Modulators of foxp3 expression

Abstract

The present embodiments provide methods, compounds, and compositions useful for inhibiting FOXP3 expression, which may be useful for treating, preventing, or ameliorating cancer.

What is claimed: 
     
         1 . A compound comprising a modified oligonucleotide 8 to 80 linked nucleosides in length having a nucleobase sequence comprising at least 8 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 9-3246. 
     
     
         2 . A compound comprising a modified oligonucleotide 9 to 80 linked nucleosides in length having a nucleobase sequence comprising at least 9 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 9-3246. 
     
     
         3 . A compound comprising a modified oligonucleotide 10 to 80 linked nucleosides in length having a nucleobase sequence comprising at least 10 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 9-3246. 
     
     
         4 . A compound comprising a modified oligonucleotide 11 to 80 linked nucleosides in length having a nucleobase sequence comprising at least 11 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 9-3246. 
     
     
         5 . A compound comprising a modified oligonucleotide 12 to 80 linked nucleosides in length having a nucleobase sequence comprising at least 12 contiguous nucleobases of any of the nucleobase sequences of SEQ ID NOs: 9-3246. 
     
     
         6 . A compound comprising a modified oligonucleotide 16 to 80 linked nucleosides in length having a nucleobase sequence comprising the nucleobase sequence of any one of SEQ ID NOs: 9-3246. 
     
     
         7 . A compound comprising a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 9-3246. 
     
     
         8 . A compound comprising a modified oligonucleotide 8 to 80 linked nucleosides in length complementary within nucleotides 2269-2284 of SEQ ID NO: 1 or within nucleotides 1233-1248, 2156-2171, 2735-2750, 4661-4676, 7307-7322, 7331-7346, 7980-7995, 11581-11596, or 12396-12411 of SEQ ID NO: 2. 
     
     
         9 . A compound comprising a modified oligonucleotide 8 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 449, 501, 544, 794, 1293, 1307, 1511, 1755, 2492, or 2575. 
     
     
         10 . A compound comprising a modified oligonucleotide having a nucleobase sequence consisting of any one of SEQ ID NOs: 449, 501, 544, 794, 1293, 1307, 1511, 1755, 2492, or 2575. 
     
     
         11 . The compound of any one of  claims 1 - 10 , wherein the modified oligonucleotide comprises at least one modified internucleoside linkage, at least one modified sugar, or at least one modified nucleobase. 
     
     
         12 . The compound of  claim 11 , wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage. 
     
     
         13 . The compound of  claim 11  or  12 , wherein the modified sugar is a bicyclic sugar. 
     
     
         14 . The compound of  claim 13 , wherein the bicyclic sugar is selected from the group consisting of: 4′-(CH 2 )—O-2′ (LNA); 4′-(CH 2 ) 2 —O-2′ (ENA); and 4′-CH(CH 3 )—O-2′ (cEt). 
     
     
         15 . The compound of  claim 11  or  12 , wherein the modified sugar is 2′-O-methoxyethyl. 
     
     
         16 . The compound of any one of  claims 11 - 15 , wherein the modified nucleobase is a 5-methylcytosine. 
     
     
         17 . The compound of any one of  claims 1 - 16 , wherein the modified oligonucleotide comprises:
 a gap segment consisting of linked deoxynucleosides;   a 5′ wing segment consisting of linked nucleosides; and   a 3′ wing segment consisting of linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.   
     
     
         18 . A compound comprising a modified oligonucleotide 16 to 80 linked nucleosides in length having a nucleobase sequence comprising any one of SEQ ID NOs: 449, 501, 544, 794, 1293, 1307, 1511, 1755, 2492, or 2575, wherein the modified oligonucleotide comprises:
 a gap segment consisting of linked deoxynucleosides;   a 5′ wing segment consisting of linked nucleosides; and   a 3′ wing segment consisting of linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.   
     
