Combination of stat3 targeting oligonucleotides and pd-l1 inhibitors
Patent Information
- Authority / Receiving Office
- EP · EP
- Patent Type
- Applications
- Current Assignee / Owner
- NOVO NORDISK AS
- Filing Date
- 2023-03-15
- Publication Date
- 2026-06-03
AI Technical Summary
Current cancer therapies, particularly chemotherapy, face challenges with multidrug resistance and limited therapeutic options due to the tumor microenvironment's immunosuppressive nature, which hampers effective treatment and leads to tumor relapse.
A combination of a STAT3 oligonucleotide conjugated to a lipid, when delivered with an anti-PD-L1 antibody, targets the tumor microenvironment, reducing tumor volume and inducing an anti-tumor memory response by enhancing CD8+ T cell activity.
The combination therapy effectively reduces tumor volume and induces a durable anti-tumor memory response, particularly in immunosuppressive and inflamed tumor models, dependent on CD8+ T cell presence, thereby overcoming multidrug resistance and improving treatment outcomes.
Smart Images

Figure IMGF000071_0001 
Figure IMGF000076_0001 
Figure IMGF000077_0001
Abstract
Description
COMBINATION OF STAT3 TARGETING OLIGONUCLEOTIDES AND PD-L1 INHIBITORS REFERENCE TO CROSS-RELATED APPLICATIONS
[0001] This application claims the priority to and the benefit of U.S. Provisional Patent Application Serial No. 63,320,163 filed March 15, 2022. The entire contents of which is incorporated herein by this reference. REFERENCE TO SEQUENCE LISTING
[0002] The contents of the electronic sequence listing (DICN_021_001WO_SeqList_ST26.xml; Size: 4,153,073 bytes; and Date of Creation: March 8, 2023) are herein incorporated by reference in its entirety. BACKGROUND OF THE DISCLOSURE
[0003] Currently, chemotherapy is the leading cancer therapy worldwide, often combined with surgery, or surgery and radiotherapy, depending on tumor type and stage (Abbas et al., AN OVERVIEW OF CANCER TREATMENT MODALITIES / INTECHOPEN, 2018). Since the discovery of several important mutations that contribute to carcinogenesis (e.g., epidermal cell alterations (Yamaoka et al., INT. J. MOL. SCI. (2017) 18(11): 2420)) these mutations and the proteins they represent have been extensively used as targets for the development of more selective drugs and drug combinations to treat cancer patients. Despite the effectiveness of these drugs, multidrug resistance (MDR) is often seen in patients, which often results in tumor relapse, limited therapeutic options and low quality of life for patients. In addition, cancer research has often been focused on tumor cells even though the effect of the tumor microenvironment and the ‘normal’ or non-cancerous cells within it that have been shown to play a key role in tumor progression, development and MDR (Klemm et al., TRENDS CELL BIOL (2015) 25(4): 198-213). Novel therapies that target different facets of the TME that contribute to tumor growth are needed. BRIEF SUMMARY OF THE DISCLOSURE
[0004] The disclosure is based, in part, on the discovery that a combination of a STAT3 oligonucleotide and a PD-L1 inhibitor provides synergistic anti-tumor efficacy for tumors of varying tumor microenvironments. Specifically, as demonstrated herein, a STAT3 oligonucleotide conjugated to a lipid, when delivered in combination with an anti-PD-L1antibody, reduced tumor volume in vivo in immunosuppressive and inflamed tumor models. Further, as shown herein, the combination of a STAT3 oligonucleotide and PD-L1 inhibitor induced an anti-tumor memory response as when mice were re-challenged with cancer cells, no tumors were established. In addition, the efficacy of the STAT3 oligonucleotide and PD- L1 inhibitor was dependent on the presence of CD8+ T cells.
[0005] Accordingly, in some aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating cancer in the subject.
[0006] In other aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating cancer in the subject.
[0007] In yet other aspects, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating the disease, disorder, or condition associated with activated STAT3 expression.
[0008] In further aspects, the disclosure provides a kit comprising an RNAi oligonucleotide, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the oligonucleotide to a subject in need thereof that has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises anantisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length.
[0009] In other aspects, the disclosure provides, a kit comprising a PD-L1 inhibitor, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the antibody to a subject in need thereof that has received or is receiving an RNAi oligonucleotide comprising an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length.
[0010] In some or any of the foregoing or related aspects, a subject has a disease, disorder, or condition associated with activated STAT3 expression. In some aspects, the disease, disorder, or condition associated with activated STAT3 expression is a cancer. In some aspects, the cancer is selected from carcinoma, sarcoma, melanoma, lymphoma, and leukemia, prostate cancer, breast cancer, hepatocellular carcinoma (HCC), colorectal cancer, pancreatic cancer and glioblastoma. In some aspects, the cancer comprises an immunosuppressive tumor microenvironment. In some aspects, the immunosuppressive tumor microenvironment has low levels of CD8+ T cell infiltration and high levels of MDSCs. In other aspects, the cancer comprises an inflamed tumor microenvironment. In some aspects, the inflamed tumor microenvironment comprises infiltrating T cells. In some aspects, the inflamed tumor microenvironment comprises high levels of CD8+ T cell infiltration and high levels of MDSCs. In some aspects, the cancer comprises a tumor resistant to immune checkpoint therapy. In some aspects, the cancer comprises a tumor partially resistant to immune checkpoint therapy. In some aspects, the cancer comprises a tumor sensitive to immune checkpoint therapy.
[0011] In some or any of the foregoing or related aspects, the methods described herein treat spontaneous tumor metastasis.
[0012] In some or any of the foregoing or related aspects, the methods described herein reduce immune suppressive genes and enhance immune activation genes. In some aspects, immune suppressive genes comprise checkpoint inhibitors, STAT3 mediated genes, suppressive cytokines, suppressive chemokines, and angiogenesis and matrix remodelingrelated genes. In some aspects, immune activation genes comprise gene related to T cell migration, T cell activation, T cell memory, and / or T cell cytotoxicity.
[0013] In some or any of the foregoing or related aspects, the PD-L1 inhibitor is an antibody. In some aspects, the antibody is an anti-PD-L1 antibody. In some aspects, the anti- PDL1 antibody is selected from FAZ053, atezolizumab, avelumab, durvalumab, envafolimab, and BMS-936559. In some aspects, the antibody is an anti-PD-1 antibody. In some aspects, the anti-PD-1 antibody is selected from nivolumab, pembrolizumab, and cemiplimab.
[0014] In some aspects, the PD-L1 inhibitor is a small molecule inhibitor. In some aspects, the PD-L1 inhibitor is a peptide. In some aspects, the PD-L1 inhibitor is a nucleic acid molecule. In some aspects, the nucleic acid molecule is selected from an antisense oligonucleotide, an siRNA, or an miRNA.
[0015] In some or any of the foregoing or related aspects, the STAT3 mRNA target sequence comprises any one of SEQ ID NOs: 89-280. In some aspects, the region of complementarity is fully complementary to the STAT3 mRNA target sequence. In some aspects, the region of complementarity comprises no more than 4 mismatches to the STAT3 mRNA target sequence.
[0016] In some or any of the foregoing or related aspects, the antisense strand is 19 to 27 nucleotides in length. In some aspects, the antisense strand is 21 to 27 nucleotides in length, optionally wherein the antisense strand is 22 nucleotides in length.
[0017] In some or any of the foregoing or related aspects, the sense strand is 19 to 40 nucleotides in length, optionally wherein the sense strand is 36 nucleotides in length.
[0018] In some or any of the foregoing or related aspects, the duplex region is at least 19 nucleotides in length. In some aspects, the duplex region is at least 20 nucleotides in length, optionally wherein the duplex region is 21 nucleotides in length.
[0019] In some or any of the foregoing or related aspects, the region of complementarity to STAT3 is at least 19 contiguous nucleotides in length. In some aspects, the region of complementarity to STAT3 is at least 21 contiguous nucleotides in length.
[0020] In some or any of the foregoing or related aspects, the sense strand comprises at its 3′ end a stem-loop set forth as: S1-L-S2, wherein S1 is complementary to S2, and wherein L forms a loop between S1 and S2 of 3 to 5 nucleotides in length. In some aspects, L is a tetraloop, optionally wherein L is 4 nucleotides in length. In some aspects, L comprises a sequence set forth as GAAA.
[0021] In some or any of the foregoing or related aspects, the antisense strand comprises a 3’ overhang sequence of one or more nucleotides in length, optionally wherein the 3’overhang sequence is 2 nucleotides in length, optionally wherein the 3’ overhang sequence is GG.
[0022] In some or any of the foregoing or related aspects, the oligonucleotide comprises at least one modified nucleotide. In some aspects, the modified nucleotide comprises a 2′- modification. In some aspects, the 2′-modification is a modification selected from 2′- aminoethyl, 2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl, and 2′-deoxy-2′-fluoro-β-d- arabinonucleic acid. In some aspects, about 10-15%, 10%, 11%, 12%, 13%, 14% or 15% of the nucleotides of the sense strand comprise a 2’-fluoro modification. In some aspects, about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the antisense strand comprise a 2’-fluoro modification. In some aspects, about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the oligonucleotide comprise a 2’-fluoro modification. In some aspects, the sense strand comprises 36 nucleotides with positions 1-36 from 5’ to 3 ’, wherein positions 8-11 comprise a 2’-fluoro modification. In some aspects, the antisense strand comprises 22 nucleotides with positions 1-22 from 3’ to 5’, and wherein positions 2, 3, 4, 5, 7, 10 and 14 comprise a 2’-fluoro modification. In some aspects, the remaining nucleotides comprise a 2’-O-methyl modification. In some aspects, all of the nucleotides of the oligonucleotide are modified.
[0023] In some or any of the foregoing or related aspects, the oligonucleotide comprises at least one modified internucleotide linkage. In some aspects, the at least one modified internucleotide linkage is a phosphorothioate linkage.
[0024] In some or any of the foregoing or related aspects, the 4′-carbon of the sugar of the 5′-nucleotide of the antisense strand comprises a phosphate analog. In some aspects, the phosphate analog is oxymethylphosphonate, vinylphosphonate or malonylphosphonate.
[0025] In some or any of the foregoing or related aspects, at least one nucleotide of the oligonucleotide is conjugated to one or more targeting ligands. In some aspects, the nucleotide is conjugated to more than one targeting ligands, wherein the targeting ligands are the same or are different. In some aspects, the one or more targeting ligands is selected from carbohydrate, amino sugar, cholesterol, polypeptide, or lipid. In some aspects, the one or more targeting ligands is a saturated or unsaturated fatty acid moiety. In some aspects, the targeting ligand is a saturated fatty acid moiety that ranges in size from C10 to C24 long. In some aspects, the targeting ligand is a C16 saturated fatty acid moiety. In some aspects, the targeting ligand is a C18 saturated fatty acid moiety. In someaspects, the targeting ligand is a C22 saturated fatty acid moiety. In some aspects, the targeting ligand comprises a N-acetylgalactosamine (GalNAc) moiety. In some aspects, the GalNAc moiety is a monovalent GalNAc moiety, a bivalent GalNAc moiety, a trivalent GalNAc moiety or a tetravalent GalNAc moiety. In some aspects, up to 4 nucleotides of L of the stem-loop are each conjugated to a monovalent GalNAc moiety.
[0026] In some or any of the foregoing or related aspects, In some or any of the foregoing or related aspects, the sense strand comprises a sequence as set forth in SEQ ID NOs: 857-946. In some aspects, the antisense strand comprises a sequence as set for in SEQ ID NOs: 947-1036.
[0027] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively.
[0028] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 861 and 951, respectively; (b) SEQ ID NOs: 857 and 947, respectively; (c) SEQ ID NOs: 858 and 948, respectively; (d) SEQ ID NOs: 859 and 949, respectively; (e) SEQ ID NOs: 860 and 950, respectively; (f) SEQ ID NOs: 862 and 952, respectively; (g) SEQ ID NOs: 863 and 953, respectively; (h) SEQ ID NOs: 864 and 954, respectively; (i) SEQ ID NOs: 865 and 955, respectively; (j) SEQ ID NOs: 866 and 956, respectively; (k) SEQ ID NOs: 867 and 957, respectively; (l) SEQ ID NOs: 868 and 958, respectively; (m) SEQ ID NOs: 869 and 959, respectively; (n) SEQ ID NOs: 870 and 960, respectively; (o) SEQ ID NOs: 871 and 961, respectively; (p) SEQ ID NOs: 872 and 962, respectively; (q) SEQ ID NOs: 873 and 963, respectively;(r) SEQ ID NOs: 874 and 964, respectively; (s) SEQ ID NOs: 875 and 965, respectively; (t) SEQ ID NOs: 876 and 966, respectively; (u) SEQ ID NOs: 877 and 967, respectively; (v) SEQ ID NOs: 878 and 968, respectively; (w) SEQ ID NOs: 879 and 969, respectively; (x) SEQ ID NOs: 880 and 970, respectively; (y) SEQ ID NOs: 881and 971, respectively; (z) SEQ ID NOs: 882 and 972, respectively; (aa) SEQ ID NOs: 883 and 973, respectively; (bb) SEQ ID NOs: 884 and 974, respectively; (cc) SEQ ID NOs: 885 and 975, respectively; (dd) SEQ ID NOs: 886 and 976, respectively; (ee) SEQ ID NOs: 887 and 977, respectively; (ff) SEQ ID NOs: 888 and 978, respectively; (gg) SEQ ID NOs: 940 and 1030, respectively; (hh) SEQ ID NOs: 896 and 986, respectively; and (ii) SEQ ID NOs: 920 and 1010, respectively.
[0029] In some or any of the foregoing or related aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 862 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 952. In some aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 875 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 965. In some aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 876 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 966. In some aspects, sense strand comprises the nucleotide sequence of SEQ ID NO: 920 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1010.
[0030] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively;(f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively.
[0031] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively.
[0032] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively.
[0033] In some or any of the foregoing or related aspects, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 11, 39, 67 and 71. In some aspects, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 12, 40, 68 and 72.
[0034] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 11 and 12, respectively; (b) SEQ ID NOs: 39 and 40, respectively; (c) SEQ ID NOs: 67 and 68, respectively; and (d) SEQ ID NOs: 71 and 72, respectively.
[0035] In some or any of the foregoing or related aspects, the sense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1042, 1055, 1056, and 1100. In some aspects, the antisense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1132, 1145, 1146, and 1190.
[0036] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1041 and 1131, respectively; (b) SEQ ID NOs: 1037 and 1127, respectively; (c) SEQ ID NOs: 1038 and 1128, respectively; (d) SEQ ID NOs: 1039 and 1129, respectively; (e) SEQ ID NOs: 1040 and 1130, respectively;(f) SEQ ID NOs: 1042 and 1132, respectively; (g) SEQ ID NOs: 1043 and 1133, respectively; (h) SEQ ID NOs: 1044 and 1134, respectively; (i) SEQ ID NOs: 1045 and 1135, respectively; (j) SEQ ID NOs: 1046 and 1136, respectively; (k) SEQ ID NOs: 1047 and 1137, respectively; (l) SEQ ID NOs: 1048 and 1138, respectively; (m) SEQ ID NOs: 1049 and 1139, respectively; (n) SEQ ID NOs: 1050 and 1140, respectively; (o) SEQ ID NOs: 1051 and 1141, respectively; (p) SEQ ID NOs: 1052 and 1142, respectively; (q) SEQ ID NOs: 1053 and 1143, respectively; (r) SEQ ID NOs: 1054 and 1144, respectively; (s) SEQ ID NOs: 1055 and 1145, respectively; (t) SEQ ID NOs: 1056 and 1146, respectively; (u) SEQ ID NOs: 1057 and 1147, respectively; (v) SEQ ID NOs: 1058 and 1148, respectively; (w) SEQ ID NOs: 1059 and 1149, respectively; (x) SEQ ID NOs: 1060 and 1150, respectively; (y) SEQ ID NOs: 1061 and 1151, respectively; (z) SEQ ID NOs: 1062 and 1152, respectively; (aa) SEQ ID NOs: 1063 and 1153, respectively; (bb) SEQ ID NOs: 1064 and 1154, respectively; (cc) SEQ ID NOs: 1065 and 1155, respectively; (dd) SEQ ID NOs: 1066 and 1156, respectively; (ee) SEQ ID NOs: 1067 and 1157, respectively; (ff) SEQ ID NOs: 1068 and 1158, respectively; (gg) SEQ ID NOs: 1120 and 1210, respectively; (hh) SEQ ID NOs: 1076 and 1166, respectively; and (ii) SEQ ID NOs: 1100 and 1190, respectively.
[0037] In some or any of the foregoing or related aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 1042 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1132. In some aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 1055 and the antisense strand comprises the nucleotide sequence ofSEQ ID NO: 1145. In some aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 1056 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1146. In some aspects, the sense strand comprises the nucleotide sequence of SEQ ID NO: 1100 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1190.
[0038] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1081 and 1171, respectively; (b) SEQ ID NOs: 1090 and 1180, respectively; (c) SEQ ID NOs: 1079 and 1169, respectively; (d) SEQ ID NOs: 1076 and 1166, respectively; (e) SEQ ID NOs: 1072 and 1162, respectively; (f) SEQ ID NOs: 1070 and 1160, respectively; and (g) SEQ ID NOs: 1069 and 1159, respectively.
[0039] In some or any of the foregoing or related aspects, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1120 and 1210, respectively; (b) SEQ ID NOs: 1117 and 1207, respectively; and (c) SEQ ID NOs: 1119 and 1209, respectively.
[0040] In some or any of the foregoing or related aspects, the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1095 and 1185, respectively; (b) SEQ ID NOs: 1104 and 1194, respectively; (c) SEQ ID NOs: 1093 and 1183, respectively; and (d) SEQ ID NOs: 1100 and 1190, respectively.
[0041] In some aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving an anti-PD-L1 antibody, the method comprising administering an RNAi oligonucleotide comprising an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 84, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 83, thereby treating cancer in the subject.
[0042] In other aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 84, wherein the antisensestrand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 83, thereby treating cancer in the subject.
[0043] In yet other aspects, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 84, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 83, thereby treating the disease, disorder, or condition associated with activated STAT3 expression.
[0044] In further aspects, the disclosure provides a kit comprising an RNAi oligonucleotide, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the oligonucleotide to a subject in need thereof that has received or is receiving an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 84, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 83.
[0045] In other aspects, the disclosure provides, a kit comprising an anti-PD-L1 antibody, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the antibody to a subject in need thereof that has received or is receiving an RNAi oligonucleotide comprising an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 84, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 83.
[0046] In some aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving an anti-PD-L1 antibody, the method comprising administering an RNAi oligonucleotide comprising an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 70, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 69, thereby treating cancer in the subject.
[0047] In other aspects, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisensestrand comprising a nucleotide sequence set forth in SEQ ID NO: 70, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 69, thereby treating cancer in the subject.
[0048] In yet other aspects, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 70, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 69, thereby treating the disease, disorder, or condition associated with activated STAT3 expression.
[0049] In further aspects, the disclosure provides a kit comprising an RNAi oligonucleotide, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the oligonucleotide to a subject in need thereof that has received or is receiving an anti-PD-L1 antibody, wherein the oligonucleotide comprises an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 70, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 69.
[0050] In other aspects, the disclosure provides, a kit comprising an anti-PD-L1 antibody, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the antibody to a subject in need thereof that has received or is receiving an RNAi oligonucleotide comprising an antisense strand comprising a nucleotide sequence set forth in SEQ ID NO: 70, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and a sense strand comprising a nucleotide sequence set forth in SEQ ID NO: 69. BRIEF DESCRIPTION OF THE DRAWINGS
[0051] FIG.1A provides structures of RNAi oligonucleotide molecules having chemical modifications with GalNAc (top) or lipid (e.g., C18 hydrocarbon chain) (bottom) conjugated to the oligonucleotide molecule to generate oligonucleotide-ligand conjugates.
[0052] FIG.1B provides structures of lipid tails suitable for conjugation to RNAi oligonucleotide molecules.
[0053] FIGs.2A and 2B are graphs showing remaining mouse Stat3 mRNA levels in the livers of mice treated with GalXC-STAT3-conjugates (GalNAc conjugates) targeting different regions of Stat3 mRNA. Mice were administered a single dose (3mg / kg) (FIG.2A) or varying doses (0.3, 1.0 or 3.0 mg / kg) to determine dose responsiveness (FIG.2B). Arrows indicate constructs selected for further study.
[0054] FIGs.3A and 3B are graphs showing mouse Stat3 mRNA expression 3 days after treatment with GalXC-STAT3-C18 conjugates in G-MDSCs and M-MDSCs derived from Pan02 xenografts implanted in mice. Tumors were dosed at 25 mg / kg (FIG.3A) and 50 mg / kg (FIG.3B).
[0055] FIGs.4A and 4B are graphs showing mouse Stat3 mRNA expression after treatment of Pan02 xenograft mice with GalXC-STAT3-C18 conjugates in bulk tumor (TME) (FIG.4A) and tumor draining lymph nodes (TdLNs) (FIG.4B) at doses of 25 and 50 mg / kg.
[0056] FIG.5A provides graphs showing the effect of GalXC-STAT3-C18-4123 on Stat3 and Pdl1 mRNA levels in G / M-MDSCs in TME and TdLNs of Pan02 xenograft mice 3 days after a dose of 25 or 50 mg / kg of the conjugated oligonucleotide.
[0057] FIG.5B provides graphs showing the effect of GalXC-STAT3-C18-4123 on Stat3 and Pdl1 mRNA levels in TdLN of Pan02 xenograft mice 7 days after a 25mg / kg dose of the conjugated oligonucleotide.
[0058] FIGs.6A and 6B are graphs showing the in vivo effect of subcutaneous treatment of a total dose of 50 mg / kg GalXC-STAT3-C18-4123 on tumor volume over time in immunocompetent mice bearing Pan02 murine pancreatic tumors. Mice were treated with either four 12.5 mg / kg (FIG.6A) or two 25mg / kg (FIG.6B) doses of the conjugated oligonucleotide.
[0059] FIG.7 provides a graph depicting the percent (%) of human STAT3 mRNA remaining in Huh7 cells endogenously expressing human STAT3, after 24-hour treatment with 1nM of DsiRNA targeting various regions of the STAT3 gene.192 DsiRNAs were designed and screened. Two primer pairs were used. Expression was normalized between samples using the HPRT and SFRS9 housekeeping genes (Forward 1- SEQ ID NO: 1219, Reverse 1- SEQ ID NO: 1220; Probe 1- SEQ ID NO: 1221; Forward 2- SEQ ID NO: 1222, Reverse 2- SEQ ID NO: 1223; Probe 2- SEQ ID NO: 1224).
[0060] FIGs.8A and 8B provide graphs depicting the percent (%) of human STAT3 mRNA remaining in Huh7 cells endogenously expressing human STAT3, after 24-hour treatment with 0.05nM, 0.3nM, or 1nM of DsiRNA targeting various regions of the STAT3gene.48 GalNAc-conjugated STAT3 oligonucleotides were assayed in FIG.8A and 34 of those oligonucleotides were selected for further testing in vivo (FIG.8B).
[0061] FIGs.9A and 9B provide graphs depicting the percent (%) of human STAT3 mRNA remaining in liver of mice exogenously expressing human STAT3 (hydrodynamic injection model) after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with 1mg / kg of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Three days post-dose mice were hydrodynamically injected (HDI) with a DNA plasmid encoding human STAT3. The level of human STAT3 mRNA was determined from livers collected 18 hours after injection. Arrows indicate oligonucleotides selected for dose response analysis. Hs / Mf = human / monkey common sequence; Hs / Mm= human / mouse common sequence; Hs / Mf / Mm= human / monkey / mouse triple common sequence.
[0062] FIG.10 provides a graph depicting the dose response of GalNAc-conjugated STAT3 oligonucleotides. The percent (%) of human STAT3 mRNA remaining in liver of mice exogenously expressing STAT3 (HDI model) after treatment with human GalNAc-conjugated STAT3 oligonucleotides at two different doses (0.3mg / kg or 1mg / kg,) was measured. The level of human STAT3 mRNA was determined from livers collected 18 hours after injection with plasmid encoding human STAT3. Arrows indicate oligonucleotides selected for dose response analysis. Hs / Mf = human / monkey common sequence; Hs / Mm= human / mouse common sequence
[0063] FIG.11 provides a graph depicting the normalized (to Ppib) relative mouse STAT3 mRNA remaining in liver of mice endogenously expressing mouse STAT3 after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with 3mg / kg of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Five days post-dose liver was collected and the level of mouse STAT3 mRNA was determined. Arrows indicate top oligonucleotides and those selected for dose response study.
[0064] FIG.12 provides a graph depicting the normalized (to Ppib) relative mouse STAT3 mRNA remaining in liver of mice endogenously expressing mouse STAT3 after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with 3mg / kg of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Five days post-dose liver was collected and the level of mouse STAT3 mRNA was determined. Arrows indicate oligonucleotides selected for dose response study.
[0065] FIGs.13A and 13B provide graphs depicting the dose response of GalNAc- conjugated STAT3 oligonucleotides. The percent (%) of mouse STAT3 mRNA remaining in liver of mice endogenously expressing STAT3 after treatment with human GalNAc-conjugated STAT3 oligonucleotides at three doses (0.3mg / kg, 1mg / kg, and 3mg / kg) was measured. The level of mouse STAT3 mRNA was determined from livers collected 5 days later. TC = triple common (mouse / human / monkey); Hs_Mm = human / mouse.
[0066] FIG.14 provides a graph depicting the percent (%) of human STAT3 mRNA remaining in liver of mice exogenously expressing human STAT3 (hydrodynamic injection model) after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with 1mg / kg of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Three days post-dose mice were hydrodynamically injected (HDI) with a DNA plasmid encoding human STAT3. The level of human STAT3 mRNA was determined from livers collected 18 hours after injection. Arrows indicate oligonucleotides selected for dose response study.
[0067] FIG.15 provides a graph depicting the dose response of GalNAc-conjugated STAT3 oligonucleotides. The percent (%) of human STAT3 mRNA remaining in liver of mice exogenously expressing human STAT3 (hydrodynamic injection model) after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with three doses (0.3mg / kg, 1mg / kg, and 3mg / kg) of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Three days post-dose mice were hydrodynamically injected (HDI) with a DNA plasmid encoding human STAT3. The level of human STAT3 mRNA was determined from livers collected 18 hours after injection. TC = triple common (mouse / human / monkey); Hs_Mm = human / mouse; Hs = human.
[0068] FIG.16 provides a graph depicting the dose response of GalNAc-conjugated STAT3 oligonucleotides. The percent (%) of human STAT3 mRNA remaining in liver of mice exogenously expressing human STAT3 (hydrodynamic injection model) after treatment with GalNAc-conjugated STAT3 oligonucleotides. Mice were dosed subcutaneously with two doses (0.3mg / kg and 1mg / kg) of the indicated GalNAc-STAT3 oligonucleotides formulated in PBS. Three days post-dose mice were hydrodynamically injected (HDI) with a DNA plasmid encoding human STAT3. The level of human STAT3 mRNA was determined from livers collected 18 hours after injection.
[0069] FIG.17 provides a graph depicting the percent (%) remaining human STAT1 mRNA in Huh7 cells endogenously expressing STAT3 and STAT1 treated with GalNAc- conjugated STAT3 oligonucleotides. Cells were treated for 24 hours with three doses (0.05nM, 0.3nM, and 1nM) of oligonucleotide.
[0070] FIG.18A provides a graph depicting tumor volume after administration of a GalXC-STAT3-C18 oligonucleotide alone or in combination with an anti-PD-L1 mAb.Immunocompetent mice bearing Pan02 murine pancreatic tumors were dosed subcutaneously (s.c.) with 25 mg / kg of GalXC-STAT3-C18-4123 with intraperitoneal (i.p.) treatment of 10 mg / kg of anti-PD-L1 mAb. Controls included GalXC-Placebo (an HBV siRNA with identical chemistry and lipid conjugation as GalXC-STAT3 oligonucleotides), GalXC-STAT3-C18- 4123 at 25 mg / kg or GalXC-Placebo at 25 mg / kg in combination with anti-PD-L1 mAb at 10 mg / kg. Mice were first administered two doses three days apart, and two weeks later were administered two more doses three days apart [(q3dx2) x2]. Arrows indicate days doses were administered.
[0071] FIG.18B provides a graph depicting tumor volume after administration of GalXC-STAT3-C18 oligonucleotide in combination with anti-PD-L1 mAb. Placebo treated mice from FIG.18A were dosed subcutaneously (s.c.) with 25 mg / kg of GalXC-STAT3- C18-4123 with intraperitoneal (i.p.) treatment of 10 mg / kg of anti-PD-L1 mAb at Day 59.
[0072] FIGs.19A-19C provide graphs depicting tumor volume after administration of a GalXC-STAT3-C18 oligonucleotide alone or in combination with an anti-PD-L1 mAb or GalXC-Placebo alone or in combination with anti-PD-L1 mAb in tumors with different immunophenotypes.4T1 (triple negative breast, checkpoint resistant) (FIG.19A), MC-38 (Colon carcinoma, partially checkpoint sensitive) (FIG.19B), or Hepa1-6 (Hepatocellular carcinoma, checkpoint sensitive) (FIG.19C) cells were implanted into mice. Tumor bearing mice were dosed s.c. with 25 mg / kg of GalXC-STAT3-C18-4123 with i.p. treatment of 10 mg / kg of anti-PD-L1 mAb. Controls included GalXC-Placebo, GalXC-STAT3-C18-4123 at 25 mg / kg or GalXC-Placebo at 25 mg / kg in combination with anti-PD-L1 mAb at 10 mg / kg.. Mice bearing MC-38 and Hepa1-6 tumors were administered two doses three days apart at 25 mg / kg and the same regimen was repeated the following week. Mice bearing 4T1 tumors were administered three doses each three days apart (q3d x 3). Arrow (5 / 5 CR) = All mice treated were complete responders.
