ASYMMETRIC SIRNA INHIBITING EXPRESSION OF PD-1
20220380774 · 2022-12-01
Inventors
Cpc classification
A61K31/7088
HUMAN NECESSITIES
A61K35/17
HUMAN NECESSITIES
C12N15/1138
CHEMISTRY; METALLURGY
International classification
C12N15/113
CHEMISTRY; METALLURGY
Abstract
The present invention relates to an asymmetric siRNA that may inhibit expression of programmed cell death protein 1 (PD-1), and a use thereof, and more specifically, to: an asymmetric siRNA including an antisense strand including a sequence complementary to mRNA encoding PD-1, and a sense strand forming complementary bonds with the antisense strand; a pharmaceutical composition for preventing or treating cancer, including the asymmetric siRNA; an immune cell in which expression of PD-1 is inhibited, obtained by treatment with the siRNA; and an immune cell therapeutic agent for treating cancer, including the immune cell.
Claims
1. An siRNA comprising: an antisense strand comprising a sequence complementary to mRNA encoding programmed cell death protein 1 (PD-1); a sense strand forming complementary bonds with the antisense strand, wherein a 5′ end of the antisense strand and a 3′ end of the sense strand form a blunt end.
2. The siRNA of claim 1, wherein the sense strand has a length of 15 nt to 17 nt, and the antisense strand has a length of 16 nt or more.
3. The siRNA of claim 2, wherein the antisense strand has a length of 16 nt to 31 nt.
4. The siRNA of claim 2, wherein the antisense strand has a length of 19 nt to 25 nt.
5. The siRNA of claim 1, wherein the sense strand is selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 77, 79, 81, 83, 85, 87, 89, and 91.
6. (canceled)
7. The siRNA of claim 1, wherein the antisense strand is selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 78, 80, 82, 84, 86, 88, 90, and 92.
8. (canceled)
9. The siRNA of claim 1, wherein the sense strand or the antisense strand comprises at least one chemical modification selected from the group consisting of (a) to (e): (a) an —OH group at a 2′ carbon position of a sugar structure of a nucleotide substituted with —CH3, —OCH3, —NH2, —F (fluorine), —O-2-methoxyethyl, —O-propyl, —O-2-methylthioethyl, —O-3-aminopropyl, or —O-3-dimethylaminopropyl; (b) oxygen in a sugar structure of a nucleotide substituted with sulfur; (c) a phosphate backbone of a nucleotide modified with phosphorothioate, boranophosphate, or methyl phosphonate; (d) a nucleotide substituted with a peptide nucleic acid (PNA), a locked nucleic acid (LNA), or an unlocked nucleic acid (UNA); and (e) a bonding of a phosphate group, a lipophilic compound, or a cell-penetrating peptide.
10. The siRNA of claim 9, wherein the lipophilic compound is selected from the group consisting of cholesterol, tocopherol, docosahexaenoic acid (DHA), palmitic acid, and long-chain fatty acids having 10 or more carbon atoms.
11. The siRNA of claim 9, comprising at least one chemical modification selected from the group consisting of: (a) an —OH group at least one 2′ carbon position of a sugar structure of a nucleotide substituted with —OCH3 or —F in the sense strand or the antisense strand; (b) at least one nucleotide bond in the sense strand or the antisense strand modified with a phosphorothioate bond; (c) a cholesterol bonded to a 3′ end of the sense strand; and (d) phosphate group bonded to a 5′ end of the antisense strand.
12. The siRNA of claim 9, wherein the sense strand is selected from the group consisting of (a) to (c) in a following table, and the antisense strand is selected from the group consisting of (d) to (o) in the following table: TABLE-US-00010 Sequence (5′.fwdarw.3′) Sense (a) mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ (b) mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ (c) mCAmUGmAGmCCmCCmAGmCA*mA*C*/chol/ Antisense (d) UCUCUCUGUCACCCmU*mG*A*G*C (e) UCUCUCUGUCACCCmU*mG*mA*mG*mC (f) UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*mG*mC*mC (g) UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*G*C*C (h) UCUCUCUGUCACCCmUmGmAmGmCmUC*U*G*C*C (i) UUCUCUCUGUCACCmC*mU*G*A*G (j) UUCUCUCUGUCACCmC*mU*mG*mA*mG (k) UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*mU*mG*mC (l) UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*U*G*C (m) UUCUCUCUGUCACCmUmUmGmAmCU*C*U*G*C (n) GUUGCUGGGGCUCAmU*mG*mC*mG*mG (o) GUUGCUGGGGCUCAmU*mG*C*G*G In the sequences above, * indicates 3 phospsorothioated bond, m indicates 2′-O-methl and /chol/ indicates cholesterol.
13. The siRNA of claim 12, wherein the sense strand is (b) in the table, the antisense strand is at least one selected from the group consisting of (i) to (m) in the table, and a 5′ end of the antisense strand is bound to a phosphate group.
14. The siRNA of claim 9, wherein the sense strand is selected from the group consisting of (a) to (c) in a following table, and the antisense strand is selected from the group consisting of (d) to (h) in the following table: TABLE-US-00011 Sequence (5′.fwdarw.3′) Sense (a) mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ (b) mA(2′-F-G)mG(2′-F-G)mU(2′-F-G)mA(2′-F-C)mA(2′- F-G)mA(2′-F-G)mA(2′-F-G)*mA*(2′-F-A)*/chol/ (c) mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ Antisense (d) 5′P-UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C (e) 5′P-mU*(2′-F-U)*mC(2′-F-U)mC(2′-F-U)mC(2′-F-U) mG(2′-F-U)mC(2′-F-A)mc(2′-F-C)mC(2′-F-U)mG(2′- F-A)mG(2′-F-C)mU*(2′-F-C)*mU*(2′-F-G)*mC (f) 5′P-mU_(2′-F-U)*(2′-F-C)(2′-F-U)(2′-F-C)(2′-F- U)(2′-F-C)(2′-F-U)(2′-F-U)(2′-F-C)A(2′-F- C)CCUmGmAmGmCU*C*U*G*C (g) 5′P-UCUCUCUGUCACCCmUmGmAmGMCmUmC*mU*mG*mC*mC (h) 5′P-UCUCUCUGUCACCCmU*mG*mA*mG*mC In the sequences above, * indicates a phosphorothioated bond, m indicates 2′-O-methyl, 2′-F- indicates 2′-F(fluorine), /chol/ indicates cholesterol and 5′P indicates a 5-phosphate group.
15. The siRNA of claim 14, wherein the sense strand is (c) in the table, the antisense strand is (g) or (h) in the table.
16. The siRNA of claim 9, wherein the sense strand is selected from the group consisting of (A) to (D) in a following table, and the antisense strand is selected from the group consisting of (E) to (H) in the following table: TABLE-US-00012 Sequence (5′.fwdarw.3′) Sense (A) GGAGmUAmUGmCmCAmCmCA*mU*mU*/chol/ (B) mG(2′F-G)m(2′F-G)mU(2′F-A)mU(2′F-G)mC(2′F-C)mA (2′F-C)mC(′2F-A)*mU*(2′F-U)*/chol/ (C) mCUmAAmACmUGmGUmACmCG*mC*A*/chol/ (D) mC(2′-F-U)mA(2′-F-A)mA(2′-F-C)mU(2′-F-G)mG(2′- F-U)mA(2′-F-C)mC(2′-F-G)*mC*(2′-F-A)*/chol/ Antisense (E) 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′ F-A)mU(2′F-A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC (F) 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′ F-A)mU(2′F-A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC (G) 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC (2′-F-A)mG(2′-F-U)mU(2′-F-U)mA*(2′-f-G)*mC* (2′-F-A)*mC (H) 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC (2′-F-A)mG(2′-F-U)mU(2′-F-U)mA*(2′-F-G)*mC* (2′-F-A)*mC In the sequences above, * indicates a phosphorotrloated bond, m indicates 2-methyl 2′-F- indicates 2′-F(fluorine), /chol/ indicates cholesterol and 5′P indicates a 5′-phosphate group
17. A pharmaceutical composition for preventing or treating cancer, comprising the siRNA according to claim 1.
18. The pharmaceutical composition of claim 17, wherein the cancer is selected from multiple myeloma, non-epithelial tumor, non-small cell lung cancer (NSCLC), melanoma, breast cancer, glioma, lymphoma, leukemia, urinary system cancer, digestive tract cancer, reproductive system tumor, refractory classic Hodgkin's lymphoma, prostate cancer, metastatic melanoma, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, urinary tract epithelial cell carcinoma, refractory B cell precursor acute lymphocytic leukemia, and diffuse large B cell lymphoma.