     
         19 . A compound comprising a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in any one of SEQ ID NOs: 449, 501, 544, 794, 1293, 1307, 1511, 1755, 2492, or 2575, wherein the modified oligonucleotide comprises:
 a gap segment consisting of ten linked deoxynucleosides;   a 5′ wing segment consisting of three linked nucleosides; and   a 3′ wing segment consisting of three linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.   
     
     
         20 . A compound comprising a modified oligonucleotide 16-80 linked nucleobases in length having a nucleobase sequence comprising the sequence recited in SEQ ID NO: 449, wherein the modified oligonucleotide comprises:
 a gap segment consisting of ten linked deoxynucleosides;   a 5′ wing segment consisting of three linked nucleosides; and   a 3′ wing segment consisting of three linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment; wherein each nucleoside of each wing segment comprises a cEt nucleoside; wherein each internucleoside linkage is a phosphorothioate linkage; and wherein each cytosine is a 5-methylcytosine.   
     
     
         21 . The compound of any one of  claims 1 - 20 , wherein the oligonucleotide is at least 80%, 85%, 90%, 95% or 100% complementary to any of SEQ ID NOs: 1-5. 
     
     
         22 . The compound of any one of  claims 1 - 21 , wherein the compound is single-stranded. 
     
     
         23 . The compound of any one of  claims 1 - 21 , wherein the compound is double-stranded. 
     
     
         24 . The compound of any one of  claims 1 - 23 , wherein the compound comprises ribonucleotides. 
     
     
         25 . The compound of any one of  claims 1 - 23 , wherein the compound comprises deoxyribonucleotides. 
     
     
         26 . The compound of any one of  claims 1 - 25 , wherein the modified oligonucleotide consists of 16 to 30 linked nucleosides. 
     
     
         27 . The compound of any preceding claim, wherein the compound consists of the modified oligonucleotide. 
     
     
         28 . A compound consisting of a pharmaceutically acceptable salt of any of the compounds of  claims 1 - 27 . 
     
     
         29 . The compound of  claim 28 , wherein the pharmaceutically acceptable salt is a sodium salt. 
     
     
         30 . The compound of  claim 28 , wherein the pharmaceutically acceptable salt is a potassium salt. 
     
     
         31 . A compound having the formula: 
       
         
           
           
               
               
           
         
       
       or a salt thereof. 
     
     
         32 . A compound having the formula: 
       
         
           
           
               
               
           
         
       
     
     
         33 . A composition comprising the compound of any one of  claims 1 - 32  and a pharmaceutically acceptable carrier. 
     
     
         34 . A composition comprising a compound or modified oligonucleotide of any preceding claim, for use in therapy. 
     
     
         35 . A method of treating or ameliorating cancer in an individual comprising administering to the individual a compound targeted to FOXP3, thereby treating or ameliorating the cancer. 
     
     
         36 . The method of  claim 35 , wherein the compound is an antisense compound targeted to FOXP3. 
     
     
         37 . The method of  claim 35  or  36 , wherein the cancer is a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         38 . The method of any of  claims 40 - 42 , wherein administering the compound inhibits or reduces immunosuppression, Treg immunosuppressive activity, cancer cell proliferation, tumor growth, or metastasis, or induces or activates anticancer or antitumor immunity; anticancer or antitumor immune response; immune cell activation or infiltration; inflammatory cell activation or infiltration; effector immune cell activation or infiltration; T cell activation or infiltration; CD8 T cell activation or infiltration; NK cell activation or infiltration; macrophage and dendritic cell activation or infiltration; inflammation; or inflammatory cytokine or chemokine expression. 
     
     
         39 . A method of inhibiting expression of FOXP3 in a cell comprising contacting the cell with a compound targeted to FOXP3, thereby inhibiting expression of FOXP3 in the cell. 
     
     
         40 . The method of  claim 39 , wherein the cell is a cancer cell. 
     