[0073] FIG.20 provides a graph depicting the effect of Hepa1-6 re-challenge in the completely eradicated tumors. After tumors in all 5 mice were completely regressed with the treatment of GalXC-STAT3-C18 (25 mg / kg, s.c.) and anti-PD-L1 mAb (10 mg / kg, i.p.) in FIG.19C, mice were rechallenged on day 51 with Hepa1-6 cells (2e6 cells / mouse) on the opposite flank of the mice and tumor volume was monitored (FIG.20). Arrow (5 / 5 CR) = All mice remained tumor free even after the re-challenge.
[0074] FIG.21 provides a graph depicting tumor volume after administration of GalXC- STAT3-C18 oligonucleotide alone or in combination with an anti-PD-L1 mAb in immunocompromised mice with no functional CD8+ T cells. Mice bearing 4T1 tumors weredosed s.c. with GalXC-STAT3-C18-4123 (25 mg / kg, three times with each dose three days apart (q3d x 3)) and i.p. with anti-PD-L1 mAb (10 mg / kg, q3d x 3). Controls included GalXC-Placebo, GalXC-STAT3-C18-4123 at 25 mg / kg or GalXC-Placebo at 25 mg / kg in combination with anti-PD-L1 mAb at 10 mg / kg.
[0075] FIG.22 provides images showing the appearance of tumors (with cell death) from mice assayed in FIG.19A, and perforin staining for positive cytotoxic CD8+ T cells in the tumors at the end of the study.
[0076] FIG.23 provides images showing lung tumor metastasis after administration of GalXC-STAT3-C18-4123 oligonucleotide alone or in combination with an anti-PD-L1 mAb as treated in FIGs.19A and 21. Mice (immunocompetent or immunocompromised) bearing 4T1 tumors were dosed s.c. with GalXC-STAT3-C18-4123 (50 mg / kg, q3d x 3) and i.p. with anti-PD-L1 mAb (10 mg / kg, q3d x 3). Controls included GalXC-Placebo, GalXC-STAT3- C18-4123 at 50 mg / kg or GalXC-Placebo at 50 mg / kg in combination with anti-PD-L1 mAb at 10 mg / kg.
[0077] FIG.24 provides a heat map showing the regulation of targets involved in immune modulation observed in CT26 tumors upon combination treatment of GalXC- STAT3-C18-4123 (s.c, 25 mg / kg, q3d x 3) and anti-PD-L1 mAb (i.p. at 10 mg / kg, q3d x 3) compared to controls including GalXC-Placebo, GalXC-STAT3-C18-4123 at 25 mg / kg or GalXC-Placebo at 25 mg / kg in combination with anti-PD-L1 mAb at 10 mg / kg. DETAILED DESCRIPTION
[0078] The present disclosure now will be described more fully hereinafter with reference to the accompanying drawings, in which illustrative embodiments of the disclosure are shown. The disclosure may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the disclosure to those skilled in the art. Definitions
[0079] The publications discussed throughout the text are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior disclosure.
[0080] As used herein, the term "and / or" includes any and all combinations of one or more of the associated listed items. Further, the singular forms and the articles "a", "an" and "the" are intended to include the plural forms as well, unless expressly stated otherwise. It will be further understood that the terms: includes, comprises, including and / or comprising, when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof. Further, it will be understood that when an element, including component or subsystem, is referred to and / or shown as being connected or coupled to another element, it can be directly connected or coupled to the other element or intervening elements may be present.
[0081] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice of the disclosed methods and compositions, exemplary methods, and materials are described herein.
[0082] General texts which describe molecular biological techniques useful herein, including the use of vectors, promoters and many other relevant topics, include Berger and Kimmel, GUIDE TO MOLECULAR CLONING TECHNIQUES, METHODS IN ENZYMOLOGY, volume 152, (Academic Press, Inc., San Diego, Calif.) ("Berger"); Sambrook et al., MOLECULAR CLONING--A LABORATORY MANUAL, 2d ed., Vol.1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, 1989 ("Sambrook") and CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, F.M. Ausubel et al., eds., CURRENT PROTOCOLS, A JOINT VENTURE BETWEEN GREENE PUBLISHING ASSOCIATES, INC. AND JOHN WILEY AND SONS, INC., (supplemented through 1999) ("Ausubel"). Examples of protocols sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR), the ligase chain reaction(LCR), Q.beta.-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA), e.g., for the production of the homologous nucleic acids of the disclosure are found in Berger, Sambrook, and Ausubel, as well as in Mullis et al., (1987) U.S. Pat. No.4,683,202; Innis et al., eds. (1990); PCR PROTOCOLS: A GUIDE TO METHODS AND APPLICATIONS (Academic Press Inc. San Diego, Calif.) ("Innis"); Arnheim and Levinson (Oct.1, 1990) Cand EN 36-47; J. NIH RES. (1991) 3:81-94; Kwoh et al., (1989) PROC. NATL. ACAD. SCI. USA 86: 1173; Guatelliet et al., (1990) PROC. NAT'L. ACAD. SCI. USA 87: 1874; Lomell et al., (1989) J. CLIN. CHEM 35: 1826; Landegren et al., (1988) SCIENCE 241: 1077-80; Van Brunt (1990) BIOTECHNOLOGY 8: 291-94; Wu and Wallace (1989) GENE 4:560; Barringer et al., (1990) GENE 89:117; and, Sooknanan and Malek(1995) BIOTECHNOLOGY 13: 563-564. Improved methods for cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No.5,426,039. Improved methods for amplifying large nucleic acids by PCR are summarized in Cheng et al., (1994) NATURE 369: 684-85 and the references cited therein, in which PCR amplicons of up to 40 kb are generated.
[0083] As used in the specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a pharmaceutical carrier" includes mixtures of two or more such carriers, and the like.
[0084] Ranges can be expressed herein as from "about" one value, and / or to "about" another value. When such a range is expressed, another embodiment includes from the one value and / or to the other value. Similarly, when values are expressed as approximations, by use of the antecedent "about," it will be understood that the value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are several values disclosed herein, and that each value is also herein disclosed as "about" that value in addition to the value itself. For example, if the value "10" is disclosed, then "about 10" is also disclosed. It is also understood that when a value is disclosed that "less than or equal to" the value, "greater than or equal to the value" and possible ranges between values are also disclosed, as appropriately understood by the skilled artisan. For example, if the value "10" is disclosed the "less than or equal to 10" as well as "greater than or equal to 10" is also disclosed. It is also understood that the throughout the application, data is provided in several different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular datapoint "10" and a particular data point 15 are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
[0085] In this specification and in the claims, which follow, reference will be made to several terms which shall be defined to have the following meanings:
[0086] The term "cancer" or "tumor" includes, but is not limited to, solid tumors and blood borne tumors. These terms include diseases of the skin, tissues, organs, bone, cartilage, blood, and vessels. These terms further encompass primary and metastatic cancers.
[0087] The term “PD-1” refers to a protein found on T cells that helps keep the immune responses in check. When PD-1 is bound to another protein called PD-L1, it helps keep T cells from killing other cells, including cancer cells. Some anticancer drugs, called immune checkpoint inhibitors, are used to block PD-1. When this protein is prevented from acting on T cells, they can act to kill cancer cells.
[0088] The term “STAT3” refers to Signal transducer and activator of transcription 3 (STAT3) which is a transcription factor which in humans is encoded by the STAT3 gene (STAT3 Human (Hs) NM_001369512.1 Genbank RefSeq #, or NM_139276.3). STAT3 mediates the expression of a variety of genes in response to cell stimuli, and thus plays a key role in many cellular processes such as cell growth and apoptosis, as well as the growth and progression of cancer.
[0089] As used herein, the term "cold tumor" or "non-inflamed tumor" refers to a tumor or tumor microenvironment wherein there is minimal to no presence of anti-tumor immune cells, such as tumor infiltrating lymphocytes (TILs), and / or contain cell subsets associated with immune suppression including regulatory T cells (Treg), myeloid-derived suppressor cells (MDSCs) and M2 macrophages. Specifically, in some embodiments, a cold tumor is characterized by a low number or even absence of infiltration of anti-tumor immune cells that such cells may be present but remain stuck in the surrounding stroma, thus unable to colonize the tumor microenvironment to provide their antitumor functions.
[0090] As used herein, “complementary” refers to a structural relationship between two nucleotides (e.g., on two opposing nucleic acids or on opposing regions of a single nucleic acid strand) that permits the two nucleotides to form base pairs with one another. For example, a purine nucleotide of one nucleic acid that is complementary to a pyrimidine nucleotide of an opposing nucleic acid may base pair together by forming hydrogen bonds with one another. In some embodiments, complementary nucleotides can base pair in the Watson-Crick manner or in any other manner that allows for the formation of stable duplexes. In some embodiments, two nucleic acids may have regions of multiple nucleotides that are complementary with each other to form regions of complementarity, as described herein.
[0091] As used herein, “species cross-reactive oligonucleotide” refers to an oligonucleotide capable of inhibiting expression of a target mRNA in more than one species.For example, in some embodiments a species cross-reactive oligonucleotide is capable of inhibiting expression of a target mRNA in human and non-human primates. Example species include but is not limited to human, non-human primates, mouse, and rat. In some embodiments, species cross-reactive oligonucleotides are capable of targeting and inhibiting mRNA in at least two, at least three, or at least four species.
[0092] As used herein, “deoxyribonucleotide” refers to a nucleotide having a hydrogen in place of a hydroxyl at the 2′ position of its pentose sugar when compared with a ribonucleotide. A modified deoxyribonucleotide is a deoxyribonucleotide having one or more modifications or substitutions of atoms other than at the 2′ position, including modifications or substitutions in or of the sugar, phosphate group or base.
[0093] As used herein, “double-stranded RNA” or “dsRNA” refers to an RNA oligonucleotide that is substantially in a duplex form. In some embodiments, the complementary base-pairing of duplex region(s) of a dsRNA oligonucleotide is formed between antiparallel sequences of nucleotides of covalently separate nucleic acid strands. In some embodiments, complementary base-pairing of duplex region(s) of a dsRNA formed between antiparallel sequences of nucleotides of nucleic acid strands that are covalently linked. In some embodiments, complementary base-pairing of duplex region(s) of a dsRNA is formed from single nucleic acid strand that is folded (e.g., via a hairpin) to provide complementary antiparallel sequences of nucleotides that base pair together. In some embodiments, a dsRNA comprises two covalently separate nucleic acid strands that are fully duplexed with one another. However, in some embodiments, a dsRNA comprises two covalently separate nucleic acid strands that are partially duplexed (e.g., having overhangs at one or both ends). In some embodiments, a dsRNA comprises antiparallel sequence of nucleotides that are partially complementary, and thus, may have one or more mismatches, which may include internal mismatches or end mismatches.
[0094] As used herein, “duplex,” in reference to nucleic acids (e.g., oligonucleotides), refers to a structure formed through complementary base pairing of two antiparallel sequences of nucleotides.
[0095] As used herein, “excipient” refers to a non-therapeutic agent that may be included in a composition, for example, to provide or contribute to a desired consistency or stabilizing effect.
[0096] As used herein, the term "hot tumor" or "inflamed tumor" refers to a tumor or tumor microenvironment wherein there is a considerable presence of anti-tumor immune cells especially TILs and thus are typically immuno-stimulatory.
[0097] As used herein, “loop” refers to an unpaired region of a nucleic acid (e.g., oligonucleotide) that is flanked by two antiparallel regions of the nucleic acid that are sufficiently complementary to one another, such that under appropriate hybridization conditions (e.g., in a phosphate buffer, in a cells), the two antiparallel regions, which flank the unpaired region, hybridize to form a duplex (referred to as a “stem”). The loop may refer to a loop comprising four nucleotides as a tetraloop (tetraL). The loop may refer to a loop comprising three nucleotides as a triloop (triL).
[0098] As used herein, “modified internucleotide linkage” refers to an internucleotide linkage having one or more chemical modifications when compared with a reference internucleotide linkage comprising a phosphodiester bond. In some embodiments, a modified nucleotide is a non-naturally occurring linkage. Typically, a modified internucleotide linkage confers one or more desirable properties to a nucleic acid in which the modified internucleotide linkage is present. For example, a modified nucleotide may improve thermal stability, resistance to degradation, nuclease resistance, solubility, bioavailability, bioactivity, reduced immunogenicity, etc.
[0099] As used herein, “modified nucleotide” refers to a nucleotide having one or more chemical modifications when compared with a corresponding reference nucleotide selected from: adenine ribonucleotide, guanine ribonucleotide, cytosine ribonucleotide, uracil ribonucleotide, adenine deoxyribonucleotide, guanine deoxyribonucleotide, cytosine deoxyribonucleotide and thymidine deoxyribonucleotide. In some embodiments, a modified nucleotide is a non-naturally occurring nucleotide. In some embodiments, a modified nucleotide has one or more chemical modification in its sugar, nucleobase and / or phosphate group. In some embodiments, a modified nucleotide has one or more chemical moieties conjugated to a corresponding reference nucleotide. Typically, a modified nucleotide confers one or more desirable properties to a nucleic acid in which the modified nucleotide is present. For example, a modified nucleotide may improve thermal stability, resistance to degradation, nuclease resistance, solubility, bioavailability, bioactivity, reduced immunogenicity, etc.
[0100] As used herein, “nicked tetraloop structure” refers to a structure of a RNAi oligonucleotide that is characterized by separate sense (passenger) and antisense (guide) strands, in which the sense strand has a region of complementarity with the antisense strand, and in which at least one of the strands, generally the sense strand, has a tetraloop configured to stabilize an adjacent stem region formed within the at least one strand.
[0101] As used herein, “oligonucleotide” refers to a short nucleic acid (e.g., less than about 100 nucleotides in length). An oligonucleotide may be single stranded (ss) or double-stranded (ds). An oligonucleotide may or may not have duplex regions. An oligonucleotide may comprise deoxyribonucleotides, ribonucleosides, or a combination of both. In some embodiments, a double-stranded oligonucleotide comprising ribonucleotides is referred to as “dsRNA”. As a set of non-limiting examples, an oligonucleotide may be, but is not limited to, a small interfering RNA (siRNA), microRNA (miRNA), short hairpin RNA (shRNA), dicer substrate interfering RNA (dsiRNA), antisense oligonucleotide, short siRNA or ss siRNA. In some embodiments, a double-stranded RNA (dsRNA) is an RNAi oligonucleotide.
[0102] The terms “RNAi oligonucleotide conjugate” and “oligonucleotide-ligand conjugate” are used interchangeably and refer to an oligonucleotide comprising one or more nucleotides conjugated with one or more targeting ligands.
[0103] As used herein, “overhang” refers to terminal non-base pairing nucleotide(s) resulting from one strand or region extending beyond the terminus of a complementary strand with which the one strand or region forms a duplex. In some embodiments, an overhang comprises one or more unpaired nucleotides extending from a duplex region at the 5′ terminus or 3′ terminus of a dsRNA. In certain embodiments, the overhang is a 3′ or 5′ overhang on the antisense strand or sense strand of a dsRNA.
[0104] As used herein, “phosphate analog” refers to a chemical moiety that mimics the electrostatic and / or steric properties of a phosphate group. In some embodiments, a phosphate analog is positioned at the 5′ terminal nucleotide of an oligonucleotide in place of a 5′-phosphate, which is often susceptible to enzymatic removal. In some embodiments, a 5′ phosphate analog contains a phosphatase-resistant linkage. Examples of phosphate analogs include, but are not limited to, 5′ phosphonates, such as 5′ methylene phosphonate (5′-MP) and 5′-(E)-vinylphosphonate (5′-VP). In some embodiments, an oligonucleotide has a phosphate analog at a 4′-carbon position of the sugar (referred to as a “4′-phosphate analog”) at a 5′-terminal nucleotide. An example of a 4′-phosphate analog is oxymethylphosphonate, in which the oxygen atom of the oxymethyl group is bound to the sugar moiety (e.g., at its 4′- carbon) or analog thereof. See, e.g., US Provisional Patent Application Nos.62 / 383,207 (filed on 2 September 2016) and 62 / 393,401 (filed on 12 September 2016). Other modifications have been developed for the 5′ end of oligonucleotides (see, e.g., Intl. Patent Application No. WO 2011 / 133871; US Patent No.8,927,513; and Prakash et al., (2015) NUCLEIC ACIDS RES.43:2993-3011).
[0105] As used herein, “reduced expression” of a gene (e.g., STAT3) refers to a decrease in the amount or level of RNA transcript (e.g., STAT3 mRNA) or protein encoded by the gene and / or a decrease in the amount or level of activity of the gene in a cell, a population of cells,a sample, or a subject, when compared to an appropriate reference (e.g., a reference cell, population of cells, sample, or subject). For example, the act of contacting a cell with an oligonucleotide herein (e.g., an oligonucleotide comprising an antisense strand having a nucleotide sequence that is complementary to a nucleotide sequence comprising STAT3 mRNA) may result in a decrease in the amount or level of STAT3 mRNA, protein and / or activity (e.g., via degradation of STAT3 mRNA by the RNAi pathway) when compared to a cell that is not treated with the dsRNA. Similarly, and as used herein, “reducing expression” refers to an act that results in reduced expression of a gene (e.g., STAT3). As used herein, “reduction of STAT3 expression” refers to a decrease in the amount or level of STAT3 mRNA, STAT3 protein and / or STAT3 activity in a cell, a population of cells, a sample or a subject when compared to an appropriate reference (e.g., a reference cell, population of cells, sample, or subject).
[0106] As used herein, “region of complementarity” refers to a sequence of nucleotides of a nucleic acid (e.g., a dsRNA) that is sufficiently complementary to an antiparallel sequence of nucleotides to permit hybridization between the two sequences of nucleotides under appropriate hybridization conditions (e.g., in a phosphate buffer, in a cell, etc.). In some embodiments, an oligonucleotide herein comprises a targeting sequence having a region of complementary to a mRNA target sequence.
[0107] As used herein, “ribonucleotide” refers to a nucleotide having a ribose as its pentose sugar, which contains a hydroxyl group at its 2′ position. A modified ribonucleotide is a ribonucleotide having one or more modifications or substitutions of atoms other than at the 2′ position, including modifications or substitutions in or of the ribose, phosphate group or base.
[0108] As used herein, “RNAi oligonucleotide” refers to either (a) a dsRNA having a sense strand (passenger) and antisense strand (guide), in which the antisense strand or part of the antisense strand is used by the Argonaute 2 (Ago2) endonuclease in the cleavage of a target mRNA or (b) a ss oligonucleotide having a single antisense strand, where that antisense strand (or part of that antisense strand) is used by the Ago2 endonuclease in the cleavage of a target mRNA.
[0109] As used herein, “strand” refers to a single, contiguous sequence of nucleotides linked together through internucleotide linkages (e.g., phosphodiester linkages or phosphorothioate linkages). In some embodiments, a strand has two free ends (e.g., a 5′ end and a 3′ end).
[0110] As used herein, “subject” means any mammal, including mice, rabbits, non- human primates (NHP), and humans. In one embodiment, the subject is a human or NHP. Moreover, “individual” or “patient” may be used interchangeably with “subject.”
[0111] As used herein, “synthetic” refers to a nucleic acid or other molecule that is artificially synthesized (e.g., using a machine (e.g., a solid-state nucleic acid synthesizer)) or that is otherwise not derived from a natural source (e.g., a cell or organism) that normally produces the molecule.
[0112] As used herein, “targeting ligand” refers to a molecule or “moiety” (e.g., a carbohydrate, amino sugar, cholesterol, polypeptide, or lipid) that selectively binds to a cognate molecule (e.g., a receptor) of a tissue or cell of interest and / or that is conjugatable to another substance for purposes of targeting the other substance to the tissue or cell of interest. For example, in some embodiments, a targeting ligand may be conjugated to an oligonucleotide for purposes of targeting the oligonucleotide to a specific tissue or cell of interest. In some embodiments, a targeting ligand selectively binds to a cell surface receptor. Accordingly, in some embodiments, a targeting ligand when conjugated to an oligonucleotide facilitates delivery of the oligonucleotide into a particular cell through selective binding to a receptor expressed on the surface of the cell and endosomal internalization by the cell of the complex comprising the oligonucleotide, targeting ligand and receptor. In some embodiments, a targeting ligand is conjugated to an oligonucleotide via a linker that is cleaved following or during cellular internalization such that the oligonucleotide is released from the targeting ligand in the cell.
[0113] As used herein, “loop”, “triloop”, or “tetraloop” refers to a loop that increases stability of an adjacent duplex formed by hybridization of flanking sequences of nucleotides. The increase in stability is detectable as an increase in melting temperature (Tm) of an adjacent stem duplex that is higher than the Tmof the adjacent stem duplex expected, on average, from a set of loops of comparable length consisting of randomly selected sequences of nucleotides. For example, a loop (e.g., a tetraloop or triloop) can confer a Tmof at least about 50°C, at least about 55°C, at least about 56°C, at least about 58°C, at least about 60°C, at least about 65°C or at least about 75°C in 10 mM NaHPO4to a hairpin comprising a duplex of at least 2 base pairs (bp) in length. In some embodiments, a loop (e.g., a tetraloop) may stabilize a bp in an adjacent stem duplex by stacking interactions. In addition, interactions among the nucleotides in a tetraloop include, but are not limited to, non-Watson- Crick base pairing, stacking interactions, hydrogen bonding and contact interactions (Cheong et al., (1990) NATURE 346:680-82; Heus and Pardi (1991) SCIENCE 253:191-94). In someembodiments, a loop comprises or consists of 3 to 6 nucleotides and is typically 4 to 5 nucleotides. In certain embodiments, a loop comprises or consists of 3, 4, 5 or 6 nucleotides, which may or may not be modified (e.g., which may or may not be conjugated to a targeting moiety). In some embodiments, a tetraloop comprises or consists of 3 to 6 nucleotides and is typically 4 to 5 nucleotides. In certain embodiments, a tetraloop comprises or consists of 3, 4, 5 or 6 nucleotides, which may or may not be modified (e.g., which may or may not be conjugated to a targeting moiety). In one embodiment, a loop consisting of 4 nucleotides is a tetraloop. Any nucleotide may be used in the loop (e.g., a tetraloop) and standard IUPAC- IUB symbols for such nucleotides may be used as described in Cornish-Bowden ((1985) NUCLEIC ACIDS RES.13:3021-3030). For example, the letter “N” may be used to mean that any base may be in that position, the letter “R” may be used to show that A (adenine) or G (guanine) may be in that position, and “B” may be used to show that C (cytosine), G (guanine), or T (thymine) may be in that position. Examples of tetraloops include the UNCG family of tetraloops (e.g., UUCG), the GNRA family of tetraloops (e.g., GAAA), and the CUUG tetraloop (Woese et al., (1990) PROC. NATL. ACAD. SCI. USA 87:8467-71; Antao et al., (1991) NUCLEIC ACIDS RES.19:5901-05). Examples of DNA tetraloops include the d(GNNA) family of tetraloops (e.g., d(GTTA), the d(GNRA)) family of tetraloops, the d(GNAB) family of tetraloops, the d(CNNG) family of tetraloops, and the d(TNCG) family of tetraloops (e.g., d(TTCG)). (See, e.g., Nakano et al., (2002) BIOCHEM.41:4281-92; Shinji et al., (2000) NIPPON KAGAKKAI KOEN YOKOSHU 78:731). In some embodiments, the tetraloop is contained within a nicked tetraloop structure.
[0114] As used herein, “treat” or “treating” refers to the act of providing care to a subject in need thereof, for example, by administering a therapeutic agent (e.g., an oligonucleotide herein) to the subject, for purposes of improving the health and / or well-being of the subject with respect to an existing condition (e.g., a disease, disorder) or to prevent or decrease the likelihood of the occurrence of a condition. In some embodiments, treatment involves reducing the frequency or severity of at least one sign, symptom or contributing factor of a condition (e.g., disease, disorder) experienced by a subject.
[0115] As used herein, the term "tumor microenvironment" relates to the cellular environment in which any given tumor exists, including the tumor stroma, surrounding blood vessels, immune cells, fibroblasts, other cells, signaling molecules, and the ECM. It is understood that the tumor microenvironment harbors and / or surrounds the tumor cells with which it interacts.Methods of Use Combination of STAT3 Oligonucleotide and PD-L1 Inhibitors
[0116] In some embodiments, the disclosure provides STAT3 oligonucleotides for use, or adaptable for use, to treat a subject (e.g., a human having a disease, disorder or condition associated with STAT3 expression) that has received or is receiving a PD-L1 inhibitor.
[0117] In some embodiments, methods described herein comprise selecting a subject having a disease, disorder or condition associated with STAT3 expression and / or PD-L1 expression or is predisposed to the same. In some instances, the methods can include selecting an individual having a marker for a disease associated with STAT3 expression and / or PD-L1 expression such as cancer or other chronic lymphoproliferative disorders.
[0118] Likewise, and as detailed herein, the methods also may include steps such as measuring or obtaining a baseline value for a marker of STAT3 expression and / or PD-L1 expression, and then comparing such obtained value to one or more other baseline values or values obtained after being administered the oligonucleotide to assess the effectiveness of treatment.
[0119] In some embodiments, the disclosure provides methods of treating a subject having, suspected of having, or at risk of developing a disease, disorder, or condition with a STAT3 oligonucleotide herein, wherein the subject has received or is receiving a PD-L1 inhibitor. In some embodiments, the disclosure provides methods of treating a subject having, suspected of having, or at risk of developing a disease, disorder, or condition with a PD-L1 inhibitor described herein, wherein the subject has received or is receiving a STAT3 oligonucleotide described herein.
[0120] In some aspects, the disclosure provides methods of treating or attenuating the onset or progression of a disease, disorder or condition associated with STAT3 expression using a STAT3 oligonucleotide herein in combination with a PD-L1 inhibitor. In other aspects, the disclosure provides methods to achieve one or more therapeutic benefits in a subject having a disease, disorder or condition associated with STAT3 expression using a STAT3 oligonucleotide herein in combination with a PD-L1 inhibitor. In some embodiments of the methods herein, the subject is treated by administering a therapeutically effective amount of a STAT3 oligonucleotide herein in combination with a PD-L1 inhibitor. In some embodiments of the methods herein, the subject is treated by administering a therapeutically effective amount of a STAT3 oligonucleotide herein to a subject that has received or isreceiving a PD-L1 inhibitor. In some embodiments of the methods herein, the subject is treated by administering a therapeutically effective amount of a PD-L1 inhibitor to a subject that has received or is receiving a STAT3 oligonucleotide herein. In some embodiments, the subject is treated therapeutically. In some embodiments, the subject is treated prophylactically.
[0121] In some embodiments of the methods herein, one or more STAT3 oligonucleotides herein, or a pharmaceutical composition comprising one or more STAT3 oligonucleotides, is administered to a subject having a disease, disorder or condition associated with STAT3 expression that has received or is receiving a PD-L1 inhibitor, such that STAT3 expression is reduced in the subject, thereby treating the subject. In some embodiments, an amount or level of STAT3 mRNA is reduced in the subject. In some embodiments, an amount or level of STAT3 and / or protein is reduced in the subject. In some embodiments of the methods herein, one or more STAT3 oligonucleotides herein, or a pharmaceutical composition comprising one or more STAT3 oligonucleotides, is administered to a subject having a disease, disorder or condition associated with STAT3 expression that has received or is receiving a PD-L1 inhibitor such that STAT3 expression and PD-L1 signaling is reduced in the subject, thereby treating the subject. In some embodiments, an amount or level of STAT3 mRNA and PD-L1 signaling is reduced in the subject. In some embodiments, an amount or level of STAT3 and / or protein is reduced in the subject and PD-L1 signaling is reduced in the subject.
[0122] In some embodiments, a therapeutically effective amount of a STAT3 oligonucleotide and / or PD-L1 inhibitor is administered to a subject. A therapeutically acceptable amount may be an amount that can therapeutically treat a disease or disorder. The appropriate dosage for any one subject will depend on certain factors, including the subject′s size, body surface area, age, the particular composition to be administered, the active ingredient(s) in the composition, time and route of administration, general health, and other drugs being administered concurrently.
[0123] In some embodiments, a subject is administered any one of the compositions herein either enterally (e.g., orally, by gastric feeding tube, by duodenal feeding tube, via gastrostomy or rectally), parenterally (e.g., subcutaneous injection, intravenous injection or infusion, intra-arterial injection or infusion, intraosseous infusion, intramuscular injection, intracerebral injection, intracerebroventricular injection, intrathecal), topically (e.g., epicutaneous, inhalational, via eye drops, or through a mucous membrane), or by directinjection into a target organ (e.g., the liver of a subject). Typically, oligonucleotides herein are administered intravenously or subcutaneously.
[0124] As a non-limiting set of examples, the oligonucleotides herein would typically be administered quarterly (once every three months), bi-monthly (once every two months), monthly or weekly. For example, the oligonucleotides may be administered every week or at intervals of two, or three weeks. Alternatively, the oligonucleotides may be administered daily. In some embodiments, a subject is administered one or more loading doses of the oligonucleotide followed by one or more maintenance doses of the oligonucleotide.
[0125] In some embodiments, a PD-L1 inhibitor (e.g., an anti-PD-L1 antibody) herein is administered quarterly (once every three months), bi-monthly (once every two months), monthly or weekly. For example, the inhibitor is administered every week or at intervals of two, or three weeks. Alternatively, the inhibitor is administered daily.
[0126] In some embodiments the oligonucleotides herein are administered in combination with a PD-L1 inhibitor. In some embodiments the oligonucleotide and inhibitor are administered in combination concurrently, sequentially (in any order), or intermittently. For example, the oligonucleotide and inhibitor may be co-administered concurrently. Alternatively, the oligonucleotide may be administered and followed any amount of time later (e.g., one hour, one day, one week or one month) by the administration of the inhibitor, or vice versa.
