protein per sample weight. In some embodiments, the baseline DKK2 protein level is indicated as a mass or percentage of DKK2 protein per sample volume. In some embodiments, the baseline DKK2 protein level is indicated as a mass or percentage of DKK2 protein per total protein within the sample. In some embodiments, the baseline DKK2 protein measurement is a baseline circulating DKK2 protein measurement. In some embodiments, the baseline DKK2 protein measurement is obtained by an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay.
In some embodiments, the baseline measurement is a baseline DKK2 mRNA measurement. In some embodiments, the baseline DKK2 mRNA measurement comprises a baseline DKK2 mRNA level. In some embodiments, the baseline DKK2 mRNA level is assessed in a baseline sample such as a baseline skin sample. In some embodiments, the baseline DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per sample weight. In some embodiments, the baseline DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per sample volume. In some embodiments, the baseline DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per total mRNA within the sample. In some embodiments, the baseline DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per total nucleic acids within the sample. In some embodiments, the baseline DKK2 mRNA level is indicated relative to another mRNA level, such as an mRNA level of a housekeeping gene, within the sample. In some embodiments, the baseline DKK2 mRNA measurement is obtained by an assay such as a polymerase chain reaction (PCR) assay. In some embodiments, the PCR comprises quantitative PCR (qPCR). In some embodiments, the PCR comprises reverse transcription of the DKK2 mRNA.
Some embodiments of the methods described herein include obtaining a sample from a subject. In some embodiments, the baseline measurement is obtained in a sample obtained from the subject. In some embodiments, the sample is obtained from the subject prior to administration or treatment of the subject with a composition described herein. In some embodiments, a baseline measurement is obtained in a sample obtained from the subject prior to administering the composition to the subject. In some embodiments, the sample is obtained from the subject in a fasted state. In some embodiments, the sample is obtained from the subject after an overnight fasting period. In some embodiments, the sample is obtained from the subject in a fed state.
In some embodiments, the sample comprises a fluid. In some embodiments, the sample is a fluid sample. In some embodiments, the sample is a blood, plasma, or serum sample. In some embodiments, the sample comprises blood. In some embodiments, the sample is a blood sample. In some embodiments, the sample is a whole-blood sample. In some embodiments, the blood is fractionated or centrifuged. In some embodiments, the sample comprises plasma. In some embodiments, the sample is a plasma sample. In some embodiments, the sample comprises serum. In some embodiments, the sample is a serum sample.
In some embodiments, the sample comprises a tissue. The tissue may be or include skin. The skin may comprise or consist of a skin layer. The skin layer may be or include a dermal layer or an epidermal layer. The skin may include epidermis. The skin may include epidermis. The skin may include scalp skin. The skin may eyebrow skin. The skin may pubic skin. The skin may include skin from a leg of the subject. The skin may include skin from an arm of the subject. The skin may include one or more hairs. The hairs may be any of scalp hairs, eyebrow hairs, pubic hairs, arm hairs, or leg hairs.
In some embodiments, the sample is a tissue sample. In some embodiments, the sample comprises skin. In some embodiments, the sample is a skin sample. For example, the baseline DKK2 mRNA measurement, or the baseline DKK2 protein measurement, may be obtained in a skin sample from the patient prior to administration of a compound or oligonucleotide disclosed herein. In some embodiments, the sample is a biopsy. In some embodiments, the biopsy is a skin biopsy. In some embodiments, the skin biopsy includes a scalp biopsy.
D. Effects
In some embodiments, the composition or administration of the composition affects a measurement such as a hair loss measurement or a measurement of a symptom of hair loss. In some embodiments, the measurement is a hair loss assessment score, a total hair count, a vellus hair count, a non-vellus hair count, a hair thickness measurement, a hair density measurement, a number of hair follicles, a hair color measurement, a gene or protein level, a DKK2 protein measurement (for example, circulating or tissue DKK2 protein levels), or a DKK2 mRNA measurement, relative to the baseline measurement.
Some embodiments of the methods described herein include obtaining the measurement from a subject. For example, the measurement may be obtained from the subject after treating the subject. In some embodiments, the measurement is obtained in a second sample (such as a fluid or tissue sample described herein) obtained from the subject after the composition is administered to the subject. In some embodiments, the measurement indicates that the disorder has been treated.
In some embodiments, the measurement is obtained non-invasively. In some embodiments, the measurement is obtained directly from the subject. In some embodiments, the measurement is obtained by observation, for example by observation of the subject or of the subject's tissue. In some embodiments, the measurement is obtained noninvasively using an imaging device. In some embodiments, the measurement is obtained using a photograph. In some embodiments, the measurement is obtained using a phototrichogram. In some embodiments, the measurement is obtained using a macrophotography analysis. In some embodiments, the measurement is obtained using a questionnaire.
In some embodiments, the measurement is obtained invasively. In some embodiments, the measurement is obtained in a second sample from the subject. In some embodiments, the measurement is obtained in a biopsy such as a scalp biopsy. In some embodiments, the measurement is obtained in one or more histological tissue sections. In some embodiments, the measurement is obtained by performing an assay on the second sample obtained from the subject. In some embodiments, the measurement is obtained by an assay, such as an assay described herein. In some embodiments, the assay is an immunoassay, a colorimetric assay, a fluorescence assay, or a PCR assay. In some embodiments, the measurement is obtained by an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay. In some embodiments, the measurement is obtained by PCR. In some embodiments, the measurement is obtained by histology. In some embodiments, the measurement is obtained by observation. In some embodiments, additional measurements are made, such as in a 3rd sample, a 4th sample, or a fifth sample.
In some embodiments, the measurement is obtained within 1 hour, within 2 hours, within 3 hours, within 4 hours, within 5 hours, within 6 hours, within 12 hours, within 18 hours, or within 24 hours after the administration of the composition. In some embodiments, the measurement is obtained within 1 day, within 2 days, within 3 days, within 4 days, within 5 days, within 6 days, or within 7 days after the administration of the composition. In some embodiments, the measurement is obtained within 1 week, within 2 weeks, within 3 weeks, within 1 month, within 2 months, within 3 months, within 6 months, within 1 year, within 2 years, within 3 years, within 4 years, or within 5 years after the administration of the composition. In some embodiments, the measurement is obtained after 1 hour, after 2 hours, after 3 hours, after 4 hours, after 5 hours, after 6 hours, after 12 hours, after 18 hours, or after 24 hours after the administration of the composition. In some embodiments, the measurement is obtained after 1 day, after 2 days, after 3 days, after 4 days, after 5 days, after 6 days, or after 7 days after the administration of the composition. In some embodiments, the measurement is obtained after 1 week, after 2 weeks, after 3 weeks, after 1 month, after 2 months, after 3 months, after 6 months, after 1 year, after 2 years, after 3 years, after 4 years, or after 5 years, following the administration of the composition.
In some embodiments, the composition reduces the measurement relative to the baseline measurement. In some embodiments, the reduction is measured in a second tissue sample obtained from the subject after administering the composition to the subject. In some embodiments, the reduction is measured directly in the subject after administering the composition to the subject. In some embodiments, the measurement is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline measurement. In some embodiments, the measurement is decreased by about 10% or more, relative to the baseline measurement. In some embodiments, the measurement is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline measurement. In some embodiments, the measurement is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline measurement. In some embodiments, the measurement is decreased by no more than about 10%, relative to the baseline measurement. In some embodiments, the measurement is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline measurement. In some embodiments, the measurement is decreased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition increases the measurement relative to the baseline measurement. In some embodiments, the increase is measured in a second tissue sample obtained from the subject after administering the composition to the subject. In some embodiments, the increase is measured directly in the subject after administering the composition to the subject. In some embodiments, the measurement is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline measurement. In some embodiments, the measurement is increased by about 10% or more, relative to the baseline measurement. In some embodiments, the measurement is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline measurement. In some embodiments, the measurement is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline measurement. In some embodiments, the measurement is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline measurement. In some embodiments, the measurement is increased by no more than about 10%, relative to the baseline measurement. In some embodiments, the measurement is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline measurement. In some embodiments, the measurement is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline measurement. In some embodiments, the measurement is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a questionnaire result. In some embodiments, the measurement is a hair loss assessment score. In some embodiments, the questionnaire result comprises a score such as a hair loss assessment score. In some embodiments, the questionnaire result is obtained from a questionnaire. In some embodiments, the questionnaire result is obtained from multiple questionnaires. In some embodiments, the questionnaire is a Men's Hair Growth Questionnaire (MHGQ). In some embodiments, the questionnaire is a Kingsley Alopecia Profile (KAP) questionnaire. The questionnaire may include questions about hair growth that the subject rates. Non-limiting examples of such ratings may include strongly agree, agree, neither agree nor disagree, disagree, and strongly disagree, where each rating is assigned a value. The score may include a sum of each value. In some embodiments, the hair loss assessment score is not based on a questionnaire. In some embodiments, the hair loss assessment score is determined by a medical practitioner. In some embodiments, the hair loss assessment score includes a semi-quantitative hair visual hair score on a numerical scale such as 1-10.
In some embodiments, the composition changes the hair loss assessment score relative to the baseline hair loss assessment score. In some embodiments, the change in the hair loss assessment score is an increase. In some embodiments, the change in the hair loss assessment score is a decrease. In some embodiments, the change is measured in the subject after administering the composition to the subject. In some embodiments, the change is measured directly by the subject after the composition is administered to the subject. In some embodiments, the hair loss assessment score is changed by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by about 10% or more, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by about 100% or more, changed by about 250% or more, changed by about 500% or more, changed by about 750% or more, or changed by about 1000% or more, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by no more than about 10%, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by no more than about 100%, changed by no more than about 250%, changed by no more than about 500%, changed by no more than about 750%, or changed by no more than about 1000%, relative to the baseline hair loss assessment score. In some embodiments, the hair loss assessment score is changed by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages. In some embodiments, the hair loss assessment score is changed by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a hair count. In some embodiments, the hair count is a total hair count. The total hair count may include a vellus hair count and a non-vellus hair count. In some embodiments, the hair count is a vellus hair count. In some embodiments, the hair count is a non-vellus hair count. In some embodiments, the hair count is determined in an area of skin. In some embodiments, the hair count is normalized based on the area of skin. In some embodiments, the hair count is assessed using photography. In some embodiments, the hair count is assessed by phototrichogram. In some embodiments, the hair count is assessed by a macrophotography analysis.
In some embodiments, the composition increases the hair count relative to the baseline hair count. In some embodiments, the increase is measured in the subject after administering the composition to the subject. In some embodiments, the increase is measured directly on the subject after administering the composition to the subject. In some embodiments, the hair count is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline hair count. In some embodiments, the hair count is increased by about 10% or more, relative to the baseline hair count. In some embodiments, the hair count is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline hair count. In some embodiments, the hair count is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline hair count. In some embodiments, the hair count is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline hair count. In some embodiments, the hair count is increased by no more than about 10%, relative to the baseline hair count. In some embodiments, the hair count is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline hair count. In some embodiments, the hair count is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline hair count. In some embodiments, the hair count is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a hair thickness measurement. In some embodiments, the hair thickness measurement is determined in an area of skin. In some embodiments, the hair thickness measurement comprises a width of an individual hair. In some embodiments, the hair thickness measurement comprises widths of multiple individual hairs. In some embodiments, the hair thickness measurement comprises an average of the widths of the multiple individual hairs. In some embodiments, the hair thickness measurement comprises a median of the widths of the multiple individual hairs. The hair thickness measurement may include a vellus hair thickness measurement. The hair thickness measurement may include a non-vellus hair thickness measurement. In some embodiments, the hair thickness measurement is assessed using photography. In some embodiments, the hair thickness measurement is assessed by phototrichogram. In some embodiments, the hair thickness measurement is assessed by a macrophotography analysis.
In some embodiments, the composition increases the hair thickness measurement relative to the baseline hair thickness measurement. In some embodiments, the increase is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the increase is measured directly on the subject after administering the composition to the subject. In some embodiments, the hair thickness measurement is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by about 10% or more, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by no more than about 10%, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline hair thickness measurement. In some embodiments, the hair thickness measurement is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a hair density measurement. In some embodiments, the hair density measurement is determined in an area of skin. In some embodiments, the hair density measurement comprises a number of hair in the area of skin. In some embodiments, the hair density measurement comprises the number of hair in the area of skin divided by the area of skin. The hair density measurement may include a vellus hair density measurement. The hair density measurement may include a non-vellus hair density measurement. In some embodiments, the hair density measurement is assessed using photography. In some embodiments, the hair density measurement is assessed by phototrichogram. In some embodiments, the hair density measurement is assessed by a macrophotography analysis.