19. An immune cell in which expression of PD-1 is suppressed, obtained by treating the immune cell with the siRNA according to claim 1.
20. The immune cell of claim 19, wherein the immune cell is selected from the group consisting of a natural killer cell (NK cell), a chimeric antigen receptor-modified NK cell (CAR-NK cell), a universal-NK cell, a tumor-infiltrating T lymphocyte (TIL), a peripheral blood mononuclear cell (PBMC), a T receptor-modified T cell (TCR-T), and a chimeric antigen receptor-modified T cell (CAR-T).
21. An immune cell therapeutic agent for treating cancer, comprising the immune cell according to claim 19 in which expression of PD-1 is suppressed.
Description
BRIEF DESCRIPTION OF DRAWINGS
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MODE OF DISCLOSURE
[0041] Unless otherwise defined, all technical and scientific terms used in this specification have the same meaning as commonly understood by an expert skilled in the art to which the present invention belongs. In general, the nomenclature used in this specification is well known and commonly used in the art.
[0042] Definitions of main terms used in the detailed description of the present invention are as follows.
[0043] The term “RNA interference (RNAi)” refers to a mechanism that inhibits expression of a target gene by inducing degradation of mRNA of the target gene by introducing a double-stranded RNA (dsRNA) consisting of a strand having a sequence homologous to mRNA of the target gene and a strand having a sequence complementary thereto.
[0044] The term “small interfering RNA (siRNA)”refers to a short double-stranded RNA (dsRNA) that mediates sequence-specific efficient gene silencing.
[0045] The term “antisense strand” is a polynucleotide that is substantially or 100% complementary to a target nucleic acid of interest, such as messenger RNA (mRNA), non-mRNA RNA sequences (e.g., microRNA, piwiRNA, tRNA, rRNA, and hnRNA), or coding or non-coding DNA sequences, which may be complementary in whole or in part.
[0046] The term “sense strand” is a polynucleotide that has an identical nucleic acid sequence to a target nucleic acid, such as messenger RNA(mRNA), non-mRNA RNA sequences (e.g., microRNA, piwiRNA, tRNA, rRNA, and hnRNA) or coding or non-coding DNA sequences, which may be identical in whole or in part.
[0047] The term “gene” should be considered in the broadest sense and may encode a structural or regulatory protein. In this case, the regulatory protein includes a transcription factor, a heat shock protein, or a protein involved in DNA/RNA replication, transcription, and/or translation.
[0048] The term “PD-1” is an abbreviation of programmed cell death protein 1 and belongs to Type I transmembrane protein of a member of the CD28 family, and the human PD-1 gene exists on 2q37.35 chromosome and contains about 55 kD of transmembrane protein. PD-1 is widely expressed on surfaces of activated T cells, B cells, mononuclear cells and dendritic cells, the structure of PD-1 has 30% homology to CTLA-4, and two tyrosine residues are present in the intracellular region, which may respectively participate in forming of one immunoreceptor tyrosine-based inhibitory motif (ITIM) at the N-terminus and one immunoreceptor tyrosine-based switch motif (ITSM) at the C-terminus. The extracellular region is consisting of one IgV-like structural region, contains a number of glycosylation sites, and is severely glycosylated, and the structural region is bound to a ligand, thereby inhibiting T cell activation. PD-L1 is expressed in excess in many cancer tissues, including non-small cell lung cancer (NSCLC), melanoma, breast cancer, glioma, lymphoma, leukemia, and various urinary system cancers, digestive tract cancers, reproductive system tumors, and the like. The high expression of PD-L1 regulates expression of proteins at a cell cycle detection point and proteins related to cell proliferation through inhibition of RAS and PI3K/AKT signaling pathways, resulting in inhibition of T cell proliferation. It is known that activation of the PD-1/PD-L1 signaling pathway in vitro and in mouse models induces specific CTL apoptosis and promotes immune escape of tumor cells by lowering sensitivity of CTL apoptosis effects.
[0049] The purpose of the present invention may be broadly expressed in two aspects. The first purpose is to design an asymmetric siRNA targeting an mRNA encoding PD-1 and select an asymmetric siRNA that most efficiently inhibits expression of PD-1 through screening. The second purpose is to introduce a chemical modification to deliver siRNA into cells without any other carrier and increase resistance to nucleases. An siRNA must be small or hydrophobic to pass through cell membrane consisting of phospholipids. However, siRNA is negatively charged by a phosphate backbone, and thus it is difficult for the siRNA to penetrate the cell membrane. In addition, it is necessary to increase resistance to nuclease s for siRNA to have a long lifetime in serum such that the amount reaching the target may be sufficient to generate effective RNAi. Therefore, by introducing chemical modifications, the siRNA delivery problem was overcome.
[0050] In one embodiment of the present invention, an asiRNA targeting PD-1 mRNA was designed, and an asiRNA having the best knockdown efficiency was identified and selected. In addition, asiRNA may be modified by introducing chemical modification to have cell-penetrating ability and resistance to nucleases without aid of a carrier, and thus, cp-asiRNA that may efficiently inhibit PD-1 expression was chosen. 4 modifications may be introduced to the chosen siRNA for asiRNA to have cell-penetrating ability and resistance to nucleases. First, cholesterol may be added to 3′ end of a sense strand to allow siRNA to penetrate cell membrane. Second, by substituting a phosphate backbone near 5′ or 3′ end of the sense strand and the antisense strand with phosphorothioate, the siRNA may have resistance to exonucleases, and absorption into cells and bioavailability of siRNA in vivo may be available. Third, by modifying 2′-OH group of sugar with 2′-O-methyl, resistance to nucleases may be obtained, and siRNA immunogenicity may be lowered, thus reducing off-target effects. Fourth, 2′ of sugar may be modified with fluorine to grant stability to double stranded duplex, thus increasing stability in serum and enabling efficient silencing in vitro and in vivo. By applying the above modification to siRNA, siRNA may have cell-penetrating ability, and siRNA may stay in serum for a longer time and allow more efficient gene suppression as sufficient amount of siRNA is delivered to target cells.
[0051] Accordingly, in an aspect of the present invention, an asymmetric siRNA may include: an antisense strand including a sequence complementary to mRNA encoding programmed cell death protein 1 (PD-1); a sense strand forming complementary bonds with the antisense strand, wherein a 5′ end of the antisense strand and a 3′ end of the sense strand may form a blunt end.
[0052] The siRNA in the present invention may include all substances having a general RNA interference (RNAi) action. Therefore, siRNA as used herein is not necessarily limited to synthetic siRNA, and may be applied to siRNA or shRNA expressed in cells using an expression vector or the like. RNAi is an intracellular gene regulation method first discovered in Caenorhabditis elegans by Fire research group in 1998. The action mechanism is that an antisense strand of an RNA double strands injected into a cell complementarily binds to an mRNA of a target gene to induce target gene degradation. Among them, synthetic RNA interference (siRNA) is one of the methods to suppress gene expression “in vitro”. siRNA having 19 bp to 21 bp is theoretically a technology that may be developed as a therapeutic agent for various gene-related diseases such as cancer, rare diseases, fibrosis, and viral infections as siRNA may selectively suppress most of genes. In mid-2002, in vivo treatment with siRNA was first attempted in mammals, and there many attempts have been performed on applied research since then. In particular, in 2018, Onpattro, the first siRNA-based RNAi treatment for multiple neuropathies of hereditary transthyretin-mediated (hATTR) amyloidosis by Alnylam Pharmaceuticals, was approved by the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA). Onpattro was previously designated as an innovative treatment and an orphan drug. Many other global pharmaceutical companies are investing more than billions of dollars on RNAi therapeutic projects, including siRNA, for various intractable diseases. However, existing RNAi therapeutics still have barriers such as 1) lack of an effective delivery system 2) off-target effect 3) immune response induction 4) saturation of intracellular RNAi pathway. Thus, there is a need to overcome these barriers. Due to these problems, although siRNA is an effective method to directly control expression of a target gene, it is difficult to develop a therapeutic agent.
[0053] To solve this, the present invention proposes an asymmetric siRNA including an antisense strand and a sense strand complementary to the antisense strand, and the siRNA according to the present invention may not cause problems such as off-target effect and saturation of RNAi mechanisms. Therefore, it is possible to stably suppress expression of the PD-1 target gene while maintaining high delivery efficiency to a desired degree.