[0127] In some embodiments, the subject to be treated is a human or non-human primate or other mammalian subject. Other exemplary subjects include domesticated animals such as dogs and cats; livestock such as horses, cattle, pigs, sheep, goats, and chickens; and animals such as mice, rats, guinea pigs, and hamsters. In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, thereby treating cancer in the subject.
[0128] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprisingadministering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0129] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, thereby treating cancer in the subject.
[0130] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0131] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, thereby treating cancer in the subject.
[0132] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0133] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, thereby treating cancer in the subject.
[0134] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0135] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, thereby treating cancer in the subject.
[0136] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0137] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, thereby treating cancer in the subject.
[0138] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0139] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, thereby treating cancer in the subject.
[0140] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0141] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, thereby treating cancer in the subject.
[0142] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO:37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0143] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, thereby treating cancer in the subject.
[0144] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0145] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, thereby treating cancer in the subject.
[0146] In some embodiments, the disclosure provides a method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0147] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and anantisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, thereby treating cancer in the subject.
[0148] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0149] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, thereby treating cancer in the subject.
[0150] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 9 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 10, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0151] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, thereby treating cancer in the subject.
[0152] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 37 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 38, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0153] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, thereby treating cancer in the subject.
[0154] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 65 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 66, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0155] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and anantisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, thereby treating cancer in the subject.
[0156] In some embodiments, the disclosure provides a method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 69 and antisense strand comprises the nucleotide sequence of SEQ ID NO: 70, and wherein a lipid moiety is conjugated to a nucleotide of the sense strand, thereby treating cancer in the subject.
[0157] In some embodiments, the methods of the disclosure increase expression of immune activation genes. In some embodiments, administering an RNAi oligonucleotide described herein with a PD-L1 inhibitor increases expression of immune activation genes. In some embodiments, the methods described herein increase expression of one or more of CD8B1, IL2Rα, TNFRSF9, CCL19, CCL27a, CD40Ig, CXCR5, CD44, STAT4, GZMB, PFR1, FASL, and HMGB1.
[0158] In some embodiments, the methods of the disclosures decrease expression of immuno-suppressive genes. In some embodiments, administering an RNAi oligonucleotide described herein with a PD-L1 inhibitor decreases expression of immune-suppressive genes. In some embodiments, the methods described herein decrease expression of one or more of CD274, LAG3, TIGIT, PDSD1IG2, CD163, PIK3R5, FOXP3, TGFBR2, IDO1, CD200R1, CCL22, CCL8, CCR9, IL10, IL33, CXCL3, CSF2RD, TNFRSF18, MMP9, LOX12, FGF18, and FAP. Cancers
[0159] In some embodiments, the STAT3 oligonucleotide and PD-L1 inhibitor target are used to treat a cancer or a tumor. In some embodiments, the tumor is a primary tumor. In some embodiments, the tumor is a metastatic tumor. In some embodiments, the tumor is a refractory tumor. In some embodiments, the tumor is a Stage I, Stage II, Stage III, or Stage IV tumor. In some embodiments, the tumor is a solid-tumor. Solid-tumors refer to conditions where the cancer forms a mass
[0160] In some embodiments, the cancer is a thyroid cancer, papillary thyroid carcinoma, head and neck cancer, liver cancer, colorectal cancer, pancreatic cancer, breastcancer, ovarian cancer, lung cancer, carcinoma, blastoma, medulloblastoma, retinoblastoma, sarcoma, liposarcoma, synovial cell sarcoma, neuroendocrine tumors, carcinoid tumors, gastrinoma, islet cell cancer, mesothelioma, schwannoma, acoustic neuroma, meningioma, adenocarcinoma, lymphoid malignancies, squamous cell cancer, epithelial squamous cell cancer, small-cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung, squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer, gastrointestinal cancer, glioblastoma, cervical cancer, bladder cancer, hepatoma, metastatic breast cancer, colon cancer, rectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, Merkel cell cancer, testicular cancer, esophageal cancer, or tumors of the biliary tract. In some embodiments, the cancer is refractory to anti-PD1, anti-PDL1 and / or anti-CTLA4 therapy. In some embodiments, the cancer is a pancreatic cancer or lung cancer. In some embodiments, the cancer comprises tumors with immunosuppressive tumor microenvironments. In some embodiments, the cancer is resistant to immune checkpoint therapy. In some embodiments, the cancer is partially resistant to immune checkpoint therapy. In some embodiments, the cancer is sensitive to immune checkpoint therapy.
[0161] In some embodiments, the STAT3 oligonucleotide and PD-L1 inhibitor reduces tumor volume. Tumor volume is measured using methods know to one of skill in the art. For example, extracted tumors are measured manually using calipers. Other methods include imagine methods such as ultrasound and MRI. In some embodiments, the oligonucleotide conjugate reduces tumor volume by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% compared to an untreated tumor. Oligonucleotide Inhibitors of STAT3
[0162] In some aspects, the disclosure provides, inter alia, oligonucleotides that reduce or inhibit STAT3 expression. In some embodiments, an oligonucleotide that inhibits STAT3 expression herein is targeted to a STAT3 mRNA. The sequence of human STAT3 mRNA (NM_001369512.1) is set forth as SEQ ID NO: 85 or NM_139276.3 (SEQ ID NO: 1217). STAT3 is a known target for conventional cancer therapies.
[0163] The tolerogenic activities of MDSCs are controlled by an oncogenic transcription factor, signal transducer and activator of transcription 3 (STAT3) (Su et al., INT J. MOL SCI (2018) 19(6): 1803). STAT3 is also known to be highly expressed across a rangeof cancer types and in in vitro and in vivo preclinical models (Huynh et al., NAT. REV. CANCER (2019) 19: 82-96). The inhibition of STAT3 leads to the selective apoptosis of tumor cells and tumor growth inhibition through modulation of downstream target genes (Wang et al., INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES, 15(3): 668–79 (2019)). STAT3 is of particular interest in immuno-oncology due to its well documented contributions to an immunosuppressive tumor microenvironment. STAT3 contributes to an immunosuppressive tumor microenvironment by upregulating the inhibitory receptor expressed by T-cells, and via expression of its ligand (PD-1 / PD-L1), through increased secretion of IFNɣ (Bu et al., JOURNAL OF DENTAL RESEARCH, 96(9): 1027–34 (2017)). It has long been known that inhibition of STAT3 signaling in antigen presenting cells (APCs) results in priming of antigen-specific CD4+ T cells in response to otherwise tolerogenic stimuli (Cheng et al., IMMUNITY, 19: 425–36 (2003)). In addition, phosphorylated STAT3 on MDSCs directly contributes to the modulation of the suppressive tumor microenvironment by regulating suppressive components such as the amino acid arginine, through transcriptional control (Vasques-Dunndel et al., J. CLIN. INVEST., 15(3): 668–79 (2013)). Over the years several methodologies have been explored to therapeutically target STAT3. While direct targeting of the protein is attractive, the true target is a protein-protein interaction that has been held up as an example of an ‘undruggable’ target due historical data showing that multiple classes of compounds have failed to effectively inhibit its activity (Lau et al., CANCERS (2019) 11(11): 1681, Zou et al., MOL CANCER (2020) 19: 145). In addition, ubiquitous expression of STAT3 across several tissues have led to concerns about severe on-target toxicities (Wong et al., EXPERT OPINION ON INVESTIGATIONAL DRUGS, 26 (8):883-87 (2017), (Kortylewski et al., CANCER IMMUNOL IMMUNOTHER (2017) 66(8): 979-88).
[0164] In some embodiments, reduction of STAT3 expression can be determined by an appropriate assay or technique to evaluate one or more properties or characteristics of a cell or population of cells associated with STAT3 expression (e.g., using an STAT3 expression biomarker) or by an assay or technique that evaluates molecules that are directly indicative of STAT3 expression (e.g., STAT3 mRNA or STAT3 protein). In some embodiments, the extent to which an oligonucleotide herein reduces STAT3 expression is evaluated by comparing STAT3 expression in a cell or population of cells contacted with the oligonucleotide to an appropriate control (e.g., an appropriate cell or population of cells not contacted with the oligonucleotide or contacted with a control oligonucleotide). In some embodiments, an appropriate control level of mRNA expression into protein, after delivery of a RNAi molecule may be a predetermined level or value, such that a control level need not bemeasured every time. The predetermined level or value can take a variety of forms. In some embodiments, a predetermined level or value can be single cut-off value, such as a median or mean.
[0165] In some embodiments, administration of an oligonucleotide herein results in a reduction in STAT3 expression in a cell or population of cells. In some embodiments, the reduction in STAT3 or STAT3 expression is about 1% or lower, about 5% or lower, about 10% or lower, about 15% or lower, about 20% or lower, about 25% or lower, about 30% or lower, about 35% or lower, about 40% or lower, about 45% or lower, about 50% or lower, about 55% or lower, about 60% or lower, about 70% or lower, about 80% or lower, or about 90% or lower when compared with an appropriate control level of mRNA. The appropriate control level may be a level of mRNA expression and / or protein translation in a cell or population of cells that has not been contacted with an oligonucleotide herein. In some embodiments, the effect of delivery of an oligonucleotide to a cell according to a method herein is assessed after a finite period. For example, levels of mRNA may be analyzed in a cell at least about 8 hours, about 12 hours, about 18 hours, about 24 hours; or at least about 1, 2, 3, 4, 5, 6, 7 or even up to 14 days after introduction of the oligonucleotide into the cell.
[0166] In some embodiments, an oligonucleotide is delivered in the form of a transgene that is engineered to express in a cell the oligonucleotide or strands comprising the oligonucleotide (e.g., its sense and antisense strands). In some embodiments, an oligonucleotide is delivered using a transgene engineered to express any oligonucleotide disclosed herein. Transgenes may be delivered using viral vectors (e.g., adenovirus, retrovirus, vaccinia virus, poxvirus, adeno-associated virus, or herpes simplex virus) or non- viral vectors (e.g., plasmids or synthetic mRNAs). In some embodiments, transgenes can be injected directly to a subject. STAT3 Target Sequences
[0167] In some embodiments, the oligonucleotide is targeted to a target sequence comprising a STAT3 mRNA. In some embodiments, the oligonucleotide, or a portion, fragment, or strand thereof (e.g., an antisense strand or a guide strand of a dsRNA) binds or anneals to a target sequence comprising a STAT3 mRNA, thereby inhibiting STAT3 expression. In some embodiments, the oligonucleotide is targeted to a STAT3 target sequence for the purpose of inhibiting STAT3 expression in vivo. In some embodiments, the amount or extent of inhibition of STAT3 expression by an oligonucleotide targeted to a STAT3 target sequence correlates with the potency of the oligonucleotide. In some embodiments, theamount or extent of inhibition of STAT3 expression by an oligonucleotide targeted to a STAT3 target sequence correlates with the amount or extent of therapeutic benefit in a subject or patient having a disease, disorder or condition associated with the expression of STAT3 treated with the oligonucleotide.
[0168] Through examination of the nucleotide sequence of mRNAs encoding STAT3, including mRNAs of multiple different species (e.g., human, cynomolgus monkey, mouse, and rat; see, e.g., Example 6) and as a result of in vitro and in vivo testing (see, e.g., Example 7 and Example 8), it has been discovered that certain nucleotide sequences of STAT3 mRNA are more amenable than others to oligonucleotide-based inhibition and are thus useful as target sequences for the oligonucleotides herein. In some embodiments, a sense strand of an oligonucleotide (e.g., a dsRNA) described herein comprises a STAT3 target sequence. In some embodiments, a portion or region of the sense strand of a dsRNA described herein comprises a STAT3 target sequence. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, a sequence of SEQ ID NO 85. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, a sequence of SEQ ID NO: 1217. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, a sequence of any one of SEQ ID NOs: 89-280. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, the sequence set forth in SEQ ID NO: 108. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, the sequence set forth in SEQ ID NO: 140. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, the sequence set forth in SEQ ID NO: 141. In some embodiments, a STAT3 mRNA target sequence comprises, or consists of, the sequence set forth in SEQ ID NO: 147. STAT3 Targeting Sequences
[0169] In some embodiments, the oligonucleotides herein have regions of complementarity to STAT3 mRNA (e.g., within a target sequence of STAT3 mRNA) for purposes of targeting the mRNA in cells and reducing or inhibiting its expression. In some embodiments, the oligonucleotides herein comprise a STAT3 targeting sequence (e.g., an antisense strand or a guide strand of a dsRNA) having a region of complementarity that binds or anneals to a STAT3 target sequence by complementary (Watson-Crick) base pairing. The targeting sequence or region of complementarity is generally of a suitable length and base content to enable binding or annealing of the oligonucleotide (or a strand thereof) to a STAT3 mRNA for purposes of inhibiting its expression. In some embodiments, the targeting sequence or region of complementarity is at least about 12, at least about 13, at least about14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 26, at least about 27, at least about 28, at least about 29 or at least about 30 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is about 12 to about 30 (e.g., 12 to 30, 12 to 22, 15 to 25, 17 to 21, 18 to 27, 19 to 27, or 15 to 30) nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 18 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 19 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 20 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 21 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 22 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 23 nucleotides in length. In some embodiments, the targeting sequence or region of complementarity is 24 nucleotides in length. In some embodiments, an oligonucleotide comprises a target sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 89-280 , and the targeting sequence or region of complementarity is 18 nucleotides in length. In some embodiments, an oligonucleotide comprises a target sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 89-280, and the targeting sequence or region of complementarity is 19 nucleotides in length. In some embodiments, an oligonucleotide comprises a target sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 473-664, and the targeting sequence or region of complementarity is 20 nucleotides in length. In some embodiments, an oligonucleotide comprises a targeting sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 473-664, and the targeting sequence or region of complementarity is 21 nucleotides in length. In some embodiments, an oligonucleotide comprises a targeting sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 473-664, and the targeting sequence or region of complementarity is 22 nucleotides in length. In some embodiments, an oligonucleotide comprises a targeting sequence or region of complementarity complementary to a sequence of any one of SEQ ID NOs: 473-664, and the targeting sequence or region of complementarity is 23 nucleotides in length. In some embodiments, an oligonucleotide comprises a targeting sequence or region ofcomplementarity complementary to a sequence of any one of SEQ ID NOs: 473-664 and the targeting sequence or region of complementarity is 24 nucleotides in length.
[0170] In some embodiments, an oligonucleotide herein comprises a targeting sequence or a region of complementarity (e.g., an antisense strand or a guide strand of a double-stranded oligonucleotide) that is fully complementary to a STAT3 target sequence. In some embodiments, the targeting sequence or region of complementarity is partially complementary to a STAT3 target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is fully complementary to a sequence of STAT3 or STAT3. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is partially complementary to a sequence of STAT3 or STAT3.
[0171] In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is fully complementary to a sequence of any one of SEQ ID NOs: 89-280. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is fully complementary to the sequence set forth in SEQ ID NOs: 108, 140, 141, and 147. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is partially complementary to a sequence of any one of SEQ ID NOs: 89-280. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is partially complementary to the sequence set forth in SEQ ID NOs: 108, 140, 141, and 147.
[0172] In some embodiments, the oligonucleotide herein comprises a targeting sequence or region of complementarity that is complementary to a contiguous sequence of nucleotides comprising a STAT3 mRNA, wherein the contiguous sequence of nucleotides is about 12 to about 30 nucleotides in length (e.g., 12 to 30, 12 to 28, 12 to 26, 12 to 24, 12 to 20, 12 to 18, 12 to 16, 14 to 22, 16 to 20, 18 to 20 or 18 to 19 nucleotides in length). In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is complementary to a contiguous sequence of nucleotides comprising a STAT3 mRNA, wherein the contiguous sequence of nucleotides is 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 nucleotides in length. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity that is complementary to a contiguous sequence of nucleotides comprising a STAT3 mRNA, wherein the contiguous sequence of nucleotides is 19 nucleotides in length.
[0173] In some embodiments, an oligonucleotide herein (e.g., an RNAi oligonucleotide) comprises a targeting sequence or a region of complementary that iscomplementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280, optionally wherein the contiguous sequence of nucleotides is 19 nucleotides in length. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 108, 140, 141, and 147, wherein the contiguous sequence of nucleotides is 19 nucleotides in length. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 473-664, wherein the contiguous sequence of nucleotides is 20 nucleotides in length. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 492, 524, 525, and 531, wherein the contiguous sequence of nucleotides is 20 nucleotides in length.
[0174] In some embodiments, a targeting sequence or region of complementarity of an oligonucleotide that is complementary to contiguous nucleotides of STAT3 or STAT3 target sequence spans the entire length of an antisense strand. In some embodiments, a region of complementarity of an oligonucleotide that is complementary to contiguous nucleotides of STAT3 or STAT3 target sequence spans a portion of the entire length of an antisense strand. In some embodiments, an oligonucleotide herein comprises a region of complementarity (e.g., on an antisense strand of a dsRNA) that is at least partially (e.g., fully) complementary to a contiguous stretch of nucleotides spanning nucleotides 1-20 of a target sequence of STAT3 or STAT3.
[0175] In some embodiments, a targeting sequence or region of complementarity of an oligonucleotide herein (e.g., an RNAi oligonucleotide) is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280 and spans the entire length of an antisense strand. In some embodiments, a targeting sequence or region of complementarity of the oligonucleotide is complementary to a contiguous sequence of nucleotides of SEQ ID NOs: 89-280 and spans a portion of the entire length of an antisense strand. In some embodiments, an oligonucleotide herein (e.g., an RNAi oligonucleotide) comprises a region of complementarity (e.g., on an antisense strand of a dsRNA) that is at least partially (e.g., fully) complementary to a contiguous stretch of nucleotides spanning nucleotides 1-19 or 1- 20 of a sequence as set forth in any one of SEQ ID NOs: 473-664.
[0176] In some embodiments, an oligonucleotide herein comprises a targeting sequence or region of complementarity having one or more bp mismatches with the corresponding STAT3 target sequence. In some embodiments, the targeting sequence orregion of complementarity may have up to about 1, up to about 2, up to about 3, up to about 4, up to about 5, etc. mismatches with the corresponding STAT3 target sequence provided that the ability of the targeting sequence or region of complementarity to bind or anneal to the STAT3 mRNA under appropriate hybridization conditions and / or the ability of the oligonucleotide to inhibit STAT3 expression is maintained. Alternatively, the targeting sequence or region of complementarity may have no more than 1, no more than 2, no more than 3, no more than 4, or no more than 5 mismatches with the corresponding STAT3 target sequence provided that the ability of the targeting sequence or region of complementarity to bind or anneal to the STAT3 mRNA under appropriate hybridization conditions and / or the ability of the oligonucleotide to inhibit STAT3 expression is maintained. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity having 1 mismatch with the corresponding target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity having 2 mismatches with the corresponding target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity having 3 mismatches with the corresponding target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity having 4 mismatches with the corresponding target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity having 5 mismatches with the corresponding target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or region of complementarity more than one mismatch (e.g., 2, 3, 4, 5 or more mismatches) with the corresponding target sequence, wherein at least 2 (e.g., all) of the mismatches are positioned consecutively (e.g., 2, 3, 4, 5 or more mismatches in a row), or where in the mismatches are interspersed throughout the targeting sequence or region of complementarity. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280, wherein the targeting sequence or region of complementarity may have up to about 1, up to about 2, up to about 3, up to about 4, up to about 5, etc. mismatches with the corresponding STAT3 target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280, wherein the targeting sequence or region of complementarity may have no more than 1, no more than 2, no more than 3, no more than 4, or no more than 5 mismatches with the corresponding STAT3target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 108, 140, 141, and 147, wherein the targeting sequence or region of complementarity may have up to about 1, up to about 2, up to about 3, up to about 4, up to about 5, etc. mismatches with the corresponding STAT3 target sequence. In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 108, 140, 141, and 147, wherein the targeting sequence or region of complementarity may have no more than 1, no more than 2, no more than 3, no more than 4, or no more than 5 mismatches with the corresponding STAT3 target sequence. Types of Oligonucleotides
[0177] A variety of oligonucleotide types and / or structures are useful for targeting a target sequence in the methods herein including, but not limited to, RNAi oligonucleotides, antisense oligonucleotides, miRNAs, etc. Any of the oligonucleotide types described herein or elsewhere are contemplated for use as a framework to incorporate a targeting sequence herein.
[0178] In some embodiments, the oligonucleotides herein inhibit expression of a target sequence by engaging with RNA interference (RNAi) pathways upstream or downstream of Dicer involvement. For example, RNAi oligonucleotides have been developed with each strand having sizes of about 19-25 nucleotides with at least one 3′ overhang of 1 to 5 nucleotides (see, e.g., US Patent No.8,372,968). Longer oligonucleotides also have been developed that are processed by Dicer to generate active RNAi products (see, e.g., US Patent No.8,883,996). Further work produced extended dsRNAs where at least one end of at least one strand is extended beyond a duplex targeting region, including structures where one of the strands includes a thermodynamically-stabilizing tetraloop structure (see, e.g., US Patent Nos.8,513,207 and 8,927,705, as well as Intl. Patent Application Publication No. WO 2010 / 033225). Such structures may include ss extensions (on one or both sides of the molecule) as well as ds extensions.
[0179] In some embodiments, the oligonucleotides herein engage with the RNAi pathway downstream of the involvement of Dicer (e.g., Dicer cleavage). In some embodiments, the oligonucleotides described herein are Dicer substrates. In some embodiments, upon endogenous Dicer processing, double-stranded nucleic acids of 19-23 nucleotide sin length capable of reducing target mRNA expression are produced. In someembodiments, the oligonucleotide has an overhang (e.g., of 1, 2, or 3 nucleotides in length) in the 3′ end of the sense strand. In some embodiments, the oligonucleotide (e.g., siRNA) comprises a 21-nucleotide guide strand that is antisense to a target RNA and a complementary passenger strand, in which both strands anneal to form a 19-bp duplex and 2 nucleotide overhangs at either or both 3′ ends. Longer oligonucleotide designs also are available including oligonucleotides having a guide strand of 23 nucleotides and a passenger strand of 21 nucleotides, where there is a blunt end on the right side of the molecule (3′ end of passenger strand / 5′ end of guide strand) and a two nucleotide 3′-guide strand overhang on the left side of the molecule (5′ end of the passenger strand / 3′ end of the guide strand). In such molecules, there is a 21 bp duplex region. See, e.g., US Patent Nos.9,012,138; 9,012,621 and 9,193,753.
[0180] In some embodiments, the oligonucleotides herein comprise sense and antisense strands that are both in the range of about 17 to 26 (e.g., 17 to 26, 20 to 25 or 21- 23) nucleotides in length. In some embodiments, the oligonucleotides herein comprise sense and antisense strands that are both in the range of about 17 to 36 (e.g., 17 to 36, 20 to 25 or 21-23) nucleotides in length. In some embodiments, the oligonucleotides described herein comprise an antisense strand of 19-30 nucleotides in length and a sense strand of 19-50 nucleotides in length, wherein the antisense and sense strands are separate strands which form an asymmetric duplex region having an overhand of 1-4 nucleotides at the 3’ terminus of the antisense strand. In some embodiments, an oligonucleotide herein comprises a sense and antisense strand that are both in the range of about 19-22 nucleotides in length. In some embodiments, the sense and antisense strands are of equal length. In some embodiments, an oligonucleotide comprises sense and antisense strands, such that there is a 3′-overhang on either the sense strand or the antisense strand, or both the sense and antisense strand. In some embodiments, for oligonucleotides that have sense and antisense strands that are both in the range of about 21-23 nucleotides in length, a 3′ overhang on the sense, antisense, or both sense and antisense strands is 1 or 2 nucleotides in length. In some embodiments, the oligonucleotide has a guide strand of 22 nucleotides and a passenger strand of 20 nucleotides, where there is a blunt end on the right side of the molecule (3′ end of passenger strand / 5′ end of guide strand) and a 2 nucleotide 3′-guide strand overhang on the left side of the molecule (5′ end of the passenger strand / 3′ end of the guide strand). In such molecules, there is a 20 bp duplex region.
[0181] Other oligonucleotide designs for use with the compositions and methods herein include: 16-mer siRNAs (see, e.g., NUCLEIC ACIDS IN CHEMISTRY ANDBIOLOGY. Blackburn (ed.), Royal Society of Chemistry, 2006), shRNAs (e.g., having 19 bp or shorter stems; (see, e.g., Moore et al., (2010) METHODS MOL. BIOL.629:141-58), blunt siRNAs (e.g., of 19 bps in length; see, e.g., Kraynack and Baker (2006) RNA 12:163-76), asymmetrical siRNAs (aiRNA; see, e.g., Sun et al., (2008) NAT. BIOTECHNOL.26:1379-82), asymmetric shorter-duplex siRNA (see, e.g., Chang et al., (2009) MOL. THER.17:725-32), fork siRNAs (see, e.g., Hohjoh (2004) FEBS LETT.557:193-98), ss siRNAs (Elsner (2012) NAT. BIOTECHNOL.30:1063), dumbbell-shaped circular siRNAs (see, e.g., Abe et al., (2007) J. AM. CHEM. SOC.129:15108-09), and small internally segmented interfering RNA (siRNA; see, e.g., Bramsen et al., (2007) NUCLEIC ACIDS RES.35:5886-97). Further non-limiting examples of an oligonucleotide structures that may be used in some embodiments to reduce or inhibit the expression of STAT3 are microRNA (miRNA), short hairpin RNA (shRNA) and short siRNA (see, e.g., Hamilton et al., (2002) EMBO J.21:4671-79; see also, US Patent Application Publication No.2009 / 0099115).
[0182] Still, in some embodiments, an oligonucleotide for reducing or inhibiting expression of a target sequence herein is ss. Such structures may include but are not limited to ss RNAi molecules. Recent efforts have demonstrated the activity of ss RNAi molecules (see, e.g., Matsui et al., (2016) MOL. THER.24:946-55). However, in some embodiments, oligonucleotides herein are antisense oligonucleotides (ASOs). An antisense oligonucleotide is a ss oligonucleotide that has a nucleobase sequence which, when written in the 5′ to 3′ direction, comprises the reverse complement of a targeted segment of a particular nucleic acid and is suitably modified (e.g., as a gapmer) to induce RNaseH-mediated cleavage of its target RNA in cells or (e.g., as a mixmer) to inhibit translation of the target mRNA in cells. ASOs for use herein may be modified in any suitable manner known in the art including, for example, as shown in US Patent No.9,567,587 (including, e.g., length, sugar moieties of the nucleobase (pyrimidine, purine), and alterations of the heterocyclic portion of the nucleobase). Further, ASOs have been used for decades to reduce expression of specific target genes (see, e.g., Bennett et al., (2017) ANNU. REV. PHARMACOL.57:81-105).
[0183] In some embodiments, the antisense oligonucleotide shares a region of complementarity with a target mRNA. In some embodiments, the antisense oligonucleotide is 15-50 nucleotides in length. In some embodiments, the antisense oligonucleotide is 15-25 nucleotides in length. In some embodiments, the antisense oligonucleotide is 22 nucleotides in length. In some embodiments, the antisense oligonucleotide is at least 15 contiguous nucleotides in length. In some embodiments, the antisense oligonucleotide is at least 19 contiguous nucleotides in length. In some embodiments, the antisense oligonucleotide is atleast 20 contiguous nucleotides in length. In some embodiments, the antisense oligonucleotide differs by 1, 2, or 3 nucleotides from the target sequence. Double-Stranded Oligonucleotides
[0184] In some embodiments, the disclosure provides double-stranded dsRNAs for targeting and inhibiting expression of a target sequence (e.g., via the RNAi pathway) comprising a sense strand (also referred to herein as a passenger strand) and an antisense strand (also referred to herein as a guide strand). In some embodiments, the sense strand and antisense strand are separate strands and are not covalently linked. In some embodiments, the sense strand and antisense strand are covalently linked. In some embodiments, the sense strand and antisense strand form a duplex region, wherein the sense strand and antisense strand, or a portion thereof, binds with one another in a complementary fashion (e.g., by Watson-Crick base pairing).
[0185] In some embodiments, the sense strand has a first region (R1) and a second region (R2), wherein R2 comprises a first subregion (S1), a loop (L), such as a tetraloop (tetraL) or triloop (triL), and a second subregion (S2), wherein L, tetraL, or triL is located between S1 and S2, and wherein S1 and S2 form a second duplex (D2). D2 may have various length. In some embodiments, D2 is about 1-6 bp in length. In some embodiments, D2 is 2-6, 3-6, 4-6, 5-6, 1-5, 2-5, 3-5 or 4-5 bp in length. In some embodiments, D2 is 1, 2, 3, 4, 5 or 6 bp in length. In some embodiments, D2 is 6 bp in length.
[0186] In some embodiments, R1 of the sense strand and the antisense strand form a first duplex (D1). In some embodiments, D1 is at least about 15 (e.g., at least 15, at least 16, at least 17, at least 18, at least 19, at least 20 or at least 21) nucleotides in length. In some embodiments, D1 is in the range of about 12 to 30 nucleotides in length (e.g., 12 to 30, 12 to 27, 15 to 22, 18 to 22, 18 to 25, 18 to 27, 18 to 30 or 21 to 30 nucleotides in length). In some embodiments, D1 is at least 12 nucleotides in length (e.g., at least 12, at least 15, at least 20, at least 25, or at least 30 nucleotides in length). In some embodiments, D1 is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length. In some embodiments, D1 is 20 nucleotides in length. In some embodiments, D1 comprising sense strand and antisense strand does not span the entire length of the sense strand and / or antisense strand. In some embodiments, D1 comprising the sense strand and antisense strand spans the entire length of either the sense strand or antisense strand or both. In certain embodiments, D1 comprising the sense strand and antisense strand spans the entire length of both the sense strand and the antisense strand.