In some embodiments, the composition increases the hair density measurement relative to the baseline hair density measurement. In some embodiments, the increase is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the increase is measured directly on the subject after administering the composition to the subject. In some embodiments, the hair density measurement is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by about 10% or more, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by no more than about 10%, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline hair density measurement. In some embodiments, the hair density measurement is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a number of hair follicles. In some embodiments, the number of hair follicles is a total number of hair follicles. In some embodiments, the number of hair follicles include a number of terminal hair follicles. In some embodiments, the number of hair follicles include a number of anagen hair follicles. In some embodiments, the number of hair follicles include a number of telogen hair follicles. In some embodiments, the number of hair follicles include a number of catagen hair follicles. In some embodiments, the number of hair follicles include a number of miniaturized hair follicles. In some embodiments, the number of hair follicles include a number of vellus miniaturized hair follicles. In some embodiments, the number of hair follicles include a number of vellus-like miniaturized hair follicles. In some embodiments, the number of hair follicles include a number of indeterminate hair follicles. In some embodiments, the number of hair follicles is determined in an area of skin. In some embodiments, the number of hair follicles is normalized based on the area of skin. In some embodiments, the number of hair follicles is assessed in a biopsy, such as a scalp biopsy. In some embodiments, the number of hair follicles is assessed using photography.
In some embodiments, the composition increases the number of hair follicles relative to the baseline number of hair follicles. In some embodiments, the increase is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the increase is measured directly on the subject after administering the composition to the subject. In some embodiments, the number of hair follicles is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by about 10% or more, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by no more than about 10%, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline number of hair follicles. In some embodiments, the number of hair follicles is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a protein level. In some embodiments, the protein level is a β-catenin protein level. In some embodiments, the protein level is a α-SMA protein level. In some embodiments, the protein level is a collagen protein level. In some embodiments, the collagen of the collagen protein level is collagen I. In some embodiments, the collagen of the collagen protein level is collagen III. In some embodiments, the protein level is assessed in a sample such as a skin sample. In some embodiments, the protein level is indicated as a mass or percentage of protein per sample weight. In some embodiments, the protein level is indicated as a mass or percentage of protein per sample volume. In some embodiments, the protein level is indicated as a mass or percentage of protein per total protein within the sample. In some embodiments, the protein measurement is a circulating protein measurement. In some embodiments, the protein measurement is obtained by an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay.
In some embodiments, the measurement is a hair color measurement. In some embodiments, the hair color measurement is determined in an area of skin. In some embodiments, the hair color measurement comprises a color of an individual hair. In some embodiments, the hair color measurement comprises colors of multiple individual hairs. In some embodiments, the hair color measurement comprises an average of the colors of the multiple individual hairs. In some embodiments, the hair color measurement comprises a median of the colors of the multiple individual hairs. The hair color measurement may include a measurement of how gray the har is, or how gray the hairs are. The hair color measurement may include a measurement of how much color is in the hair, or how much color is in the hairs. The hair color measurement may include a measurement of how white the har is, or how white the hairs are. The hair color measurement may include a hair pigmentation measurement. The hair color measurement may include a hair contrast measurement. The hair color measurement may include a vellus hair color measurement. The hair color measurement may include a non-vellus hair color measurement. In some embodiments, the hair color measurement is assessed using photography. In some embodiments, the hair color measurement is assessed by phototrichogram. In some embodiments, the hair color measurement is assessed by a macrophotography analysis. The hair color measurement may be a qualitative measurement. The hair color measurement may be a quantitative measurement. The hair color measurement may be a number, such as an amount of hair color. The hair color measurement may be a rate, such as a rate of hair color loss.
In some embodiments, the composition increases the hair color measurement relative to the baseline hair color measurement. In some embodiments, the increase is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the increase is measured directly on the subject after administering the composition to the subject. In some embodiments, the hair color measurement is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by about 10% or more, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by no more than about 10%, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline hair color measurement. In some embodiments, the hair color measurement is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition reduces the protein level relative to the baseline protein level. In some embodiments, the reduction is measured in a second tissue or fluid sample (e.g. a skin, blood, serum, or plasma sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the protein level is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline protein level. In some embodiments, the protein level is decreased by about 10% or more, relative to the baseline protein level. In some embodiments, the protein level is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline protein level. In some embodiments, the protein level is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline protein level. In some embodiments, the protein level is decreased by no more than about 10%, relative to the baseline protein level. In some embodiments, the protein level is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline protein level. In some embodiments, the protein level is decreased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition increases the protein level relative to the baseline protein level. In some embodiments, the increase is measured in a second tissue or fluid sample (e.g. a skin, blood, serum, or plasma sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the protein level is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline protein level. In some embodiments, the protein level is increased by about 10% or more, relative to the baseline protein level. In some embodiments, the protein level is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline protein level. In some embodiments, the protein level is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline protein level. In some embodiments, the protein level is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline protein level. In some embodiments, the protein level is increased by no more than about 10%, relative to the baseline protein level. In some embodiments, the protein level is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline protein level. In some embodiments, the protein level is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline protein level. In some embodiments, the protein level is increased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a mRNA level. In some embodiments, the mRNA level is a β-catenin mRNA level. In some embodiments, the mRNA level is a α-SMA mRNA level. In some embodiments, the mRNA level is a collagen mRNA level. In some embodiments, the collagen of the collagen mRNA level is collagen I. In some embodiments, the collagen of the collagen mRNA level is collagen III. In some embodiments, the mRNA level is assessed in a sample such as a skin sample. In some embodiments, the mRNA level is indicated as a mass or percentage of mRNA per sample weight. In some embodiments, the mRNA level is indicated as a mass or percentage of mRNA per sample volume. In some embodiments, the mRNA level is indicated as a mass or percentage of mRNA per total mRNA within the sample. In some embodiments, the mRNA level is indicated as a mass or percentage of mRNA per total nucleic acids within the sample. In some embodiments, the mRNA level is indicated relative to another mRNA level, such as an mRNA level of a housekeeping gene, within the sample. In some embodiments, the mRNA measurement is obtained by an assay such as a polymerase chain reaction (PCR) assay. In some embodiments, the PCR comprises quantitative PCR (qPCR). In some embodiments, the PCR comprises reverse transcription of the mRNA.
In some embodiments, the composition reduces the mRNA level relative to the baseline mRNA level. In some embodiments, the reduction is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the mRNA level is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by about 10% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by no more than about 10%, relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline mRNA level. In some embodiments, the mRNA level is decreased by 2.5%, 5%, 7.5%1, 0%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the composition increases the mRNA level relative to the baseline mRNA level. In some embodiments, the increase is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the mRNA level is increased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by about 10% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by about 100% or more, increased by about 250% or more, increased by about 500% or more, increased by about 750% or more, or increased by about 1000% or more, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by no more than about 10%, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by no more than about 100%, increased by no more than about 250%, increased by no more than about 500%, increased by no more than about 750%, or increased by no more than about 1000%, relative to the baseline mRNA level. In some embodiments, the mRNA level is increased by 2.5%, 5%, 7.5%, 10, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 250%, 500%, 750%, or 1000%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a DKK2 protein measurement. In some embodiments, the DKK2 protein measurement comprises a DKK2 protein level. In some embodiments, the DKK2 protein level is assessed in a sample such as a skin sample or a fluid sample (e.g. blood, serum, or plasma). In some embodiments, the DKK2 protein level is indicated as a mass or percentage of DKK2 protein per sample weight. In some embodiments, the DKK2 protein level is indicated as a mass or percentage of DKK2 protein per sample volume. In some embodiments, the DKK2 protein level is indicated as a mass or percentage of DKK2 protein per total protein within the sample. In some embodiments, the DKK2 protein measurement is a circulating DKK2 protein measurement. In some embodiments, the DKK2 protein measurement is obtained by an assay such as an immunoassay, a colorimetric assay, or a fluorescence assay.
In some embodiments, the composition reduces the DKK2 protein level relative to the baseline DKK2 protein level. In some embodiments, the reduction is measured in a second tissue or fluid sample (e.g. a skin, blood, serum, or plasma sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the DKK2 protein level is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by about 10% or more, relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by no more than about 10%, relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline DKK2 protein level. In some embodiments, the DKK2 protein level is decreased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages.
In some embodiments, the measurement is a DKK2 mRNA measurement. In some embodiments, the DKK2 mRNA measurement comprises a DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is assessed in a sample such as a skin sample. In some embodiments, the DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per sample weight. In some embodiments, the DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per sample volume. In some embodiments, the DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per total mRNA within the sample. In some embodiments, the DKK2 mRNA level is indicated as a mass or percentage of DKK2 mRNA per total nucleic acids within the sample. In some embodiments, the DKK2 mRNA level is indicated relative to another mRNA level, such as an mRNA level of a housekeeping gene, within the sample. In some embodiments, the DKK2 mRNA measurement is obtained by an assay such as a polymerase chain reaction (PCR) assay. In some embodiments, the PCR comprises quantitative PCR (qPCR). In some embodiments, the PCR comprises reverse transcription of the DKK2 mRNA.
In some embodiments, the composition reduces the DKK2 mRNA level relative to the baseline DKK2 mRNA level. In some embodiments, the reduction is measured in a second tissue sample (e.g. a skin sample as described herein) obtained from the subject after administering the composition to the subject. In some embodiments, the DKK2 mRNA level is decreased by about 2.5% or more, about 5% or more, or about 7.5% or more, relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by about 10% or more, relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by about 20% or more, about 30% or more, about 40% or more, about 50% or more, about 60% or more, about 70% or more, about 80% or more, about 90% or more, relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by no more than about 2.5%, no more than about 5%, or no more than about 7.5%, relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by no more than about 10%, relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by no more than about 20%, no more than about 30%, no more than about 40%, no more than about 50%, no more than about 60%, no more than about 70%, no more than about 80%, no more than about 90%, or no more than about 100% relative to the baseline DKK2 mRNA level. In some embodiments, the DKK2 mRNA level is decreased by 2.5%, 5%, 7.5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or by a range defined by any of the two aforementioned percentages.
III. Definitions
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 some 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.
Throughout this application, various embodiments may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
As used in the specification and claims, the singular forms “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a sample” includes a plurality of samples, including mixtures thereof.
The terms “determining,” “measuring,” “evaluating,” “assessing,” “assaying,” and “analyzing” are often used interchangeably herein to refer to forms of measurement. The terms include determining if an element is present or not (for example, detection). These terms can include quantitative, qualitative or quantitative and qualitative determinations. Assessing can be relative or absolute. “Detecting the presence of” can include determining the amount of something present in addition to determining whether it is present or absent depending on the context.
The terms “subject,” and “patient” may be used interchangeably herein. A “subject” can be a biological entity containing expressed genetic materials. The biological entity can be a plant, animal, or microorganism, including, for example, bacteria, viruses, fungi, and protozoa. The subject can be a mammal. The mammal can be a human. The subject may be diagnosed or suspected of being at high risk for a disease. In some cases, the subject is not necessarily diagnosed or suspected of being at high risk for the disease.
As used herein, the term “about” a number refers to that number plus or minus 10% of that number. The term “about” a range refers to that range minus 10% of its lowest value and plus 10% of its greatest value.
As used herein, the terms “treatment” or “treating” are used in reference to a pharmaceutical or other intervention regimen for obtaining beneficial or desired results in the recipient. Beneficial or desired results include but are not limited to a therapeutic benefit and/or a prophylactic benefit. A therapeutic benefit may refer to eradication or amelioration of symptoms or of an underlying disorder being treated. Also, a therapeutic benefit can be achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. A prophylactic effect includes delaying, preventing, or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof. For prophylactic benefit, a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease may undergo treatment, even though a diagnosis of this disease may not have been made.
Some embodiments refer to nucleic acid sequence information. In some embodiments, any uracil (U) may be interchanged with any thymine (T), and vice versa. For example, in an siRNA with a nucleic acid sequence comprising one or more Us, in some embodiments any of the Us may be replaced with Ts. Similarly, in an siRNA with a nucleic acid sequence comprising one or more Ts, in some embodiments any of the Ts may be replaced with Us. In some embodiments, an oligonucleotide such as an siRNA disclosed herein comprises or consists of RNA. In some embodiments, the oligonucleotide may comprise or consist of DNA.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
IV. Sequence Information
Some embodiments include one or more nucleic acid sequences in the following table:
VI. Examples Example 1: Variants in DKK2 are Associated with Decreased Risk of Male Pattern Baldness
Variants in DKK2 were evaluated for associations with male pattern baldness (MBP) in approximately 206,000 male individuals with genotype data from the UK Biobank cohort. Variants evaluated included (1) rs76067940, a low-frequency (AAF=0.0365) intronic variant, and (2) rs35290077, a low-frequency (AAF=0.0428) missense variant (G96R) that is predicted to be deleterious to the DKK2 protein and is a DKK2 protein quantitative trait locus (pQTL) with the alternative (G) allele associated with decreased circulating plasma DKK2. The two variants were considered to be hypomorphic or loss of function variants that may result in a decrease in the abundance or activity of the DKK2 gene product. Stepwise conditional analyses, as well as direct evaluation of linkage disequilibrium, confirmed that they are independent variants.