[0054] In the present invention, the sense strand of the siRNA may have a length of 15 nt to 17 nt, and the antisense strand may have a length of 16 nt or more. Although not limited thereto, the antisense strand may have a length of 16 nt to 31 nt or preferably a length of 19 nt to 25 nt. More preferably, the sense strand may have a length of 16 nt, and the antisense strand complementary thereto may have a length of 19 nt, 21 nt, or 25 nt, but is not limited thereto. 3′ end of the sense strand and 5′ end of the antisense strand may form a blunt end. 3′ end of the antisense strand may include, for example, overhang of 1 nt to 16 nt.
[0055] In some embodiments, 36 asiRNAs were designed to suppress PD-1 expression, and inhibition in HeLa-PD-1 cell expressing PD-1 in mRNA level and protein level were identified.
[0056] In the present invention, the sense strand may be selected from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 77, 79, 81, 83, 85, 87, 89, and 91. Preferably, an siRNA including the sense strand selected from the group consisting of SEQ ID NOs:43, 47, 49, 77, and 89 and an antisense strand to complementary the sense strand was found to be most effective in inhibiting PD-1 expression.
[0057] In the present invention, the antisense strand may be selected from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 78, 80, 82, 84, 86, 88, 90, and 92. Preferably, the antisense strand may be selected from the group consisting of SEQ ID NOs:44, 48, 50, 78, and 80.
[0058] More preferably, the sense strand of the siRNA of the present invention may be SEQ ID NO:43, 47, 49, 77, or 89, and the antisense strand of the siRNA may be SEQ ID NO:44, 48, 50, 78, or 90.
[0059] In the present invention, the sense strand or the antisense strand of the siRNA may include at least one chemical modification.
[0060] General siRNA may not pass through cell membrane due to high molecular weight and high negative charge due to the phosphate backbone structure, and it is difficult to deliver a sufficient amount for RNAi induction to the actual target site because general siRNA is rapidly degraded and removed from the blood. Currently, in the case of in vitro delivery, many high-efficiency delivery methods using cationic lipids and cationic polymers have been developed, but in the case of in vivo, it is difficult to deliver siRNA with as high efficiency as in vitro, and there is a problem in that siRNA delivery efficiency decreases due to interaction with various proteins present in vivo.
[0061] Accordingly, the present inventors have developed an asiRNA construct (cp-asiRNA) having an effective and self-transmitting ability capable of intracellular delivery without a separate carrier by introducing chemical modifications to an asymmetric siRNA structure.
[0062] In the present invention, chemical modification in the sense strand or the antisense strand may include at least one selected from the group consisting of: —OH group at 2′ carbon position in a sugar structure of a nucleotide substituted with methyl (—CH.sub.3), methoxy (—OCH.sub.3), —NH.sub.2, —F (fluorine), —O-2-methoxyethyl-O-propyl, —O-2-methylthioethyl, —O-3-aminopropyl, —O-3-dimethylaminopropyl; oxygen in a sugar structure of a nucleotide substituted with sulfur; a phosphate bond of a nucleotide modified with phosphorothioate, phosphorodithioate, boranophosphate, or methyl phosphonate; substitution with a peptide nucleic acid (PNA), a locked nucleic acid (LNA), or an unlocked nucleic acid (UNA); and a phosphate group, lipophilic compound, or cell-penetrating peptide bond.
[0063] In the present invention, the lipophilic compound may be selected from the group consisting of cholesterol, tocopherol, docosahexaenoic acid (DHA), palmitic acid, and long-chain fatty acids having 10 or more carbon atoms. Preferably, the lipophilic compound may be cholesterol, but embodiments are not limited thereto.
[0064] In some embodiments, the sense strand or the antisense strand may include at least one modification selected from the group consisting of: —OH group at 2′ carbon position in a sugar structure of a nucleotide substituted with methoxy (—OCH.sub.3) or —F (fluorine); at least one nucleotide bond in the sense strand or the antisense strand modified with phosphorothioate; 3′ end of the sense strand modified with a lipophilic compound bond; and 5′ end of the antisense strand modified with a phosphate group bond.
[0065] The sense strand in the siRNA in the present invention may be selected from the group consisting of (a) to (c), and the antisense strand may be selected from the group consisting of (d) to (o).
TABLE-US-00001 Sequence (5′.fwdarw.3′) Sense (a) mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ (b) mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ (c) mCAmUGmAGmCCmCCmAGmCA*mA*C*/chol/ Antisense (d) UCUCUCUGUCACCCmU*mG*A*G*C (e) UCUCUCUGUCACCCmU*mG*mA*mG*mC (f) UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*mG*mC*mC (g) UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*G*C*C (h) UCUCUCUGUCACCCmUmGmAmGmCmUC*U*G*C*C (i) UUCUCUCUGUCACCmC*mU*G*A*G (j) UUCUCUCUGUCACCmC*mU*mG*mA*mG (k) UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*mU*mG*mC (l) UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*U*G*C (m) UUCUCUCUGUCACCmUmUmGmAmCU*C*U*G*C (n) GUUGCUGGGGCUCAmU*mG*mC*mG*mG (o) GUUGCUGGGGCUCAmU*mG*C*G*G
[0066] In the table above, * indicates a phosphorothioated bond, m indicates 2′-O-methyl, and /chol/ indicates cholesterol. Specifically, “*” refers to an existing phosphodiester bond substituted with a phosphorothioate bond, “m” refers to 2′-OH substituted with 2′-O-methyl. In the case of “2′-F-”, for example, “2′-F-G” refers to existing 2′-OH of guanine (G) substituted with fluorine, and “Chol” refers to a form in which cholesterol is added at 3′-end. 5′ end of the antisense strand may further be bonded with 1 to 3 phosphate group(s).
[0067] Preferably, the sense strand may be (b) in the table, and the antisense strand may be (i) or (m) in the table.
[0068] More preferably, the sense strand may be selected from the group consisting of (a) to (c), and the antisense strand may be selected from the group consisting of (d) to (h):
TABLE-US-00002 Sequence (5′.fwdarw.3′) Sense (a) mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ (b) mA(2′-F-G)mG(2′-F-G)mU(2′-F-G)mA(2′-F-C)mA(2′- F-G)mA(2′-F-G)mA(2′-F-G)*mA*(2′-F-A)*/chol/ (c) mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ Antisense (d) 5′P-UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C (e) 5′P-mU*(2′-F-U)*mC(2′-F-U)mC(2′-F-U)mC(2′-F-U) mG(2′-F-U)mC(2′-F-A)mc(2′-F-C)mC(2′-F-U)mG(2′- F-A)mG(2′-F-C)mU*(2′-F-C)*mU*(2′-F-G)*mC (f) 5′P-mU_(2′-F-U)*(2′-F-C)(2′-F-U)(2′-F-C)(2′-F- U)(2′-F-C)(2′-F-U)(2′-F-U)(2′-F-C)A(2′-F- C)CCUmGmAmGmCU*C*U*G*C (g) 5′P-UCUCUCUGUCACCCmUmGmAmGMCmUmC*mU*mG*mC*mC (h) 5′P-UCUCUCUGUCACCCmU*mG*mA*mG*mC
[0069] In the table above, * indicates a phosphorothioated bond, m indicates 2′-O-methyl, 2′-F- indicates 2′-fluoro, /chol/ indicates cholesterol, and 5′P indicates a 5′-phosphate group.
[0070] Most preferably, the sense strand may be (c) in the table, and the antisense strand may be (g) or (h) in the table.
[0071] Preferably, the sense strand may be one selected from the group consisting of (A) to (D), antisense strand may be one selected from the group consisting of (E) to (H), and more preferably, the siRNA may be: Sense Strand (A) and Antisense Strand (E); Sense Strand (B) and Antisense Strand (F); Sense Strand (C) and Antisense Strand (G); or Sense Strand (D) and Antisense Strand (H).