[0187] It should be appreciated that, in some embodiments, sequences presented in the Sequence Listing may be referred to in describing the structure of an oligonucleotide or other nucleic acid. In such embodiments, the actual oligonucleotide or other nucleic acid may have one or more alternative nucleotides (e.g., an RNA counterpart of a DNA nucleotide or a DNA counterpart of an RNA nucleotide) and / or one or more modified nucleotides and / or one or more modified internucleotide linkages and / or one or more other modification when compared with the specified sequence while retaining essentially same or similar complementary properties as the specified sequence.
[0188] In some embodiments, a double-stranded RNA (dsRNA) herein comprises a 25-nucleotide sense strand and a 27-nucleotide antisense strand that when acted upon by a Dicer enzyme results in an antisense strand that is incorporated into the mature RISC. In some embodiments, the sense strand of the dsRNA is longer than 27 nucleotides (e.g., 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides). In some embodiments, the sense strand of the dsRNA is longer than 27 nucleotides (e.g., 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides). In some embodiments, the sense strand of the dsRNA is longer than 25 nucleotides (e.g., 26, 27, 28, 29 or 30 nucleotides).
[0189] In some embodiments, oligonucleotides herein have one 5′ end that is thermodynamically less stable when compared to the other 5′ end. In some embodiments, an asymmetry oligonucleotide is provided that includes a blunt end at the 3′ end of a sense strand and a 3′-overhang at the 3′ end of an antisense strand. In some embodiments, the 3′- overhang on the antisense strand is about 1-8 nucleotides in length (e.g., 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides in length). Typically, an oligonucleotide for RNAi has a two-nucleotide overhang on the 3′ end of the antisense (guide) strand. However, other overhangs are possible. In some embodiments, an overhang is a 3′-overhang comprising a length of between 1 and 6 nucleotides, optionally 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 6, 3 to 5, 3 to 4, 4 to 6, 4 to 5, 5 to 6 nucleotides, or 1, 2, 3, 4, 5 or 6 nucleotides. However, in some embodiments, the overhang is a 5′-overhang comprising a length of between 1 and 6 nucleotides, optionally 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 6, 3 to 5, 3 to 4, 4 to 6, 4 to 5, 5 to 6 nucleotides, or 1, 2, 3, 4, 5 or 6 nucleotides.
[0190] In some embodiments, two terminal nucleotides on the 3′ end of an antisense strand are modified. In some embodiments, the two terminal nucleotides on the 3′ end of the antisense strand are complementary with the target mRNA. In some embodiments, the two terminal nucleotides on the 3′ end of the antisense strand are not complementary with thetarget mRNA. In some embodiments, the two terminal nucleotides on the 3′ end of the antisense strand of an oligonucleotide herein comprise an unpaired GG. In some embodiments, the two (2) terminal nucleotides on the 3′ end of an antisense strand of an oligonucleotide herein are not complementary to the target mRNA. In some embodiments, two terminal nucleotides on each 3′ end of an oligonucleotide in the nicked tetraloop structure are GG. In some embodiments, one or both of the two (2) terminal GG nucleotides on each 3′ end of an oligonucleotide herein is not complementary with the target mRNA. Typically, one or both two terminal GG nucleotides on each 3′ end of an oligonucleotide is not complementary with the target.
[0191] In some embodiments, there is one or more (e.g., 1, 2, 3, 4 or 5) mismatch between a sense and antisense strand. If there is more than one mismatch between a sense and antisense strand, they may be positioned consecutively (e.g., 2, 3 or more in a row), or interspersed throughout the region of complementarity. In some embodiments, the 3′ end of the sense strand contains one or more mismatches. In one embodiment, two mismatches are incorporated at the 3′ end of the sense strand. In some embodiments, base mismatches, or destabilization of segments at the 3′ end of the sense strand of the oligonucleotide improved the potency of synthetic duplexes in RNAi, possibly through facilitating processing by Dicer. a. Antisense Strands
[0192] In some embodiments, a dsRNA comprises an antisense strand of up to about 40 nucleotides in length (e.g., up to 40, up to 35, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17 or up to 12 nucleotides in length). In some embodiments, an oligonucleotide herein (e.g., an RNAi oligonucleotide) comprises an antisense strand of up to about 50 nucleotides in length (e.g., up to 50, up to 40, up to 35, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17 or up to 12 nucleotides in length). In some embodiments, an oligonucleotide may have an antisense strand of at least about 12 nucleotides in length (e.g., at least 12, at least 15, at least 19, at least 21, at least 22, at least 25, at least 27, at least 30, at least 35 or at least 38 nucleotides in length). In some embodiments, an oligonucleotide may have an antisense strand in a range of about 12 to about 40 (e.g., 12 to 40, 12 to 36, 12 to 32, 12 to 28, 15 to 40, 15 to 36, 15 to 32, 15 to 28, 17 to 22, 17 to 25, 19 to 27, 19 to 30, 20 to 40, 22 to 40, 25 to 40 or 32 to 40) nucleotides in length. In some embodiments, an oligonucleotide comprises antisense strand of 15 to 30 nucleotides in length. In some embodiments, an oligonucleotide may have an antisense strand of 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides in length.
[0193] In some embodiments, an antisense strand of an oligonucleotide may be referred to as a “guide strand.” For example, if an antisense strand can engage with RNA- induced silencing complex (RISC) and bind to an Argonaute protein such as Ago2, or engage with or bind to one or more similar factors, and direct silencing of a target gene, it may be referred to as a guide strand. In some embodiments, a sense strand complementary to a guide strand may be referred to as a “passenger strand.”
[0194] In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 281-472. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 281-472. In some embodiments, an oligonucleotide disclosed herein (e.g., an RNAi oligonucleotide) for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 665-856. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 665-856. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 947-1036. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 947-1036. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 10, 38, 66, and 70. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 10, 38, 66, and 70. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strandcomprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 281-472. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 281-472. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 952, 965, 966, and 1010. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 952, 965, 966, and 1010. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 991, 1000, 989, 986, 982, 980, and 979. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 991, 1000, 989, 986, 982, 980, and 979. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 1030, 1027, and 1029. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 1030, 1027, and 1029. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 1005, 1014, 1003, and 1010. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 1005, 1014, 1003, and 1010.
[0195] b. Sense Strands
[0196] In some embodiments, an oligonucleotide disclosed herein (e.g., and RNAi oligonucleotide) for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence as set forth in in any one of SEQ ID NOs: 89-280. In some embodiments, an oligonucleotide herein has a sense strand that comprise at least about 12 (e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in in any one of SEQ ID NOs: 89-280. In some embodiments, an oligonucleotide disclosed herein (e.g., an RNAi oligonucleotide) for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence a set forth in any one of SEQ ID NOs: 473- 664. In some embodiments, an oligonucleotide herein has a sense strand that comprise at least about 12 (e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in in any one of SEQ ID NOs: 473-664. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence as set forth in any one of SEQ ID NOs: 857-946. In some embodiments, an oligonucleotide herein has a sense strand comprised of least about 12 (e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 857-946. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence as set forth in any one of SEQ ID NOs: 9, 37, 65, and 69. In some embodiments, an oligonucleotide herein has a sense strand comprised of least about 12 (e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 9, 37, 65, and 69. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence as set forth in any one of SEQ ID NOs: 862, 875, 876, and 920. In some embodiments, an oligonucleotide herein has a sense strand that comprise at least about 12 (e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 862, 875, 876, and 920. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 mRNA and inhibiting STAT3 expression comprises a sense strand sequence as set forth in any one of SEQ ID NOs: 901, 910, 899, 896, 892, 890, and 889. In some embodiments, an oligonucleotide herein has a sense strand that comprise at least about 12(e.g., at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 901, 910, 899, 896, 892, 890, and 889. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 940, 937, and 939. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 940, 937, and 939. In some embodiments, an oligonucleotide disclosed herein for targeting STAT3 comprises an antisense strand comprising or consisting of a sequence as set forth in any one of SEQ ID NOs: 915, 924, 913, and 920. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising at least about 12 (e.g., at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22 or at least 23) contiguous nucleotides of a sequence as set forth in any one of SEQ ID NOs: 915, 924, 913, and 920.
[0197] In some embodiments, an oligonucleotide comprises a sense strand (or passenger strand) of up to about 40 nucleotides in length (e.g., up to 40, up to 36, up to 30, up to 27, up to 25, up to 21, up to 19, up to 17 or up to 12 nucleotides in length). In some embodiments, an oligonucleotide may have a sense strand of at least about 12 nucleotides in length (e.g., at least 12, at least 15, at least 19, at least 21, at least 25, at least 27, at least 30, at least 36 or at least 38 nucleotides in length). In some embodiments, an oligonucleotide may have a sense strand in a range of about 12 to about 40 (e.g., 12 to 40, 12 to 36, 12 to 32, 12 to 28, 15 to 40, 15 to 36, 15 to 32, 15 to 28, 17 to 21, 17 to 25, 19 to 27, 19 to 30, 20 to 40, 22 to 40, 25 to 40 or 32 to 40) nucleotides in length. In some embodiments, an oligonucleotide herein comprises a sense strand of 15 to 50 nucleotides in length. In some embodiments, an oligonucleotide herein comprises a sense strand of 18 to 36 nucleotides in length. In some embodiments, an oligonucleotide may have a sense strand of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides in length. In some embodiments, an oligonucleotide comprises a sense strand of 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length. In some embodiments, an oligonucleotide herein comprises a sense strand of 36 nucleotides in length.
[0198] In some embodiments, an oligonucleotide provided herein (e.g., an RNAi oligonucleotide) comprises a sense strand comprising a stem-loop structure at the 3′ end of the sense strand. In some embodiments, the stem-loop is formed by intrastrand base pairing. In some embodiments, a sense strand comprises a stem-loop structure at its 5′ end. In some embodiments, the stem of the stem-loop comprises a duplex of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 2 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 3 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 4 nucleotides in length. In some embodiments, the stem of the stem- loop comprises a duplex of 5 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 6 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 7 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 8 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 9 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 10 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 11 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 12 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 13 nucleotides in length. In some embodiments, the stem of the stem-loop comprises a duplex of 14 nucleotides in length.
[0199] In some embodiments, a stem-loop provides the oligonucleotide protection against degradation (e.g., enzymatic degradation), facilitates or improves targeting and / or delivery to a target cell, tissue, or organ (e.g., the liver), or both. For example, in some embodiments, the loop of a stem-loop is comprised of nucleotides comprising one or more modifications that facilitate, improve, or increase targeting to a target, inhibition of target gene expression, and / or delivery, uptake, and / or penetrance into a target cell, tissue, or organ (e.g., the liver), or a combination thereof. In some embodiments, the stem-loop itself or modification(s) to the stem-loop do not affect or do not substantially affect the inherent gene expression inhibition activity of the oligonucleotide, but facilitates, improves, or increases stability (e.g., provides protection against degradation) and / or delivery, uptake, and / or penetrance of the oligonucleotide to a target cell, tissue, or organ. In certain embodiments, an oligonucleotide herein comprises a sense strand comprising (e.g., at its 3′ end) a stem-loop set forth as: S1-L-S2, in which S1 is complementary to S2, and in which L forms a single- stranded loop of linked nucleotides between S1 and S2 of up to about 10 nucleotides in length(e.g., 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in length). In some embodiments, the loop (L) is 3 nucleotides in length (referred to herein as “triloop”. In some embodiments, the loop (L) is 4 nucleotides in length (referred to herein as “tetraloop”). In some embodiments, the loop (L) is 5 nucleotides in length. In some embodiments, the loop (L) is 6 nucleotides in length. In some embodiments, the loop (L) is 7 nucleotides in length. In some embodiments, the loop (L) is 8 nucleotides in length. In some embodiments, the loop (L) is 9 nucleotides in length. In some embodiments, the loop (L) is 10 nucleotides in length.
[0200] In some embodiments, an oligonucleotide provided herein (e.g., an RNAi oligonucleotide) comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280, and the oligonucleotide comprises a sense strand comprising (e.g., at its 3′ end) a stem-loop set forth as: S1-L-S2, in which S1 is complementary to S2, and in which L forms a single- stranded loop between S1 and S2 of up to about 10 nucleotides in length (e.g., 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in length). In some embodiments, the oligonucleotide comprises a targeting sequence or a region of complementary that is complementary to a contiguous sequence of nucleotides of any one of SEQ ID NOs: 89-280, and the oligonucleotide comprises a sense strand comprising (e.g., at its 3′ end) a stem-loop set forth as: S1-L-S2, in which S1 is complementary to S2, and in which L forms a single-stranded loop between S1 and S2 of 4 nucleotides in length.
[0201] In some embodiments, the tetraloop comprises the sequence 5’-GAAA-3’. In some embodiments, the stem loop comprises the sequence 5’-GCAGCCGAAAGGCUGC-3’ (SEQ ID NO: 86).
[0202] In some embodiments, a sense strand comprises a stem-loop structure at its 3′ end. In some embodiments, a sense strand comprises a stem-loop structure at its 5′ end. In some embodiments, a stem is a duplex of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 bp in length. In some embodiments, a stem-loop provides the molecule protection against degradation (e.g., enzymatic degradation) and facilitates targeting characteristics for delivery to a target cell. For example, in some embodiments, a loop provides added nucleotides on which modification can be made without substantially affecting the gene expression inhibition activity of an oligonucleotide. In certain embodiments, an oligonucleotide is herein in which the sense strand comprises (e.g., at its 3′ end) a stem-loop set forth as: S1-L- S2, in which S1 is complementary to S2, and in which L forms a loop between S1 and S2 of up to about 10 nucleotides in length (e.g., 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in length). FIG. 1A depicts non-limiting examples of such an oligonucleotide.
[0203] In some embodiments, a loop (L) of a stem-loop having the structure S1-L-S2 as described herein is a triloop. In some embodiments, the triloop comprises ribonucleotides, deoxyribonucleotides, modified nucleotides, ligands (e.g., delivery ligands), and combinations thereof.
[0204] In some embodiments, a loop of a stem-loop is a tetraloop (e.g., within a nicked tetraloop structure). A tetraloop may contain ribonucleotides, deoxyribonucleotides, modified nucleotides and combinations thereof. Typically, a tetraloop has 4 to 5 nucleotides. Duplex Length
[0205] In some embodiments, a duplex formed between a sense and antisense strand is at least 12 (e.g., at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21) nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length). In some embodiments, a duplex formed between a sense and antisense strand is 12, 13, 14, 15, 16, 17, 18, 19, 29, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 12 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 13 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 14 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 15 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 16 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 17 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 18 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 19 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 20 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 21 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 22 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 23 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 24 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 25 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 26 nucleotides in length. In some embodiments, a duplex formedbetween a sense and antisense strand is 27 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 28 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 29 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand is 30 nucleotides in length. In some embodiments, a duplex formed between a sense and antisense strand does not span the entire length of the sense strand and / or antisense strand. In some embodiments, a duplex between a sense and antisense strand spans the entire length of either the sense or antisense strands. In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand.
[0206] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, the sense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 861 and 951, respectively; (b) SEQ ID NOs: 857 and 947, respectively; (c) SEQ ID NOs: 858 and 948, respectively; (d) SEQ ID NOs: 859 and 949, respectively; (e) SEQ ID NOs: 860 and 950, respectively; (f) SEQ ID NOs: 862 and 952, respectively; (g) SEQ ID NOs: 863 and 953, respectively; (h) SEQ ID NOs: 864 and 954, respectively; (i) SEQ ID NOs: 865 and 955, respectively; (j) SEQ ID NOs: 866 and 956, respectively; (k) SEQ ID NOs: 867 and 957, respectively; (l) SEQ ID NOs: 868 and 958, respectively; (m) SEQ ID NOs: 869 and 959, respectively; (n) SEQ ID NOs: 870 and 960, respectively; (o) SEQ ID NOs: 871 and 961, respectively; (p) SEQ ID NOs: 872 and 962, respectively; (q) SEQ ID NOs: 873 and 963, respectively; (r) SEQ ID NOs: 874 and 964, respectively; (s) SEQ ID NOs: 875 and 965, respectively; (t) SEQ ID NOs: 876 and 966, respectively; (u) SEQ ID NOs: 877 and 967, respectively;(v) SEQ ID NOs: 878 and 968, respectively; (w) SEQ ID NOs: 879 and 969, respectively; (x) SEQ ID NOs: 880 and 970, respectively; (y) SEQ ID NOs: 881and 971, respectively; (z) SEQ ID NOs: 882 and 972, respectively; (aa) SEQ ID NOs: 883 and 973, respectively; (bb) SEQ ID NOs: 884 and 974, respectively; (cc) SEQ ID NOs: 885 and 975, respectively; (dd) SEQ ID NOs: 886 and 976, respectively; (ee) SEQ ID NOs: 887 and 977, respectively; (ff) SEQ ID NOs: 888 and 978, respectively; (gg) SEQ ID NOs: 940 and 1030, respectively; (hh) SEQ ID NOs: 896 and 986, respectively; and (ii) SEQ ID NOs: 920 and 1010, respectively, wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length).
[0207] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, the sense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 857 and 947, respectively; (b) SEQ ID NOs: 858 and 948, respectively; (c) SEQ ID NOs: 859 and 949, respectively; (d) SEQ ID NOs: 860 and 950, respectively; (e) SEQ ID NOs: 862 and 952, respectively; (f) SEQ ID NOs: 867 and 957, respectively; (g) SEQ ID NOs: 875 and 965, respectively; and (h) SEQ ID NOs: 876 and 966, respectively, wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length).
[0208] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, thesense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively. wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length).
[0209] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, the sense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively. wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length).
[0210] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, the sense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively. wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length).
[0211] In some embodiments, a duplex between a sense and antisense strand spans the entire length of both the sense strand and the antisense strand. In some embodiments, the sense and antisense strands of an oligonucleotide comprise nucleotides sequences selected from the group consisting of: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively. wherein a duplex formed between a sense and antisense strand is in the range of 12-30 nucleotides in length (e.g., 12 to 30, 12 to 27, 12 to 22, 15 to 25, 18 to 30, 18 to 22, 18 to 25, 18 to 27, 18 to 30, 19 to 30 or 21 to 30 nucleotides in length). Oligonucleotide Termini
[0212] In some embodiments, an oligonucleotide disclosed herein (e.g., an RNAi oligonucleotide) comprises a sense strand and an antisense strand, wherein the termini of either or both strands comprise a blunt end. In some embodiments, an oligonucleotide herein comprises sense and antisense strands that are separate strands which form an asymmetric duplex region having an overhang at the 3’ terminus of the antisense strand. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the termini of either or both strands comprise an overhang comprising one or more nucleotides. In some embodiments, the one or more nucleotides comprising the overhang are unpaired nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the 3’ termini of the sense strand and the 5’ termini of the antisense strand comprise a blunt end. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the 5’ termini of the sense strand and the 3’ termini of the antisense strand comprise a blunt end.
[0213] In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the 3’ terminus of either or both strands comprise a 3’-overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the sense strand comprises a 3’- overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the antisense strand comprises a 3’-overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein both thesense strand and the antisense strand comprises a 3’-overhang comprising one or more nucleotides.
[0214] In some embodiments, the 3’-overhang is about one (1) to twenty (20) nucleotides in length (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or about 20 nucleotides in length). In some embodiments, the 3’ overhang is about one (1) to nineteen (19), one (1) to eighteen (18), one (1) to seventeen (17), one (1) to sixteen (16), one (1) to fifteen (15), one (1) to fourteen (14), one (1) to thirteen (13), one (1) to twelve (12), one (1) to eleven (11), one (1) to ten (10), one (1) to nine (9), one (1) to eight (8), one (1) to seven (7), one (1) to six (6), one (1) to five (5), one (1) to four (4), one (1) to three (3), or about one (1) to two (2) nucleotides in length. In some embodiments, the 3’-overhang is (1) nucleotide in length. In some embodiments, the 3’-overhang is two (2) nucleotides in length. In some embodiments, the 3’-overhang is three (3) nucleotides in length. In some embodiments, the 3’-overhang is four (4) nucleotides in length. In some embodiments, the 3’- overhang is five (5) nucleotides in length. In some embodiments, the 3’-overhang is six (6) nucleotides in length. In some embodiments, the 3’-overhang is seven (7) nucleotides in length. In some embodiments, the 3’-overhang is eight (8) nucleotides in length. In some embodiments, the 3’-overhang is nine (9) nucleotides in length. In some embodiments, the 3’- overhang is ten (10) nucleotides in length. In some embodiments, the 3’-overhang is eleven (11) nucleotides in length. In some embodiments, the 3’-overhang is twelve (12) nucleotides in length. In some embodiments, the 3’-overhang is thirteen (13) nucleotides in length. In some embodiments, the 3’-overhang is fourteen (14) nucleotides in length. In some embodiments, the 3’-overhang is fifteen (15) nucleotides in length. In some embodiments, the 3’-overhang is sixteen (16) nucleotides in length. In some embodiments, the 3’-overhang is seventeen (17) nucleotides in length. In some embodiments, the 3’-overhang is eighteen (18) nucleotides in length. In some embodiments, the 3’-overhang is nineteen (19) nucleotides in length. In some embodiments, the 3’-overhang is twenty (20) nucleotides in length.
[0215] In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the 5’ terminus of either or both strands comprise a 5’-overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the sense strand comprises a 5’- overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein the antisense strand comprises a 5’-overhang comprising one or more nucleotides. In some embodiments, an oligonucleotide herein comprises a sense strand and an antisense strand, wherein both thesense strand and the antisense strand comprises a 5’-overhang comprising one or more nucleotides.
[0216] In some embodiments, the 5’-overhang is about one (1) to twenty (20) nucleotides in length (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or about 20 nucleotides in length). In some embodiments, the 5’ overhang is about one (1) to nineteen (19), one (1) to eighteen (18), one (1) to seventeen (17), one (1) to sixteen (16), one (1) to fifteen (15), one (1) to fourteen (14), one (1) to thirteen (13), one (1) to twelve (12), one (1) to eleven (11), one (1) to ten (10), one (1) to nine (9), one (1) to eight (8), one (1) to seven (7), one (1) to six (6), one (1) to five (5), one (1) to four (4), one (1) to three (3), or about one (1) to two (2) nucleotides in length. In some embodiments, the 5’-overhang is (1) nucleotide in length. In some embodiments, the 5’-overhang is two (2) nucleotides in length. In some embodiments, the 5’-overhang is three (3) nucleotides in length. In some embodiments, the 5’-overhang is four (4) nucleotides in length. In some embodiments, the 5’- overhang is five (5) nucleotides in length. In some embodiments, the 5’-overhang is six (6) nucleotides in length. In some embodiments, the 5’-overhang is seven (7) nucleotides in length. In some embodiments, the 5’-overhang is eight (8) nucleotides in length. In some embodiments, the 5’-overhang is nine (9) nucleotides in length. In some embodiments, the 5’- overhang is ten (10) nucleotides in length. In some embodiments, the 5’-overhang is eleven (11) nucleotides in length. In some embodiments, the 5’-overhang is twelve (12) nucleotides in length. In some embodiments, the 5’-overhang is thirteen (13) nucleotides in length. In some embodiments, the 5’-overhang is fourteen (14) nucleotides in length. In some embodiments, the 5’-overhang is fifteen (15) nucleotides in length. In some embodiments, the 5’-overhang is sixteen (16) nucleotides in length. In some embodiments, the 5’-overhang is seventeen (17) nucleotides in length. In some embodiments, the 5’-overhang is eighteen (18) nucleotides in length. In some embodiments, the 5’-overhang is nineteen (19) nucleotides in length. In some embodiments, the 5’-overhang is twenty (20) nucleotides in length.
[0217] In some embodiments, one or more (e.g., 2, 3, 4, 5, or more) nucleotides comprising the 3’ terminus or 5’ terminus of a sense and / or antisense strand are modified. For example, in some embodiments, one or two terminal nucleotides of the 3’ terminus of the antisense strand are modified. In some embodiments, the last nucleotide at the 3’ terminus of an antisense strand is modified, such that it comprises 2’ modification, or it comprises, a 2’- O-methoxyethyl. In some embodiments, the last one or two terminal nucleotides at the 3’ terminus of an antisense strand are complementary with the target. In some embodiments, thelast one or two nucleotides at the 3’ terminus of the antisense strand are not complementary with the target.
[0218] In some embodiments, an oligonucleotide disclosed herein (e.g., an RNAi oligonucleotide) comprises a sense strand and an antisense strand, wherein the 3’ terminus of the sense strand comprises a step-loop described herein and the 3’ terminus of the antisense strand comprises a 3’-overhang described herein. In some embodiments, an oligonucleotide herein (e.g., an RNAi oligonucleotide) comprises a sense strand and an antisense strand that form a nicked tetraloop structure described herein, wherein the 3’ terminus of the sense strand comprises a stem-loop, wherein the loop is a tetraloop described herein, and wherein the 3’ terminus of the antisense strand comprises a 3’-overhang described herein. In some embodiments, the 3’-overhang is two (2) nucleotides in length. In some embodiments, the two (2) nucleotides comprising the 3’-overhang both comprise guanine (G) nucleobases. Typically, one or both of the nucleotides comprising the 3’-overhang of the antisense strand are not complementary with the target mRNA. Oligonucleotide Modifications a. Sugar Modifications
[0219] In some embodiments, a modified sugar (also referred herein to a sugar analog) includes a modified deoxyribose or ribose moiety in which, for example, one or more modifications occur at the 2′, 3′, 4′ and / or 5′ carbon position of the sugar. In some embodiments, a modified sugar may also include non-natural alternative carbon structures such as those present in locked nucleic acids (“LNA”; see, e.g., Koshkin et al., (1998) TETRAHEDON 54:3607-3630), unlocked nucleic acids (“UNA”; see, e.g., Snead et al., (2013) MOL. THER-NUCL. ACIDS 2:e103) and bridged nucleic acids (“BNA”; see, e.g., Imanishi and Obika (2002) CHEM COMMUN. (CAMB) 21:1653-1659).
[0220] In some embodiments, a nucleotide modification in a sugar comprises a 2′- modification. In some embodiments, a 2′-modification may be 2′-O-propargyl, 2′-O- propylamin, 2′-amino, 2′-ethyl, 2′-fluoro (2′-F), 2′-aminoethyl (EA), 2′-O-methyl (2′-OMe), 2′-O-methoxyethyl (2′-MOE), 2′-O-[2-(methylamino)-2-oxoethyl] (2′-O-NMA) or 2′-deoxy- 2′-fluoro-β-d-arabinonucleic acid (2′-FANA). In some embodiments, the modification is 2′- F, 2′-OMe or 2′-MOE. In some embodiments, a modification in a sugar comprises a modification of the sugar ring, which may comprise modification of one or more carbons of the sugar ring. For example, a modification of a sugar of a nucleotide may comprise a 2′- oxygen of a sugar is linked to a 1′-carbon or 4′-carbon of the sugar, or a 2′-oxygen is linked tothe 1′-carbon or 4′-carbon via an ethylene or methylene bridge. In some embodiments, a modified nucleotide has an acyclic sugar that lacks a 2′-carbon to 3′-carbon bond. In some embodiments, a modified nucleotide has a thiol group, e.g., in the 4′ position of the sugar.
[0221] In some embodiments, the oligonucleotide described herein comprises at least about 1 modified nucleotide (e.g., at least 1, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, or more). In some embodiments, the sense strand of the oligonucleotide comprises at least about 1 modified nucleotide (e.g., at least 1, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, or more). In some embodiments, the antisense strand of the oligonucleotide comprises at least about 1 modified nucleotide (e.g., at least 1, at least 5, at least 10, at least 15, at least 20, or more).
[0222] In some embodiments, all the nucleotides of the sense strand of the oligonucleotide are modified. In some embodiments, all the nucleotides of the antisense strand of the oligonucleotide are modified. In some embodiments, all the nucleotides of the oligonucleotide (i.e., both the sense strand and the antisense strand) are modified. In some embodiments, the modified nucleotide comprises a 2′-modification (e.g., a 2′-F or 2′-OMe, 2′-MOE, and 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid). In some embodiments, the modified nucleotide comprises a 2′-modification (e.g., a 2′-F or 2′-OMe).
[0223] In some embodiments, the disclosure provides oligonucleotides having different modification patterns. In some embodiments, an oligonucleotide herein comprises a sense strand having a modification pattern as set forth in the Examples and Sequence Listing and an antisense strand having a modification pattern as set forth in the Examples and Sequence Listing.
[0224] In some embodiments, an oligonucleotide disclosed herein (e.g., an RNAi oligonucleotide) comprises an antisense strand having nucleotides that are modified with 2′- F. In some embodiments, an oligonucleotide herein comprises an antisense strand comprising nucleotides that are modified with 2′-F and 2′-OMe. In some embodiments, an oligonucleotide disclosed herein comprises a sense strand having nucleotides that are modified with 2′-F. In some embodiments, an oligonucleotide disclosed herein comprises a sense strand comprises nucleotides that are modified with 2′-F and 2′-OMe.
[0225] In some embodiments, an oligonucleotide described herein comprises a sense strand with about 10-15%, 10%, 11%, 12%, 13%, 14% or 15% of the nucleotides of the sense strand comprising a 2’-fluoro modification. In some embodiments, about 11% of the nucleotides of the sense strand comprise a 2-fluoro modification. In some embodiments, anoligonucleotide described herein comprises an antisense strand with about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the antisense strand comprising a 2’-fluoro modification. In some embodiments, about 32% of the nucleotides of the antisense strand comprise a 2’-fluoro modification. In some embodiments, the oligonucleotide has about 15-25%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, or 25% of its nucleotides comprising a 2’-fluoro modification. In some embodiments, about 19% of the nucleotides in the dsRNAi oligonucleotide comprise a 2’-fluoro modification.