These analyses resulted in the identification of genome-wide significant MBP-protective associations for the two variants in DKK2 (Table 3). The directional consistency between the protective effects of the two independent DKK2 variants, together with the known effects of the rs35290077 (G96R) variant on reduced levels of circulating DKK2 protein, indicate that loss-of-function or abundance of DKK2 results in protection from male pattern baldness, and that pharmacological inhibition of DKK2 may be therapeutic for MBP and related traits or diseases.
Protective Variants in DKK2 Result in a Reduction of DKK2 mRNA Following Induction with Vitamin D
Lymphoblastoid cell lines (LCLs) from three age and gender-matched donors with known rs35290077 (G96R) genotypes, including a donor that was hom*ozygous for the reference allele (rs35290077 C/C), a donor that was heterozygous (rs35290077 C/G) and a donor that was hom*ozygous for alternative allele (rs35290077 G/G), were seeded at 500,000 cells/well in 24 well plate in complete growth media and grown overnight. LCLs were treated with 25 nM Vitamin D or vehicle (100% EtOH) for 2 days, and then harvested.
Cell lysates from Vitamin D and vehicle-treated LCLs were assayed to evaluate DKK2 mRNA expression by qPCR. LCLs from the rs35290077 hom*ozygous reference allele donor (C/C) demonstrate an approximately 2.4-fold increase of DKK2 mRNA expression with Vitamin D treatment compared with vehicle treatment, LCLs from the rs35290077 heterozygous donor (C/G) demonstrate an approximately 1.8-fold increase of DKK2 mRNA expression with Vitamin D treatment compared with vehicle treatment and LCLs from the rs35290077 hom*ozygous alternative allele donor (G/G) demonstrate an approximately 1.2-fold increase of DKK2 mRNA expression with Vitamin D treatment compared with vehicle treatment (
These data provide experimental verification that DKK2 gene variants associated with protection from MBP result in loss of DKK2 mRNA abundance or function. Accordingly, in some cases therapeutic inhibition or modulation of DKK2 may be an effective genetically-informed method of treatment for MBP and related traits or diseases.
Example 2: Bioinformatic Selection of Sequences in Order to Identify Therapeutic siRNAs to Downmodulate Expression of the DKK2 mRNA
Screening sets were defined based on bioinformatic analysis. Therapeutic siRNAs were designed to target human DKK2. Predicted specificity in human, rhesus monkey, cynomolgus monkey, mouse, rat, rabbit, and dog was determined for sense (S) and antisense (AS) strands. These were assigned a “specificity score” which considers the likelihood of unintended downregulation of any other transcript by full or partial complementarity of an siRNA strand (up to 2 mismatches within positions 2-18) as well as the number and positions of mismatches. Thus, off-target(s) transcripts for antisense and sense strands of each siRNA were identified. As identified, siRNAs with high specificity and a low number of predicted off-targets provided a benefit of increased targeting specificity.
In addition to selecting siRNA sequences with high sequence specificity to DKK2 mRNA, siRNA sequences within the seed region were analyzed for similarity to seed regions of known miRNAs. siRNAs can function in a miRNA like manner via base-pairing with complementary sequences within the 3′-UTR of mRNA molecules. The complementarity typically encompasses the 5′-bases at positions 2-7 of the miRNA (seed region). To circumvent siRNAs to act via functional miRNA binding sites, siRNA strands containing natural miRNA seed regions can be avoided. Seed regions identified in miRNAs from human, mouse, rat, rhesus monkey, dog, rabbit, and pig are referred to as “conserved”. Combining the “specificity score” with miRNA seed analysis yielded a “specificity category”. This is divided into categories 1-4, with 1 having the highest specificity and 4 having the lowest specificity. Each strand of the siRNA is assigned to a specificity category.
Analysis of the Genome Aggregation Database (gnomAD) to identify siRNAs targeting regions with known SNPs was also carried out to identify siRNAs that may be non-functional in individuals containing the SNP. Information regarding the positions of SNPs within the target sequence as well as minor allele frequency (MAF) in case data was obtained in this analysis.
Initial analysis of the relevant DKK2 mRNA sequence revealed few sequences that fulfil the specificity parameters and at the same time target DKK2 mRNA in all the analyzed relevant species. Therefore, independent screening subsets were designed for the therapeutic siRNAs.
The siRNAs in these subsets recognized at least the human DKK2 sequences. Therefore, the siRNAs in these subsets can be used to target human DKK2 in a therapeutic setting.
The number of siRNA sequences derived from human DKK2 mRNA (ENST00000285311, SEQ ID NO: 7599) without consideration of specificity or species cross-reactivity was 3636 (sense and antisense strand sequences included in SEQ ID NOS: 1-3636 and 3637-7272, respectively).
Prioritizing sequences for target specificity, absence of miRNA seed region sequences and SNPs as described above yielded subset A. Subset A contained 741 siRNAs, including siRNAs 12, 13, 21, 22, 24, 27, 29, 30, 31, 34, 35, 36, 38, 39, 40, 42, 43, 46, 47, 48, 51, 53, 54, 60, 63, 64, 65, 66, 67, 68, 69, 70, 74, 76, 77, 81, 84, 93, 94, 95, 98, 102, 103, 104, 105, 107, 117, 118, 119, 122, 124, 130, 131, 132, 135, 136, 137, 142, 144, 145, 149, 150, 156, 157, 159, 160, 161, 164, 165, 166, 167, 168, 169, 170, 175, 179, 180, 181, 184, 186, 188, 189, 190, 191, 192, 193, 196, 197, 198, 203, 204, 205, 211, 219, 220, 228, 229, 231, 233, 241, 242, 243, 245, 278, 283, 297, 303, 304, 308, 312, 314, 316, 317, 319, 323, 324, 325, 331, 332, 333, 335, 336, 338, 339, 340, 341, 350, 351, 411, 418, 421, 422, 425, 428, 435, 436, 439, 440, 442, 443, 445, 446, 447, 450, 455, 456, 457, 458, 459, 462, 463, 470, 472, 505, 512, 513, 514, 517, 518, 519, 520, 521, 522, 524, 525, 531, 532, 535, 537, 539, 543, 571, 572, 573, 574, 576, 577, 583, 586, 605, 609, 611, 616, 618, 666, 669, 670, 671, 677, 678, 680, 682, 698, 701, 703, 707, 712, 717, 718, 720, 721, 722, 724, 727, 728, 733, 735, 736, 737, 739, 762, 764, 784, 785, 788, 791, 792, 793, 794, 795, 798, 799, 800, 801, 802, 803, 807, 808, 809, 810, 811, 812, 813, 822, 824, 827, 831, 839, 850, 851, 852, 856, 862, 864, 865, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 882, 883, 886, 892, 895, 896, 897, 898, 899, 900, 902, 903, 904, 905, 906, 908, 912, 918, 924, 925, 938, 939, 940, 941, 943, 949, 950, 951, 958, 963, 964, 970, 973, 974, 976, 978, 981, 983, 984, 1010, 1011, 1013, 1021, 1022, 1036, 1042, 1045, 1049, 1051, 1052, 1053, 1063, 1073, 1076, 1078, 1081, 1083, 1089, 1090, 1094, 1095, 1097, 1118, 1119, 1125, 1130, 1136, 1162, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1180, 1182, 1197, 1203, 1214, 1218, 1219, 1221, 1223, 1227, 1229, 1236, 1257, 1262, 1263, 1265, 1266, 1268, 1270, 1274, 1292, 1295, 1298, 1302, 1303, 1305, 1308, 1309, 1319, 1320, 1325, 1328, 1340, 1346, 1347, 1352, 1354, 1355, 1361, 1362, 1368, 1369, 1370, 1371, 1373, 1374, 1376, 1377, 1378, 1379, 1383, 1384, 1389, 1424, 1425, 1426, 1427, 1436, 1437, 1443, 1446, 1447, 1481, 1487, 1488, 1489, 1496, 1498, 1504, 1505, 1511, 1512, 1519, 1530, 1550, 1562, 1565, 1566, 1567, 1571, 1574, 1595, 1597, 1604, 1605, 1607, 1608, 1610, 1611, 1612, 1615, 1616, 1617, 1619, 1646, 1651, 1654, 1656, 1658, 1661, 1664, 1665, 1666, 1668, 1707, 1708, 1711, 1731, 1736, 1744, 1752, 1753, 1772, 1783, 1790, 1804, 1808, 1809, 1812, 1818, 1835, 1838, 1851, 1859, 1862, 1866, 1867, 1871, 1874, 1875, 1876, 1877, 1878, 1881, 1883, 1885, 1886, 1887, 1888, 1889, 1891, 1892, 1895, 1896, 1910, 1913, 1915, 1916, 1918, 1919, 1926, 1928, 1929, 1932, 1933, 1934, 1962, 1985, 1992, 1999, 2013, 2020, 2021, 2024, 2032, 2033, 2038, 2043, 2047, 2048, 2084, 2089, 2098, 2103, 2108, 2111, 2112, 2113, 2119, 2120, 2126, 2157, 2183, 2190, 2198, 2206, 2207, 2210, 2232, 2233, 2236, 2237, 2238, 2242, 2248, 2250, 2253, 2254, 2259, 2267, 2270, 2276, 2281, 2282, 2317, 2319, 2320, 2321, 2324, 2331, 2334, 2342, 2348, 2352, 2366, 2367, 2379, 2380, 2382, 2385, 2401, 2402, 2405, 2407, 2410, 2413, 2414, 2462, 2467, 2469, 2470, 2522, 2531, 2535, 2537, 2558, 2561, 2564, 2565, 2566, 2570, 2588, 2589, 2590, 2614, 2615, 2616, 2629, 2638, 2644, 2668, 2671, 2675, 2678, 2682, 2686, 2696, 2703, 2704, 2708, 2709, 2712, 2717, 2718, 2719, 2720, 2721, 2722, 2723, 2724, 2725, 2726, 2727, 2729, 2730, 2731, 2735, 2758, 2761, 2768, 2770, 2774, 2796, 2809, 2810, 2811, 2813, 2819, 2821, 2822, 2823, 2829, 2832, 2842, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2860, 2861, 2864, 2867, 2868, 2871, 2914, 2916, 2918, 2919, 2920, 2921, 2922, 2923, 2924, 2926, 2929, 2941, 2948, 2962, 2969, 2983, 2988, 2992, 2993, 2996, 2997, 2998, 2999, 3000, 3003, 3004, 3006, 3013, 3022, 3028, 3032, 3037, 3042, 3054, 3055, 3057, 3064, 3065, 3071, 3073, 3080, 3128, 3129, 3136, 3137, 3164, 3169, 3179, 3199, 3201, 3204, 3205, 3218, 3219, 3220, 3224, 3257, 3269, 3292, 3314, 3317, 3318, 3320, 3322, 3324, 3327, 3328, 3329, 3333, 3341, 3350, 3352, 3353, 3354, 3357, 3358, 3362, 3363, 3364, 3386, 3388, 3404, 3433, 3441, 3453, 3457, 3508, 3525, 3545, 3547, 3555, 3556, 3564, 3572, 3579, and 3636.
The siRNAs in subset A had the following characteristics: Cross-reactivity: With 19mer in human DKK2 mRNA; Specificity category: For human: AS2 or better, SS3 or better; and miRNA seeds: AS+SS strand: seed region not conserved in human, mouse, and rat and not present in >4 species; Off-target frequency: ≤30 human off-targets matched with 2 mismatches in antisense strand; and SNPs: siRNA target sites do not harbor SNPs with a MAF≥1% (pos. 2-18).