TABLE-US-00003 Sequence (5′.fwdarw.3′) Sense (A) GGAGmUAmUGmCmCAmCmCA*mU*mU*/chol/ (B) mG(2′F-G)m(2′F-G)mU(2′F-A)mU(2′F-G)mC(2′F-C)mA (2′F-C)mC(′2F-A)*mU*(2′F-U)*/chol/ (C) mCUmAAmACmUGmGUmACmCG*mC*A*/chol/ (D) mC(2′-F-U)mA(2′-F-A)mA(2′-F-C)mU(2′-F-G)mG(2′- F-U)mA(2′-F-C)mC(2′-F-G)*mC*(2′-F-A)*/chol/ Antisense (E) 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′ F-A)mU(2′F-A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC (F) 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′ F-A)mU(2′F-A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC (G) 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC (2′-F-A)mG(2′-F-U)mU(2′-F-U)mA*(2′-f-G)*mC* (2′-F-A)*mC (H) 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC (2′-F-A)mG(2′-F-U)mU(2′-F-U)mA*(2′-F-G)*mC* (2′-F-A)*mC
[0072] In the table above, * indicates a phosphorothioated bond, m indicates 2′-methyl, 2′-F- indicates 2′-fluorine (F), /chol/ indicates cholesterol, and 5′P indicates a 5′-phosphate group.
[0073] Another aspect of the present invention provides a pharmaceutical composition for preventing or treating cancer including the siRNA.
[0074] In the present invention, the cancer may be selected from multiple myeloma, non-epithelial tumor, non-small cell lung cancer (NSCLC), melanoma, breast cancer, glioma, lymphoma, leukemia, urinary system cancer, digestive tract cancer, reproductive system tumor, refractory classic Hodgkin's lymphoma, prostate cancer, metastatic melanoma, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, urinary tract epithelial cell carcinoma, refractory B cell precursor acute lymphocytic leukemia, and diffuse large B cell lymphoma, but is not limited thereto, and any cancer known to express PD-1 ligand represented by PD-L1 may be treated with a composition for preventing or treating cancer without any limitation.
[0075] The pharmaceutical composition may be prepared by including one or more pharmaceutically acceptable carriers in addition to siRNA as an active ingredient. The pharmaceutically acceptable carrier is compatible with the active ingredient of the present invention and may include saline, sterile water, Ringer's solution, buffered saline, dextrose solution, maltodextrin solution, glycerol, ethanol, or a mixture of two or more of these ingredients. Any other general additives such as antioxidants, buffers, and bacteriostatic agents may be added according to a need. In addition, diluents, dispersants, surfactants, binders, and lubricants may be additionally added to formulate injectable formulations such as aqueous solutions, suspensions, and emulsions. In particular, it is preferable to provide a formulation in a lyophilized form. For the preparation of the lyophilized formulation, a method commonly known in the art may be used, and a stabilizer for lyophilization may be added.
[0076] The method of administering the pharmaceutical composition may be determined by one of ordinary skill in the art based on symptoms and severity of the disease of a typical patient. In addition, the pharmaceutical composition may be formulated in various forms such as powders, tablets, capsules, liquids, injections, ointments, syrups, or the like, and the pharmaceutical composition may be provided in unit-dose or multi-dose containers, such as sealed ampoules and bottles.
[0077] The pharmaceutical composition of the present invention may be administered orally or parenterally. The route of administration of the composition according to the present invention may be, for example, oral, intravenous, intramuscular, intraarterial, intramedullary, intrathecal, intracardiac, transdermal, subcutaneous, intraperitoneal, intestinal, sublingual, or topical administration, but is not limited thereto. The dosage of the composition according to the present invention may vary depending on the patient's weight, age, sex, health status, diet, administration time, method, excretion rate, or severity of disease and may be determined by one of ordinary skill in the art. In addition, the composition of the present invention may be formulated into a suitable formulation using known techniques for clinical administration.
[0078] In another aspect, the present invention relates to a method of preventing or treating cancer including administering the siRNA to an individual. Since the configuration included in improving or treating according to the present invention is the same as the configuration included in the invention described above, the above description may be identically applied to the improvement or treatment method.
[0079] In another aspect, the present invention relates to an immune cell, in which expression of PD-1 is inhibited, obtained by treating the immune cell with the siRNA.
[0080] The term “immune cell” as used herein refers to a cell involved in an immune response expressing PD-1. Preferably, an immune cell may be an immune cell used for tumor immunotherapy, but is not limited thereto.
[0081] In the present invention, the immune cell may be selected from the group consisting of a natural killer cell (NK cell), a chimeric antigen receptor-modified NK cell (CAR-NK cell), a universal-NK cell, a cytotoxic T lymphocyte (CTL), a tumor-infiltrating T lymphocyte (TIL), a peripheral blood mononuclear cell (PBMC), a T receptor-modified T cell (TCR-T), and a chimeric antigen receptor-modified T cells (CAR-T). Preferably, the immune cell may be CD8+ T cell, but is not limited thereto.
[0082] The term “chimeric antigen receptor-T cell (CAR-T cell)” or “CAR-NK cell” as used herein respectively refers to a T cell or NK cell expressing a ‘chimeric antigen receptor’.
[0083] The term “chimeric antigen receptor (CAR)” as used herein refers to a recombinant polypeptide construct that may provide a target cell and intracellular signal generation to a cell in an immune effector cell. CAR is a molecule that combines antibody-based specificity for a target antigen (e.g., a tumor antigen) with a receptor-activated intracellular domain of T cells or NK cells to produce chimeric proteins that exhibit specific anti-tumor cell immune activity.
[0084] The term “chimera” of the present invention refers to a composition of parts of different proteins or DNAs of different origins. The CAR may include at least an extracellular binding domain, a transmembrane domain, and an intracellular signaling domain.
[0085] This immune cell-based tumor immunotherapy has been successfully used in clinical practice and has shown unprecedented clinical efficacy. Despite the remarkable effect of immune cell-based tumor immunotherapy, problems have been raised due to various difficulties in the actual tumor treatment process, and one of the most important reasons is the above-described PD-1/PD-L1 inhibitory immune checkpoints. The immune checkpoints significantly reduce effectiveness of the immune cell-based tumor immunotherapy by inhibiting immune activity of immune cells in association with inhibitory signal transduction.
[0086] Accordingly, the present inventors developed immune cells with suppressed PD-1 expression obtained by treatment with the siRNA to prevent reduction of the effects of immune cell-based tumor immunotherapy due to inhibitory immune checkpoints with PD-ligand expressed by cancer cells.
[0087] In one embodiment of the present invention, when cp-asiRNA was treated on an effector T cell expressing PD-1, a satisfactory activity recovery effect was confirmed even in the presence of PD-L1 expressing cells. In this light, even when the expression of PD-1 is suppressed by siRNA against any of the above-described immune cells such as NK cells, CAR-NK cells, CAR-T, or TCR-T, recovery of the activity of immune cells may be expected.
[0088] In another aspect, the present invention relates to an immune cell therapeutic agent for cancer including immune cells in which expression of PD-1 is suppressed.
[0089] The term “immune cell therapeutic agent” as used herein refers to a drug used for treating diseases by activating immune response in a body using immune cells such as dendritic cell, natural killer cells, or T cells. The immune cell therapeutic agent is mainly developed as an indication for cancer treatment, and the therapeutic mechanism and efficacy of the immune cell therapeutic agent are differentiated from surgical therapy, therapy using anticancer drugs, or radiation therapy in the related art used in cancer treatment, because therapeutic effects may be obtained by activating immune function by administering immune cells directly to the patient. Thus, the immune cell therapeutic agent occupies a major part of new bio drugs.
[0090] According to characteristics of genes introduced into cells during the manufacturing process and characteristics of immune cells used, the immune cell therapeutic agent may include dendritic immunomodulatory cell therapy, natural killer cells (NK cells), and chimeric antigen receptor-modified NK cells (CAR-NK cells). Universal-NK cells, lymphokine activated killers (LAK), tumor-infiltrating T lymphocytes (TIL), T cell receptor-modified T cells (TCR-T), and chimeric antigen receptor-modified T cells (CAR-T) may be included, but is not limited thereto.
[0091] In the present invention, the cancer may include breast cancer, multiple myeloma, non-epithelial tumor, NSCLC, melanoma, glioma, lymphoma, leukemia, urinary system cancer, digestive tract cancer, and reproductive system tumor, refractory classic Hodgkin's lymphoma, prostate cancer, metastatic melanoma, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, urinary tract epithelial cell carcinoma, refractory B cell precursor acute lymphocytic leukemia, and diffuse large B cell lymphoma, but is not limited thereto, and any cancer known to express PD-1 ligand represented by PD-L1 may be treated with the immune cell therapeutic agent without any limitation.
[0092] Hereinafter, the present invention will be described in further detail with reference to Examples. The Examples are for illustrative purposes only, and it will be apparent to one of ordinary skill in the art that the scope of the present invention is not construed as being limited by these examples.