[0226] In some embodiments, the modified oligonucleotides comprise a sense strand sequence having a modification pattern as set forth in FIG 1A or Example 7 and an antisense strand having a modification pattern as set forth in FIG 1A or Example 7. In some embodiments, for these oligonucleotides, one or more of positions 8, 9, 10 or 11 of the sense strand is modified with a 2′-F group. In other embodiments, for these oligonucleotides, the sugar moiety at each of nucleotides at positions 1-7 and 12-20 in the sense strand is modified with a 2′-OMe.
[0227] In some embodiments, the antisense strand has 3 nucleotides that are modified at the 2′-position of the sugar moiety with a 2′-F. In some embodiments, the sugar moiety at positions 2, 5 and 14 and optionally up to 3 of the nucleotides at positions 1, 3, 7 and 10 of the antisense strand are modified with a 2′-F. In some embodiments, the sugar moiety at positions 2, 5 and 14 and optionally up to 3 of the nucleotides at positions 3, 4, 7 and 10 of the antisense strand are modified with a 2′-F. In other embodiments, the sugar moiety at each of the positions at positions 2, 5 and 14 of the antisense strand is modified with the 2′-F. In other embodiments, the sugar moiety at each of the positions at positions 1, 2, 5 and 14 of the antisense strand is modified with the 2′-F. In other embodiments, the sugar moiety at each of the positions at positions 2, 4, 5 and 14 of the antisense strand is modified with the 2′-F. In still other embodiments, the sugar moiety at each of the positions at positions 1, 2, 3, 5, 7 and 14 of the antisense strand is modified with the 2′-F. In other embodiments, the sugar moiety at each of the positions at positions 2, 3, 4, 5, 7 and 14 of the antisense strand is modified with the 2′-F. In yet another embodiment, the sugar moiety at each of the positions at positions 1, 2, 3, 5, 10 and 14 of the antisense strand is modified with the 2′-F. In other embodiments, the sugar moiety at each of the positions at positions 2, 3, 4, 5, 10 and 14 of the antisense strand is modified with the 2′-F. In another embodiment, the sugar moiety at each of the positions at positions 2, 3, 5, 7, 10 and 14 of the antisense strand is modified with the2′-F. In yet another embodiment, the sugar moiety at each of the positions at positions 2, 3, 4, 5, 7, 10 and 14 of the antisense strand is modified with the 2′-F.
[0228] In some embodiments, an oligonucleotide provided herein comprises an antisense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, or position 22 modified with 2′-F.
[0229] In some embodiments, an oligonucleotide provided herein comprises an antisense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, or position 22 modified with 2′-OMe.
[0230] In some embodiments, an oligonucleotide provided herein comprises an antisense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, or position 22 modified with a modification selected from the group consisting of 2′-O-propargyl, 2′-O-propylamin, 2′-amino, 2′-ethyl, 2’-aminoethyl (EA), 2′-O- methyl (2′-OMe), 2′-O-methoxyethyl (2′-MOE), 2′-O-[2-(methylamino)-2-oxoethyl] (2′-O- NMA), and 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′-FANA).
[0231] In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at positions 8-11 modified with 2′-F. In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at positions 3, 8, 9, 10, 12, 13 and 17 modified with 2′-F. In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at positions 1-7 and 12-17 or 12-20 modified with 2’OMe. In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at positions 1-7, 12-27 and 31-36 modified with 2’OMe. In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety of each of the nucleotides at positions 1-7 and 12-17 or 12-20 of the sense strand modified with a modification selected from the group consisting of 2′-O-propargyl, 2′-O-propylamin, 2′-amino, 2′-ethyl, 2’-aminoethyl (EA), 2′-O- methyl (2′-OMe), 2′-O-methoxyethyl (2′-MOE), 2′-O-[2-(methylamino)-2-oxoethyl] (2′-O- NMA), and 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′-FANA). In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety atpositions 1-2, 4-7, 11, 14-16 and 18-20 modified with 2’OMe. In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety of each of the nucleotides at positions 1-2, 4-7, 11, 14-16 and 18-20 of the sense strand modified with a modification selected from the group consisting of 2′-O-propargyl, 2′-O-propylamin, 2′- amino, 2′-ethyl, 2’-aminoethyl (EA), 2′-O-methyl (2′-OMe), 2′-O-methoxyethyl (2′-MOE), 2′-O-[2-(methylamino)-2-oxoethyl] (2′-O-NMA), and 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′-FANA).
[0232] In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, position 22, position 23, position 24, position 25, position 26, position 27, position 28, position 29, position 30, position 31, position 32, position 33, position 34, position 35, or position 36 modified with 2′-F.
[0233] In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, position 22, position 23, position 24, position 25, position 26, position 27, position 28, position 29, position 30, position 31, position 32, position 33, position 34, position 35, or position 36 modified with 2′-OMe.
[0234] In some embodiments, an oligonucleotide provided herein comprises a sense strand having the sugar moiety at position 1, position 2, position 3, position 4, position 5, position 6, position 7, position 8, position 9, position 10, position 11, position 12, position 13, position 14, position 15, position 16, position 17, position 18, position 19, position 20, position 21, position 22, position 23, position 24, position 25, position 26, position 27, position 28, position 29, position 30, position 31, position 32, position 33, position 34, position 35, or position 36 modified with a modification selected from the group consisting of 2′-O-propargyl, 2′-O-propylamin, 2′-amino, 2′-ethyl, 2’-aminoethyl (EA), 2′-O-methyl (2′- OMe), 2′-O-methoxyethyl (2′-MOE), 2′-O-[2-(methylamino)-2-oxoethyl] (2′-O-NMA), and 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′-FANA). b. 5′ Terminal Phosphates
[0235] In some embodiments, 5′-terminal phosphate groups of oligonucleotides enhance the interaction with Ago2. However, oligonucleotides comprising a 5′-phosphate group may be susceptible to degradation via phosphatases or other enzymes, which can limit their bioavailability in vivo. In some embodiments, oligonucleotides include analogs of 5′ phosphates that are resistant to such degradation. In some embodiments, a phosphate analog may be oxymethylphosphonate, vinylphosphonate or malonyl phosphonate. In certain embodiments, the 1′ end of an oligonucleotide strand is attached to chemical moiety that mimics the electrostatic and steric properties of a natural 5′-phosphate group (“phosphate mimic”).
[0236] In some embodiments, an oligonucleotide has a phosphate analog at a 4′- carbon position of the sugar (referred to as a “4′-phosphate analog”). See, e.g., Intl. Patent Application Publication No. WO 2018 / 045317. In some embodiments, an oligonucleotide herein comprises a 4′-phosphate analog at a 5′-terminal nucleotide. In some embodiments, a phosphate analog is an oxymethylphosphonate, in which the oxygen atom of the oxymethyl group is bound to the sugar moiety (e.g., at its 4′-carbon) or analog thereof. In other embodiments, a 4′-phosphate analog is a thiomethyl phosphonate or an amino methyl phosphonate, in which the sulfur atom of the thiomethyl group or the nitrogen atom of the amino methyl group is bound to the 4′-carbon of the sugar moiety or analog thereof. In certain embodiments, a 4′-phosphate analog is an oxymethyl phosphonate. In some embodiments, an oxymethyl phosphonate is represented by the formula –O–CH2–PO(OH)2or –O–CH2–PO(OR)2, in which R is independently selected from H, CH3, an alkyl group, CH2CH2CN, CH2OCOC(CH3)3, CH2OCH2CH2Si (CH3)3 or a protecting group. In certain embodiments, the alkyl group is CH2CH3. More typically, R is independently selected from H, CH3 or CH2CH3.
[0237] In some embodiments, an oligonucleotide provided herein comprises an antisense strand comprising a 4′-phosphate analog at the 5′-terminal nucleotide, wherein 5’- terminal nucleotide comprises the following structure (Chem 1):4’-O-monomethylphosphonate-2’-O-methyluridine phosphorothioate [MePhosphonate- 4O-mUs]. Chem 1 c. Modified Internucleotide Linkages
[0238] In some embodiments, an oligonucleotide may comprise a modified internucleoside linkage. In some embodiments, phosphate modifications or substitutions may result in an oligonucleotide that comprises at least about 1 (e.g., at least 1, at least 2, at least 3 or at least 5) modified internucleotide linkage. In some embodiments, any one of the oligonucleotides disclosed herein comprises about 1 to about 10 (e.g., 1 to 10, 2 to 8, 4 to 6, 3 to 10, 5 to 10, 1 to 5, 1 to 3 or 1 to 2) modified internucleotide linkages. In some embodiments, any one of the oligonucleotides disclosed herein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 modified internucleotide linkages.
[0239] A modified internucleotide linkage may be a phosphorodithioate linkage, 4′- O-methylene phosphonate linkage, a phosphorothioate linkage, a phosphotriester linkage, a thionoalkylphosphonate linkage, a thionalkylphosphotriester linkage, a phosphoramidite linkage, a phosphonate linkage or a boranophosphate linkage. In some embodiments, at least one modified internucleotide linkage of any one of the oligonucleotides as disclosed herein is a phosphorothioate linkage. In some embodiments, at least one modified internucleotide linkage of any one of the oligonucleotides as disclosed herein is a 4′-O-methylene phosphonate linkage.
[0240] In some embodiments, the oligonucleotide described herein has a phosphorothioate linkage between one or more of positions 1 and 2 of the sense strand, positions 1 and 2 of the antisense strand, positions 2 and 3 of the antisense strand, positions 3and 4 of the antisense strand, positions 20 and 21 of the antisense strand, and positions 21 and 22 of the antisense strand. In some embodiments, the oligonucleotide described herein has a phosphorothioate linkage between each of positions 1 and 2 of the sense strand, positions 1 and 2 of the antisense strand, positions 2 and 3 of the antisense strand, positions 20 and 21 of the antisense strand, and positions 21 and 22 of the antisense strand. d. Base Modifications
[0241] In some embodiments, oligonucleotides herein have one or more modified nucleobases. In some embodiments, modified nucleobases (also referred to herein as base analogs) are linked at the 1′ position of a nucleotide sugar moiety. In certain embodiments, a modified nucleobase is a nitrogenous base. In certain embodiments, a modified nucleobase does not contain nitrogen atom. See, e.g., US Patent Application Publication No. 2008 / 0274462. In some embodiments, a modified nucleotide comprises a universal base. However, in certain embodiments, a modified nucleotide does not contain a nucleobase (abasic).
[0242] In some embodiments, a universal base is a heterocyclic moiety located at the 1′ position of a nucleotide sugar moiety in a modified nucleotide, or the equivalent position in a nucleotide sugar moiety substitution, that, when present in a duplex, can be positioned opposite more than one type of base without substantially altering structure of the duplex. In some embodiments, compared to a reference single-stranded nucleic acid (e.g., oligonucleotide) that is fully complementary to a target nucleic acid, a single-stranded nucleic acid containing a universal base forms a duplex with the target nucleic acid that has a lower Tmthan a duplex formed with the complementary nucleic acid. However, in some embodiments, when compared to a reference single-stranded nucleic acid in which the universal base has been replaced with a base to generate a single mismatch, the single- stranded nucleic acid containing the universal base forms a duplex with the target nucleic acid that has a higher Tmthan a duplex formed with the nucleic acid comprising the mismatched base.
[0243] Non-limiting examples of universal-binding nucleotides include, but are not limited to, inosine, 1-β-D-ribofuranosyl-5-nitroindole and / or 1-β-D-ribofuranosyl-3- nitropyrrole (see, US Patent Application Publication No.2007 / 0254362; Van Aerschot et al., (1995) NUCLEIC ACIDS RES.23:4363-4370; Loakes et al., (1995) NUCLEIC ACIDS RES. 23:2361-66; and Loakes and Brown (1994) NUCLEIC ACIDS RES.22:4039-43).e. Reversible Modifications
[0244] While certain modifications to protect an oligonucleotide from the in vivo environment before reaching target cells can be made, they can reduce the potency or activity of the oligonucleotide once it reaches the cytosol of the target cell. Reversible modifications can be made such that the molecule retains desirable properties outside of the cell, which are then removed upon entering the cytosolic environment of the cell. Reversible modification can be removed, for example, by the action of an intracellular enzyme or by the chemical conditions inside of a cell (e.g., through reduction by intracellular glutathione).
[0245] In some embodiments, a reversibly modified nucleotide comprises a glutathione-sensitive moiety. Typically, nucleic acid molecules have been chemically modified with cyclic disulfide moieties to mask the negative charge created by the internucleotide diphosphate linkages and improve cellular uptake and nuclease resistance. See US Patent Application Publication No.2011 / 0294869, Intl. Patent Application Publication Nos. WO 2014 / 088920 and WO 2015 / 188197, and Meade et al., (2014) NAT. BIOTECHNOL.32:1256-63. This reversible modification of the internucleotide diphosphate linkages is designed to be cleaved intracellularly by the reducing environment of the cytosol (e.g., glutathione). Earlier examples include neutralizing phosphotriester modifications that were reported to be cleavable inside cells (see, Dellinger et al., (2003) J. AM. CHEM. SOC. 125:940-50).
[0246] In some embodiments, such a reversible modification allows protection during in vivo administration (e.g., transit through the blood and / or lysosomal / endosomal compartments of a cell) where the oligonucleotide will be exposed to nucleases and other harsh environmental conditions (e.g., pH). When released into the cytosol of a cell where the levels of glutathione are higher compared to extracellular space, the modification is reversed, and the result is a cleaved oligonucleotide. Using reversible, glutathione-sensitive moieties, it is possible to introduce sterically larger chemical groups into the oligonucleotide of interest when compared to the options available using irreversible chemical modifications. This is because these larger chemical groups will be removed in the cytosol and, therefore, should not interfere with the biological activity of the oligonucleotides inside the cytosol of a cell. As a result, these larger chemical groups can be engineered to confer various advantages to the nucleotide or oligonucleotide, such as nuclease resistance, lipophilicity, charge, thermal stability, specificity, and reduced immunogenicity. In some embodiments, the structure of the glutathione-sensitive moiety can be engineered to modify the kinetics of its release.
[0247] In some embodiments, a glutathione-sensitive moiety is attached to the sugar of the nucleotide. In some embodiments, a glutathione-sensitive moiety is attached to the 2′- carbon of the sugar of a modified nucleotide. In some embodiments, the glutathione- sensitive moiety is located at the 5′-carbon of a sugar, particularly when the modified nucleotide is the 5′-terminal nucleotide of the oligonucleotide. In some embodiments, the glutathione-sensitive moiety is located at the 3′-carbon of sugar, particularly when the modified nucleotide is the 3′-terminal nucleotide of the oligonucleotide. In some embodiments, the glutathione-sensitive moiety comprises a sulfonyl group. See, e.g., US Provisional Patent Application No.62 / 378,635, entitled Compositions Comprising Reversibly Modified Oligonucleotides and Uses Thereof, which was filed on August 23, 2016. Targeting Ligands
[0248] In some embodiments, it is desirable to target the STAT3 targeting oligonucleotides of the disclosure to one or more cells or one or more organs. Such a strategy can help to avoid undesirable effects in other organs or avoid undue loss of the oligonucleotide to cells, tissue or organs that would not benefit from the oligonucleotide. Targeting of oligonucleotides to one or more cells or one or more organs can be achieved through a variety of approaches. Conjugation of oligonucleotides to tissue or cell specific antibodies, small molecules or targeting ligands can facilitate delivery to and modify accumulation of the oligonucleotide in one or more target cells or tissues (Chernolovskaya et al., (2019) FRONT PHARMACOL.10:444). For example, conjugation of an oligonucleotide to a saturated fatty acid (e.g., C22) may facilitate delivery to cells or tissues like adipose tissue or immune cells which uptake such ligands more readily than conventional oligonucleotide ligands. Accordingly, in some embodiments, oligonucleotides disclosed herein are modified to facilitate targeting and / or delivery of a tissue, cell, or organ (e.g., to facilitate delivery of the oligonucleotide to the liver). In certain embodiments, oligonucleotides disclosed herein are modified to facilitate delivery of the oligonucleotide to cells of the immune system. In certain embodiments, oligonucleotides disclosed herein are modified to facilitate delivery of the oligonucleotide to myeloid derived suppressor cells. In some embodiments, an oligonucleotide comprises at least one nucleotide (e.g., 1, 2, 3, 4, 5, 6 or more nucleotides) conjugated to one or more targeting ligand(s).
[0249] In some embodiments, the targeting ligand comprises a carbohydrate, amino sugar, cholesterol, peptide, polypeptide, protein, or part of a protein (e.g., an antibody or antibody fragment), or lipid. In some embodiments, the targeting ligand is an aptamer. Forexample, a targeting ligand may be an RGD peptide that is used to target tumor vasculature or glioma cells, CREKA peptide to target tumor vasculature or stoma, transferring, lactoferrin, or an aptamer to target transferrin receptors expressed on CNS vasculature, or an anti-EGFR antibody to target EGFR on glioma cells. In certain embodiments, the targeting ligand is one or more GalNAc moieties.
[0250] In some embodiments, 1 or more (e.g., 1, 2, 3, 4, 5 or 6) nucleotides of an oligonucleotide are each conjugated to a separate targeting ligand. In some embodiments, 2 to 4 nucleotides of an oligonucleotide are each conjugated to a separate targeting ligand. In some embodiments, targeting ligands are conjugated to 2 to 4 nucleotides at either ends of the sense or antisense strand (e.g., targeting ligands are conjugated to a 2 to 4 nucleotide overhang or extension on the 5′ or 3′ end of the sense or antisense strand) such that the targeting ligands resemble bristles of a toothbrush and the oligonucleotide resembles a toothbrush. For example, an oligonucleotide may comprise a stem-loop at either the 5′ or 3′ end of the sense strand and 1, 2, 3 or 4 nucleotides of the loop of the stem may be individually conjugated to a targeting ligand. In some embodiments, an oligonucleotide (e.g., a dsRNA) provided by the disclosure comprises a stem-loop at the 3′ end of the sense strand, wherein the loop of the stem-loop comprises a triloop or a tetraloop, and wherein the 3 or 4 nucleotides comprising the triloop or tetraloop, respectfully, are individually conjugated to a targeting ligand. In some embodiments, an oligonucleotide provided by the disclosure (e.g., a RNAi oligonucleotide) comprises a stem-loop at the 3′ terminus of the sense strand, wherein the loop of the stem-loop comprises a tetraloop, and wherein 3 nucleotides of the tetraloop are individually conjugated to a targeting ligand.
[0251] GalNAc is a high affinity ligand for the ASGPR, which is primarily expressed on the sinusoidal surface of hepatocyte cells and has a major role in binding, internalizing and subsequent clearing circulating glycoproteins that contain terminal galactose or GalNAc residues (asialoglycoproteins). Conjugation (either indirect or direct) of GalNAc moieties to oligonucleotides of the instant disclosure can be used to target these oligonucleotides to the ASGPR expressed on cells. In some embodiments, an oligonucleotide of the instant disclosure is conjugated to at least one or more GalNAc moieties, wherein the GalNAc moieties target the oligonucleotide to an ASGPR expressed on human liver cells (e.g., human hepatocytes). In some embodiments, the GalNAc moiety target the oligonucleotide to the liver.
[0252] In some embodiments, an oligonucleotide of the instant disclosure is conjugated directly or indirectly to a monovalent GalNAc. In some embodiments, theoligonucleotide is conjugated directly or indirectly to more than one monovalent GalNAc (i.e., is conjugated to 2, 3 or 4 monovalent GalNAc moieties, and is typically conjugated to 3 or 4 monovalent GalNAc moieties). In some embodiments, an oligonucleotide is conjugated to one or more bivalent GalNAc, trivalent GalNAc or tetravalent GalNAc moieties.
[0253] In some embodiments, 1 or more (e.g., 1, 2, 3, 4, 5 or 6) nucleotides of an oligonucleotide are each conjugated to a GalNAc moiety. In some embodiments, 2 to 4 nucleotides of a tetraloop are each conjugated to a separate GalNAc. In some embodiments, 1 to 3 nucleotides of a triloop are each conjugated to a separate GalNAc. In some embodiments, targeting ligands are conjugated to 2 to 4 nucleotides at either ends of the sense or antisense strand (e.g., ligands are conjugated to a 2 to 4 nucleotide overhang or extension on the 5′ or 3′ end of the sense or antisense strand) such that the GalNAc moieties resemble bristles of a toothbrush and the oligonucleotide resembles a toothbrush. In some embodiments, GalNAc moieties are conjugated to a nucleotide of the sense strand. For example, 4 GalNAc moieties can be conjugated to nucleotides in the tetraloop of the sense strand where each GalNAc moiety is conjugated to 1 nucleotide.
[0254] In some embodiments, the tetraloop is any combination of adenine and guanine nucleotides.
[0255] In some embodiments, the tetraloop (tetraL) has a monovalent GalNAc moiety attached to any one or more guanine nucleotides of the tetraloop via any linker described herein, as depicted below in Chem 2 (X=heteroatom):Chem 2
[0256] In some embodiments, the tetraloop (tetraL) has a monovalent GalNAc attached to any one or more adenine nucleotides of the tetraloop via any linker described herein, as depicted below in Chem 3 (X=heteroatom):Chem 3
[0257] In some embodiments, an oligonucleotide herein comprises a monovalent GalNAc attached to a guanine nucleotide referred to as [ademG-GalNAc] or 2′- aminodiethoxymethanol-Guanine-GalNAc, as depicted below in Chem 4:
[0258] In some embodiments, an oligonucleotide herein comprises a monovalent GalNAc attached to an adenine nucleotide, referred to as [ademA-GalNAc] or 2′- aminodiethoxymethanol-Adenine-GalNAc, as depicted below in Chem 5:Chem 5
[0259] An example of such conjugation is shown below (Chem 6) for a loop comprising from 5′ to 3′ the nucleotide sequence GAAA (L = linker, X = heteroatom) stem attachment points are shown. Such a loop may be present, for example, at positions 27-30 of the sense strand as shown in FIG.1A. In the chemical formula,is used to describe an attachment point to the oligonucleotide strand (Chem 6).Chem 6
[0260] Appropriate methods or chemistry (e.g., click chemistry) can be used to link a targeting ligand to a nucleotide. In some embodiments, a targeting ligand is conjugated to a nucleotide using a click linker. In some embodiments, an acetal-based linker is used to conjugate a targeting ligand to a nucleotide of any one of the oligonucleotides described herein. Acetal-based linkers are disclosed, for example, in Intl. Patent Application Publication No. WO 2016 / 100401. In some embodiments, the linker is a labile linker. However, in other embodiments, the linker is stable. Examples are shown below for a loop comprising from 5′ to 3′ the nucleotides GAAA, in which GalNAc moieties are attached to nucleotides of the loop using an acetal linker (Chem 7 and Chem 8). Such a loop may be present, for example, at positions 27-30 of the any one of the sense strand as shown in FIG.1. In the chemical formula,is an attachment point to the oligonucleotide strand (Chem 7 and Chem 8).
[0261] As mentioned, various appropriate methods or chemistry synthetic techniques (e.g., click chemistry) can be used to link a targeting ligand to a nucleotide. In some embodiments, a targeting ligand is conjugated to a nucleotide using a click linker. In some embodiments, an acetal-based linker is used to conjugate a targeting ligand to a nucleotide of any one of the oligonucleotides described herein. Acetal-based linkers are disclosed, for example, in Intl. Patent Application Publication No. WO 2016 / 100401. In some embodiments, the linker is a labile linker. However, in other embodiments, the linker is a stable linker.
[0262] In some embodiments, a duplex extension (e.g., of up to 3, 4, 5 or 6 bp in length) is provided between a targeting ligand (e.g., a GalNAc moiety) and a dsRNA. In some embodiments, the oligonucleotides herein do not have a GalNAc conjugated thereto. Structure of Conjugated STAT3 Targeting Oligonucleotides
[0263] In some embodiments, a STAT3 targeting oligonucleotide described hereincomprises a nucleotide sequence having a region of complementarity to a STAT3 mRNA target sequence and one or more targeting ligands, wherein the nucleotide sequence comprises one or more nucleosides (nucleic acids) conjugated with one or more targeting ligands represented by formula I-a:or a pharmaceutically acceptable salt thereof, wherein: B is a nucleobase or hydrogen; R1and R2are independently hydrogen, halogen, RA, -CN, -S(O)R, -S(O)2R, -Si(OR)2R, - Si(OR)R2, or -SiR3; or R1and R2on the same carbon are taken together with their intervening atoms to form a 3-7 membered saturated or partially unsaturated ring having 0-3 heteroatoms, independently selected from nitrogen, oxygen, and sulfur; each RAis independently an optionally substituted group selected from C1-6aliphatic, phenyl, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; each R is independently hydrogen, a suitable protecting group, or an optionally substituted group selected from C1-6aliphatic, phenyl, a 4-7 membered saturated or partially unsaturated heterocyclic having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or two R groups on the same atom are taken together with their intervening atoms to form a 4-7 membered saturated, partially unsaturated, or heteroaryl ring having 0-3 heteroatoms, independently selected from nitrogen, oxygen, silicon, and sulfur; each targeting ligand is selected from lipid conjugate moiety (LC), carbohydrate, amino sugar or GalNAc; and wherein each LC is independently a lipid conjugate moiety comprising a saturated or unsaturated, straight, or branched C1-50hydrocarbon chain, wherein 0-10methylene units of the hydrocarbon chain are independently replaced by -Cy-, -O-, - C(O)NR-, -NR-, -S-, -C(O)-, -C(O)O-, -S(O)-, -S(O)2-, -P(O)OR-, -P(S)OR-; each -Cy- is independently an optionally substituted bivalent ring selected from phenylenyl, an 8-10 membered bicyclic arylenyl, a 4-7 membered saturated or partially unsaturated carbocyclylenyl, a 4-11 membered saturated or partially unsaturated spiro carbocyclylenyl, an 8-10 membered bicyclic saturated or partially unsaturated carbocyclylenyl, a 4-7 membered saturated or partially unsaturated heterocyclylenyl having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 4- 11 membered saturated or partially unsaturated spiro heterocyclylenyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, an 8-10 membered bicyclic saturated or partially unsaturated heterocyclylenyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, a 5-6 membered heteroarylenyl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or an 8-10 membered bicyclic heteroarylenyl having 1-5 heteroatoms independently selected from nitrogen, oxygen, or sulfur; n is 1-10; L is a covalent bond or a bivalent saturated or unsaturated, straight or branched C1-50hydrocarbon chain, wherein 0-10 methylene units of the hydrocarbon chain are independently replaced by -Cy-, -O-, -C(O)NR-, -NR-, -S-, -C(O)-, -C(O)O-, -S(O)-, - S(O)2-, -P(O)OR-, -P(S)OR-, -V1CR2W1-, orm is 1-50; X1, V1and W1are independently -C(R)2-, -OR, -O-, -S-, -Se-, or -NR-; Y is hydrogen, a suitable hydroxyl protecting group,; R3is hydrogen, a suitable protecting group, a suitable prodrug, or an optionally substituted group selected from C1-6aliphatic, phenyl, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; X2is O, S, or NR; X3is -O-, -S-, -BH2-, or a covalent bond;Y1is a linking group attaching to the 2′- or 3′-terminal of a nucleoside, a nucleotide, or an oligonucleotide; Y2is hydrogen, a suitable protecting group, a phosphoramidite analogue, an internucleotide linking group attaching to the 5′-terminal of a nucleoside, a nucleotide, or an oligonucleotide, or a linking group attaching to a solid support; and Z is -O-, -S-, -NR-, or -CR2-.
[0264] In some embodiments, the STAT3 targeting oligonucleotide comprises one or more nucleic acids conjugated with targeting ligands represented by formula II-a:or a pharmaceutically acceptable salt thereof.
[0265] In some embodiments, the STAT3 targeting oligonucleotide comprises one or more nucleic acids conjugated with targeting ligands represented by formula II-b or II-c:II-c or a pharmaceutically acceptable salt thereof, wherein: L1is a covalent bond, a monovalent or a bivalent saturated or unsaturated, straight or branched C1-50hydrocarbon chain, wherein 0-10 methylene units of the hydrocarbon chain are independently replaced by -Cy-, -O-, -C(O)NR-, -NR-, -S-, -C(O)-, -C(O)O-, -S(O)-, -S(O)2-, -P(O)OR-, -P(S)OR-, orR4is hydrogen, RA, or a suitable amine protection group; andR5is adamantyl, or a saturated or unsaturated, straight, or branched C1-50hydrocarbon chain, wherein 0-10 methylene units of the hydrocarbon chain are independently replaced by -O-, - C(O)NR-, -NR-, -S-, -C(O)-, -C(O)O-, -S(O)-, -S(O)2-, -P(O)OR-, or -P(S)OR.
[0266] In some embodiments, R5is selected from
[0267] In some embodiments, R5is selected from:
[0268] In some embodiments, R5is. In some. ,embodiments,. In some embodiments, R5issome embodiments, R5issome embodiments, R5is. In some embodiments, R5is.
[0269] In some embodiments, the STAT3 targeting oligonucleotide comprises one or more nucleic acids conjugated with targeting ligands represented by formula II-Ib or II-Ic:II-Ic or a pharmaceutically acceptable salt thereof; wherein B is a nucleobase or hydrogen; m is 1-50; X1is -O-, or -S-; Y is hydrogen,R3is hydrogen, or a suitable protecting group; X2is O, or S; X3is -O-, -S-, or a covalent bond; Y1is a linking group attaching to the 2′- or 3′-terminal of a nucleoside, a nucleotide, or an oligonucleotide; Y2is hydrogen, a phosphoramidite analogue, an internucleotide linking group attaching to the 5′-terminal of a nucleoside, a nucleotide, or an oligonucleotide, or a linking group attaching to a solid support; R5is adamantyl, or a saturated or unsaturated, straight, or branched C1-50hydrocarbon chain, wherein 0-10 methylene units of the hydrocarbon chain are independently replaced by -O-, - C(O)NR-, -NR-, -S-, -C(O)-, -C(O)O-, -S(O)-, -S(O)2-, -P(O)OR-, or -P(S)OR-; and R is hydrogen, a suitable protecting group, or an optionally substituted group selected from C1-6aliphatic, phenyl, a 4-7 membered saturated or partially unsaturated heterocyclic having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and a 5-6membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
[0270] In some embodiments, R5is selected from.