The siRNA sequences in subset A were selected for more stringent specificity to yield subset B. Subset B included 735 siRNAs, including siRNAs 12, 13, 21, 22, 24, 27, 29, 30, 31, 34, 35, 36, 38, 39, 40, 42, 43, 46, 47, 48, 51, 53, 54, 60, 63, 64, 65, 66, 67, 68, 69, 70, 74, 76, 77, 81, 84, 93, 94, 95, 98, 102, 103, 104, 105, 107, 117, 118, 119, 124, 130, 131, 132, 135, 136, 137, 142, 144, 145, 149, 150, 156, 157, 159, 160, 161, 164, 165, 166, 167, 168, 169, 170, 175, 179, 180, 181, 184, 186, 188, 189, 190, 191, 192, 193, 196, 197, 198, 203, 204, 205, 211, 219, 220, 228, 229, 231, 233, 242, 243, 245, 278, 283, 303, 304, 308, 312, 314, 316, 317, 319, 323, 324, 325, 331, 332, 333, 335, 336, 338, 339, 340, 341, 350, 351, 411, 418, 421, 422, 425, 428, 435, 436, 439, 440, 442, 443, 445, 446, 447, 450, 455, 456, 457, 458, 459, 462, 463, 470, 472, 505, 512, 513, 514, 517, 518, 519, 520, 521, 522, 524, 525, 531, 532, 535, 537, 539, 543, 571, 572, 573, 574, 576, 577, 583, 586, 605, 609, 611, 616, 618, 666, 669, 670, 671, 677, 678, 680, 682, 698, 701, 703, 707, 712, 717, 718, 720, 721, 722, 724, 727, 728, 733, 735, 736, 737, 739, 762, 764, 784, 785, 788, 791, 792, 793, 794, 795, 798, 799, 800, 801, 802, 803, 807, 808, 809, 810, 811, 812, 813, 822, 824, 827, 831, 839, 850, 851, 852, 856, 862, 864, 865, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 882, 883, 886, 892, 895, 896, 897, 898, 899, 900, 902, 903, 904, 905, 906, 908, 912, 918, 924, 925, 938, 939, 940, 941, 943, 949, 950, 951, 958, 963, 964, 970, 973, 974, 976, 978, 981, 983, 984, 1010, 1011, 1013, 1021, 1022, 1036, 1042, 1045, 1049, 1051, 1052, 1053, 1063, 1073, 1076, 1078, 1081, 1083, 1089, 1090, 1094, 1095, 1097, 1118, 1119, 1125, 1130, 1136, 1162, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1180, 1182, 1197, 1203, 1214, 1218, 1219, 1221, 1223, 1227, 1229, 1236, 1257, 1262, 1263, 1265, 1266, 1268, 1270, 1274, 1292, 1295, 1298, 1302, 1303, 1305, 1308, 1309, 1319, 1320, 1325, 1328, 1340, 1346, 1347, 1352, 1354, 1355, 1361, 1362, 1368, 1369, 1370, 1371, 1373, 1374, 1376, 1377, 1378, 1379, 1383, 1384, 1389, 1424, 1425, 1426, 1427, 1436, 1437, 1443, 1446, 1447, 1481, 1487, 1488, 1489, 1496, 1498, 1504, 1505, 1511, 1512, 1519, 1530, 1550, 1562, 1565, 1566, 1567, 1571, 1574, 1595, 1597, 1604, 1605, 1607, 1608, 1610, 1611, 1612, 1615, 1616, 1617, 1619, 1651, 1654, 1656, 1658, 1661, 1664, 1665, 1666, 1668, 1707, 1708, 1711, 1731, 1736, 1744, 1752, 1753, 1772, 1783, 1790, 1804, 1808, 1809, 1812, 1818, 1835, 1838, 1851, 1859, 1862, 1866, 1871, 1874, 1875, 1876, 1877, 1878, 1881, 1883, 1885, 1886, 1887, 1888, 1889, 1891, 1892, 1895, 1896, 1910, 1913, 1915, 1916, 1918, 1919, 1926, 1928, 1929, 1932, 1933, 1934, 1962, 1985, 1992, 1999, 2013, 2020, 2021, 2024, 2032, 2033, 2038, 2043, 2047, 2048, 2084, 2089, 2098, 2103, 2108, 2111, 2112, 2113, 2119, 2120, 2126, 2157, 2183, 2190, 2198, 2206, 2207, 2210, 2232, 2233, 2236, 2237, 2238, 2242, 2248, 2250, 2253, 2254, 2259, 2267, 2270, 2276, 2281, 2282, 2317, 2319, 2320, 2321, 2324, 2331, 2334, 2342, 2348, 2352, 2366, 2367, 2379, 2380, 2382, 2385, 2401, 2402, 2405, 2407, 2410, 2413, 2414, 2462, 2467, 2469, 2470, 2522, 2531, 2535, 2537, 2558, 2561, 2564, 2565, 2566, 2570, 2588, 2589, 2590, 2614, 2615, 2616, 2629, 2638, 2644, 2668, 2671, 2675, 2678, 2682, 2686, 2696, 2703, 2704, 2708, 2709, 2712, 2717, 2718, 2719, 2720, 2721, 2722, 2723, 2724, 2725, 2726, 2727, 2729, 2730, 2731, 2735, 2758, 2761, 2768, 2770, 2774, 2796, 2809, 2810, 2811, 2813, 2819, 2821, 2822, 2823, 2829, 2832, 2842, 2847, 2848, 2849, 2850, 2851, 2852, 2853, 2854, 2860, 2861, 2864, 2867, 2868, 2871, 2914, 2916, 2918, 2919, 2920, 2921, 2922, 2923, 2924, 2926, 2929, 2941, 2948, 2962, 2969, 2983, 2988, 2992, 2993, 2996, 2997, 2998, 2999, 3000, 3003, 3004, 3006, 3013, 3022, 3028, 3032, 3037, 3042, 3054, 3055, 3057, 3064, 3065, 3071, 3073, 3080, 3128, 3129, 3136, 3137, 3164, 3169, 3179, 3199, 3201, 3204, 3205, 3218, 3219, 3220, 3224, 3257, 3269, 3292, 3314, 3317, 3318, 3320, 3322, 3324, 3327, 3328, 3329, 3333, 3341, 3350, 3352, 3353, 3354, 3357, 3358, 3362, 3363, 3364, 3386, 3388, 3404, 3433, 3441, 3453, 3457, 3508, 3545, 3547, 3555, 3556, 3564, 3572, 3579, and 3636.
The siRNAs in subset B had the following characteristics: Cross-reactivity: With 19mer in human DKK2 mRNA; Specificity category: For human: AS2 or better, SS3 or better; miRNA seeds: AS+SS strand: seed region not conserved in human, mouse, and rat and not present in >4 species; Off-target frequency: ≤20 human off-targets matched with 2 mismatches in antisense strand; and SNPs: siRNA target sites do not harbor SNPs with a MAF≥1% (pos. 2-18).
The siRNA sequences in subset B were further selected for absence of seed regions in the AS strand that are identical to a seed region of known human miRNA to yield subset C. Subset C includes 489 siRNAs, including siRNAs 12, 13, 21, 22, 24, 27, 29, 30, 31, 35, 36, 40, 43, 46, 47, 48, 51, 53, 54, 60, 63, 64, 65, 66, 67, 68, 69, 74, 76, 81, 84, 93, 94, 95, 102, 103, 105, 107, 119, 122, 130, 131, 132, 135, 136, 142, 144, 149, 150, 156, 157, 159, 160, 165, 166, 167, 168, 170, 175, 184, 186, 188, 190, 191, 192, 198, 203, 220, 228, 229, 231, 233, 241, 242, 243, 278, 283, 297, 308, 312, 314, 316, 317, 324, 331, 332, 333, 338, 340, 351, 418, 422, 425, 435, 439, 440, 445, 446, 456, 457, 459, 462, 470, 472, 513, 514, 517, 518, 521, 522, 524, 525, 535, 539, 543, 571, 572, 573, 576, 586, 605, 611, 616, 669, 677, 678, 680, 682, 698, 703, 707, 712, 717, 720, 722, 724, 728, 735, 736, 737, 739, 762, 764, 784, 785, 788, 791, 792, 793, 794, 795, 798, 799, 800, 801, 807, 809, 810, 811, 813, 822, 824, 850, 851, 864, 865, 867, 869, 872, 874, 875, 876, 877, 879, 880, 882, 883, 886, 892, 895, 896, 897, 898, 899, 902, 903, 904, 905, 908, 918, 924, 938, 940, 949, 951, 963, 964, 970, 973, 974, 976, 1011, 1022, 1045, 1049, 1051, 1063, 1076, 1083, 1089, 1090, 1094, 1097, 1125, 1130, 1136, 1162, 1167, 1168, 1169, 1170, 1171, 1172, 1176, 1180, 1182, 1218, 1219, 1221, 1229, 1262, 1263, 1266, 1270, 1274, 1292, 1295, 1298, 1302, 1308, 1309, 1325, 1328, 1340, 1347, 1352, 1355, 1361, 1362, 1368, 1370, 1371, 1376, 1377, 1379, 1384, 1389, 1424, 1426, 1427, 1436, 1437, 1443, 1446, 1447, 1481, 1487, 1488, 1489, 1496, 1498, 1504, 1511, 1512, 1519, 1562, 1565, 1566, 1571, 1574, 1595, 1597, 1604, 1605, 1607, 1610, 1611, 1612, 1616, 1617, 1646, 1651, 1654, 1656, 1658, 1661, 1666, 1668, 1707, 1708, 1711, 1731, 1744, 1772, 1783, 1804, 1808, 1812, 1818, 1838, 1851, 1859, 1862, 1866, 1874, 1876, 1877, 1878, 1881, 1883, 1885, 1886, 1887, 1888, 1892, 1895, 1910, 1913, 1916, 1919, 1926, 1928, 1929, 1932, 1933, 1962, 1985, 1999, 2013, 2032, 2033, 2038, 2043, 2047, 2048, 2084, 2089, 2108, 2113, 2120, 2126, 2157, 2183, 2190, 2207, 2210, 2232, 2233, 2236, 2237, 2238, 2248, 2250, 2254, 2259, 2267, 2270, 2281, 2282, 2319, 2324, 2331, 2334, 2348, 2380, 2382, 2385, 2401, 2402, 2405, 2414, 2462, 2467, 2470, 2522, 2531, 2535, 2537, 2558, 2561, 2564, 2565, 2570, 2588, 2589, 2590, 2614, 2615, 2616, 2629, 2638, 2671, 2675, 2682, 2686, 2717, 2718, 2720, 2721, 2722, 2723, 2724, 2726, 2731, 2735, 2770, 2774, 2796, 2809, 2821, 2823, 2829, 2847, 2848, 2849, 2853, 2854, 2860, 2861, 2868, 2914, 2920, 2921, 2922, 2923, 2941, 2948, 2962, 2969, 2983, 2988, 2992, 2993, 2996, 2998, 2999, 3000, 3004, 3013, 3022, 3028, 3032, 3042, 3054, 3055, 3064, 3071, 3080, 3128, 3129, 3136, 3137, 3179, 3201, 3218, 3219, 3220, 3257, 3314, 3317, 3329, 3333, 3341, 3352, 3353, 3354, 3358, 3363, 3364, 3386, 3388, 3404, 3508, 3525, 3545, 3556, 3564, 3572, and 3636.
The siRNAs in subset C had the following characteristics: Cross-reactivity: With 19mer in human DKK2 mRNA; Specificity category: For human: AS2 or better, SS3 or better; miRNA seeds: AS+SS strand: seed region not conserved in human, mouse, and rat and not present in >4 species. AS strand: seed region not identical to seed region of known human miRNA; Off-target frequency: ≤30 human off-targets matched with 2 mismatches by antisense strand; and SNPs: siRNA target sites do not harbor SNPs with a MAF≥1% (pos. 2-18).