     
         41 . The method of  claim 40 , wherein the cancer is a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         42 . A method of reducing or inhibiting immunosuppression, Treg immunosuppressive activity, cancer cell proliferation, tumor growth, or metastasis in an individual having cancer comprising administering a compound targeted to FOXP3 to the individual, thereby reducing or inhibiting immunosuppression, Treg immunosuppressive activity, cancer cell proliferation, tumor growth, or metastasis in the individual. 
     
     
         43 . A method of inducing or activating anticancer or antitumor immunity; anticancer or antitumor immune response; immune cell activation or infiltration; inflammatory cell activation or infiltration; effector immune cell activation or infiltration; T cell activation or infiltration; CD8 T cell activation or infiltration; NK cell activation or infiltration; macrophage and dendritic cell activation or infiltration; inflammation; or inflammatory cytokine or chemokine expression in an individual having cancer comprising administering a compound targeted to FOXP3 to the individual. 
     
     
         44 . The method of  claim 43 , wherein the individual has a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         45 . The method of any one of  claims 35 - 44 , wherein the compound is an antisense compound targeted to FOXP3. 
     
     
         46 . The method of any one of  claims 35 - 45 , wherein the compound is the compound of any one of  claims 1 - 34  or composition of  claim 35  or  36 . 
     
     
         47 . The method of any of  claims 35 - 46 , wherein the compound is administered parenterally. 
     
     
         48 . Use of a compound targeted to FOXP3 for treating, preventing, or ameliorating cancer. 
     
     
         49 . The use of  claim 48 , wherein the cancer is a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         50 . The use of  claim 48  or  49 , wherein the compound is an antisense compound targeted to FOXP3. 
     
     
         51 . The use of any one of  claims 48 - 50 , wherein the compound is the compound of any one of  claims 1 - 32  or composition of  claim 33  or  34 . 
     
     
         52 . Use of a compound targeted to FOXP3 in the manufacture of a medicament for treating or ameliorating cancer. 
     
     
         53 . The use of  claim 51 , wherein the cancer is a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         54 . The use of  claim 52  or  53 , wherein the compound is an antisense compound targeted to FOXP3. 
     
     
         55 . The use of any one of  claims 52 - 54 , wherein the compound is the compound of any one of  claims 1 - 32  or composition of  claim 33  or  34 . 
     
     
         56 . Use of a compound targeted to FOXP3 in the preparation of a medicament for treating or ameliorating cancer. 
     
     
         57 . The use of  claim 56 , wherein the cancer is a cancer having FOXP3 positive (FOXP3+) Tregs in the microenvironment or stroma or tumor draining lymph nodes, lung cancer, non-small cell lung carcinoma (NSCLC), small-cell lung carcinoma (SCLC), squamous cell carcinoma (SCC), head and neck cancer, head and neck squamous cell carcinoma (HNSCC), gastrointestinal cancer, large intestinal cancer, small intestinal cancer, stomach cancer, colon cancer, colorectal cancer, bladder cancer, liver cancer, hepatocellular carcinoma (HCC), esophageal cancer, pancreatic cancer, biliary tract cancer, gastric cancer, urothelial cancer, breast cancer, triple-negative breast cancer (TNBC), ovarian cancer, endometrial cancer, cervical cancer, prostate cancer, mesothelioma, sarcomas (e.g. epitheloid, rhabdoid and synovial), chordoma, renal cancer, renal cell carcinoma (RCC), brain cancer, neuroblastoma, glioblastoma, skin cancer, melanoma, basal cell carcinoma, merkel cell carcinoma, blood cancer, hematopoetic cancer, myeloma, multiple myeloma (MM), B cell malignancies, lymphoma, B cell lymphoma, Hodgkin lymphoma, T cell lymphoma, leukemia, or acute lymphocytic leukemia (ALL). 
     
     
         58 . The use of  claim 56  or  57 , wherein the compound is an antisense compound targeted to FOXP3. 
     
     
         59 . The use of any one of  claims 56 - 58 , wherein the compound is the compound of any one of  claims 1 - 32  or composition of  claim 33  or  34 .