[0271] In some embodiments, R5is.
[0273] In some embodiments, the nucleotide sequence of the STAT3 targeting oligonucleotide comprises 1-10 targeting ligands. In some embodiments, the nucleotide sequence comprises 1, 2 or 3 targeting ligands.
[0274] In some embodiments, the STAT3 targeting oligonucleotide is a double- stranded molecule. In some embodiments, the STAT3 targeting oligonucleotide is an RNAi molecule. In some embodiments, the STAT3 targeting double stranded oligonucleotide comprises a stem loop. In some embodiments, the ligand is conjugated to any of the nucleotides in the stem loop. In some embodiments, the ligand is conjugated to the first nucleotide from 5’ to 3’, in the stem loop. In some embodiments, the ligand is conjugated to the second nucleotide from 5’ to 3’ in the stem loop. In some embodiments, the ligand is conjugated to the third nucleotide from 5’ to 3’ in the stem loop. In some embodiments, the ligand is conjugated to the fourth nucleotide from 5’ to 3’ in the stem loop. In some embodiments, the ligand is conjugated to one, two, three, or four of the nucleotides in the stem loop. In some embodiments, the ligand is conjugated to three of the nucleotides in the stem loop.
[0275] In some embodiments, the STAT3 targeting double stranded oligonucleotide comprises a stem loop, wherein one or more lipids are conjugated to one or more nucleotides of the stem loop. In some embodiments, the STAT3 targeting double stranded oligonucleotide comprises a stem loop, wherein one or more C16 lipids are conjugated to one or more nucleotides of the stem loop. In some embodiments, the STAT3 targeting double stranded oligonucleotide comprises a stem loop, wherein one or more C18 lipids are conjugated to one or more nucleotides of the stem loop.
[0276] In some embodiments, the STAT3 targeting oligonucleotide comprises a sense strand of 36 nucleotides with positions numbered 1-36 from 5’ to 3’. In some embodiments, the STAT3 targeting oligonucleotide comprises a lipid conjugated to position 27 of a 36- nucleotide sense strand. In some embodiments, STAT3 targeting oligonucleotide comprises a lipid conjugated to position 28 of a 36-nucleotide sense strand. In some embodiments, theSTAT3 targeting oligonucleotide comprises a lipid conjugated to position 29 of a 36- nucleotide sense strand. In some embodiments, the STAT3 targeting oligonucleotide comprises a lipid conjugated to position 30 of a 36-nucleotide sense strand. In some embodiments, a 36-nucleotide sense strand forms a stem loop having a loop with positions 27-30. In some embodiments, a lipid is conjugated to more than one position of the loop (e.g., positions 27 and 28 of a 36-nucleotide sense strand).
[0277] In some embodiments, the STAT3 targeting oligonucleotide comprises a C16 lipid conjugated to position 27 of a 36-nucleotide sense strand. In some embodiments, STAT3 targeting oligonucleotide comprises a C16 lipid conjugated to position 28 of a 36- nucleotide sense strand. In some embodiments, the STAT3 targeting oligonucleotide comprises a C16 lipid conjugated to position 29 of a 36-nucleotide sense strand. In some embodiments, the STAT3 targeting oligonucleotide comprises a C16 lipid conjugated to position 30 of a 36-nucleotide sense strand. In some embodiments, a 36-nucleotide sense strand forms a stem loop having a loop with positions 27-30. In some embodiments, a C16 lipid is conjugated to more than one position of the loop (e.g., positions 27 and 28 of a 36- nucleotide sense strand).
[0278] In some embodiments, the STAT3 targeting oligonucleotide comprises a C18 lipid conjugated to position 27 of a 36-nucleotide sense strand. In some embodiments, STAT3 targeting oligonucleotide comprises a C18 lipid conjugated to position 28 of a 36- nucleotide sense strand. In some embodiments, the STAT3 targeting oligonucleotide comprises a C18 lipid conjugated to position 29 of a 36-nucleotide sense strand. In some embodiments, the STAT3 targeting oligonucleotide comprises a C18 lipid conjugated to position 30 of a 36-nucleotide sense strand. In some embodiments, a 36-nucleotide sense strand forms a stem loop having a loop with positions 27-30. In some embodiments, a C18 lipid is conjugated to more than one position of the loop (e.g., positions 27 and 28 of a 36- nucleotide sense strand).
[0279] In some embodiments, a STAT3 targeting oligonucleotide comprises an antisense strand of 15 to 30 nucleotides and a sense strand of 15 to 40 nucleotide, wherein the sense and antisense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence expressed in an immune cell associated with a tumor microenvironment, wherein the sense strand comprises at its 3’ end a stem-loop comprising a tetraloop comprising 4 nucleosides, wherein one or more of the 4 nucleosides is represented by formula II-Ib:, wherein B is selected from an adenine and a guanine nucleobase, and wherein R5is a hydrocarbon chain. In some embodiments, m is 1, X1 is O, Y2 is an internucleotide linking group attaching to the 5’ terminal of a nucleoside, Y1Y is represented by, Y1 is a linking group attaching to the 2’ or 3’ terminal of a nucleotide, X2 is O, X3 is O, and R3 is H.
[0280] In some embodiments, the hydrocarbon chain is a C8-C30 hydrocarbon chain. In some embodiments, the hydrocarbon chain is a C16 hydrocarbon chain. In some embodiments, the C16 hydrocarbon chain is represented by. In some embodiments, the hydrocarbon chain is a C18 hydrocarbon chain. In some embodiments, the C18 hydrocarbon chain is represented by.
[0281] In some embodiments, the oligonucleotide comprises a sense strand comprising a sequence selected from SEQ ID NOs: 89-280, wherein the sense strand comprises a C18 lipid. In some embodiments, the 4 nucleosides of the tetraloop are numbered 1-4 from 5’ to 3’ and position 1 is represented by formula II-Ib. In some embodiments, position 2 is represented by formula II-Ib. In some embodiments, position 3 is represented by formula II-Ib. In some embodiments, position 4 is represented by formula II- Ib. In some embodiments, the sense strand is 36 nucleotides with positions numbered 1-36 from 5’ to 3’, wherein the stem-loop comprises nucleotides at positions 21-36, and wherein one or more nucleosides at positions 27-30 are represented by formula II-Ib. In some embodiments, the antisense strand is 22 nucleotides. Exemplary STAT3 Targeting Oligonucleotides
[0282] In some embodiments, an oligonucleotide targeting STAT3 comprises a sense strand and an antisense strand as set forth in Tables 1, 2, 3, 8, 9, 10, 11, and 12, wherein the oligonucleotide comprises a stem loop structure having a double-stranded stem of about 2-6 base pairs and a loop of 3-4 nucleotides, and wherein the sense and antisense strands comprise the modification pattern set forth in FIG.1A or Example 7. In some embodiments, an oligonucleotide targeting STAT3 comprises a sense strand and an antisense strand as set forth in Tables 1, 2, 3, 8, 9, 10, 11, and 12, wherein the oligonucleotide comprises a stem loop structure having a double-stranded stem of about 2-6 base pairs and a loop of 3-4 nucleotides, wherein the sense and antisense strands comprise the modification pattern set forth in FIG.1A, and wherein antisense strand is modified with an oxymethylphosphonate at the 4’ carbon of the 5’ terminal nucleotide. In some embodiments, the oligonucleotide comprises a stem loop comprising the nucleotide sequence of SEQ ID NO: 86. In some embodiments, the oligonucleotide comprises a double-stranded stem of 6 base pairs and a stem loop of 4 nucleotides comprising one, two, three or four GalNAc conjugated nucleotides. In some embodiments, the GalNAc conjugated nucleotide is a monovalent GalNAc conjugated to an adenine nucleotide, referred to as [ademA-GalNAc] or 2′- aminodiethoxymethanol-Adenine-GalNAc, as depicted below:
[0283] In some embodiments, the stem loop comprises a double-stranded stem of 6 base pairs and a loop comprising the nucleotide sequence GAAA, wherein each adenine nucleotide is ademA-GalNAc.
[0284] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively.
[0285] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand and an antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively, wherein the sense and antisense strands are modified based on the pattern below Sense Strand: [mXs][mX][mX][mX][mX][mX][mX][fX][fX][fX][fX][mX][mX][mX][mX][mX][mX][ mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][ademX-C#] [mX] [mX] [mX] [mX] [mX] [mX][mX][mX] Hybridized to Antisense Strand: [MePhosphonate-4O-mXs][fXs][fX][fX][fX][mX][fX][mX][mX] [fX][mX][mX][mX][fX][mX][mX][mX][mX][mX][mXs][mXs][mX] (key provided in Table 7). In some embodiments, C# is C16 or C18.
[0286] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand and an antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 862 and 952, respectively; (b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the sense and antisense strands are modified based on the pattern below Sense Strand: [mXs][mX][mX][mX][mX][mX][mX][fX][fX][fX][fX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][ademX-C#] [mX] [mX] [mX] [mX] [mX] [mX][mX][mX] Hybridized to Antisense Strand: [MePhosphonate-4O-mXs][fXs][fX][fX][fX][mX][fX][mX][mX] [fX][mX][mX][mX][fX][mX][mX][mX][mX][mX][mXs][mXs][mX] (key provided in Table 7). In some embodiments, C# is C16 or C18.
[0287] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand and an antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 862 and 952, respectively; (b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the sense and antisense strands are modified based on the pattern below Sense Strand: [mXs][mX][mX][mX][mX][mX][mX][fX][fX][fX][fX][mX][mX][mX][mX][mX][mX][ mX][mX][mX][mX][mX][mX][mX][mX][mX][mX][ademX-C#] [mX] [mX] [mX] [mX] [mX] [mX][mX][mX] Hybridized to Antisense Strand: [MePhosphonate-4O-mXs][fXs][fXs][fX][fX][mX][fX][mX][mX] [fX][mX][mX][mX][fX][mX][mX][mX][mX][mX][mXs][mXs][mX] (key provided in Table 7). In some embodiments, C# is C16 or C18.
[0288] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 11 and 12, respectively; (b) SEQ ID NOs: 39 and 40, respectively; (c) SEQ ID NOs: 67 and 68, respectively; and (d) SEQ ID NOs: 71 and 72, respectively.
[0289] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sequence set forth in SEQ ID NO: 81. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sequence set forth in SEQ ID NO: 82. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sequence set forth in SEQ ID NO: 83. In some embodiments, anoligonucleotide for reducing expression of STAT3 mRNA comprises the sequence set forth in SEQ ID NO: 84.
[0290] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand having nucleotide sequences set forth in SEQ ID NOs: 87 and 68, respectively. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand having nucleotide sequences set forth in SEQ ID NOs: 88 and 71, respectively.
[0291] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 89-280. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 857-946. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 857-888. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 889-912. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 913-934. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 935-946.
[0292] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 947-1036. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 947-978. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 979-1002. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 1003-1024. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 1025-1036.
[0293] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 857-946 and an antisense strand selected from SEQ ID NOs: 947-1036. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 857-888 and an antisense strand selected from SEQ ID NOs: 947-978. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNAcomprises a sense strand sequence selected from SEQ ID NOs: 889-912 and an antisense strand selected from SEQ ID NOs: 979-1002. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 913-934 and an antisense strand selected from SEQ ID NOs:1003-1024. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 935-946 and an antisense strand selected from SEQ ID NOs:1025-1036.
[0294] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1037-1126. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1037-1068. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs:1069-1092. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1093-1114. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs:1115-1126.
[0295] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 1127-1216. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 1127-1158. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs: 1159-1182. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs:1183-1204. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises an antisense strand sequence selected from SEQ ID NOs:1205-1216.
[0296] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1037-1126 and an antisense strand selected from SEQ ID NOs: 1127-1216. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1037-1068 and an antisense strand selected from SEQ ID NOs: 1127-1182. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1069-1092 and an antisense strand selected from SEQ ID NOs: 1159-1182. In some embodiments, anoligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1093-1114 and an antisense strand selected from SEQ ID NOs:1183-1204. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense strand sequence selected from SEQ ID NOs: 1115-1126 and an antisense strand selected from SEQ ID NOs:1205-1216.
[0297] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 857 and 947, respectively; (b) SEQ ID NOs: 858 and 948, respectively; (c) SEQ ID NOs: 859 and 949, respectively; (d) SEQ ID NOs: 860 and 950, respectively; (e) SEQ ID NOs: 862 and 952, respectively; (f) SEQ ID NOs: 867 and 957, respectively; (g) SEQ ID NOs: 875 and 965, respectively; and (h) SEQ ID NOs: 876 and 966, respectively.
[0298] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively.
[0299] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively.
[0300] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively.
[0301] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 862 and 952, respectively; (b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively.
[0302] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 862 and the antisense strand comprises the sequence of SEQ ID NO: 952.
[0303] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 875 and the antisense strand comprises the sequence of SEQ ID NO: 965.
[0304] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 876 and the antisense strand comprises the sequence of SEQ ID NO: 966.
[0305] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 920 and the antisense strand comprises the sequence of SEQ ID NO: 1010.
[0306] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1037 and 1127, respectively; (b) SEQ ID NOs: 1038 and 1128, respectively; (c) SEQ ID NOs: 1039 and 1129, respectively; (d) SEQ ID NOs: 1040 and 1130, respectively; (e) SEQ ID NOs: 1042 and 1132, respectively; (f) SEQ ID NOs: 1047 and 1137, respectively; (g) SEQ ID NOs: 1055 and 1145, respectively; and (h) SEQ ID NOs: 1056 and 1146, respectively.
[0307] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1081 and 1171, respectively; (b) SEQ ID NOs: 1090 and 1180, respectively; (c) SEQ ID NOs: 1079 and 1169, respectively; (d) SEQ ID NOs: 1076 and 1166, respectively; (e) SEQ ID NOs: 1072 and 1162, respectively; (f) SEQ ID NOs: 1070 and 1160, respectively; and (g) SEQ ID NOs: 1069 and 1159, respectively.
[0308] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1120 and 1210, respectively; (b) SEQ ID NOs: 1117 and 1207, respectively; and (c) SEQ ID NOs: 1119 and 1209, respectively.
[0309] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1095 and 1185, respectively; (b) SEQ ID NOs: 1104 and 1194, respectively; (c) SEQ ID NOs: 1093 and 1183, respectively; and (d) SEQ ID NOs: 1100 and 1190, respectively.
[0310] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1042 and 1132, respectively; (b) SEQ ID NOs: 1055 and 1145, respectively; (c) SEQ ID NOs: 1056 and 1146, respectively; and (d) SEQ ID NOs: 1100 and 1190, respectively.
[0311] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 1042 and the antisense strand comprises the sequence of SEQ ID NO: 1132.
[0312] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 1055 and the antisense strand comprises the sequence of SEQ ID NO: 1145.
[0313] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 1056 and the antisense strand comprises the sequence of SEQ ID NO: 1146.
[0314] In some embodiments, the sense strand comprises the sequence of SEQ ID NO: 1100 and the antisense strand comprises the sequence of SEQ ID NO: 1190.
[0315] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand comprising nucleotide sequences selected from: (a) SEQ ID NOs: 1042 and 4, respectively; (b) SEQ ID NOs: 1055 and 5, respectively; (c) SEQ ID NOs: 1056 and 6, respectively; and (d) SEQ ID NOs: 1100 and 7, respectively.
[0316] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA described herein comprises minimal off-target effects. For example, in some embodiments, an oligonucleotide described herein reduces STAT3 expression and does not reduce STAT1 expression or reduces STAT1 expression less than STAT3 expression. In some embodiments, the oligonucleotide comprises a sense strand comprising the nucleotide sequence set forth in SEQ ID NO: 862 and an antisense strand comprising the nucleotide sequence set forth in SEQ ID NO: 952, wherein the oligonucleotide reduces STAT3 expression and does not reduce STAT1 expression or reduces STAT1 expression less than STAT3 expression. In some embodiments, the oligonucleotide comprises a sense strand comprising the nucleotide sequence set forth in SEQ ID NO: 1042 and an antisense strand comprising the nucleotide sequence set forth in SEQ ID NO: 1132, wherein the oligonucleotide reduces STAT3 expression and does not reduce STAT1 expression or reduces STAT1 expression less than STAT3 expression. In some embodiments, the oligonucleotide comprises a sense strand comprising the nucleotide sequence set forth in SEQ ID NO: 875 and an antisense strand comprising the nucleotide sequence set forth in SEQ ID NO: 965, wherein the oligonucleotide reduces STAT3 expression and does not reduce STAT1 expression or reduces STAT1 expression less than STAT3 expression. In some embodiments, the oligonucleotide comprises a sense strand comprising the nucleotide sequence set forth in SEQ ID NO: 1055 and an antisense strand comprising the nucleotide sequence set forth in SEQ ID NO: 1145, wherein the oligonucleotide reduces STAT3 expression and does not reduce STAT1 expression or reduces STAT1 expression less than STAT3 expression.
[0317] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA described herein is a species cross-reactive oligonucleotide. In some embodiments, an oligonucleotide described herein is capable of reducing expression of STAT3 mRNA of at least two different species. In some embodiments, an oligonucleotide described herein is capable of reducing expression of STAT3 mRNA of at least two different species but does not cross-react with non-STAT3 mRNA (e.g., STAT1). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA is cross-reactive between at least two species. In some embodiments, an oligonucleotide for reducing expression of STAT3 cross-reacts with human, non-human primate, and mouse STAT3 mRNA. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA cross-reacts with human and mouse STAT3 mRNA. In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA cross-reacts with human and non-human primate STAT3 mRNA.
[0318] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.
[0319] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50% to at least 75% in human, non-human primate, and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% in human, non-human primate, and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 80%, at least 85%, at least 90%, or at least 95% in human, non-human primate, and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0320] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50% to at least 75% in human and non-human primate (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% in human and non-human primate (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 80%, at least 85%, at least 90%, or at least 95% inhuman and non-human primate (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0321] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50% to at least 75% in human and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% in human and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA reduces STAT3 mRNA by at least 80%, at least 85%, at least 90%, or at least 95% in human and mouse (i.e. the oligonucleotide is a species cross-reactive oligonucleotide). In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0322] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0323] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and(d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0324] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0325] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide reduces STAT3 mRNA in humans.
[0326] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide reduces STAT3 mRNA in humans.
[0327] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide reduces STAT3 mRNA in humans.
[0328] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 857 and 947, respectively; (b) SEQ ID NOs: 858 and 948, respectively; (c) SEQ ID NOs: 859 and 949, respectively; (d) SEQ ID NOs: 860 and 950, respectively; (e) SEQ ID NOs: 862 and 952, respectively; (f) SEQ ID NOs: 867 and 957, respectively; (g) SEQ ID NOs: 875 and 965, respectively; and (h) SEQ ID NOs: 876 and 966, respectively, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0329] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively;(c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0330] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0331] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0332] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 862 and 952, respectively; (b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0333] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0334] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide reduces STAT3 mRNA by at least
[0335] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0336] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide reduces STAT3 mRNA by at least 75%.
[0337] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 857 and 947, respectively; (b) SEQ ID NOs: 858 and 948, respectively; (c) SEQ ID NOs: 859 and 949, respectively; (d) SEQ ID NOs: 860 and 950, respectively; (e) SEQ ID NOs: 862 and 952, respectively; (f) SEQ ID NOs: 867 and 957, respectively; (g) SEQ ID NOs: 875 and 965, respectively; and (h) SEQ ID NOs: 876 and 966, respectively, wherein the oligonucleotide is conjugated to a lipid.
[0338] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0339] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively,wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0340] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0341] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 862 and 952, respectively; (b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0342] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0343] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0344] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0345] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a lipid on the sense strand.
[0346] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 857 and 947, respectively;(b) SEQ ID NOs: 858 and 948, respectively; (c) SEQ ID NOs: 859 and 949, respectively; (d) SEQ ID NOs: 860 and 950, respectively; (e) SEQ ID NOs: 862 and 952, respectively; (f) SEQ ID NOs: 867 and 957, respectively; (g) SEQ ID NOs: 875 and 965, respectively; and (h) SEQ ID NOs: 876 and 966, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0347] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0348] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0349] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0350] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 862 and 952, respectively;(b) SEQ ID NOs: 875 and 965, respectively; (c) SEQ ID NOs: 876 and 966, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0351] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0352] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0353] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0354] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand.
[0355] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0356] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively;(b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0357] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide reduces STAT3 mRNA in humans by at least 75%.
[0358] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0359] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide reduces STAT3 mRNA in humans by at least 75%.
[0360] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide reduces STAT3 mRNA in humans by at least 75%.
[0361] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide reduces STAT3 mRNA in humans by at least 75%.
[0362] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively;(e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross- reactive oligonucleotide).
[0363] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0364] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans.
[0365] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0366] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans.
[0367] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strandsequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans.
[0368] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans.
[0369] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0370] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0371] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans.
[0372] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide).
[0373] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a C18 on the sense strand lipid and reduces STAT3 mRNA in humans.
[0374] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans.
[0375] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans.
[0376] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross- reactive oligonucleotide) by at least 75%.
[0377] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively,wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0378] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0379] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0380] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0381] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strand sequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0382] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0383] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively;(e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans, non-human primates, and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0384] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans and mice (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0385] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises a sense and antisense strand selected from: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0386] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 862 and the antisense strand sequence of SEQ ID NO: 952, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans and non-human primates (i.e. the oligonucleotide is a species cross-reactive oligonucleotide) by at least 75%.
[0387] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 875 and the antisense strand sequence of SEQ ID NO: 965, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0388] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 876 and the antisense strandsequence of SEQ ID NO: 966, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%.
[0389] In some embodiments, an oligonucleotide for reducing expression of STAT3 mRNA comprises the sense strand sequence of SEQ ID NO: 920 and the antisense strand sequence of SEQ ID NO: 1010, wherein the oligonucleotide is conjugated to a C18 lipid on the sense strand and reduces STAT3 mRNA in humans by at least 75%. Formulations
[0390] Various formulations have been developed to facilitate oligonucleotide use. For example, oligonucleotides can be delivered to a subject or a cellular environment using a formulation that minimizes degradation, facilitates delivery and / or uptake, or provides another beneficial property to the oligonucleotides in the formulation. In some embodiments, an oligonucleotide is formulated in buffer solutions such as phosphate buffered saline solutions, liposomes, micellar structures, and capsids.
[0391] Formulations of oligonucleotides with cationic lipids can be used to facilitate transfection of the oligonucleotides into cells. For example, cationic lipids, such as lipofectin, cationic glycerol derivatives, and polycationic molecules (e.g., polylysine, can be used. Suitable lipids include Oligofectamine, Lipofectamine (Life Technologies), NC388 (Ribozyme Pharmaceuticals, Inc., Boulder, Colo.), or FuGene 6 (Roche) all of which can be used according to the manufacturer′s instructions.
[0392] Accordingly, in some embodiments, a formulation comprises a lipid nanoparticle. In some embodiments, an excipient comprises a liposome, a lipid, a lipid complex, a microsphere, a microparticle, a nanosphere or a nanoparticle, or may be otherwise formulated for administration to the cells, tissues, organs, or body of a subject in need thereof (see, e.g., Remington: THE SCIENCE AND PRACTICE OF PHARMACY, 22nd edition, Pharmaceutical Press, 2013).
[0393] In some embodiments, the formulations herein comprise an excipient. In some embodiments, an excipient confers to a composition improved stability, improved absorption, improved solubility and / or therapeutic enhancement of the active ingredient. In some embodiments, an excipient is a buffering agent (e.g., sodium citrate, sodium phosphate, a tris base, or sodium hydroxide) or a vehicle (e.g., a buffered solution, petrolatum, dimethyl sulfoxide, or mineral oil). In some embodiments, an oligonucleotide is lyophilized for extending its shelf-life and then made into a solution before use (e.g., administration to a subject). Accordingly, an excipient in a composition comprising any one of theoligonucleotides described herein may be a lyoprotectant (e.g., mannitol, lactose, polyethylene glycol or polyvinylpyrrolidone) or a collapse temperature modifier (e.g., dextran, Ficoll™ or gelatin).
[0394] In some embodiments, a pharmaceutical composition is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral (e.g., intravenous, intramuscular, intraperitoneal, intradermal, subcutaneous), oral (e.g., inhalation), transdermal (e.g., topical), transmucosal and rectal administration.
[0395] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohol’s such as mannitol, sorbitol, sodium chloride in the composition. Sterile injectable solutions can be prepared by incorporating the oligonucleotides in a required amount in a selected solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
[0396] In some embodiments, a composition may contain at least about 0.1% of the therapeutic agent or more, although the percentage of the active ingredient(s) may be between about 1% to about 80% or more of the weight or volume of the total composition. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.
[0397] Even though several embodiments are directed to liver-targeted delivery of any of the oligonucleotides herein, targeting of other tissues is also contemplated. Programmed Death Ligand 1 (PD-L1) Inhibitors
[0398] In some embodiments, the disclosure provides a PD-L1 inhibitor for use in combination with an oligonucleotide described herein. In some embodiments, a PD-L1 inhibitor is a small molecule, a peptide, a protein, an antibody, or nucleic acid molecule suchas an siRNA, miRNA, or an antisense RNA. In some embodiments, the PD-L1 inhibitor inhibits association of PD-L1 and PD-1. In some embodiments, the PD-L1 inhibitor is specific for PD-L1.
[0399] In some embodiments, the PD-L1 inhibitor is an anti-PD-L1 antibody. In some embodiments, the PD-L1 inhibitor is specific for PD-1. In some embodiments, the PD-L1 inhibitor is an anti-PD-1 antibody. In some embodiments, the antibody is a full-length antibody. In some embodiments, the antibody is an antibody fragment. In some embodiments, the PD- L1 inhibitor is a small molecule.
[0400] In some embodiments, the anti-PD-L1 antibody is atezolizumab. Atezolizumab (MPDL3280A) is a fully humanized, engineered IgG1 monoclonal antibody to PD-L1. In some embodiments, the anti-PD-L1 antibody is avelumab. Avelumab (MSB0010718C) is a fully humanized, engineered IgG1 monoclonal antibody to PD-L1. In some embodiments, the anti-PD-L1 antibody is envafolimab. In some embodiments, the anti- PD-L1 antibody is durvalumab. Duvalumab (MEDI4736) is a human monoclonal antibody to PD-L1. In some embodiments, the anti-PD-L1 antibody is TSR-042. TSR-042 refers to an engineered chimeric antibody directed against the PD-1 / PD-L1 pathway. In some embodiments, the anti-PD-L1 antibody is KD-033. KD-033 refers to a bifunctional anti-PD- L1 / IL-15 fusion protein, wherein the anti-PD-L1 antibody binds to the cytokine IL-15 by the sushi domain of the IL-15 receptor connected at the tail. In some embodiments, the anti-PD- L1 antibody is STI-1014. STI-1014 refers to an anti-PD-L1 antibody. In some embodiments, the anti-PD-L1 antibody is KY-1003. KY-1003 is a monoclonal antibody against PD-L1. In some embodiments, the anti-PD-L1 antibody is YW243.55.S70. Antibody YW243.55.S70 is an anti-PDL1 described in U.S. Patent No.9,920,123, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-L1 antibody is MDX-1106. MDX- 1106, also known as MDX-1106-04, ONO-4538 or BMS-936558, is an anti-PD 1 antibody described in U.S. Patent No.8,008,449, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-L1 antibody is Merck 3745. Merck 3745, also known as MK-3475 or SCH-900475, is an anti-PD1 antibody described in U.S. Patent No. 8,168,757, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-L1 antibody is CT-011. CT-011, also known as hBAT or hBAT-1, is an anti-PD1 antibody described in U.S. Patent No.8,747,847, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-L1 antibody is AMP- 224. AMP-224, also known as B7-DClg, is a PDL2-Fc fusion soluble receptor describedin U.S. Pub. No.2011 / 0223188 and U.S. Pub. No.2013 / 0017199, the contents of which are incorporated herein in their entirety.
[0401] In some embodiments, the anti-PD-L1 antibody is any anti-PD-L1 antibody known in the art, including, but not limited to, the anti-PD-L1 antibodies disclosed in Akinleye & Rasool “Immune checkpoint inhibitors of PD-L1 as cancer therapeutics” J. of Hematology & Oncology.12(92): 2019. In some embodiments, the anti-PD-L1 antibody is BMS-936559. BMS-936559 (MDX-1105) is a fully human IgG4 monoclonal antibody against PD-L1 and is described in U.S. Patent No.7,943,743, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-L1 antibody is CK- 301. In some embodiments, the anti-PD-L1 antibody is CS-1001. In some embodiments, the anti-PD-L1 antibody is SHR-1316. In some embodiments, the anti-PD-L1 antibody is BG- A333. In some embodiments, the anti-PD-L1 antibody is an antibody disclosed in International Pub. No. WO 2021 / 231741, the contents of which are incorporated herein in their entirety.
[0402] In some embodiments, the anti-PD-1 antibody is nivolumab. Nivolumab (BMS-936558) is an IgG4 monoclonal antibody described in U.S. Patent No.8,008,449, the contents of which are incorporated herein in their entirety. In some embodiments, the anti- PD-1 antibody is pembrolizumab. Pembrolizumab is an IgG4 monoclonal antibody described in U.S. Patent No.8,354,509, the contents of which are incorporated herein in their entirety. In some embodiments, the anti-PD-1 antibody is cemiplimab. Cemiplimab (REGN2810) is an IgG4 monoclonal antibody described in U.S. Patent No.9,987,500, the contents of which are incorporated herein in their entirety.