The siRNA sequences in subset C were also selected for absence of seed regions in the AS or S strands that are identical to a seed region of known human miRNA in addition to having an off-target frequency of ≤30 human off-targets matched with 2 mismatches by antisense strand to yield subset D. Subset D includes 311 siRNAs, including siRNAs 12, 24, 29, 30, 31, 35, 36, 40, 43, 46, 47, 51, 64, 65, 66, 74, 76, 94, 95, 103, 105, 122, 130, 131, 142, 144, 160, 166, 167, 168, 186, 190, 192, 220, 229, 233, 241, 242, 243, 283, 308, 324, 338, 340, 351, 418, 422, 435, 445, 446, 456, 459, 462, 470, 472, 514, 517, 518, 521, 522, 524, 543, 571, 572, 576, 586, 605, 616, 669, 680, 707, 712, 720, 722, 724, 728, 737, 739, 764, 785, 791, 792, 795, 798, 801, 807, 809, 810, 811, 813, 824, 864, 865, 867, 872, 874, 875, 876, 877, 879, 883, 892, 895, 905, 908, 918, 940, 963, 964, 970, 1011, 1022, 1045, 1051, 1083, 1089, 1090, 1094, 1097, 1125, 1130, 1136, 1167, 1168, 1169, 1170, 1176, 1180, 1218, 1221, 1229, 1274, 1298, 1302, 1308, 1309, 1340, 1347, 1355, 1361, 1362, 1370, 1376, 1379, 1384, 1389, 1424, 1437, 1443, 1446, 1447, 1487, 1488, 1489, 1496, 1498, 1512, 1519, 1562, 1574, 1595, 1597, 1604, 1605, 1607, 1610, 1611, 1616, 1646, 1651, 1654, 1656, 1661, 1666, 1668, 1708, 1772, 1783, 1804, 1808, 1812, 1838, 1851, 1859, 1862, 1866, 1874, 1877, 1878, 1881, 1885, 1886, 1887, 1895, 1910, 1913, 1916, 1926, 1928, 1929, 1932, 1933, 1962, 1985, 1999, 2033, 2038, 2043, 2047, 2084, 2089, 2113, 2120, 2126, 2157, 2190, 2207, 2210, 2233, 2236, 2248, 2250, 2259, 2267, 2270, 2282, 2319, 2324, 2331, 2334, 2348, 2380, 2382, 2402, 2405, 2414, 2462, 2467, 2531, 2537, 2558, 2564, 2570, 2589, 2590, 2614, 2671, 2675, 2682, 2686, 2718, 2720, 2721, 2722, 2723, 2735, 2770, 2774, 2796, 2809, 2847, 2848, 2849, 2854, 2860, 2861, 2868, 2914, 2920, 2921, 2923, 2941, 2948, 2962, 2969, 2983, 2988, 2993, 2996, 2998, 2999, 3000, 3004, 3013, 3032, 3042, 3054, 3055, 3080, 3128, 3129, 3136, 3218, 3219, 3317, 3329, 3333, 3341, 3352, 3353, 3354, 3358, 3363, 3364, 3388, 3404, 3508, 3525, 3556, 3564, and 3572.
The siRNA sequences in subset D were also selected to have an off-target frequency of ≤20 human off-targets matched with 2 mismatches by antisense strand to yield subset E. Subset E includes 307 siRNAs, including siRNAs 12, 24, 29, 30, 31, 35, 36, 40, 43, 46, 47, 51, 64, 65, 66, 74, 76, 94, 95, 103, 105, 130, 131, 142, 144, 160, 166, 167, 168, 186, 190, 192, 220, 229, 233, 242, 243, 283, 308, 324, 338, 340, 351, 418, 422, 435, 445, 446, 456, 459, 462, 470, 472, 514, 517, 518, 521, 522, 524, 543, 571, 572, 576, 586, 605, 616, 669, 680, 707, 712, 720, 722, 724, 728, 737, 739, 764, 785, 791, 792, 795, 798, 801, 807, 809, 810, 811, 813, 824, 864, 865, 867, 872, 874, 875, 876, 877, 879, 883, 892, 895, 905, 908, 918, 940, 963, 964, 970, 1011, 1022, 1045, 1051, 1083, 1089, 1090, 1094, 1097, 1125, 1130, 1136, 1167, 1168, 1169, 1170, 1176, 1180, 1218, 1221, 1229, 1274, 1298, 1302, 1308, 1309, 1340, 1347, 1355, 1361, 1362, 1370, 1376, 1379, 1384, 1389, 1424, 1437, 1443, 1446, 1447, 1487, 1488, 1489, 1496, 1498, 1512, 1519, 1562, 1574, 1595, 1597, 1604, 1605, 1607, 1610, 1611, 1616, 1651, 1654, 1656, 1661, 1666, 1668, 1708, 1772, 1783, 1804, 1808, 1812, 1838, 1851, 1859, 1862, 1866, 1874, 1877, 1878, 1881, 1885, 1886, 1887, 1895, 1910, 1913, 1916, 1926, 1928, 1929, 1932, 1933, 1962, 1985, 1999, 2033, 2038, 2043, 2047, 2084, 2089, 2113, 2120, 2126, 2157, 2190, 2207, 2210, 2233, 2236, 2248, 2250, 2259, 2267, 2270, 2282, 2319, 2324, 2331, 2334, 2348, 2380, 2382, 2402, 2405, 2414, 2462, 2467, 2531, 2537, 2558, 2564, 2570, 2589, 2590, 2614, 2671, 2675, 2682, 2686, 2718, 2720, 2721, 2722, 2723, 2735, 2770, 2774, 2796, 2809, 2847, 2848, 2849, 2854, 2860, 2861, 2868, 2914, 2920, 2921, 2923, 2941, 2948, 2962, 2969, 2983, 2988, 2993, 2996, 2998, 2999, 3000, 3004, 3013, 3032, 3042, 3054, 3055, 3080, 3128, 3129, 3136, 3218, 3219, 3317, 3329, 3333, 3341, 3352, 3353, 3354, 3358, 3363, 3364, 3388, 3404, 3508, 3556, 3564, and 3572.
Therapeutic siRNAs were designed to target human DKK2 as described above and, in some cases, the DKK2 sequence of at least one toxicology-relevant species, in this case, the non-human primate (NHP) cynomolgus monkey. The siRNAs included in subset F had the following characteristics: Cross-reactivity: With 19mer in human DKK2 mRNA, with 17mer/19mer in NHP DKK2; Specificity category: For human and NHP: AS2 or better, SS3 or better.
Subset F includes 40 siRNAs, including siRNAs 822, 824, 827, 918, 949, 950, 951, 1083, 1180, 1182, 1203, 1214, 1218, 1219, 1221, 1223, 1227, 1229, 1236, 1292, 1319, 1320, 1325, 1328, 1443, 1446, 1550, 2348, 2588, 2589, 2590, 3508, 3525, 3545, 3547, 3555, 3556, 3564, 3572, and 3579.
In some cases, the sense strand of any of the siRNAs of subset F comprises siRNA with a particular modification pattern. In this modification pattern, position 9 counting from the 5′ end of the of the sense strand is has the 2′F modification. If position 9 of the sense strand is a pyrimidine, then all purines in the sense strand have the 2′OMe modification. If position 9 is the only pyrimidine between positions 5 and 11 of the sense stand, then position 9 is the only position with the 2′F modification in the sense strand. If position 9 and only one other base between positions 5 and 11 of the sense strand are pyrimidines, then both of these pyrimidines are the only two positions with the 2′F modification in the sense strand. If position 9 and only two other bases between positions 5 and 11 of the sense strand are pyrimidines, and those two other pyrimidines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. If there are >2 pyrimidines between positions 5 and 11 of the sense strand, then all combinations of pyrimidines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that the sense strand does not have three 2′F modifications in a row.
If position 9 of the sense strand is a purine, then all purines in the sense strand have the 2′OMe modification. If position 9 is the only purine between positions 5 and 11 of the sense stand, then position 9 is the only position with the 2′F modification in the sense strand. If position 9 and only one other base between positions 5 and 11 of the sense strand are purines, then both of these purines are the only two positions with the 2′F modification in the sense strand. If position 9 and only two other bases between positions 5 and 11 of the sense strand are purines, and those two other purines are in adjacent positions so that there would be not three 2′F modifications in a row, then any combination of 2′F modifications can be made that give three 2′F modifications in total. If there are >2 purines between positions 5 and 11 of the sense strand, then all combinations of purines having the 2′F modification are allowed that have three to five 2′F modifications in total, provided that the sense strand does not have three 2′F modifications in a row.
In some cases, position 9 of the sense strand can be a 2′deoxy. In these cases, 2′F and 2′OMe modifications may occur at the other positions of the sense strand.
In some cases, the sense strand of any of the siRNAs of subset F comprises a modification pattern which conforms to these sense strand rules (Table 4).
In some cases, the antisense strand of any of the siRNAs of subset F comprise a modification or modification pattern. Some such examples are included in Table 4. Table 5 includes some additional sense strand modifications of the siRNAs in subset F. The siRNAs in subset F may comprise any other modification pattern(s). In Table 4 and Table 5, Nf (e.g. At Cf, Gf, Tf, or Uf) is a 2′ fluoro-modified nucleoside, dN (e.g. dA, dC, dG, dT, or dU) is a 2′ deoxy-modified nucleoside, n (e.g. a, c, g, t, or u) is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage.
Any siRNA among any of subsets A-H may comprise any modification pattern described herein. If a sequence has a different number of nucleotides in length than a modification pattern, the modification pattern may still be used with the appropriate number of additional nucleotides added 5′ or 3′ to match the number of nucleotides in the modification pattern. For example, if a sense or antisense strand of the siRNA among any of subsets A-H comprises 19 nucleotides, and a modification pattern comprises 21 nucleotides, UU may be added onto the 5′ end of the sense or antisense strand.
Example 3: In Vivo Delivery of siRNA in C57 Mice
A published model of hair growth where application of dexamethasone was used to assess the ability of DKK2 mRNA reduction to prevent catagen phase (Paus, R; Handjiski, B; Czarnetzki, B.; Eichmüller, S A Murine Model for Inducing and Manipulating Hair Follicle Regression (Catagen): Effects of Dexamethasone and Cyclosporin A Journal of Investigative Dermatology 1994, 103, 143-147.) On day 0 of study groups of two groups of four using 59-day-old mice had an area on their back shaved and depilated using hair removal cream containing urea and potassium thioglycolate (Nad's for Men Hair Removal cream). Following hair removal, 30 ug ETD01043 or ETD01551 formulated in 10 ul of 1 part azone: 32 parts propylene glycol was applied to the shaved area. ETD01043 was used as a control and targeted human ANGPTL7, and ETD01551 targeted DKK2. The application of siRNA's was repeated on days, 2, 5 and 7. On day 9 of study, formulations containing 30 ug ETD01043 or ETD01551, and 10 ug dexamethasone acetate formulated in 10 ul of 1 part azone: 32 parts propylene glycol were applied to the shaved areas. The formulations containing dexamethasone and siRNA were repeated on days 10, 11, 12, 13 and 14.
Pictures of the hair growth area were taken on day 14 of study. The animals treated with ETD01043, which did not target DKK2 mRNA, showed pronounced graying indicative of the catagen phase, while ETD01551, which targeted DKK2, did not show graying (
On day 16 of the study, the animals were euthanized, and skin samples of the siRNA-applied areas were obtained by punch biopsy and placed into RNAlater. Total skin RNA was prepared by hom*ogenizing the tissue in hom*ogenization buffer (Maxwell RSC simplyRNA Tissue Kit) using a Percellys 24 tissue hom*ogenizer (Bertin Instruments) set at 5000 rpm for two 10 second cycles. The hom*ogenate was centrifuged for 10′ at 16,000×g at 4 C and the lower liquid layer was removed to a fresh tube. The sample was centrifuged two additional times, each time removing the lower liquid layer to a fresh tube. Total RNA from the lysate was purified on a Maxwell RSC 48 platform (Promega Corporation) according to the manufacturer's recommendations. Preparation ofcDNA was performed using Quanta uScript cDNA SuperMix (VWR, Catalog #95048-500) according to the manufacturer's instructions. The relative levels of mouse DKK2 mRNA were assessed by RT-qPCR in triplicate on a QuantStudio™ 6 Pro Real-Time PCR System using and the mouse housekeeping gene PPIA (TheroFisher, assaysMm02342430g1). Data were normalized to the level in animals receiving ETD01043, which showed that an average DKK2 knockdown of 87% for the animals treated with DKK2-targeting ETD01551.
Some example siRNAs are shown in Table 6, where Nf (e.g. Af, Cf, Gf, Tf, or Uf) is a 2′ fluoro-modified nucleoside, n (e.g. a, c, g, t, or u) is a 2′ O-methyl modified nucleoside, and “s” is a phosphorothioate linkage. In addition to ETD01043 and ETD01551, this table includes additional siRNAs that may be tested as described above, or which may be used in a method disclosed herein. The siRNAs in this table may target mouse DKK2.
Example 4: siRNA-Mediated Knockdown of DKK2 in Dermal Fibroblast Cell Line
In this prophetic experiment, siRNAs targeted to the DKK2 mRNA that downregulate levels of DKK2 mRNA are transfected into cultured dermal fibroblast cell. Downregulation of DKK2 mRNA (and ultimately protein) subsequently leads to an increase in protein levels of β-catenin, α-SMA, and collagens I and III in cultured dermal fibroblast cells.