EXAMPLE 1
Screening of 36 RNAi-Induced Double-Stranded Nucleic Acid Molecules Targeting PD-1
[0093] 1.1. Confirmation of PD-1 Expression in HeLa-PD-1 Cell Line
[0094] Prior to designing asiRNAs and verifying inhibitory effects thereof on PD-1 mRNA expression, expression of PD-1 in HeLa-PD-1 cell lines was confirmed using PCR and ELISA. HeLa-PD-1 stably overexpresses PD-1 with a cell line selected using hygromycin B (Gold Biotechnology Inc.), which is a selection marker, after transfection of a plasmid encoding mRNA of PD-1 into HeLa (ATCC). This feature overcomes the limitation of PD-1 that transcription is induced only by stimulation, rather than being always expressed, and enables smooth screening.
[0095] 1.2. Selection of Target PD-1 Gene and Design and Production of 36 asiRNAs
[0096] In order to secure a double-stranded nucleic acid molecule that induces high-efficiency RNAi interference targeting PD-1, asiRNA was designed after selecting a target sequence for the PD-1 gene. asiRNA structure has different secondary structure, GC contents (%), 5′ end stability difference, or the like, as compared with commonly known siRNA. Thus, when designing a base sequence of asiRNA using a general siRNA design program, it may be difficult to design an optimized asiRNA. Therefore, designing of the candidate asiRNA of the present invention was carried out in the following method.
[0097] PD-1 gene information was obtained through NCBI database search (mRNA accession number: NM_005018.2). In consideration of animal experiments, base sequences showing 100% homology based on a base sequence having a common target with a mouse was first selected, and then base sequences allowing mismatch in the antisense strand except for the seed region (base sequence No. 2 to 8 based on 5′) were further selected. Then, 36 asiRNAs were designed and synthesized in 10-nanomole-scale by OliX Pharmaceuticals, Inc. (Korea). The 36 designed asiRNAs each had a base sequence as shown in Table 1. Each of the asiRNAs was diluted to an appropriate concentration in 5× siRNA duplex (available from Bioneer) and annealed through an incubation process at 95° C. for 5 minutes and 37° C. for 1 hour. After performing 12% polyacrylamide gel electrophoresis (PAGE) thereon, QC through a ChemiDoc UV transilluminator (available from Biorad) was carried out. The 36 screened asiRNAs base sequences are shown in Table 1.
TABLE-US-00004 TABLE 1 SEQ ID asiRNA name Sequence(5′.fwdarw.3′) NO. asiPD-1-4 sense CUGUGGGGCCAUCUCC 1 antisense GGAGAUGGCCCCACAGAGGUA 2 asiPD-1-5 sense UCUGUGGGGCCAUCUC 3 antisense GAGAUGGCCCCACAGAGGUAG 4 asiPD-1-11 sense CCUUCACCUGCAGCUU 5 antisense AAGCUGCAGGUGAAGGUGGCG 6 asiPD-1-13 sense ACCUUCACCUGCAGCU 7 antisense AGCUGCAGGUGAAGGUGGCGU 8 asiPD-1-15 sense CACCUUCACCUGCAGC 9 antisense GCUGCAGGUGAAGGUGGCGUU 10 asiPD-1-17 sense CUCUGUGGGGCCAUCU 11 antisense AGAUGGCCCCACAGAGGUAGG 12 asiPD-1-19 sense CCUCUGUGGGGCCAUC 13 antisense GAUGGCCCCACAGAGGUAGGU 14 asiPD-1-21 sense ACCUCUGUGGGGCCAU 15 antisense AUGGCCCCACAGAGGUAGGUG 16 asiPD-1-31 sense CCACCUUCACCUGCAG 17 antisense CUGCAGGUGAAGGUGGCGUUG 18 asiPD-1-33 sense GCCCCAGCAACCAGAC 19 antisense GUCUGGUUGCUGGGGCUCAUG 20 asiPD-1-35 sense AGCCCCAGCAACCAGA 21 antisense UCUGGUUGCUGGGGCUCAUGC 22 asiPD-1-51 sense GGCACCUACCUCUGUG 23 antisense CACAGAGGUAGGUGCCGCUGU 24 asiPD-1-53 sense CGGCACCUACCUCUGU 25 antisense ACAGAGGUAGGUGCCGCUGUC 26 asiPD-1-55 sense GCGGCACCUACCUCUG 27 antisense CAGAGGUAGGUGCCGCUGUCA 28 asiPD-1-57 sense AGCGGCACCUACCUCU 29 antisense AGAGGUAGGUGCCGCUGUCAU 30 asiPD-1-59 sense CGUGACUUCCACAUGA 31 antisense UCAUGUGGAAGUCACGCCCGU 32 asiPD-1-65 sense GGGCGUGACUUCCACA 33 antisense UGUGGAAGUCACGCCCGUUGG 34 asiPD-1-77 sense ACUAUGGGGAGCUGGA 35 antisense UCCAGCUCCCCAUAGUCCACA 36 asiPD-1-79 sense GACACUGCUCUUGGCC 37 antisense GGCCAAGAGCAGUGUCCAUCC 38 asiPD-1-85 sense GCCACCUUCACCUGCA 39 antisense UGCAGGUGAAGGUGGCGUUGU 40 asiPD-1-87 sense CGCCACCUUCACCUGC 41 antisense GCAGGUGAAGGUGGCGUUGUC 42 asiPD-1-89 sense CAUGAGCCCCAGCAAC 43 antisense GUUGCUGGGGCUCAUGCGGUA 44 asiPD-1-91 sense GCAUGAGCCCCAGCAA 45 antisense UUGCUGGGGCUCAUGCGGUAC 46 asiPD-1-93 sense AGGGUGACAGAGAGAA 47 antisense UUCUCUCUGUCACCCUGAGCU 48 asiPD-1-95 sense CAGGGUGACAGAGAGA 49 antisense UCUCUCUGUCACCCUGAGCUC 50 asiPD-1-97 sense UCAGGGUGACAGAGAG 51 antisense CUCUCUGUCACCCUGAGCUCU 52 asiPD-1-99 sense GACUAUGGGGAGCUGG 53 antisense CCAGCUCCCCAUAGUCCACAG 54 asiPD-1-101 sense AGUGGCGAGAGAAGAC 55 antisense GUCUUCUCUCGCCACUGGAAA 56 asiPD-1-103 sense CAGUGGCGAGAGAAGA 57 antisense UCUUCUCUCGCCACUGGAAAU 58 asiPD-1-105 sense CCAGUGGCGAGAGAAG 59 antisense CUUCUCUCGCCACUGGAAAUC 60 asiPD-1-107 sense UCCAGUGGCGAGAGAA 61 antisense UUCUCUCGCCACUGGAAAUCC 62 asiPD-1-109 sense UCUGCAGACCCUCCAC 63 antisense GUGGAGGGUCUGCAGAACACU 64 asiPD-1-116 sense ACGCCACCUUCACCUG 65 antisense CAGGUGAAGGUGGCGUUGUCC 66 asiPD-1-118 sense AACGCCACCUUCACCU 67 antisense AGGUGAAGGUGGCGUUGUCCC 68 asiPD-1-138 sense UUCUGCAGACCCUCCA 69 antisense UGGAGGGUCUGCAGAACACUG 70 asiPD-1-134 sense GGACUAUGGGGAGCUG 71 antisense CAGCUCCCCAUAGUCCACAGA 72
[0098] 1.3. Confirmation of PD-1 mRNA Expression Inhibitory Effects of 36 asiRNAs
[0099] To identify gene inhibitory efficiency at an mRNA level, transfection with 36 selected asiRNAs at concentrations of 10 nM and 1 nM into HeLa-PD-1 cell lines were performed, and then qRT-PCR was performed thereon to measure the expression level of PD-1 mRNA.