[0403] In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 30nM to about 100nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 30nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 40nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 50nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 60nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 70nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 80nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 90nM. In some embodiments, the anti-PD-L1 antibody described herein binds to PD-L1 with an affinity of about 100nM.
[0404] In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 30nM to about 100nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 30nM. In some embodiments, the anti- PD-1 antibody described herein binds to PD-1 with an affinity of about 40nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 50nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 60nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 70nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 80nM. In some embodiments, the anti- PD-1 antibody described herein binds to PD-1 with an affinity of about 90nM. In some embodiments, the anti-PD-1 antibody described herein binds to PD-1 with an affinity of about 100nM.
[0405] In some embodiments, the antibody is generated using display technologies. Display technologies used to generate antibody polypeptides include any of the display techniques (e.g. display library screening techniques). In some embodiments, synthetic antibodies are designed, selected, or optimized by screening target antigens using display technologies (e.g. phage display technologies). Phage display libraries may comprise millions to billions of phage vectors, each expressing unique antibody fragments on their viral coats. Such libraries may provide richly diverse resources that are used to select potentially hundreds of antibody fragments with diverse levels of affinity for one or more antigens of interest (McCafferty, et al., 1990. Nature.348:552-4; Edwards, B.M. et al., 2003. JMB.334: 103-18; Schofield, D. et al., 2007. Genome Biol.8, R254 and Pershad, K. et al., 2010. Protein Engineering Design and Selection.23:279-88; the contents of each of which are herein incorporated by reference in their entirety). Often, the antibody fragments present in such libraries comprise scFv antibody fragments, comprising a fusion protein of VHand VL antibody domains joined by a flexible linker. In some cases, scFvs may contain the same sequence with the exception of unique sequences encoding variable loops of the CDRs. In some cases, scFvs are expressed as fusion proteins, linked to viral coat proteins (e.g. the N- terminus of the viral pill coat protein). VL chains may be expressed separately for assembly with VH chains in the periplasm prior to complex incorporation into viral coats. Precipitated library members may be sequenced from the bound phage to obtain cDNA encoding desired scFvs. Antibody variable domains or CDRs from such sequences may be directly incorporated into antibody sequences for recombinant antibody production or mutated and utilized for further optimization through in vitro affinity maturation.
[0406] In some embodiments, the sequences of the polypeptides to be encoded in the viral genomes are produced using yeast surface display technology. In some embodiments, recombinant antibodies are developed by displaying the antibody fragment of interest as a fusion to on the surface of the yeast, where the protein interacts with proteins and small molecules in a solution. scFvs with affinity toward desired receptors may be isolated from the yeast surface using magnetic separation and flow cytometry. Several cycles of yeast surface display and isolation may be done to attain scFvs with desired properties through directed evolution.
[0407] Methods for determining the affinity of an antibody for its antigen are known in the art. An exemplary method for determining binding affinity employs surface plasmon resonance. Surface plasmon resonance is an optical phenomenon that allows for the analysis of realtime biospecific interactions by detection of alterations in protein concentrations within a biosensor matrix, for example using the BIAcore system (Pharmacia Biosensor AB, Uppsala, Sweden and Piscataway, N.J.). For further descriptions, see Jonsson, U., et al. (1993) Ann. Biol. Clin.51: 19-26; Jonsson, U., i (1991) Biotechniques 11 :620-627; Johnsson, B., et al. (1995) J. Mol.Recognit.8: 125-131; and Johnsson, B., et al. (1991) Anal. Biochem.198:268-277.
[0408] In some embodiments, the PD-L1 inhibitor is an siRNA molecule. In some embodiments, the PD-L1 inhibitor is ALN-PDL. In some embodiments, the PD-L1 inhibitor is a PD-L1 inhibitor described in U.S. Patent No.10,889,813, U.S. Patent No.10,745,704, U.S. Pub. No.2021 / 0277403, U.S. Pub. No.2006 / 0276422A1, U.S.2021 / 0277403, International Pub. No. WO2019 / 000149, or International Pub. No. WO2019 / 000149, the contents of which are incorporated herein in their entirety. In some embodiments, the PD-L1 inhibitor is an siRNA molecule described in Barati, M., et al. A review of PD-1 / PD-L1 siRNA delivery systems in immune T cells and cancer cells, International Immunopharmacology, 2022, vol.111. In some embodiments, the siRNA molecule for inhibition of PD-L1 is an siRNA molecule generated using methods known to those of skill in the art.
[0409] In some embodiments, the PD-L1 inhibitor is an antisense oligonucleotide. In some embodiments, the PD-L1 inhibitor is an antisense oligonucleotide described in U.S. Patent No.10,745,480, U.S. Patent. No.10,982,215, U.S. Pub. No.2021 / 0269797A1, or U.S. Pub. No. US20220220485A1, the contents of which are incorporated herein in their entirety. In some embodiments, the antisense oligonucleotide for inhibition of PD-L1 is an antisense oligonucleotide generated using methods known to those of skill in the art.
[0410] In some embodiments, the PD-L1 inhibitor is a small molecule. In some embodiments, the small molecule is CA-170. CA-170 is a small molecule antagonist of PD- L1 and VISTA. In some embodiments, the small molecule is CA-327. CA-327 refers to small molecule antagonists of PD-L1 and TIM3. In some embodiments, the small molecule is BMS-1001. In some embodiments, the small molecule is BMS-1166. In some embodiments, the small molecule is BMS-8. In some embodiments, the small molecule is BMS-37. In some embodiments, the small molecule is BMS-202. In some embodiments, the small molecule is BMS-200. In some embodiments, the small molecule is Incyte-001. In some embodiments, the small molecule is Incyte-011. In some embodiments, the small molecule is INCB086550. In some embodiments, the small molecule is LH1306. In some embodiments, the small molecule is LH1307. In some embodiments, the small molecule is ARB-272572. In some embodiments, the PD-L1 inhibitor is a small molecule described in Sasikumar, P. et al. Small Molecule Agents Targeting PD-1 Checkpoint Pathway for Cancer Immunotherapy: Mechanisms of Action and Other Considerations for Their Advanced Development, Front. Immunol.2022, 13:752065. In some embodiments, the PD-L1 inhibitor is a small molecule described in U.S. Patent No.11,130,740, U.S. Patent No.10,590,105, International Pub. No. WO2019 / 076343, U.S. Patent No.11,555,029, or U.S. Pub. No.2018 / 0305315, the contents of which are incorporated herein in their entirety. In some embodiments, the small molecule is a small molecule described in Wu, Q. et al. Small molecule inhibitors targeting the PD- 1 / PD-L1 signaling pathway, Acta Pharmacologica Sinica.2021, 42: 1-9. In some embodiments, the small molecule is a small molecule described in Wang, Y. et al. A Small Molecule Antagonist of PD-1 / PD-L1 Interactions Acts as an Immune Checkpoint Inhibitor for NSCLC and Melanoma Immunotherapy, Front. Immuno.2021. Vol.12. In some embodiments, the small molecule inhibitor is a stereoisomer, a tautomer, a pharmaceutically acceptable salt, a hydrate, or a solvent of a small molecule described herein. In some embodiments, the small molecule for inhibition of PD-L1 is a small molecule generated using methods known to those of skill in the art.
[0411] In some embodiments, the PD-L1 inhibitor is a peptide. In some embodiments, the PD-L1 inhibitor is a peptide inhibitor described in U.S. Patent No.9,422,339 or U.S. Patent No.9,850,283, the contents of which are incorporated herein in their entirety. In some embodiments, the PD-L1 inhibitor is a peptide inhibitor described in Yin, H. et al. Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy, J. Am. Chem. Soc.2021, 143: 44, 18536-18547. In some embodiments, the PD-L1 inhibitor is a peptide inhibitor described in Lin, X., et al. Progress in PD-1 / PD-L1pathway inhibitors: From biomacromolecules to small molecules, Euro. J. Med. Chem.2020, vol.186. In some embodiments, the inhibitor peptide for inhibition of PD-L1 is a peptide generated using methods known to those of skill in the art.
[0412] The person skilled in the art knows how to determine whether a compound is a PD1 and / or PDL1 inhibitor by testing it in an appropriate assay. Binding of inhibitors to PD1 and / or PDL1 and / or PDL2 can e.g., be measured in ELISA-type assays that are well known in the art. Bioassays to measure the biological effect of PD1 and / or PDL1 and / or PDL2 inhibition are well known by the person skilled in the art. Kits
[0413] In some embodiments, the disclosure provides a kit comprising a STAT3 oligonucleotide herein, and instructions for administering the STAT3 oligonucleotide to a subject that has received or is receiving a PD-L1 inhibitor. In some embodiments, the kit comprises, in a suitable container, an oligonucleotide herein, one or more controls, and various buffers, reagents, enzymes and other standard ingredients well known in the art. In some embodiments, the container comprises at least one vial, well, test tube, flask, bottle, syringe, or other container means, into which the oligonucleotide is placed, and in some instances, suitably aliquoted. In some embodiments where an additional component is provided, the kit contains additional containers into which this component is placed. The kits can also include a means for containing the oligonucleotide and any other reagent in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained. Containers and / or kits can include labeling with instructions for use and / or warnings.
[0414] In some embodiments, a kit comprises a STAT3 oligonucleotide herein, and a pharmaceutically acceptable carrier, or a pharmaceutical composition comprising the oligonucleotide and instructions for treating or delaying progression of a disease, disorder or condition associated with STAT3 expression in a subject in need thereof, wherein the subject has received or is receiving a PD-L1 inhibitor. In some embodiments, a kit comprises a STAT3 oligonucleotide herein, and a pharmaceutically acceptable carrier, or a pharmaceutical composition comprising the oligonucleotide and instructions for treating or delaying progression of a cancer in a subject in need thereof, wherein the subject has received or is receiving a PD-L1 inhibitor.
[0415] In some embodiments, a kit comprises a PD-L1 inhibitor, and a pharmaceutically acceptable carrier, or a pharmaceutical composition comprising theoligonucleotide and instructions for treating or delaying progression of a disease, disorder or condition in a subject in need thereof, wherein the subject has received or is receiving a STAT3 oligonucleotide described herein. In some embodiments, a kit comprises a PD-L1 inhibitor, and a pharmaceutically acceptable carrier, or a pharmaceutical composition comprising the oligonucleotide and instructions for treating or delaying progression of a cancer in a subject in need thereof, wherein the subject has received or is receiving a STAT3 oligonucleotide described herein. EXAMPLES
[0416] While the disclosure has been described with reference to the specific embodiments set forth in the following Examples, it should be understood by those skilled in the art that various changes may be made, and equivalents may be substituted without departing from the true spirit and scope of the disclosure. Further, the following Examples are offered by way of illustration and are not intended to limit the scope of the disclosure in any manner. In addition, modifications may be made to adapt to a situation, material, composition of matter, process, process step or steps, to the objective, spirit, and scope of the disclosure. All such modifications are intended to be within the scope of the disclosure. Standard techniques well known in the art or the techniques specifically described below were utilized. Abbreviations Ac: acetyl AcOH: acetic acid ACN: acetonitrile Ad: adamantyl AIBN: 2,2'-azo bisisobutyronitrile Anhyd: anhydrous Aq: aqueous B2Pin2: bis (pinacolato)diboron -4,4,4',4',5,5,5',5'-octamethyl-2,2'-bi(1,3,2- dioxaborolane) BINAP: 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl BH3: Borane Bn: benzyl Boc: tert-butoxycarbonylBoc2O: di-tert-butyl dicarbonate BPO: benzoyl peroxide BuOH: n-butanol CDI: carbonyldiimidazole COD: cyclooctadiene d: days DABCO: 1,4-diazobicyclo[2.2.2]octane DAST: diethylaminosulfur trifluoride dba: dibenzylideneacetone DBU: 1,8-diazobicyclo[5.4.0]undec-7-ene DCE: 1,2-dichloroethane DCM: dichloromethane DEA: diethylamine DHP: dihydropyran DIBAL-H: diisobutylaluminum hydride DIPA: diisopropylamine DIPEA or DIEA: N,N-diisopropylethylamine DMA: N,N-dimethylacetamide DME: 1,2-dimethoxyethane DMAP: 4-dimethylaminopyridine DMF: N,N-dimethylformamide DMP: Dess-Martin periodinane DMSO-dimethyl sulfoxide DMTr: 4,4’-dimethyoxytrityl DPPA: diphenylphosphoryl azide dppf: 1,1’-bis(diphenylphosphino)ferrocene EDC or EDCI: 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride ee: enantiomeric excess ESI: electrospray ionization EA: ethyl acetate EtOAc: ethyl acetate EtOH: ethanol FA: formic acid h or hrs: hoursHATU: N,N,N’,N’-tetramethyl-O-(7-azabenzotriazol-1-yl)uronium hexafluorophosphate HCl: hydrochloric acid HPLC: high performance liquid chromatography HOAc: acetic acid IBX: 2-iodoxybenzoic acid IPA: isopropyl alcohol KHMDS: potassium hexamethyldisilazide K2CO3: potassium carbonate LAH: lithium aluminum hydride LDA: lithium diisopropylamide L-DBTA: dibenzoyl-L-tartaric acid m-CPBA: meta-chloroperbenzoic acid M: molar MeCN: acetonitrile MeOH: methanol Me2S: dimethyl sulfide MeONa: sodium methylate MeI: iodomethane min: minutes mL: milliliters mM: millimolar mmol: millimoles MPa: mega pascal MOMCl: methyl chloromethyl ether MsCl: methanesulfonyl chloride MTBE: methyl tert-butyl ether nBuLi: n-butyllithium NaNO2: sodium nitrite NaOH: sodium hydroxide Na2SO4: sodium sulfate NBS: N-bromosuccinimide NCS: N-chlorosuccinimide NFSI: N-FluorobenzenesulfonimideNMO: N-methylmorpholine N-oxide NMP: N-methylpyrrolidine NMR: Nuclear Magnetic ResonanceoC: degrees Celsius Pd / C: Palladium on Carbon Pd(OAc)2: Palladium Acetate PBS: phosphate buffered saline PE: petroleum ether POCl3: phosphorus oxychloride PPh3: triphenylphosphine PyBOP: (Benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate Rel: relative R.T. or rt: room temperature s or sec: second sat: saturated SEMCl: chloromethyl-2-trimethylsilylethyl ether SFC: supercritical fluid chromatography SOCl2: sulfur dichloride tBuOK: potassium tert-butoxide TBAB: tetrabutylammonium bromide TBAF: tetrabutylammmonium fluoride TBAI: tetrabutylammonium iodide TEA: triethylamine Tf: trifluoromethanesulfonate TfAA, TFMSA or Tf2O: trifluoromethanesulfonic anhydride TFA: trifluoroacetic acid TIBSCl: 2,4,6-triisopropylbenzenesulfonyl chloride TIPS: triisopropylsilyl THF: tetrahydrofuran THP: tetrahydropyran TLC: thin layer chromatography TMEDA: tetramethylethylenediamine pTSA: para-toluenesulfonic acid UPLC: Ultra Performance Liquid Chromatographywt: weight Xantphos: 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene Example 1: Preparation of Double-Stranded RNAi Oligonucleotides General Synthetic Methods
[0417] The following examples are intended to illustrate the disclosure and are not to be construed as being limitations thereon. Temperatures are given in degrees centigrade (C). If not mentioned otherwise, all evaporations are performed under reduced pressure, preferably between about 15 mm Hg and 100 mm Hg (= 20-133 mbar). The structure of final products, intermediates and starting materials was confirmed by standard analytical methods, e.g., microanalysis and spectroscopic characteristics, e.g., MS, IR, NMR. Abbreviations used are those conventional in the art.
[0418] All starting materials, building blocks, reagents, acids, bases, dehydrating agents, solvents, and catalysts utilized to synthesis the nucleic acid or analogues thereof of the present disclosure are either commercially available or can be produced by organic synthesis methods known to one of ordinary skill in the art (METHODS OF ORGANIC SYNTHESIS, Thieme, Volume 21 (Houben-Weyl 4th Ed.1952)). Further, the nucleic acid or analogues thereof of the present disclosure can be produced by organic synthesis methods known to one of ordinary skill in the art as shown in the following examples.
[0419] All reactions are carried out under nitrogen or argon unless otherwise stated.
[0420] Proton NMR (1H NMR) was conducted in deuterated solvent. In certain nucleic acid or analogues thereof disclosed herein, one or more1H shifts overlap with residual proteo solvent signals; these signals have not been reported in the experimental provided hereinafter.
[0421] As depicted in the Examples below, in certain exemplary embodiments, the nucleic acid or analogues thereof were prepared according to the following general procedures. It will be appreciated that, although the general methods depict the synthesis of certain nucleic acid or analogues thereof of the present disclosure, the following general methods, and other methods known to one of ordinary skill in the art, can be applied to all nucleic acid or analogues thereof and subclasses and species of each of these nucleic acid or analogues thereof, as described herein. Example^1a:^Synthesis^of^2‐(2‐((((6aR,8R,9R,9aR)‐8‐(6‐benzamido‐9H‐purin‐9‐yl)‐2,2,4,4‐ tetraisopropyltetrahydro‐6H‐furo[3,2‐f][1,3,5,2,4]trioxadisilocin‐9‐yl)oxy)methoxy)ethoxy)^ethan‐1‐ammonium^formate^(1‐6)
[0422] A solution of compound 1-1 (25.00 g, 67.38 mmol) in 20 mL of DMF was treated with pyridine (11 mL, 134.67 mmol) and tetraisopropyldisiloxane dichloride (22.63 mL, 70.75 mmol) at 10 °C. The resulting mixture was stirred at 25 °C for 3 h and quenched with 20% citric acid (50 mL). The aqueous layer was extracted with EtOAc (3X50 mL) and the combined organic layers were concentrated in vacuo. The crude residue was recrystallized from a mixture of MTBE and n-heptane (1:15, 320 mL) to afford compound 1- 2 (37.20 g, 90%) as a white oily solid.
[0423] A solution of compound 1-2 (37.00 g, 60.33 mmol) in 20 mL of DMSO was treated with AcOH (20 mL, 317.20 mmol) and Ac2O (15 mL, 156.68 mmol). The mixture was stirred at 25 °C for 15 h. The reaction was diluted with EtOAc (100 mL) and quenched with sat. K2CO3(50 mL). The aqueous layer was extracted with EtOAc (3X50 mL). The combined organic layers were concentrated and recrystallized with ACN (30 mL) to afford compound 1-3 (15.65 g, 38.4%) as a white solid.
[0424] A solution of compound 1-3 (20.00 g, 29.72 mmol) in 120 mL of DCM was treated with Fmoc-amino-ethoxy ethanol (11.67 g, 35.66 mmol) at 25 °C. The mixture was stirred to afford a clear solution and then treated with 4Å molecular sieves (20.0 g), N-iodosuccinimide (8.02 g, 35.66 mmol), and TfOH (5.25 mL, 59.44 mmol). The mixture was stirred at 30 °C until the HPLC analysis indicated >95% consumption of compound 1-3. The reaction was quenched with TEA (6 mL) and filtered. The filtrate was diluted with EtOAc, washed with sat. NaHCO3(2X100 mL), sat. Na2SO3(2X100 mL), and water (2X100 mL) and concentrated in vacuo to afford crude compound 1-4 (26.34 g, 93.9%) as a yellow solid, which was used directly for the next step without further purification.
[0425] A solution of compound 1-4 (26.34 g, 27.62 mmol) in a mixture of DCM / water (10:7, 170 mL) was treated with DBU (7.00 mL, 45.08 mmol) at 5 °C. The mixture was stirred at 5-25 °C for 1 h. The organic layer was then separated, washed with water (100 mL), and diluted with DCM (130 mL). The solution was treated with fumaric acid (7.05 g, 60.76 mmol) and 4Å molecular sieves (26.34 g) in four portions. The mixture was stirred for 1 h, concentrated, and recrystallized from a mixture of MTBE and DCM (5:1) to afford compound 1-6 (14.74 g, 62.9%) as a white solid:1H NMR (400 MHz, d6-DMSO) 8.73 (s, 1H), 8.58 (s, 1H), 8.15-8.02 (m, 2H), 7.65-7.60 (m, 1H), 7.59-7.51 (m, 2H), 6.52 (s, 2H), 6.15(s, 1H), 5.08-4.90 (m, 3H), 4.83-4.78 (m, 1H), 4.15-3.90 (m, 3H), 3.79-3.65 (m, 2H), 2.98-2.85 (m, 6H), 1.20-0.95 (m, 28H). Example 1b: Synthesis of (2R,3R,4R,5R)‐5‐(6‐benzamido‐9H‐purin‐9‐yl)‐2‐((bis(4‐ methoxyphenyl)(phenyl)methoxy)methyl)‐4‐((2‐(2‐[lipid]‐ amidoethoxy)ethoxy)methoxy) tetrahydrofuran‐3‐yl (2‐cyanoethyl)^ diisopropylphosphoramidite(2‐4a^to^2‐4e)^
[0426] A solution of compound 1-6 (50.00 g, 59.01 mmol) in 150 mL of 2- methyltetrahydrofuran was washed with ice cold aqueous K2HPO4 (6%, 100 mL) and brine (20%, 2X100 mL). The organic layer was separated and treated with hexanoic acid (10.33 mL, 82.61 mmol), HATU (33.66 g, 88.52 mmol), and DMAP (10.81 g, 147.52 mmol) at 0 °C. The resulting mixture was warmed to 25 °C and stirred for 1 h. The solution was washed with water (2X100 mL), brine (100 mL), and concentrated in vacuo to afford a crude residue. Flash chromatography on silica gel (1:1 hexanes / acetone) gave compound 2-1a (34.95 g, 71.5%) as a white solid.
[0427] A mixture of compound 2-1a (34.95 g, 42.19 mmol) and TEA (9.28 mL, 126.58 mmol) in 80 mL of THF was treated with triethylamine trihydrofluoride (20.61 mL, 126.58 mmol) dropwise at 10 °C. The mixture was warmed to 25 °C and stirred for 2 h. The reaction was concentrated, dissolved in DCM (100 mL), and washed with sat. NaHCO3(5X20 mL) and brine (50 mL). The organic layer was concentrated in vacuo to afford crude compound 2-2a (24.72 g, 99%), which was used directly for the next step without further purification.
[0428] A solution of compound 2-2a (24.72 g, 42.18 mmol) in 50 mL of DCM was treated with N-methylmorpholine (18.54 mL, 168.67 mmol) and DMTr-Cl (15.69 g, 46.38 mmol). The mixture was stirred at 25 °C for 2 h and quenched with sat. NaHCO3(50 mL). The organic layer was separated, washed with water, concentrated to afford a slurry crude. Flash chromatography on silica gel (1:1 hexanes / acetone) gave compound 2-3a (30.05 g, 33.8 mmol, 79.9%) as a white solid.
[0429] A solution of compound 2-3a (25.00 g, 28.17 mmol) in 50 mL of DCM was treated with N-methylmorpholine (3.10 mL, 28.17 mmol) and tetrazole (0.67 mL, 14.09 mmol) under nitrogen atmosphere. Bis(diisopropylamino) chlorophosphine (9.02 g, 33.80 mmol) was added to the solution dropwise and the resulting mixture was stirred at 25 °C for 4 h. The reaction was quenched with water (15 mL), and the aqueous layer was extracted with DCM (3X50 mL). The combined organic layers were washed with sat. NaHCO3(50 mL), concentrated to afford a crude solid that was recrystallized from a mixture of DCM / MTBE / n- hexane (1:4:40) to afford compound 2-4a (25.52 g, 83.4%) as a white solid:1H NMR (400 MHz, d6-DMSO) 11.25 (s, 1H), 8.65-8.60 (m, 2 H), 8.09-8.02 (m, 2H), 7.71 (s, 1H), 7.67- 7.60 (m, 1H), 7.59-7.51 (m, 2H), 7.38-7.34 (m, 2H), 7.30-7.25 (m, 7H), 6.85-6.79 (m, 4H), 6.23-6.20 (m, 1H), 5.23-5.14 (m, 1H), 4.80-4.69 (m, 3H), 4.33-4.23 (m, 2H), 3.90-3.78 (m, 1H), 3.75 (s, 6H), 3.74-3.52 (m, 3H), 3.50-3.20 (m, 6H), 3.14-3.09 (m, 2H), 3.09 (s, 1H), 2.82-2.80 (m, 1H), 2.65-2.60 (m, 1H), 2.05-1.96 (m, 2H), 1.50-1.39 (m, 2H), 1.31-1.10 (m, 14H), 1.08-1.05 (m, 2 H), 0.85-0.79 (m, 3H);31P NMR (162 MHz, d6-DMSO) 149.43, 149.18.
[0430] Compound 2-4b, 2-4c, 2-4d, and 2-4e were prepared using similar procedures described above for compound 2-4a. Compound 2-4b was obtained (25.50 g, 85.4%) as a white solid:1H NMR (400 MHz, d6-DMSO) 11.23 (s, 1H), 8.65-8.60 (m, 2 H), 8.05-8.02 (m, 2H), 7.73-7.70 (m, 1H), 7.67-7.60 (m, 1H), 7.59-7.51 (m, 2H), 7.38-7.34 (m, 2H), 7.30-7.25 (m, 7H), 6.89-6.80 (m, 4H), 6.21-6.15 (m, 1H), 5.23-5.17 (m, 1H), 4.80-4.69 (m, 3H), 4.40- 4.21 (m, 2H), 3.91-3.80 (m, 1H), 3.74 (s, 6H), 3.74-3.52 (m, 3H), 3.50-3.20 (m, 6H), 3.14- 3.09 (m, 2H), 3.09 (s, 1H), 2.83-2.79 (m, 1H), 2.68-2.62 (m, 1H), 2.05-1.97 (m, 2H), 1.50- 1.38 (m, 2H), 1.31-1.10 (m, 18H), 1.08-1.05 (m, 2H), 0.85-0.78 (m, 3H);31P NMR (162 MHz, d6-DMSO) 149.43, 149.19.
[0431] Compound 2-4c was obtained (36.60 g, 66.3%) as an off-white solid:1H NMR (400 MHz, d6-DMSO) 11.22 (s, 1H), 8.64-8.59 (m, 2H), 8.05-8.00 (m, 2H), 7.73-7.70 (m, 1H), 7.67-7.60 (m, 1H), 7.59-7.51 (m, 2H), 7.38-7.34 (m, 2H), 7.30-7.25 (m, 7H), 6.89-6.80 (m, 4H), 6.21-6.15 (m, 1H), 5.25-5.17 (m, 1H), 4.80-4.69 (m, 3H), 4.40-4.21 (m, 2H), 3.91-3.80 (m, 1H), 3.74 (s, 6H), 3.74-3.50 (m, 3H), 3.50-3.20 (m, 6H), 3.14-3.09 (m, 2H), 3.09 (s, 1H), 2.83-2.79 (m, 1H), 2.68-2.62 (m, 1H), 2.05-1.99 (m, 2H), 1.50-1.38 (m, 2H), 1.33-1.12 (m, 38H), 1.08-1.05 (m, 2 H), 0.86-0.80 (m, 3H);31P NMR (162 MHz, d6-DMSO) 149.42, 149.17.
[0432] Compound 2-4d was obtained (26.60 g, 72.9%) as an off-white solid:1H NMR (400 MHz, d6-DMSO) 11.22 (s, 1H), 8.64-8.59 (m, 2H), 8.05-8.00 (m, 2H), 7.73-7.70 (m, 1H), 7.67-7.60 (m, 1H), 7.59-7.51 (m, 2H), 7.38-7.33 (m, 2H), 7.30-7.25 (m, 7H), 6.89- 6.80 (m, 4H), 6.21-6.15 (m, 1H), 5.22-5.17 (m, 1H), 4.80-4.69 (m, 3H), 4.40-4.21 (m, 2H), 3.91-3.80 (m, 1H), 3.74 (s, 6H), 3.74-3.52 (m, 3H), 3.50-3.20 (m, 6H), 3.14-3.09 (m, 2H), 3.09 (s, 1H), 2.83-2.79 (m, 1H), 2.68-2.62 (m, 1H), 2.05-1.99 (m, 2H), 1.50-1.38 (m, 2H), 1.35-1.08 (m, 38H), 1.08-1.05 (m, 2 H), 0.85-0.79 (m, 3H);31P NMR (162 MHz, d6-DMSO) 149.47, 149.22.
[0433] Compound 2-4e was obtained (38.10 g, 54.0%) as a white solid:1H NMR (400 MHz, d6-DMSO) 11.21 (s, 1H), 8.64-8.59 (m, 2H), 8.05-8.00 (m, 2H), 7.73-7.70 (m, 1H), 7.67-7.60 (m, 1H), 7.59-7.51 (m, 2H), 7.38-7.34 (m, 2H), 7.30-7.25 (m, 7H), 6.89-6.80 (m, 4H), 6.21-6.15 (m, 1H), 5.23-5.17 (m, 1H), 4.80-4.69 (m, 3H), 4.40-4.21 (m, 2H), 3.91-3.80 (m, 1H), 3.73 (s, 6H), 3.74-3.52 (m, 3H), 3.47-3.22 (m, 6H), 3.14-3.09 (m, 2H), 3.09 (s, 1H), 2.83-2.79 (m, 1H), 2.68-2.62 (m, 1H), 2.05-1.99 (m, 2H), 1.50-1.38 (m, 2H), 1.35-1.06 (m, 46H), 1.08-1.06 (m, 2 H), 0.85-0.77 (m, 3H);31P NMR (162 MHz, d6-DMSO) 149.41, 149.15. Example^2.^^Synthesis^of^GalXC^RNAi^Oligonucleotide‐Lipid^ConjugatesScheme^1. Synthesis of GalXC RNAi oligonucleotide-lipid conjugates with mono-lipid (linear andbranched) conjugated to the tetraloop. Post-synthetic conjugation was realized through amidecoupling reactions.R1COOH group represents fatty acid C8:0, C10:0, C11:0, C12:0, C14:0, C16:0, C17:0, C18:0, C18:1,C18:2, C22:5, C22:0, C24:0, C26:0, C22:6, C24:1, diacyl C16:0 or diacyl C18:1
[0434] Synthesis Sense 1 and Antisense 1 were prepared by solid-phase synthesis. Synthesis of Conjugated Sense 1a-1i.