On Day 0, the dermal fibroblast cells are seeded at 150,000 cells/mL into a Falcon 24-well tissue culture plate (Cat. No. 353047) at 0.5 mL per well.
On Day 1, the DKK2 siRNA and negative control siRNA master mixes are prepared. The DKK2 siRNA master mix contains 350 uL of Opti-MEM (ThermoFisher Cat. No. 4427037—s1288 Lot No. AS02B02D) and 3.5 ul of a mixture of the two DKK2 siRNAs (10 uM stock). The negative control siRNA master mix contains 350 uL of Opti-MEM and 3.5 ul of negative control siRNA (ThermoFisher Cat. No. 4390843, 10 uM stock). Next, 3 uL of TransIT-X2 (Mirus Cat. No. MIR6000) is added to each master mix. The mixes are incubated for 15 minutes to allow transfection complexes to form, then 51 ul of the appropriate master mix+TransIT-X2 is added to quadruplicate wells of dermal fibroblast cells with a final siRNA concentration of 10 nM.
On Day 3, 48 hours post transfection, duplicate wells of dermal fibroblast cells are lysed using the Cells-to-Ct kit according to the manufacturer's protocol (ThermoFisher Cat. No. 4399002). In brief, cells are washed with 50 ul using cold 1×PBS and lysed by adding 49.5 ul of Lysis Solution and 0.5 ul DNase I per well and pipetting up and down 5 times and incubating for 5 minutes at room temperature. The Stop Solution (5 ul/well) is added to each well and mixed by pipetting up and down five times and incubating at room temperature for 2 minutes. The reverse transcriptase reaction is performed using 22.5 ul of the lysate according to the manufacturer's protocol. Samples are stored at −80° C. until real-time qPCR is performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems FAM/DKK2 using a BioRad iCycler).
On Day 3, 48 hours post transfection, corresponding duplicate wells to the those lysed with the Cells-to-Ct kit are lysed with (1×PBS, 1% NP-40, 0.1% sodium dodecylsulfate (SDS), 5 mM EDTA, 0.5% sodium deoxycholate, and 1 mM sodium orthovanadate) with protease inhibitors (Pierce). In brief, cells are washed with 50 ul using cold 1×PBS and lysed by adding 100 ul of RIPA buffer and triturated 5 times by manual pipet. The protein concentrations in the cell lysates are determined by BCA Protein Assay Kit (Pierce). SDS-PAGE is done in 8% glycine gels (Bio-rad) loading equal amount of proteins per lane. After electrophoresis, separated proteins are transferred to nitrocellulose membrane (Bio-rad) and blocked with 5% non-fat milk in TBST buffer for 1 h. After that, the membranes are incubated with DKK2 (1:600; CST), β-Catenin (1:800; CST), alpha smooth muscle Actin (1:800; abeam), Collagen I (1:800; abeam), Collagen III (1:800; abeam) and GAPDH (1:2,000; CST), loading control, antibodies overnight at 4° C., and then anti-rabbit IgG monoclonal antibody conjugated with horseradish peroxidase (Pierce) at 1:2000 dilution for 1 h at room temperature. Protein bands are detected using the West Femto system (Pierce).
A decrease in DKK2 mRNA expression in the dermal fibroblast cells is expected after transfection with the DKK2 siRNAs compared to DKK2 mRNA levels in dermal fibroblast cells transfected with the non-specific control siRNA 48 hours after transfection. There is an expected increase in protein levels of 3-catenin, α-SMA, and collagens I and III in wells containing dermal fibroblast s cells transfected with the DKK2 siRNAs relative to the amount of β-catenin, α-SMA, and collagens I and III in wells containing dermal fibroblast cells transfected with a non-specific control siRNA 48 hours after transfection. These results show that the DKK2 siRNAs elicit knockdown of DKK2 mRNA in dermal fibroblast cells and that the decrease in DKK2 expression is correlated with an increase in β-catenin, α-SMA, and collagens I and III production.
Example 5: ASO-Mediated Knockdown of DKK2 in Dermal Fibroblast Cell Line
In this prophetic experiment, ASOs targeted to the DKK2 mRNA that downregulate levels of DKK2 mRNA are transfected into cultured dermal fibroblast cell. Downregulation of DKK2 mRNA (and ultimately protein) subsequently leads to an increase in protein levels of β-catenin, α-SMA, and collagens I and III in cultured dermal fibroblast cells.
On Day 0, the dermal fibroblast cells are seeded at 150,000 cells/mL into a Falcon 24-well tissue culture plate (Cat. No. 353047) at 0.5 mL per well.
On Day 1, the DKK2 ASO and negative control ASO master mixes are prepared. The DKK2 ASO master mix contains 350 uL of Opti-MEM (ThermoFisher Cat. No. 4427037—s1288 Lot No. AS02B02D) and 3.5 ul of a mixture of the two DKK2 ASOs (10 uM stock). The negative control ASO master mix contains 350 uL of Opti-MEM and 3.5 ul of negative control ASO (ThermoFisher Cat. No. 4390843, 10 uM stock). Next, 3 uL of TransIT-X2 (Mirus Cat. No. MIR6000) is added to each master mix. The mixes are incubated for 15 minutes to allow transfection complexes to form, then 51 ul of the appropriate master mix+TransIT-X2 is added to quadruplicate wells of dermal fibroblast cells with a final ASO concentration of 10 nM.
On Day 3, 48 hours post transfection, duplicate wells of dermal fibroblast cells are lysed using the Cells-to-Ct kit according to the manufacturer's protocol (ThermoFisher Cat. No. 4399002). In brief, cells are washed with 50 ul using cold 1×PBS and lysed by adding 49.5 ul of Lysis Solution and 0.5 ul DNase I per well and pipetting up and down 5 times and incubating for 5 minutes at room temperature. The Stop Solution (5 ul/well) is added to each well and mixed by pipetting up and down five times and incubating at room temperature for 2 minutes. The reverse transcriptase reaction is performed using 22.5 ul of the lysate according to the manufacturer's protocol. Samples are stored at −80° C. until real-time qPCR is performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems FAM/DKK2 using a BioRad iCycler).
On Day 3, 48 hours post transfection, corresponding duplicate wells to the those lysed with the Cells-to-Ct kit are lysed with (1×PBS, 1% NP-40, 0.1% sodium dodecylsulfate (SDS), 5 mM EDTA, 0.5% sodium deoxycholate, and 1 mM sodium orthovanadate) with protease inhibitors (Pierce). In brief, cells are washed with 50 ul using cold 1×PBS and lysed by adding 100 ul of RIPA buffer and triturated 5 times by manual pipet. The protein concentrations in the cell lysates are determined by BCA Protein Assay Kit (Pierce). SDS-PAGE is done in 8% glycine gels (Bio-rad) loading equal amount of proteins per lane. After electrophoresis, separated proteins are transferred to nitrocellulose membrane (Bio-rad) and blocked with 5% non-fat milk in TBST buffer for 1h. After that, the membranes are incubated with DKK2 (1:600; CST), β-Catenin (1:800; CST), alpha smooth muscle Actin (1:800; abeam), Collagen I (1:800; abeam), Collagen III (1:800; abeam) and GAPDH (1:2,000; CST), loading control, antibodies overnight at 4° C., and then anti-rabbit IgG monoclonal antibody conjugated with horseradish peroxidase (Pierce) at 1:2000 dilution for 1 h at room temperature. Protein bands are detected using the West Femto system (Pierce).
A decrease in DKK2 mRNA expression in the dermal fibroblast cells is expected after transfection with the DKK2 ASOs compared to DKK2 mRNA levels in dermal fibroblast cells transfected with the non-specific control ASO 48 hours after transfection. There is an expected increase in protein levels of β-catenin, α-SMA, and collagens I and III in wells containing dermal fibroblast s cells transfected with the DKK2 ASOs relative to the amount of β-catenin, α-SMA, and collagens I and III in wells containing dermal fibroblast cells transfected with a non-specific control ASO 48 hours after transfection. These results show that the DKK2 ASOs elicit knockdown of DKK2 mRNA in dermal fibroblast cells and that the decrease in DKK2 expression is correlated with an increase in β-catenin, α-SMA, and collagens I and III production.
Example 6: Inhibition of DKK2 in a Mouse Model of Hair Regrowth Using Modified DKK2 siRNAs and ASOs
In this prophetic experiment, a mouse model of hair regrowth is used to evaluate the effect of siRNA and ASO inhibition of DKK2. The model involves treatment of shaved skin in 50 day old C57BL mice. Mice typically begin telogen at approximately post-natal day 50, and enter anagen 4-5 weeks later.
Briefly, mice are divided into four groups: Group 1—a group treated with non-targeting control siRNA, Group 2—a group treated with non-targeting control ASO, Group 3—a group treated with DKK2 siRNA1, Group 4—a group treated with DKK2 ASO1. Each group contains eight mice (4 males, 4 females). Each group has an equal portion of the hind limb shaved divided visually into 12 sections. Each section is assessed weekly and given a s.
Administration of siRNA or ASO is achieved with a topical application of siRNA or ASO resuspended in vehicle at concentration of 10 uM to the portion of the mouse skin initially exposed by shaving. On Study Day 0, Group 1 mice will be treated with non-targeting control siRNA, Group 2 mice will be treated with non-targeting control ASO, Group 3 mice will be treated with siRNA1 targeting human DKK2, Group 4 mice will be treated with ASO1 targeting human DKK2, and Group 5 mice will be treated with vehicle. Mice are treated once a week for 7 weeks with the final assessment taken 7 days after final treatment.
7 days after the final treatment, the mice are sacrificed by cervical dislocation following an intraperitoneal injection of 0.3 ml Nembutal (5 mg/ml). The shaved portion of skin tissue is collected and stored in RNAlater.
mRNA is isolated from tissue placed in RNAlater solution using the PureLink kit according to the manufacturer's protocol (ThermoFisher Cat. No. 12183020). The reverse transcriptase reaction is performed according to the manufacturer's protocol. Samples are stored at −80° C. until real-time qPCR is performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems FAM/DKK2 using a BioRad iCycler). There is an expected decrease in DKK2 mRNA expression in skin tissue from mice dosed with the DKK2 siRNA1 or ASO1 compared to DKK2 mRNA levels in the skin tissue from mice dosed with the non-specific controls. There is an expected increase in hair growth in the mice that receive the DKK2 siRNA or ASO compared to the hair growth in mice that receive the non-specific control. These results show that the DKK2 siRNA or ASO elicit knockdown of DKK2 mRNA in a mouse model of hair regrowth and that the decrease in DKK2 expression is correlated with a shortened telogen and accelerated anagen phase resulting in an increase in total hair regrowth.
Example 7: Clinical Experiments of Inhibition of DKK2 on Hair Loss
In this prophetic experiment, human subjects with hair loss (including male pattern baldness, alopecia areata, or non-scarring hair loss) are treated topically with an siRNA or ASO targeting DKK2, or with a control such as a placebo. For example, a topical formulation comprising the siRNA or ASO is administered to the scalp of the subject.
Signs and symptoms of hair loss are observed before, during, and after the treatment. For example, any one or more of the following may be determined: Men's Hair Growth Questionnaire (MHGQ) results, Kingsley Alopecia Profile (KAP) results, total hair counts, vellus hair counts, non-vellus hair counts, hair thickness measurements, hair density measurements, numbers of hair follicles (including total hair follicles, terminal hair follicles, anagen hair follicles, telogen hair follicles, catagen hair follicles, vellus or vellus-like miniaturized hair follicles, and indeterminate hair follicles), and protein and mRNA levels for β-catenin, α-SMA, collagen I, and collagen III. Additionally, DKK2 protein (circulating and skin) levels and DKK2 mRNA (skin) levels are determined. The topical treatment with either the siRNA or the ASO is expected to improve these measurements.
Example 8: Oligonucleotide Synthesis
Oligonucleotides such as siRNAs may be synthesized according to phosphoramidite technology on a solid phase. For example, a K&A oligonucleotide synthesizer may be used. Syntheses may be performed on a solid support made of controlled pore glass (CPG, 500 Å or 600 Å, obtained from AM Chemicals, Oceanside, CA, USA). All 2′-OMe and 2′-F phosphoramidites may be purchased from Hongene Biotech (Union City, CA, USA). All phosphoramidites may be dissolved in anhydrous acetonitrile (100 mM) and molecular sieves (3 Å) may be added. 5-Benzylthio-1H-tetrazole (BTT, 250 mM in acetonitrile) or 5-Ethylthio-1H-tetrazole (ETT, 250 mM in acetonitrile) may be used as activator solution. Coupling times may be 9-18 min (e.g. with a GalNAc such as ETL17), 6 min (e.g. with 2′OMe and 2′F). In order to introduce phosphorothioate linkages, a 100 mM solution of 3-phenyl 1,2,4-dithiazoline-5-one (POS, obtained from PolyOrg, Inc., Leominster, Mass., USA) in anhydrous acetonitrile may be employed.