[0100] Specifically, HeLa-PD-1 cells were cultured in Dulbecco's modified Eagle's medium (Gibco) to which 10% fetal bovine serum (Gibco) and 0.2 g/L hygromycin B were added in a 100 mm cell culture dish. HeLa-PD-1 cells cultured 24 hours before transfection were seeded in a 12-well plate. Thereafter, 36 asiRNAs of 1 nM or 10 nM (Table 1) were transfected using RNAimax (Invitrogen) based on the protocol provided by the manufacturer. After 24 hours, the total RNA was extracted using Tri-RNA reagent (FAVORGEN), and 500 ng of RNA was used for cDNA synthesis. cDNA was synthesized by using a High-capacity cDNA reverse transcription kit (Applied Biosystems) according to the protocol provided by the manufacturer. The synthesized cDNA was then subjected to qRT-PCR using the StepOne real-time PCR system (Applied Biosystems). By using the primers of Table 2 and SYBR green PCR master Mix (Applied Biosystems), the amount of PD-1 expression in the asiRNA transfection sample, compared with non-treated sample (NT), was converted into percentage (
TABLE-US-00005 TABLE 2 Name Sequence(5′.fwdarw.3′) SEQ ID NO. Tubulin Forward GACCAAGCGTACCATCCAGT 73 Reverse ACGTTTGGCATACATCAGG 74 PD-1 Forward CCCTGGTGGTTGGTGTCGT 75 Reverse GCCTGGCTCCTATTGTCCCTC 76
[0101] The experiment was independently performed three times, and the gene suppression efficiencies of asiRNA against 36 types of sequences targeting PD-1 mRNA are shown in
[0102] 1.4. Confirmation of Protein Expression Inhibitory Effect Through Quantification of PD-1 Protein Level of 3 asiRNAs
[0103] From the results of 36 asiRNA screening, the two most efficient asiRNAs (asiPD-1-93 and asiPD-1-95) and additional asiPD-1-89 were selected. After transfection at 1 nM concentration, the PD-1 protein level was identified through a human programmed death 1 (PD-1) ELISA kit (Mybiosoure).
[0104] Specifically, HeLa-PD-1 cells were cultured in Dulbecco's modified Eagle's medium (Gibco) to which 10% fetal bovine serum (Gibco) and 0.2 g/L hygromycin B were added in a 100 mm cell culture dish. HeLa-PD-1 cells cultured 24 hours before transfection were seeded in a 12-well plate. Thereafter, 1 nM of 3 asiRNAs (asiPD-1-89, asiPD-1-93, and asiPD-1-95) were transfected using RNAimax (Invitrogen) based on the protocol provided by the manufacturer. After 24 hours after transfection, the media was replaced with a new medium, and at 48 hours, passage was performed with a 12-well plate again. After that, at 96 hours, harvest was performed to prepare cell lysate using 5× RIPA (self-made) buffer. After quantification through BCA assay (Pierce), the PD-1 protein level was identified by using human programmed death 1 (PD-1) ELISA kit (Mybiosource) according to the protocol provided by the manufacturer.
[0105] The experiment was independently performed four times, and the PD-1 protein levels (% of control) for the three selected candidate groups are shown in
EXAMPLE 2
Screening of RNAi-Induced Asymmetric Double-Stranded Nucleic Acid Molecules (cp-asiRNA) Having Cell-Penetrating Ability Targeting PD-1
[0106] 2.1. Design and Production of 12 cp-asiRNAs Having Cell-Penetrating Ability
[0107] Chemical modification, which promote penetration into cells and improve stability of RNA structure, were selected and applied to the three candidate asiRNAs targeting PD-1 (asiPD-1-89, asiPD-1-93, and asiPD-1-95) through two processes. In the first chemical modification, cholesterol was conjugated to the nucleotide at the 3′ end of the sense strand, which is 16 nt, and the three phosphate backbones present in the 5′ direction were substituted with phosphorothioates. Each hydroxyl group at the 2′ position of the ribose of 8 nucleotides of the 16 nucleotides of the sense strand was substituted with an —O-methyl group. In addition, the antisense strand is consisting of 19 nt or 25 nt in length, the hydroxyl group at the 2′ position of ribose of 2 nt to 11 nt nucleotides was substituted with —O-methyl group, and the phosphate backbone of 4 nucleotides present in the 3′ end direction were substituted with phosphorothioate, thereby designing 12 cp-asiRNAs. The 12 cp-asiRNA nucleotide sequences designed in this manner are shown in Table 3. cp-asiPD-1-1 to cp-asiPD-1-5 were designed based on asiPD-1-95 in Table 1, cp-asiPD-1-6 to cp-asiPD-1-10 were designed based on asiPD-1-93 in Table 1, and cp-asiPD-1-11 to cp-asiPD-1-12 were designed based on asiPD-1-89 in Table 1. Each of the designed cp-asiRNAs was diluted to an appropriate concentration for OptiMEM (Gipco) and annealed through an incubation process at 95° C. for 5 minutes and 37° C. for 1 hour. After performing 12% polyacrylamide gel electrophoresis (PAGE) thereon, QC through a ChemiDoc UV transilluminator (available from Biorad) was carried out.
TABLE-US-00006 TABLE 3 cp-asiRNA name Sequence(5′.fwdarw.3′) cp-asiPD-1-1 sense mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ antisense UCUCUCUGUCACCCmU*mG*A*G*C cp-asiPD-1-2 sense mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ antisense UCUCUCUGUCACCCmU*mG*mA*mG*mC cp-asiPD-1-3 sense mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ antisense UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*mG*mC*mC cp-asiPD-1-4 sense mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ antisense UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*G*C*C cp-asiPD-1-5 sense mCAmGGmGUmGAmCAmGAmGA*mG*A*/chol/ antisense UCUCUCUGUCACCCmUmGmAmGmCmUC*U*G*C*C cp-asiPD-1-6 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense UUCUCUCUGUCACCmC*mU*G*A*G cp-asiPD-1-7 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense UUCUCUCUGUCACCmC*mU*mG*mA*mG cp-asiPD-1-8 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*mU*mG*mC cp-asiPD-1-9 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense UUCUCUCUGUCACCmCmUmGmAmGmCmU*mC*U*G*C cp-asiPD-1-10 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C cp-asiPD-1-11 sense mCAmUGmAGmCCmCCmAGmCA*mA*C*/chol/ antisense GUUGCUGGGGCUCAmU*mG*mC*mG*mG cp-asiPD-1-12 sense mCAmUGmAGmCCmCCmAGmCA*mA*C*/chol/ antisense GUUGCUGGGGCUCAmU*mG*C*G*G m: 2′-O-CH.sub.3(methyl) modification, *phosphorothioate linkage, /chol/: cholesterol
[0108] 2.2. Verification of Toxicity and Verification of Cell Penetrating Ability and PD-1 Expression Inhibitory Efficiency at Protein Level for 12 cp-asiRNAs
[0109] To confirm the gene inhibitory efficiency at a protein level, cp-asiRNA was treated at a concentration of 1 μM, and then the toxicity caused by cp-asiRNA was identified 24 hours later, and the expression level of PD-1 protein was measured 96 hours after the treatment.
[0110] Specifically, first, HeLa-PD-1 cells were cultured in Dulbecco's modified Eagle's medium (Gibco) to which 10% fetal bovine serum (Gibco) and 0.2 g/L hygromycin B (Gold Biotechnology Inc.) were added in a 100 mm petri dish. HeLa-PD-1 cells cultured 24 hours before the treatment were seeded in a 12-well plate. After seeding, 12 types of cp-asiRNAs were treated at a concentration of 1 μM without a separate carrier.
[0111] To confirm toxicity, toxicity caused by cp-asiRNA was confirmed 24 hours after treatment, at 24 hours, the media was changed to new media, and MTT (Sigma-Aldrich) dissolved in Dulbecco's phosphate-buffered saline (DPBS, Gibco) was added thereto such that the final concentration was 5 mg/mL. After incubation at 37° C. for 2 hours, all the solutions were removed, DMSO (Sigma-Aldrich) was added, and then incubation was further performed at 37° C. for 10 minutes, and absorbance at 570 nm was measured. As a result, it was confirmed that there was no cytotoxicity induced by the prepared cp-asiRNA.
[0112] To measure expression of PD-1 protein, the cells were harvested 96 hours after treatment to obtain cell lysate. After quantification using the Thermo Scientific Pierce BCA Protein Assay Kit (Thermo Scientific), the PD-1 protein level was confirmed by Western blotting. Anti-PD1 antibody (Abcam) was used as the primary antibody, and Goat anti-Rabbit igG H&L (HRP) (Abcam) was used as the secondary antibody.