[0435] Conjugated Sen...
Claims
Claims 1. A method of treating cancer in a subject that has received or is receiving a PD-L1 inhibitor, the method comprising administering an RNAi oligonucleotide comprising an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating cancer in the subject.
2. A method of treating cancer in a subject that has received or is receiving an RNAi oligonucleotide, the method comprising administering a PD-L1 inhibitor, wherein the oligonucleotide comprises an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating cancer in the subject.
3. A method of treating a disease, disorder or condition associated with activated STAT3 expression, comprising administering to a subject in need thereof an RNAi oligonucleotide, wherein the subject has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length, thereby treating cancer in the subject.
4. The method of claim 3, wherein the disease, disorder, or condition associated with activated STAT3 expression is a cancer.
5. The method of any one of claims 1-2 and 4, wherein the cancer is selected from carcinoma, sarcoma, melanoma, lymphoma, and leukemia, prostate cancer, breast cancer, hepatocellular carcinoma (HCC), colorectal cancer, pancreatic cancer and glioblastoma.
6. The method of any one of claims 1-2 and 4-5, wherein the cancer comprises an immunosuppressive tumor microenvironment.
7. The method of any one of claims 1-2 and 4-5, wherein the cancer comprises an inflamed tumor microenvironment.
8. The method of claim 7, wherein the inflamed tumor microenvironment comprises infiltrating T cells.
9. The method of any one of claims 1-8, wherein the PD-L1 inhibitor is an antibody.
10. The method of claim 9, wherein the antibody is an anti-PD-L1 antibody.
11. The method of claim 10, wherein the anti-PDL1 antibody is selected from FAZ053, atezolizumab, avelumab, durvalumab, envafolimab, and BMS-936559.
12. The method of claim 9, wherein the antibody is an anti-PD-1 antibody.
13. The method of claim 12, wherein the anti-PD-1 antibody is selected from nivolumab, pembrolizumab, and cemiplimab.
14. The method of any one of claims 1-8, wherein the PD-L1 inhibitor is a small molecule inhibitor.
15. The method of any one of claims 1-8, wherein the PD-L1 inhibitor is a peptide.
16. The method of any one of claims 1-8, wherein the PD-L1 inhibitor is a nucleic acid molecule.
17. The method of claim 16, wherein the nucleic acid molecule is selected from an antisense oligonucleotide, an siRNA, or an miRNA.
18. The method of any one of claims 1-17, wherein the STAT3 mRNA target sequence comprises any one of SEQ ID NOs: 89-280.
19. The method of any one of claims 1-18, wherein the region of complementarity is fully complementary to the STAT3 mRNA target sequence.
20. The method of any one of claims 1-18, wherein the region of complementarity comprises no more than 4 mismatches to the STAT3 mRNA target sequence.
21. The method of any one of claims 1-20, wherein the antisense strand is 19 to 27 nucleotides in length.
22. The method of any one of claims 1-21, wherein the antisense strand is 21 to 27 nucleotides in length, optionally wherein the antisense strand is 22 nucleotides in length.
23. The method of any one of claims 1-22, wherein the sense strand is 19 to 40 nucleotides in length, optionally wherein the sense strand is 36 nucleotides in length.
24. The method of any one of claims 1-23, wherein the duplex region is at least 19 nucleotides in length.
25. The method of any one of claims 1-24, wherein the duplex region is at least 20 nucleotides in length, optionally wherein the duplex region is 21 nucleotides in length.
26. The method of any one of claims 1-25, wherein the region of complementarity to STAT3 is at least 19 contiguous nucleotides in length.
27. The method of any one of claims 1-26, wherein the region of complementarity to STAT3 is at least 21 contiguous nucleotides in length.
28. The method of any one of claims 1-27, wherein the sense strand comprises at its 3′ end a stem-loop set forth as: S1-L-S2, wherein S1 is complementary to S2, and wherein L forms a loop between S1 and S2 of 3 to 5 nucleotides in length.
29. The method of claim 28, wherein L is a tetraloop, optionally wherein L is 4 nucleotides in length.
30. The method of claim 28 or 29, wherein L comprises a sequence set forth as GAAA.
31. The method of any one of claims 1-30, wherein the antisense strand comprises a 3’ overhang sequence of one or more nucleotides in length, optionally wherein the 3’ overhang sequence is 2 nucleotides in length, optionally wherein the 3’ overhang sequence is GG.
32. The method of any one of claims 1-31, wherein the oligonucleotide comprises at least one modified nucleotide.
33. The method of claim 32, wherein the modified nucleotide comprises a 2′- modification.
34. The method of claim 33, wherein the 2′-modification is a modification selected from 2′-aminoethyl, 2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl, and 2′-deoxy-2′-fluoro-β- d-arabinonucleic acid.
35. The method of any one of claims 33-34, wherein about 10-15%, 10%, 11%, 12%, 13%, 14% or 15% of the nucleotides of the sense strand comprise a 2’-fluoro modification.
36. The method of any one of claims 33-35, wherein about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the antisense strand comprise a 2’-fluoro modification.
37. The method of any one of claims 33-36, wherein about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the oligonucleotide comprise a 2’-fluoro modification.
38. The method of any one of claims 33-37, wherein the sense strand comprises 36 nucleotides with positions 1-36 from 5’ to 3 ’, wherein positions 8-11 comprise a 2’- fluoro modification.
39. The method of any one of claims 33-38, wherein the antisense strand comprises 22 nucleotides with positions 1-22 from 3’ to 5’, and wherein positions 2, 3, 4, 5, 7, 10 and 14 comprise a 2’-fluoro modification.
40. The method of any one of claims 33-39, wherein the remaining nucleotides comprise a 2’-O-methyl modification.
41. The method of any one of claims 33-40, wherein all of the nucleotides of the oligonucleotide are modified.
42. The method of any one of claims 1-41, wherein the oligonucleotide comprises at least one modified internucleotide linkage.
43. The method of claim 42, wherein the at least one modified internucleotide linkage is a phosphorothioate linkage.
44. The method of any one of claims 1-43, wherein the 4′-carbon of the sugar of the 5′-nucleotide of the antisense strand comprises a phosphate analog.
45. The method of claim 44, wherein the phosphate analog is oxymethylphosphonate, vinylphosphonate or malonylphosphonate.
46. The method of claim 44, wherein the phosphate analog is oxymethylphosphonate.
47. The method of any one of claims 1-46, wherein at least one nucleotide of the oligonucleotide is conjugated to one or more targeting ligands.
48. The method of claim 47, wherein the nucleotide is conjugated to more than one targeting ligands, wherein the targeting ligands are the same or are different.
49. The method of claim 47 or 48, wherein the one or more targeting ligands is selected from carbohydrate, amino sugar, cholesterol, polypeptide, or lipid.
50. The method of claim 47 or 48, wherein the one or more targeting ligands is a saturated or unsaturated fatty acid moiety.
51. The method of claim 47 or 48, wherein the targeting ligand is a saturated fatty acid moiety that ranges in size from C10 to C24 long.
52. The method of claim 51, wherein the targeting ligand is a C16 saturated fatty acid moiety.
53. The method of claim 51, wherein the targeting ligand is a C18 saturated fatty acid moiety.
54. The method of claim 51, wherein the targeting ligand is a C22 saturated fatty acid moiety.
55. The method of claim 47 or 48, wherein the targeting ligand comprises a N- acetylgalactosamine (GalNAc) moiety.
56. The method of claim 55, wherein the GalNAc moiety is a monovalent GalNAc moiety, a bivalent GalNAc moiety, a trivalent GalNAc moiety or a tetravalent GalNAc moiety.
57. The method of any one of claims 28-48, wherein up to 4 nucleotides of L of the stem-loop are each conjugated to a monovalent GalNAc moiety.
58. The method of any one of claims 1-57, wherein the sense strand comprises a sequence as set forth in SEQ ID NOs: 857-946.
59. The method of any one of claims 1-58, wherein the antisense strand comprises a sequence as set for in SEQ ID NOs: 947-1036.
60. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 9 and 10, respectively;(b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively.
61. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 861 and 951, respectively; (b) SEQ ID NOs: 857 and 947, respectively; (c) SEQ ID NOs: 858 and 948, respectively; (d) SEQ ID NOs: 859 and 949, respectively; (e) SEQ ID NOs: 860 and 950, respectively; (f) SEQ ID NOs: 862 and 952, respectively; (g) SEQ ID NOs: 863 and 953, respectively; (h) SEQ ID NOs: 864 and 954, respectively; (i) SEQ ID NOs: 865 and 955, respectively; (j) SEQ ID NOs: 866 and 956, respectively; (k) SEQ ID NOs: 867 and 957, respectively; (l) SEQ ID NOs: 868 and 958, respectively; (m) SEQ ID NOs: 869 and 959, respectively; (n) SEQ ID NOs: 870 and 960, respectively; (o) SEQ ID NOs: 871 and 961, respectively; (p) SEQ ID NOs: 872 and 962, respectively; (q) SEQ ID NOs: 873 and 963, respectively; (r) SEQ ID NOs: 874 and 964, respectively; (s) SEQ ID NOs: 875 and 965, respectively; (t) SEQ ID NOs: 876 and 966, respectively; (u) SEQ ID NOs: 877 and 967, respectively; (v) SEQ ID NOs: 878 and 968, respectively; (w) SEQ ID NOs: 879 and 969, respectively; (x) SEQ ID NOs: 880 and 970, respectively; (y) SEQ ID NOs: 881and 971, respectively; (z) SEQ ID NOs: 882 and 972, respectively; (aa) SEQ ID NOs: 883 and 973, respectively; (bb) SEQ ID NOs: 884 and 974, respectively;(cc) SEQ ID NOs: 885 and 975, respectively; (dd) SEQ ID NOs: 886 and 976, respectively; (ee) SEQ ID NOs: 887 and 977, respectively; (ff) SEQ ID NOs: 888 and 978, respectively; (gg) SEQ ID NOs: 940 and 1030, respectively; (hh) SEQ ID NOs: 896 and 986, respectively; and (ii) SEQ ID NOs: 920 and 1010, respectively.
62. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 862 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
952.
63. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 875 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
965.
64. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 876 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
966.
65. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 920 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1010.
66. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively.
67. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively.
68. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively.
69. The method of any one of claims 1-57, wherein the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 11, 39, 67 and 71.
70. The method of any one of claims 1-57, wherein the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 12, 40, 68 and 72.
71. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 11 and 12, respectively; (b) SEQ ID NOs: 39 and 40, respectively; (c) SEQ ID NOs: 67 and 68, respectively; and (d) SEQ ID NOs: 71 and 72, respectively.
72. The method of any one of claims 1-57, wherein the sense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1042, 1055, 1056, and 1100.
73. The method of any one of claims 1-57 and 72, wherein the antisense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1132, 1145, 1146, and 1190.
74. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1041 and 1131, respectively; (b) SEQ ID NOs: 1037 and 1127, respectively; (c) SEQ ID NOs: 1038 and 1128, respectively; (d) SEQ ID NOs: 1039 and 1129, respectively; (e) SEQ ID NOs: 1040 and 1130, respectively; (f) SEQ ID NOs: 1042 and 1132, respectively; (g) SEQ ID NOs: 1043 and 1133, respectively; (h) SEQ ID NOs: 1044 and 1134, respectively; (i) SEQ ID NOs: 1045 and 1135, respectively; (j) SEQ ID NOs: 1046 and 1136, respectively; (k) SEQ ID NOs: 1047 and 1137, respectively; (l) SEQ ID NOs: 1048 and 1138, respectively; (m) SEQ ID NOs: 1049 and 1139, respectively; (n) SEQ ID NOs: 1050 and 1140, respectively; (o) SEQ ID NOs: 1051 and 1141, respectively; (p) SEQ ID NOs: 1052 and 1142, respectively; (q) SEQ ID NOs: 1053 and 1143, respectively; (r) SEQ ID NOs: 1054 and 1144, respectively; (s) SEQ ID NOs: 1055 and 1145, respectively; (t) SEQ ID NOs: 1056 and 1146, respectively; (u) SEQ ID NOs: 1057 and 1147, respectively; (v) SEQ ID NOs: 1058 and 1148, respectively; (w) SEQ ID NOs: 1059 and 1149, respectively; (x) SEQ ID NOs: 1060 and 1150, respectively; (y) SEQ ID NOs: 1061 and 1151, respectively; (z) SEQ ID NOs: 1062 and 1152, respectively; (aa) SEQ ID NOs: 1063 and 1153, respectively; (bb) SEQ ID NOs: 1064 and 1154, respectively; (cc) SEQ ID NOs: 1065 and 1155, respectively; (dd) SEQ ID NOs: 1066 and 1156, respectively; (ee) SEQ ID NOs: 1067 and 1157, respectively; (ff) SEQ ID NOs: 1068 and 1158, respectively;(gg) SEQ ID NOs: 1120 and 1210, respectively; (hh) SEQ ID NOs: 1076 and 1166, respectively; and (ii) SEQ ID NOs: 1100 and 1190, respectively.
75. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1042 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1132.
76. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1055 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1145.
77. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1056 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1146.
78. The method of any one of claims 1-57, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1100 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1190.
79. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1081 and 1171, respectively; (b) SEQ ID NOs: 1090 and 1180, respectively; (c) SEQ ID NOs: 1079 and 1169, respectively; (d) SEQ ID NOs: 1076 and 1166, respectively; (e) SEQ ID NOs: 1072 and 1162, respectively; (f) SEQ ID NOs: 1070 and 1160, respectively; and (g) SEQ ID NOs: 1069 and 1159, respectively.
80. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1120 and 1210, respectively; (b) SEQ ID NOs: 1117 and 1207, respectively; and(c) SEQ ID NOs: 1119 and 1209, respectively.
81. The method of any one of claims 1-57, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1095 and 1185, respectively; (b) SEQ ID NOs: 1104 and 1194, respectively; (c) SEQ ID NOs: 1093 and 1183, respectively; and (d) SEQ ID NOs: 1100 and 1190, respectively.
82. A kit comprising an RNAi oligonucleotide, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the oligonucleotide to a subject in need thereof that has received or is receiving a PD-L1 inhibitor, wherein the oligonucleotide comprises an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length.
83. A kit comprising a PD-L1 inhibitor, an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administering the antibody to a subject in need thereof that has received or is receiving an RNAi oligonucleotide comprising an antisense strand of 15 to 30 nucleotides in length and a sense strand of 15 to 40 nucleotides in length, wherein the antisense and sense strands form a duplex region, wherein the antisense strand comprises a region of complementarity to a STAT3 mRNA target sequence, and wherein the region of complementarity is at least 15 contiguous nucleotides in length.
84. The kit of 82 or 83, wherein the subject has a disease, disorder, or condition associated with activated STAT3 expression.
85. The kit of any one of claims 82-84, wherein the subject has cancer.
86. The kit of claim 85, wherein the cancer is selected from carcinoma, sarcoma, melanoma, lymphoma, and leukemia, prostate cancer, breast cancer, hepatocellular carcinoma (HCC), colorectal cancer, pancreatic cancer and glioblastoma.
87. The kit of any one of claims 82-86, wherein the cancer comprises an immunosuppressive tumor microenvironment.
88. The kit of any one of claims 82-86, wherein the cancer comprises an inflamed tumor microenvironment.
89. The kit of claim 88, wherein the inflamed tumor microenvironment comprises infiltrating T cells.
90. The kit of any one of claims 82-89, wherein the PD-L1 inhibitor is an antibody.
91. The kit of claim 90, wherein the antibody is an anti-PD-L1 antibody.
92. The kit of claim 91, wherein the anti-PDL1 antibody is selected from FAZ053, atezolizumab, avelumab, durvalumab, envafolimab, and BMS-936559.
93. The kit of claim 90, wherein the antibody is an anti-PD-1 antibody.
94. The kit of claim 93, wherein the anti-PD-1 antibody is selected from nivolumab, pembrolizumab, and cemiplimab.
95. The kit of any one of claims 82-89, wherein the PD-L1 inhibitor is a small molecule inhibitor.
96. The kit of any one of claims 82-89, wherein the PD-L1 inhibitor is a peptide.
97. The kit of any one of claims 82-89, wherein the PD-L1 inhibitor is a nucleic acid molecule.
98. The kit of any one of claims 82-89, wherein the nucleic acid molecule is selected from an antisense oligonucleotide, an siRNA, or an miRNA.
99. The kit of any one of claims 82-94, wherein the STAT3 mRNA target sequence comprises any one of SEQ ID NOs: 89-280.
100. The kit of any one of claims 82-99, wherein the region of complementarity is fully complementary to the STAT3 mRNA target sequence.
101. The kit of any one of claims 82-99, wherein the region of complementarity comprises no more than 4 mismatches to the STAT3 mRNA target sequence.
102. The kit of any one of claims 82-101, wherein the antisense strand is 19 to 27 nucleotides in length.
103. The kit of any one of claims 82-102, wherein the antisense strand is 21 to 27 nucleotides in length, optionally wherein the antisense strand is 22 nucleotides in length.
104. The kit of any one of claims 82-103, wherein the sense strand is 19 to 40 nucleotides in length, optionally wherein the sense strand is 36 nucleotides in length.
105. The kit of any one of claims 82-104, wherein the duplex region is at least 19 nucleotides in length.
106. The kit of any one of claims 82-105, wherein the duplex region is at least 20 nucleotides in length, optionally wherein the duplex region is 21 nucleotides in length.
107. The kit of any one of claims 82-106, wherein the region of complementarity to STAT3 is at least 19 contiguous nucleotides in length.
108. The kit of any one of claims 82-107, wherein the region of complementarity to STAT3 is at least 21 contiguous nucleotides in length.
109. The kit of any one of claims 82-108, wherein the sense strand comprises at its 3′ end a stem-loop set forth as: S1-L-S2, wherein S1 is complementary to S2, and wherein L forms a loop between S1 and S2 of 3 to 5 nucleotides in length.
110. The kit of claim 109, wherein L is a tetraloop, optionally wherein L is 4 nucleotides in length.
111. The kit of claim 109 or 110, wherein L comprises a sequence set forth as GAAA.
112. The kit of any one of claims 82-111, wherein the antisense strand comprises a 3’ overhang sequence of one or more nucleotides in length, optionally wherein the 3’ overhang sequence is 2 nucleotides in length, optionally wherein the 3’ overhang sequence is GG.
113. The kit of any one of claims 82-112, wherein the oligonucleotide comprises at least one modified nucleotide.
114. The kit of claim 113, wherein the modified nucleotide comprises a 2′- modification.
115. The kit of claim 114, wherein the 2′-modification is a modification selected from 2′-aminoethyl, 2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl, and 2′-deoxy-2′-fluoro-β-d- arabinonucleic acid.
116. The kit of any one of claims 114-115, wherein about 10-15%, 10%, 11%, 12%, 13%, 14% or 15% of the nucleotides of the sense strand comprise a 2’-fluoro modification.
117. The kit of any one of claims 114-116, wherein about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the antisense strand comprise a 2’-fluoro modification.
118. The kit of any one of claims 114-117, wherein about 25-35%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34% or 35% of the nucleotides of the oligonucleotide comprise a 2’-fluoro modification.
119. The kit of any one of claims 114-118, wherein the sense strand comprises 36 nucleotides with positions 1-36 from 5’ to 3 ’, wherein positions 8-11 comprise a 2’- fluoro modification.
120. The kit of any one of claims 114-119, wherein the antisense strand comprises 22 nucleotides with positions 1-22 from 3’ to 5’, and wherein positions 2, 3, 4, 5, 7, 10 and 14 comprise a 2’-fluoro modification.
121. The kit of any one of claims 114-120, wherein the remaining nucleotides comprise a 2’-O-methyl modification.
122. The kit of any one of claims 114-121, wherein all of the nucleotides of the oligonucleotide are modified.
123. The kit of any one of claims 82-122, wherein the oligonucleotide comprises at least one modified internucleotide linkage.
124. The kit of claim 123, wherein the at least one modified internucleotide linkage is a phosphorothioate linkage.
125. The kit of any one of claims 82-124, wherein the 4′-carbon of the sugar of the 5′- nucleotide of the antisense strand comprises a phosphate analog.
126. The kit of claim 125, wherein the phosphate analog is oxymethylphosphonate, vinylphosphonate or malonylphosphonate.
127. The kit of any one of claims 82-126, wherein at least one nucleotide of the oligonucleotide is conjugated to one or more targeting ligands.
128. The kit of claim 127, wherein the nucleotide is conjugated to more than one targeting ligands, wherein the targeting ligands are the same or are different.
129. The kit of claim 127 or 128, wherein the one or more targeting ligands is selected from carbohydrate, amino sugar, cholesterol, polypeptide, or lipid.
130. The kit of claim 127 or 128, wherein the one or more targeting ligands is a saturated or unsaturated fatty acid moiety.
131. The kit of claim 127 or 128, wherein the targeting ligand is a saturated fatty acid moiety that ranges in size from C10 to C24 long.
132. The kit of claim 131, wherein the targeting ligand is a C16 saturated fatty acid moiety.
133. The kit of claim 131, wherein the targeting ligand is a C18 saturated fatty acid moiety.
134. The kit of claim 131, wherein the targeting ligand is a C22 saturated fatty acid moiety.
135. The kit of claim 127 or 128, wherein the targeting ligand comprises a N- acetylgalactosamine (GalNAc) moiety.
136. The kit of claim 135, wherein the GalNAc moiety is a monovalent GalNAc moiety, a bivalent GalNAc moiety, a trivalent GalNAc moiety or a tetravalent GalNAc moiety.
137. The kit of any one of claims 109-129, wherein up to 4 nucleotides of L of the stem-loop are each conjugated to a monovalent GalNAc moiety.
138. The kit of any one of claims 82-137, wherein the sense strand comprises a sequence as set forth in SEQ ID NOs: 857-946.
139. The kit of any one of claims 82-138, wherein the antisense strand comprises a sequence as set for in SEQ ID NOs: 947-1036.
140. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of:(a) SEQ ID NOs: 9 and 10, respectively; (b) SEQ ID NOs: 37 and 38, respectively; (c) SEQ ID NOs: 65 and 66, respectively; and (d) SEQ ID NOs: 69 and 70, respectively.
141. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 861 and 951, respectively; (b) SEQ ID NOs: 857 and 947, respectively; (c) SEQ ID NOs: 858 and 948, respectively; (d) SEQ ID NOs: 859 and 949, respectively; (e) SEQ ID NOs: 860 and 950, respectively; (f) SEQ ID NOs: 862 and 952, respectively; (g) SEQ ID NOs: 863 and 953, respectively; (h) SEQ ID NOs: 864 and 954, respectively; (i) SEQ ID NOs: 865 and 955, respectively; (j) SEQ ID NOs: 866 and 956, respectively; (k) SEQ ID NOs: 867 and 957, respectively; (l) SEQ ID NOs: 868 and 958, respectively; (m) SEQ ID NOs: 869 and 959, respectively; (n) SEQ ID NOs: 870 and 960, respectively; (o) SEQ ID NOs: 871 and 961, respectively; (p) SEQ ID NOs: 872 and 962, respectively; (q) SEQ ID NOs: 873 and 963, respectively; (r) SEQ ID NOs: 874 and 964, respectively; (s) SEQ ID NOs: 875 and 965, respectively; (t) SEQ ID NOs: 876 and 966, respectively; (u) SEQ ID NOs: 877 and 967, respectively; (v) SEQ ID NOs: 878 and 968, respectively; (w) SEQ ID NOs: 879 and 969, respectively; (x) SEQ ID NOs: 880 and 970, respectively; (y) SEQ ID NOs: 881and 971, respectively; (z) SEQ ID NOs: 882 and 972, respectively; (aa) SEQ ID NOs: 883 and 973, respectively;(bb) SEQ ID NOs: 884 and 974, respectively; (cc) SEQ ID NOs: 885 and 975, respectively; (dd) SEQ ID NOs: 886 and 976, respectively; (ee) SEQ ID NOs: 887 and 977, respectively; (ff) SEQ ID NOs: 888 and 978, respectively; (gg) SEQ ID NOs: 940 and 1030, respectively; (hh) SEQ ID NOs: 896 and 986, respectively; and (ii) SEQ ID NOs: 920 and 1010, respectively.
142. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 862 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
952.
143. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 875 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
965.
144. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 876 and the antisense strand comprises the nucleotide sequence of SEQ ID NO:
966.
145. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 920 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1010.
146. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 901 and 991, respectively; (b) SEQ ID NOs: 910 and 1000, respectively; (c) SEQ ID NOs: 899 and 989, respectively; (d) SEQ ID NOs: 896 and 986, respectively; (e) SEQ ID NOs: 892 and 982, respectively; (f) SEQ ID NOs: 890 and 980, respectively; and (g) SEQ ID NOs: 889 and 979, respectively.
147. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 940 and 1030, respectively; (b) SEQ ID NOs: 937 and 1027, respectively; and (c) SEQ ID NOs: 939 and 1029, respectively.
148. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 915 and 1005, respectively; (b) SEQ ID NOs: 924 and 1014, respectively; (c) SEQ ID NOs: 913 and 1003, respectively; and (d) SEQ ID NOs: 920 and 1010, respectively.
149. The kit of any one of claims 82-137, wherein the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 11, 39, 67 and 71.
150. The kit of any one of claims 82-137, wherein the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 12, 40, 68 and 72.
151. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 11 and 12, respectively; (b) SEQ ID NOs: 39 and 40, respectively; (c) SEQ ID NOs: 67 and 68, respectively; and (d) SEQ ID NOs: 71 and 72, respectively.
152. The kit of any one of claims 82-137, wherein the sense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1042, 1055, 1056, and 1100.
153. The kit of any one of claims 82-137 and 152, wherein the antisense strand comprises a nucleotide sequence selected from SEQ ID NOs: 1132, 1145, 1146, and 11154. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1041 and 1131, respectively; (b) SEQ ID NOs: 1037 and 1127, respectively; (c) SEQ ID NOs: 1038 and 1128, respectively; (d) SEQ ID NOs: 1039 and 1129, respectively; (e) SEQ ID NOs: 1040 and 1130, respectively; (f) SEQ ID NOs: 1042 and 1132, respectively; (g) SEQ ID NOs: 1043 and 1133, respectively; (h) SEQ ID NOs: 1044 and 1134, respectively; (i) SEQ ID NOs: 1045 and 1135, respectively; (j) SEQ ID NOs: 1046 and 1136, respectively; (k) SEQ ID NOs: 1047 and 1137, respectively; (l) SEQ ID NOs: 1048 and 1138, respectively; (m) SEQ ID NOs: 1049 and 1139, respectively; (n) SEQ ID NOs: 1050 and 1140, respectively; (o) SEQ ID NOs: 1051 and 1141, respectively; (p) SEQ ID NOs: 1052 and 1142, respectively; (q) SEQ ID NOs: 1053 and 1143, respectively; (r) SEQ ID NOs: 1054 and 1144, respectively; (s) SEQ ID NOs: 1055 and 1145, respectively; (t) SEQ ID NOs: 1056 and 1146, respectively; (u) SEQ ID NOs: 1057 and 1147, respectively; (v) SEQ ID NOs: 1058 and 1148, respectively; (w) SEQ ID NOs: 1059 and 1149, respectively; (x) SEQ ID NOs: 1060 and 1150, respectively; (y) SEQ ID NOs: 1061 and 1151, respectively; (z) SEQ ID NOs: 1062 and 1152, respectively; (aa) SEQ ID NOs: 1063 and 1153, respectively; (bb) SEQ ID NOs: 1064 and 1154, respectively; (cc) SEQ ID NOs: 1065 and 1155, respectively; (dd) SEQ ID NOs: 1066 and 1156, respectively; (ee) SEQ ID NOs: 1067 and 1157, respectively; (ff) SEQ ID NOs: 1068 and 1158, respectively;(gg) SEQ ID NOs: 1120 and 1210, respectively; (hh) SEQ ID NOs: 1076 and 1166, respectively; and (ii) SEQ ID NOs: 1100 and 1190, respectively.
155. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1042 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1132.
156. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1055 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1145.
157. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1056 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1146.
158. The kit of any one of claims 82-137, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO: 1100 and the antisense strand comprises the nucleotide sequence of SEQ ID NO: 1190.
159. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1081 and 1171, respectively; (b) SEQ ID NOs: 1090 and 1180, respectively; (c) SEQ ID NOs: 1079 and 1169, respectively; (d) SEQ ID NOs: 1076 and 1166, respectively; (e) SEQ ID NOs: 1072 and 1162, respectively; (f) SEQ ID NOs: 1070 and 1160, respectively; and (g) SEQ ID NOs: 1069 and 1159, respectively.
160. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1120 and 1210, respectively; (b) SEQ ID NOs: 1117 and 1207, respectively; and(c) SEQ ID NOs: 1119 and 1209, respectively.
161. The kit of any one of claims 82-137, wherein the sense strand and antisense strand comprise nucleotide sequences selected from the group consisting of: (a) SEQ ID NOs: 1095 and 1185, respectively; (b) SEQ ID NOs: 1104 and 1194, respectively; (c) SEQ ID NOs: 1093 and 1183, respectively; and (d) SEQ ID NOs: 1100 and 1190, respectively.