After solid phase synthesis, the dried solid support may be treated with a 1:1 volume solution of 40 wt. % methylamine in water and 28% ammonium hydroxide solution (Aldrich) for two hours at 30° C. The solution may be evaporated and the solid residue may be reconstituted in water and purified by anionic exchange HPLC using a TKSgel SuperQ-5PW 13u column. Buffer A may be 20 mM Tris, 5 mM EDTA, pH 9.0 and contained 20% Acetonitrile and buffer B may be the same as buffer A with the addition of 1 M sodium chloride. UV traces at 260 nm may be recorded. Appropriate fractions may be pooled then desalted using Sephadex G-25 medium.
Equimolar amounts of sense and antisense strand may be combined to prepare a duplex. The duplex solution may be prepared in 0.1×PBS (Phosphate-Buffered Saline, 1×, Gibco). The duplex solution may be annealed at 95° C. for 5 min, and cooled to room temperature slowly. Duplex concentration may be determined by measuring the solution absorbance on a UV-Vis spectrometer at 260 nm in 0.1×PBS. For some experiments, a conversion factor may be calculated from an experimentally determined extinction coefficient.
Example 9: GalNAc Ligand for Hepatocyte Targeting of Oligonucleotides
Without limiting the disclosure to these individual methods, there are at least two general methods for attachment of multivalent N-acetylgalactosamine (GalNAc) ligands to oligonucleotides: solid or solution-phase conjugations. GalNAc ligands may be attached to solid phase resin for 3′ conjugation or at the 5′ terminus using GalNAc phosphoramidite reagents. GalNAc phosphoramidites may be coupled on solid phase as for other nucleosides in the oligonucleotide sequence at any position in the sequence. Reagents for GalNAc conjugation to oligonucleotides are shown in Table 7.
In solution phase conjugation, the oligonucleotide sequence—including a reactive conjugation site—is formed on the resin. The oligonucleotide is then removed from the resin and GalNAc is conjugated to the reactive site.
The carboxy GalNAc derivatives may be coupled to amino-modified oligonucleotides. The peptide coupling conditions are known to the skilled in the art using a carbodiimide coupling agent like DCC (N,N′-Dicyclohexylcarbodiimide), EDC (N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide) or EDC·HCl (N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride and an additive like HOBt (1-hydroxybenztriazole), HOSu (N-hydroxysuccinimide), TBTU (N,N,N′,N′-Tetramethyl-O-(benzotriazol-1-yl)uronium tetrafluoroborate, HBTU (2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate) or HOAt (1-Hydroxy-7-azabenzotriazole and common combinations thereof such as TBTU/HOBt or HBTU/HOAt to form activated amine-reactive esters.
Amine groups may be incorporated into oligonucleotides using a number of known, commercially available reagents at the 5′ terminus, 3′ terminus or anywhere in between.
Non-limiting examples of reagents for oligonucleotide synthesis to incorporate an amino group include:
-
- 5′ attachment:
- 6-(4-Monomethoxytritylamino)hexyl-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite CAS Number: 114616-27-2
- 5′-Amino-Modifier TEG CE-Phosphoramidite
- 10-(O-trifluoroacetamido-N-ethyl)-triethyleneglycol-1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
- 3′ attachment:
- 3′-Amino-Modifier Serinol CPG
- 3-Dimethoxytrityloxy-2-(3-(fluorenylmethoxycarbonylamino)propanamido)propyl-1-O-succinyl-long chain alkylamino-CPG (where CPG stands for controlled-pore glass and is the solid support)
- Amino-Modifier Serinol Phosphoramidite
- 3-Dimethoxytrityloxy-2-(3-(fluorenylmethoxycarbonylamino)propanamido)propyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
Internal (base modified):
-
- Amino-Modifier C6 dT
- 5′-Dimethoxytrityl-5-[N-(trifluoroacetylaminohexyl)-3-acrylimido]-2′-deoxyUridine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite. CAS Number: 178925-21-8
Solution phase conjugations may occur after oligonucleotide synthesis via reactions between non-nucleosidic nucleophilic functional groups that are attached to the oligonucleotide and electrophilic GalNAc reagents. Examples of nucleophilic groups include amines and thiols, and examples of electrophilic reagents include activated esters (e.g. N-hydroxysuccinimide, pentafluorophenyl) and maleimides.
Example 10: GalNAc Ligands for Hepatocyte Targeting of Oligonucleotides
Without limiting the disclosure to these individual methods, there are at least two general methods for attachment of multivalent N-acetylgalactosamine (GalNAc) ligands to oligonucleotides: solid or solution-phase conjugations. GalNAc ligands may be attached to solid phase resin for 3′ conjugation or at the 5′ terminus using GalNAc phosphoramidite reagents. GalNAc phosphoramidites may be coupled on solid phase as for other nucleosides in the oligonucleotide sequence at any position in the sequence. A non-limiting example of a phosphoramidite reagent for GalNAc conjugation to a 5′ end oligonucleotide is shown in Table 8.
The following includes examples of synthesis reactions used to create a GalNAc moiety:
Scheme for the Preparation of NAcegal-Linker-TMSOTf
General Procedure for Preparation of Compound 2A
To a solution of Compound 1A (500 g, 4.76 mol, 476 mL) in 2-Methyl-THF (2.00 L) is added CbzCl (406 g, 2.38 mol, 338 mL) in 2-Methyl-THF (750 mL) dropwise at 0° C. The mixture is stirred at 25° C. for 2 hrs under N2 atmosphere. TLC (DCM:MeOH=20:1, PMA) may indicate CbzCl is consumed completely and one new spot (Rf=0.43) formed. The reaction mixture is added HCl/EtOAc (1 N, 180 mL) and stirred for 30 mins, white solid is removed by filtration through celite, the filtrate is concentrated under vacuum to give Compound 2A (540 g, 2.26 mol, 47.5% yield) as a pale yellow oil and used into the next step without further purification. 1H NMR: δ 7.28-7.41 (m, 5H), 5.55 (br s, 1H), 5.01-5.22 (m, 2H), 3.63-3.80 (m, 2H), 3.46-3.59 (m, 4H), 3.29-3.44 (m, 2H), 2.83-3.02 (m, 1H).
General Procedure for Preparation of Compound 4A
To a solution of Compound 3A (1.00 kg, 4.64 mol, HCl) in pyridine (5.00 L) is added acetyl acetate (4.73 kg, 46.4 mol, 4.34 L) dropwise at 0° C. under N2 atmosphere. The mixture is stirred at 25° C. for 16 hrs under N2 atmosphere. TLC (DCM:MeOH=20:1, PMA) indicated Compound 3A is consumed completely and two new spots (Rf=0.35) formed. The reaction mixture is added to cold water (30.0 L) and stirred at 0° C. for 0.5 hr, white solid formed, filtered and dried to give Compound 4A (1.55 kg, 3.98 mol, 85.8% yield) as a white solid and used in the next step without further purification. 1H NMR: δ 7.90 (d, J=9.29 Hz, 1H), 5.64 (d, J=8.78 Hz, 1H), 5.26 (d, J=3.01 Hz, 1H), 5.06 (dd, J=11.29, 3.26 Hz, 1H), 4.22 (t, J=6.15 Hz, 1H), 3.95-4.16 (m, 3H), 2.12 (s, 3H), 2.03 (s, 3H), 1.99 (s, 3H), 1.90 (s, 3H), 1.78 (s, 3H).
General Procedure for Preparation of Compound 5A
To a solution of Compound 4A (300 g, 771 mmol) in DCE (1.50 L) is added TMSOTf (257 g, 1.16 mol, 209 mL) and stirred for 2 hrs at 60° C., and then stirred for 1 hr at 25° C. Compound 2A (203 g, 848 mmol) is dissolved in DCE (1.50 L) and added 4 Å powder molecular sieves (150 g) stirring for 30 mins under N2 atmosphere. Then the solution of Compound 4A in DCE is added dropwise to the mixture at 0° C. The mixture is stirred at 25° C. for 16 hrs under N2 atmosphere. TLC (DCM:MeOH=25:1, PMA) indicated Compound 4A is consumed completely and new spot (Rf=0.24) formed. The reaction mixture is filtered and washed with sat. NaHCO3 (2.00 L), water (2.00 L) and sat. brine (2.00 L). The organic layer is dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue is triturated with 2-Me-THE/heptane (5/3, v/v, 1.80 L) for 2 hrs, filtered and dried to give Compound 5A (225 g, 389 mmol, 50.3% yield, 98.4% purity) as a white solid. 1H NMR: δ 7.81 (d, J=9.29 Hz, 1H), 7.20-7.42 (m, 6H), 5.21 (d, J=3.26 Hz, 1H), 4.92-5.05 (m, 3H), 4.55 (d, J=8.28 Hz, 1H), 3.98-4.07 (m, 3H), 3.82-3.93 (m, 1H), 3.71-3.81 (m, 1H), 3.55-3.62 (m, 1H), 3.43-3.53 (m, 2H), 3.37-3.43 (m, 2H), 3.14 (q, J=5.77 Hz, 2H), 2.10 (s, 3H), 1.99 (s, 3H), 1.89 (s, 3H), 1.77 (s, 3H).
General Procedure for Preparation of NAcegal-Linker-Tosylate Salt
To a solution of Compound 5A (200 g, 352 mmol) in THF (1.0 L) is added dry Pd/C (15.0 g, 10% purity) and TsOH (60.6 g, 352 mmol) under N2 atmosphere. The suspension is degassed under vacuum and purged with H2 several times. The mixture is stirred at 25° C. for 3 hrs under H2 (45 psi) atmosphere. TLC (DCM:MeOH=10:1, PMA) indicated Compound 5A is consumed completely and one new spot (Rf=0.04) is formed. The reaction mixture is filtered and concentrated (≤40° C.) under reduced pressure to give a residue. Diluted with anhydrous DCM (500 mL, dried overnight with 4 Å molecular sieves (dried at 300° C. for 12 hrs)) and concentrate to give a residue and run Karl Fisher (KF) to check for water content. This is repeated 3 times with anhydrous DCM (500 mL) dilutions and concentration to give NAcegal-Linker-TMSOTf (205 g, 95.8% yield, TsOH salt) as a foamy white solid. 1H NMR: δ 7.91 (d, J=9.03 Hz, 1H), 7.53-7.86 (m, 2H), 7.49 (d, J=8.03 Hz, 2H), 7.13 (d, J=8.03 Hz, 2H), 5.22 (d, J=3.26 Hz, 1H), 4.98 (dd, J=11.29, 3.26 Hz, 1H), 4.57 (d, J=8.53 Hz, 1H), 3.99-4.05 (m, 3H), 3.87-3.94 (m, 1H), 3.79-3.85 (m, 1H), 3.51-3.62 (m, 5H), 2.96 (br t, J=5.14 Hz, 2H), 2.29 (s, 3H), 2.10 (s, 3H), 2.00 (s, 3H), 1.89 (s, 3H), 1.78 (s, 3H).
Scheme for the Preparation of TRIS-PEG2-CBZ
General Procedure for Preparation of Compound 5B
To a solution of Compound 4B (400 g, 1.67 mol, 1.00 eq) and NaOH (10 M, 16.7 mL, 0.10 eq) in THF (2.00 L) is added Compound 4B_2 (1.07 kg, 8.36 mol, 1.20 L, 5.00 eq), the mixture is stirred at 30° C. for 2 hrs. LCMS showed the desired MS is given. Five batches of solution are combined to one batch, then the mixture is diluted with water (6.00 L), extracted with ethyl acetate (3.00 L*3), the combined organic layer is washed with brine (3.00 L), dried over Na2SO4, filtered and concentrated under vacuum. The crude is purified by column chromatography (SiO2, petroleum ether:ethyl acetate=100:1-10:1, Rf=0.5) to give Compound 5B (2.36 kg, 6.43 mol, 76.9% yield) as light yellow oil. HNMR: δ 7.31-7.36 (m, 5H), 5.38 (s, 1H), 5.11-5.16 (m, 2H), 3.75 (t, J=6.4 Hz), 3.54-3.62 (m, 6H), 3.39 (d, J=5.2 Hz), 2.61 (t, J=6.0 Hz).