[0113] The protein level confirmation was independently performed three times, and
EXAMPLE 3
Screening of RNAi-Induced Asymmetric Double-Stranded Nucleic Acid Molecules (cp-asiRNA) Having Cell-Penetrating Ability Targeting PD-1
[0114] 3.1. Design and Production of 11 cp-asiRNAs of cp-asiPD-1-6 to cp-asiPD-1-10 Further Chemically Modified
[0115] cp-asiPD-1-6 to cp-asiPD-1-10 added with chemical modification to asiPD-1-93 of the 7 types, showing the lowest expression level of PD-1 protein among the 12 cp-asiRNAs that were confirmed to be effective in
TABLE-US-00007 TABLE 4 Cp-asiRNA name Sequence(5′.fwdarw.3′) cp-asiPD-1-13 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense 5′P-UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C cp-asiPD-1-14 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense 5′P-mU*(2′-F-U)*mC(2′-F-U)mC(2′-F-U)mC(2′-F-U)mG(2′-F-U)mC(2′-F-A)mC(2′-F- c)mC(2′-F-U)mG(2′-F-A)mG(2′-F-c)mU*(2′-F-c)*mU*(2′-F-G)*mC cp-asiPD-1-15 sense mAGmGGmUGmACmAGmAGmAG*mA*A*/chol/ antisense 5′P-mU*(2′-F-U)*(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)G(2′-F-U)(2′-F- c)A(2′-F-c)CCUmGmAmGmCU*C*U*G*C cp-asiPD-1-16 sense mA(2′-F-G)mG(2′-F-G)mU(2′-F-G)mA(2′-F-c)mA(2′-F-G)mA(2′-F-G)mA(2′-F- G)*mA*(2′-F-A)*/chol/ antisense 5’P-UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C cp-asiPD-1-17 sense mA(2′-F-G)mG(2′-F-G)mU(2′-F-G)mA(2′-F-c)mA(2′-F-G)mA(2′-F-G)mA(2′-F- G)*mA*(2′-F-A)*/chol/ antisense 5′P-mU*(2′-F-U)*mC(2′-F-U)mC(2′-F-U)mC(2′-F-U)mG(2′-F-U)mC(2′-F-A)mC(2′-F- c)mC(2′-F-U)mG(2′-F-A)mG(2′-F-c)mU*(2′-F-c)*mU*(2′-F-G)*mC cp-asiPD-1-18 sense mA(2′-F-G)mG(2′-F-G)mU(2′-F-G)mA(2′-F-c)mA(2′-F-G)mA(2′-F-G)mA(2′-F- G)*mA*(2′-F-A)*/chol/ antisense 5′P-mU*(2′-F-U)*(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)G(2′-F-U)(2′-F- c)A(2′-F-c)CCUmGmAmGmCU*C*U*G*C cp-asiPD-1-19 sense mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ antisense 5′P-UUCUCUCUGUCACCmCmUmGmAmGmCU*C*U*G*C cp-asiPD-1-20 sense mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ antisense 5′P-mU*(2′-F-U)*mC(2′-F-U)mC(2′-F-U)mC(2′-F-U)mG(2′-F-U)mC(2′-F-A)mC(2′-F- c)mC(2′-F-U)mG(2′-F-A)mG(2′-F-c)mU*(2′-F-c)*mU*(2′-F-G)*mC cp-asiPD-1-21 sense mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ antisense 5′P-mU*(2′-F-U)*(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)(2′-F-c)(2′-F-U)G(2′-F-U)(2′-F- c)A(2′-F-c)CCUmGmAmGmCU*C*U*G*C cp-asiPD-1-22 sense mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ antisense 5′-P-UCUCUCUGUCACCCmUmGmAmGmCmUmC*mU*mG*mC*mC cp-asiPD-1-23 sense mAmGmGGmUGAmCAGAGAmG*mA*mA*/chol/ antisense 5′-P-UCUCUCUGUCACCCmU*mG*mA*mG*mC 5′P: 5′-phosphate, m: 2′-O-CH.sub.3 modification, (2′-F-N): 2′-F modification, *phosphorothioatelinkage, /chol/: cholesterol
[0116] 3.2. Verification of Toxicity and Verification of Cell Penetrating Ability and PD-1 Expression Inhibitory Efficiency at Protein Level for Additionally Produced 11 cp-asiRNAs
[0117] In the same manner as in Example 2.2, the verification of toxicity of 11 additionally produced cp-asiRNAs and verification of the cell penetrating ability and PD-1 expression inhibitory efficiency at the protein level were performed. The experiment was independently conducted three times, and
EXAMPLE 4
Duration Test for 2 cp-asiRNAs (cp-asiPD-1-22 and cp-asiPD-1-23)
[0118] As shown in Example 3, a duration test was performed to confirm the increase in the ability to sustain the effect according to chemical modification to cp-asiPD-1-22 and cp-asiPD-1-23, which showed the best PD-1 expression inhibitory effect. asiPD-1-93 was used as a control, and cp-asiPIN1 was used as a negative control as a cp-asiRNA targeting a gene other than PD-1.
[0119] Specifically, HeLa-PD-1 cells were cultured in Dulbecco's modified Eagle's medium (Gibco) to which 10% fetal bovine serum (Gibco) and 0.2 g/L hygromycin B were added in a 100 mm cell culture dish. HeLa-PD-1 cells cultured 24 hours before transfection were seeded in a 12-well plate. After 24 hours of the seeding, asiRNA (asiPD-1-93) was transfected using RNAimax (Invitrogen) based on the protocol provided by the manufacturer, and cp-asiPD-1-22 and cp-asiPD-1-23 were treated without a separate carrier. Thereafter, the PD-1 protein level was confirmed through Western blotting in the same manner as in Example 2.2 (
[0120] As shown in
EXAMPLE 5
Functional Assay for T Cell Activation Ability of 2 Types of cp-asiRNAs (cp-asiPD-1-22 and cp-asiPD-1-23)
[0121] It was confirmed whether the inhibition of PD-1 gene expression using two cp-asiRNAs (cp-asiPD-1-22 and cp-asiPD-1-23) shown in
[0122] 5.1. Functional Assay for T Cell Activation Ability of Two cp-asiRNAs (cp-asiPD-1-22 and cp-asiPD-1-23) (96 hours)
[0123] Specifically, effector cells expressing PD-1 were treated with asiPD-1-93 at concentrations of 3 μM, 1 μM, and 0.5 μM in the same manner as in Example 1.3, and cp-asiPD-1-22 and cp-asiPD-1-23 were treated at the same concentration in the same manner as in Example 2.2. After 96 hours after treatment, co-incubation with PD-L1 cells was performed for 6 hours, and then the luminescence was measured to determine the luminescence measurement value of each sample compared to the non-treated sample (NT) as an average relative light unit (RLU). This measurement was performed using PD-1/PD-L1 Blockade Bioassays (Promega) and was carried out according to the protocol provided by the manufacturer. Nivolumab used as a positive control was used at a concentration of 1 μg/mL. The experiment was independently conducted three times, and
[0124] As shown in
[0125] 5.2. Functional Assay for T Cell Activation Ability of two cp-asiRNAs (cp-asiPD-1-22 and cp-asiPD-1-23) (72 hours)
[0126] As confirmed in Example 4 (
[0127] As shown in
EXAMPLE 6
Screening of 8 RNAi-Induced Double-Stranded Nucleic Acid Molecules Targeting PD-1
[0128] 6.1. Design and Production of 8 asiRNAs
[0129] In this Example, an RNAi-induced double-stranded nucleic acid molecule targeting PD-1 was designed and produced in the same manner as in Example 1.2. The nucleic acid molecule consisted of a sense strand of 16 nt and an antisense strand of 19 nt, and the screened 8 asiRNAs base sequences and target regions are shown in Table 5.