General procedure for preparation of 3-oxo-1-phenyl-2,7,10-trioxa-4-azatridecan-13-oic acid (Compound 2B below)
To a solution of Compound 5B (741 g, 2.02 mol, 1.00 eq) in DCM (2.80 L) is added TFA (1.43 kg, 12.5 mol, 928 mL, 6.22 eq), the mixture is stirred at 25° C. for 3 hrs. LCMS showed the desired MS is given. The mixture is diluted with DCM (5.00 L), washed with water (3.00 L*3), brine (2.00 L), the combined organic layer is dried over Na2SO4, filtered and concentrated under vacuum to give Compound 2B (1800 g, crude) as light yellow oil. HNMR: δ 9.46 (s, 5H), 7.27-7.34 (m, 5H), 6.50-6.65 (m, 1H), 5.71 (s, 1H), 5.10-5.15 (m, 2H), 3.68-3.70 (m, 14H), 3.58-3.61 (m, 6H), 3.39 (s, 2H), 2.55 (s, 6H), 2.44 (s, 2H).
General Procedure for Preparation of Compound 3B
To a solution of Compound 2B (375 g, 999 mmol, 83.0% purity, 1.00 eq) in DCM (1.80 L) is added HATU (570 g, 1.50 mol, 1.50 eq) and DIEA (258 g, 2.00 mol, 348 mL, 2.00 eq) at 0° C., the mixture is stirred at 0° C. for 30 min, then Compound 1B (606 g, 1.20 mol, 1.20 eq) is added, the mixture is stirred at 25° C. for 1 hr. LCMS showed desired MS is given. The mixture is combined to one batch, then the mixture is diluted with DCM (5.00 L), washed with 1 N HCl aqueous solution (2.00 L*2), then the organic layer is washed with saturated Na2CO3 aqueous solution (2.00 L*2) and brine (2.00 L), the organic layer is dried over Na2SO4, filtered and concentrated under vacuum to give Compound 3B (3.88 kg, crude) as yellow oil.
General Procedure for Preparation of TRIS-PEG2-CBZ.
A solution of Compound 3B (775 g, 487 mmol, 50.3% purity, 1.00 eq) in HCl/dioxane (4 M, 2.91 L, 23.8 eq) is stirred at 25° C. for 2 hrs. LCMS showed the desired MS is given. The mixture is concentrated under vacuum to give a residue. Then the combined residue is diluted with DCM (5.00 L), adjusted to pH=8 with 2.5 M NaOH aqueous solution, and separated. The aqueous phase is extracted with DCM (3.00 L) again, then the aqueous solution is adjusted to pH=3 with 1 N HCl aqueous solution, then extracted with DCM (5.00 L*2), the combined organic layer is washed with brine (3.00 L), dried over Na2SO4, filtered and concentrated under vacuum. The crude is purified by column chromatography (SiO2, DCM:MeOH=0:1-12:1, 0.1% HOAc, Rf=0.4). The residue is diluted with DCM (5.00 L), adjusted to pH=8 with 2.5 M NaOH aqueous solution, separated, the aqueous solution is extracted with DCM (3.00 L) again, then the aqueous solution is adjusted to pH=3 with 6 N HCl aqueous solution, extracted with DCM:MeOH=10:1 (5.00 L*2), the combined organic layer is washed with brine (2.00 L), dried over Na2SO4, filtered and concentrated under vacuum to give a residue. Then the residue is diluted with MeCN (5.00 L), concentrated under vacuum, repeat this procedure twice to remove water to give TRIS-PEG2-CBZ (1.25 kg, 1.91 mol, 78.1% yield, 95.8% purity) as light yellow oil. 1HNMR: 400 MHz, MeOD, δ 7.30-7.35 (5H), 5.07 (s, 2H), 3.65-3.70 (m, 16H), 3.59 (s, 4H), 3.45 (t, J=5.6 Hz), 2.51 (t, J=6.0 Hz), 2.43 (t, 6.4 Hz).
Scheme for the Preparation of TriNGal-TRIS-Pes2-Phosph 8c
TriGNal-TRIS-Peg2-Phosph 8c General Procedure for Preparation of Compound 3C
To a solution of Compound 1C (155 g, 245 mmol, 1.00 eq) in ACN (1500 mL) is added TBTU (260 g, 811 mmol, 3.30 eq), DIEA (209 g, 1.62 mol, 282 mL, 6.60 eq) and Compound 2C (492 g, 811 mmol, 3.30 eq, TsOH) at 0° C., the mixture is stirred at 15° C. for 16 hrs. LCMS showed the desired MS is given. The mixture is concentrated under vacuum to give a residue, then the mixture is diluted with DCM (2000 mL), washed with 1 N HCl aqueous solution (700 mL*2), then saturated NaHCO3 aqueous solution (700 mL*2) and concentrated under vacuum. The crude is purified by column chromatography to give Compound 3C (304 g, 155 mmol, 63.1% yield, 96.0% purity) as a yellow solid.
General Procedure for Preparation of Compound 4C
Two batches solution of Compound 3C (55.0 g, 29.2 mmol, 1.00 eq) in MeOH (1600 mL) is added Pd/C (6.60 g, 19.1 mmol, 10.0% purity) and TFA (3.34 g, 29.2 mmol, 2.17 mL, 1.00 eq), the mixture is degassed under vacuum and purged with H2. The mixture is stirred under H2 (15 psi) at 15° C. for 2 hours. LCMS showed the desired MS is given. The mixture is filtered and the filtrate is concentrated under vacuum to give Compound 4C (106 g, 54.8 mmol, 93.7% yield, 96.2% purity, TFA) as a white solid.
General Procedure for Preparation of Compound 5C
Two batches in parallel. To a solution of EDCI (28.8 g, 150 mmol, 1.00 eq) in DCM (125 mL) is added compound 4a (25.0 g, 150 mmol, 1.00 eq) dropwise at 0° C., then the mixture is added to compound 4 (25.0 g, 150 mmol, 1.00 eq) in DCM (125 mL) at 0° C., then the mixture is stirred at 25° C. for 1 hr. TLC (Petroleum ether:Ethyl acetate=3:1, Rf=0.45) showed the reactant is consumed and one new spot is formed. The reaction mixture is diluted with DCM (100 mL) then washed with aq.NaHCO3 (250 mL*1) and brine (250 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue is purified by column chromatography (SiO2, Petroleum ether:Ethyl acetate=100:1 to 3:1), TLC (SiO2, Petroleum ether:Ethyl acetate=3:1), Rf=0.45, then concentrated under reduced pressure to give a residue. Compound 5C (57.0 g, 176 mmol, 58.4% yield, 96.9% purity) is obtained as colorless oil and confirmed 1HNMR: EW33072-2-P1A, 400 MHz, DMSO δ 9.21 (s, 1H), 7.07-7.09 (m, 2H), 6.67-6.70 (m, 2H), 3.02-3.04 (m, 2H), 2.86-2.90 (m, 2H)
General Procedure for Preparation of Compound 6
To a mixture of compound 3 (79.0 g, 41.0 mmol, 96.4% purity, 1.00 eq, TFA) and compound 6C (14.2 g, 43.8 mmol, 96.9% purity, 1.07 eq) in DCM (800 mL) is added TEA (16.6 g, 164 mmol, 22.8 mL, 4.00 eq) dropwise at 0° C., the mixture is stirred at 15° C. for 16 hrs. LCMS (EW33072-12-P1B, Rt=0.844 min) showed the desired mass is detected. The reaction mixture is diluted with DCM (400 mL) and washed with aq.NaHCO3 (400 mL*1) and brine (400 mL*1), then the mixture is diluted with DCM (2.00 L) and washed with 0.7 M Na2CO3 (1000 mL*3) and brine (800 mL*3), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue is used to next step directly without purification. Compound 6 (80.0 g, crude) is obtained as white solid and confirmed via 1HNMR: EW33072-12-P1A, 400 MHz, MeOD δ 7.02-7.04 (m, 2H), 6.68-6.70 (m, 2H), 5.34-5.35 (s, 3H), 5.07-5.08 (d, J=4.00 Hz, 3H), 4.62-4.64 (d, J=8.00 Hz, 3H), 3.71-4.16 (m, 16H), 3.31-3.70 (m, 44H), 2.80-2.83 (m, 2H), 2.68 (m, 2H), 2.46-2.47 (m, 10H), 2.14 (s, 9H), 2.03 (s, 9H), 1.94-1.95 (d, J=4.00 Hz, 18H).
General Procedure for Preparation of TriGNal-TRIS-Peg2-Phosph 8c
Two batches are synthesized in parallel. To a solution of compound 6C (40.0 g, 21.1 mmol, 1.00 eq in DCM (600 mL) is added diisopropylammonium tetrazolide (3.62 g, 21.1 mmol, 1.00 eq) and compound 7c (6.37 g, 21.1 mmol, 6.71 mL, 1.00 eq) in DCM (8.00 mL) drop-wise, the mixture is stirred at 30° C. for 1 hr, then added compound 7c (3.18 g, 10.6 mmol, 3.35 mL, 0.50 eq) in DCM (8.00 mL) drop-wise, the mixture is stirred at 30° C. for 30 mins, then added compound 7c (3.18 g, 10.6 mmol, 3.35 mL, 0.50 eq) in DCM (8.00 mL) drop-wise, the mixture is stirred at 30° C. for 1.5 hrs. LCMS (EW33072-17-P1C1, Rt=0.921 min) showed the desired MS+1 is detected. LCMS (EW33072-17-P1C2, Rt=0.919 min) showed the desired MS+1 is detected. Two batches are combined for work-up. The mixture is diluted with DCM (1.20 L), washed with saturated NaHCO3 aqueous solution (1.60 L*2), 3% DMF in H2O (1.60 L*2), H2O (1.60 L*3), brine (1.60 L), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue is purified by column chromatography (SiO2, DCM:MeOH:TEA=100:3:2) TLC (SiO2, DCM:MeOH=10:1, Rf=0.45), then concentrated under reduced pressure to give a residue. Compound 8C (76.0 g, 34.8 mmol, 82.5% yield, 96.0% purity) is obtained as white solid and confirmed via 1HNMR: EW33072-19-P1C, 400 MHz, MeOD δ 7.13-7.15 (d, J=8.50 Hz, 2H), 6.95-6.97 (dd, J=8.38, 1.13 Hz, 2H), 5.34 (d, J=2.88 Hz, 3H), 0.09 (dd, J=11.26, 3.38 Hz, 3H), 4.64 (d, J=8.50 Hz, 3H), 3.99-4.20 (m, 12H), 3.88-3.98 (m, 5H), 3.66-3.83 (m, 20H), 3.51-3.65 (m, 17H), 3.33-3.50 (m, 9H), 2.87 (t, J=7.63 Hz, 2H), 2.76 (t, J=5.94 Hz, 2H), 2.42-2.50 (m, 10H), 2.14 (s, 9H), 2.03 (s, 9H), 1.94-1.95 (d, J=6.13 Hz, 18H), 1.24-1.26 (d, J=6.75 Hz, 6H), 1.18-1.20 (d, J=6.75 Hz, 6H).
Example 11: Modification Motif 1
An example DKK2 siRNA includes a combination of the following modifications:
-
- Position 9 (from 5′ to 3′) of the sense strand is 2′ F.
- If position 9 is a pyrimidine then all purines in the Sense Strand are 2′OMe, and 1-5 pyrimidines between positions 5 and 11 are 2′ F provided that there are never three 2′F modifications in a row.
- If position 9 is a purine then all pyrimidines in the Sense Strand are 2′OMe, and 1-5 purines between positions 5 and 11 are 2′ F provided that there are never three 2′F modifications in a row.
- Antisense strand odd-numbered positions are 2′OMe and even-numbered positions are a mixture of 2′ F, 2′OMe and 2′ deoxy.
Example 12: Modification Motif 2
An example DKK2 siRNA includes a combination of the following modifications:
-
- Position 9 (from 5′ to 3′) of the sense strand is 2′ deoxy.
- Sense strand positions 5, 7 and 8 are 2′ F.
- All pyrimidines in positions 10-21 are 2′ OMe, and purines are a mixture of 2′ OMe and 2′ F. Alternatively, all purines in positions 10-21 are 2′ OMe and all pyrimidines in positions 10-21 are a mixture of 2′ OMe and 2′ F.
- Antisense strand odd-numbered positions are 2′OMe and even-numbered positions are a mixture of 2′ F, 2′OMe and 2′ deoxy.
While preferred embodiments of the present invention 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 invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and compositions within the scope of these claims and their equivalents be covered thereby.