TABLE-US-00008 TABLE 5 asiRNA name Secuence(5′.fwdarw.3′) SEQ ID NO. 8-039 sense CUAAACUGGUACCGCA 77 antisense UGCGGUACCAGUUUAGCAC 78 8-046 sense GGAGAGCUUCGUGCUA 79 antisense UAGCACGAAGCUCUCCGAU 80 8-048 sense CGGAGAGCUUCGUGCU 81 antisense AGCACGAAGCUCUCCGAUG 82 8-050 sense UCUGGGCGGUGCUACA 83 antisense UGUAGCACCGCCCAGACGA 84 8-053 sense CGCAGAUCAAAGAGAG 85 antisense CUCUCUUUGAUCUGCGCCU 86 8-054 sense GCAGAUCAAAGAGAGC 87 antisense GCUCUCUUUGAUCUGCGCC 88 8-068 sense GGAGUAUGCCACCAUU 89 antisense AAUGGUGGCAUACUCCGUC 90 8-070 sense CCAUUGUCUUUCCUAG 91 antisense CUAGGAAAGACAAUGGUGG 92
[0130] 6.2. Confirmation of PD-1 mRNA Expression Inhibitory Effect
[0131] In this example, to confirm the efficiency of gene inhibitory effect at the mRNA level, 8 types of asiRNAs were used to transfect a HeLa-PD-1 cell line at a concentration of 1 nM in the same manner as in Example 1.3, followed by performing qRT-PCR and measuring the PD-1 mRNA expression level. Specifically, 24 hours after seeding HeLa-PD-1 cells in a 12-well plate, asiRNA was transfected at a concentration of 1 nM using RNAimax (Thermo) according to a protocol provided by the manufacturer. After 24 hours of the transfection, RNA was extracted using Tri-RNA reagent (FAVORGEN), and cDNA was synthesized using High-capacity cDNA reverse transcription kit (Applied Biosystems). Thereafter, the efficiency of asiRNA to inhibit PD-1 expression was evaluated through qRT-PCR at the mRNA level.
[0132] As a result, as shown in
[0133] 6.3. Confirmation of PD-1 Protein Expression Inhibitory Effect
[0134] In this Example, asiRNAs (8-039, 8-046, 8-048, 8-053, 8-068, and 8-070) showing a gene inhibitory efficiency of about 70% or higher according to the results of Example 6.2 were transfected into the HeLa-PD-1 cell line, and then, the cells obtained 48 hours later were evaluated for the inhibitory efficiency of asiRNAs to PD-1 expression at the protein level in the same manner as in Example 1.4.
[0135] As a result, as shown in
EXAMPLE 7
Screening of RNAi-Induced Asymmetric Double-Stranded Nucleic Acid Molecules (cp-asiRNA) Having Cell-Penetrating Ability Targeting PD-1
[0136] 7.1. Design and Production of 12 cp-asiRNAs of 8-039 and 8-068 Further Chemically Modified
[0137] Chemical modifications were introduced in the same manner as in Example 3.1 for 8-068 and 8-039, which showed excellent PD-1 expression inhibitory efficiency among the 8 asiRNAs in Example 6. A total of 12 cp-asiRNAs were additionally designed and produced, and the nucleotide sequences thereof are shown in Table 6.
TABLE-US-00009 TABLE 6 cp-asiRNA name Sequence(5′.fwdarw.3′) 8-068-2 sense GGAGmUAmUGmCmCAmCmCA*mU*mU*/chol/ antisense 5′P-mAAmUGmGUmGGmCAmUAmCUmC*C*mG*U*mC 8-068-3 sense GGAGmUAmUGmCmCAmCmCA*mU*mU*/chol/ antisense 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′F-A)mU(2′F- A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC 8-068-5 sense GGAGmUAmUGmCmCAmCmCA*mU*mU*/chol/ antisense 5′P-AAUGGUGGCAUACUmC*mC*mG*mU*mC 8-068-7 sense mGGmAGmUAmUGmCCmACmCA*mU*U*/chol/ antisense 5′P-mAAmUGmGUmGGmCAmUAmCUmC*C*mG*U*mC 8-068-8 sense mGGmAGmUAmUGmCCmACmCA*mU*U*/chol/ antisense 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′F-A)mU(2′F- A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC 8-068-13 sense mG(2′F-G)mA(2′F-G)mU(2′F-A)mU(2′F-G)mC(2′F-C)mA(2′F-C)mC(2′F- A)*mU*(2′F-U)*/chol/ antisense 5′P-mA(2′F-A)mU(2′F-G)mG(2′F-U)mG(2′F-G)mC(2′F-A)mU(2′F- A)mC(2′F-U)mC*(2′F-C)*mG*(2′F-U)*mC 8-068-15 sense mG(2′F-G)mA(2′F-G)mU(2′F-A)mU(2′F-G)mC(2′F-C)mA(2′F-C)mC(2′F- A)*mU*(2′F-U)*/chol/ antisense 5′P-AAUGGUGGCAUACUmC*mC*mG*mU*mC 8-039-3 sense mCmUAAAmCmUGGmUAmCmCG*mC*A*/chol/ antisense 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC(2′-F-A)mG(2′-F- U)mU(2′-F-U)mA*(2′-F-G)*mC*(2′-F-A)*mC 8-039-8 sense mCUmAAmACmUGmGUmACmCG*mC*A*/chol/ antisense 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC(2′-F-A)mG(2′-F- U)mU(2′-F-U)mA*(2′-F-G)*mC*(2′-F-A)*mC 8-039-13 sense mC(2′-F-U)mA(2′-F-A)mA(2′-F-C)mU(2′-F-G)mG(2′-F-U)mA(2′-F- C)mC(2′-F-G)*mC*(2′-F-A)*/chol/ antisense 5′P-mU(2′-F-G)mC(2′-F-G)mG(2′-F-U)mA(2′-F-C)mC(2′-F-A)mG(2′-F- U)mU(2′-F-U)mA*(2′-F-G)*mC*(2′-F-A)*mC 8-039-14 sense mC(2′-F-U)mA(2′-F-A)mA(2′-F-C)mU(2′-F-G)mG(2′-F-U)mA(2′-F- C)mC(2′-F-G)*mC*(2′-F-A)*/chol/ antisense 5′P-(2′-F-U)mG(2′-F-C)mGmG(2′-F-U)mA(2′-F-C)(2′-F-C)mAmG(2′-F- U)(2′-F-U)(2′-F-U)mA*mG*(2′-F-C)*mA*(2′-F-C) 8-039-15 sense mC(2′-F-U)mA(2′-F-A)mA(2′-F-C)mU(2′-F-G)mG(2′-F-U)mA(2′-F- C)mC(2′-F-G)*mC*(2′-F-A)*/chol/ antisense 5’P-UGCGGUACCAGUUUmA*mG*mC*mA*mC
[0138] 7.2. Confirmation of PD-1 mRNA Expression Inhibitory Effect
[0139] In this example, to confirm the efficiency of gene inhibitory effect at the mRNA level, 12 types of cp-asiRNAs were used to treat a HeLa-PD-1 cell line at a concentration of 1 μM, followed by performing qRT-PCR and measuring the PD-1 mRNA expression level. Specifically, 24 hours after seeding of HeLa-PD-1 cells in a 12-well plate, cp-asiRNA was treated without a separate carrier. After 24 hours of the treatment, RNA was extracted using Tri-RNA reagent (FAVORGEN), and cDNA was synthesized using High-capacity cDNA reverse transcription kit (Applied Biosystems). Thereafter, the efficiency of cp-asiRNA to inhibit PD-1 expression was evaluated through qRT-PCR at the mRNA level. 4 types, i.e., 8-068-3, 8-068-13, 8-039-8, and 8-039-13, selected from the 12 types of cp-asiRNAs were used to treat a HeLa-PD-1 cell line at a concentration of 1 μM or 2 μM, followed by evaluation of the PD-1 expression inhibitory efficiency at the mRNA level.
[0140] As a result, as shown in
[0141] 7.3. Confirmation of PD-1 mRNA Protein Expression Inhibitory Effect
[0142] In this Example, 4 types of cp-asiRNAs showing excellent gene inhibitory efficiency according to the results of Example 7.1 were treated with HeLa-PD-1 cell lines, and then cells obtained after incubation for 24 hours were evaluated for the PD-1 expression inhibitory effects of cp-asiRNA at the protein level in the same manner as in Example 1.4.
[0143] As a result, as shown in
EXAMPLE 8
Functional Assay for T Cell Activation Ability of cp-asiRNAs
[0144] In this Example, T cells were treated with 8-068-3, 8-068-13, 8-039-8, and 8-039-13, which showed excellent PD-1 expression inhibitory efficiency among the cp-asiRNAs in Example 7, to confirm whether the inhibition of PD-1 gene expression leads to an increase in T cell activity. In particular, T cells were recovered for 18 to 20 hours by using frozen human T cells (available from Stem Cell Technologies). Then, the recovered human T cells were treated with CD3/Cd28 magnetic beads (Dynabeads) and 200 IU of IL-2 in CTS OpTmizer (Thermo) containing 2% human serum to activate the T cells for 72 hours. After 72 hours of cp-asiRNA treatment on 20,000 activated T cells in a 12-well plate, RNA was extracted using Tri-RNA reagent (FAVORGEN), and cDNA was synthesized using High-capacity cDNA reverse transcription kit (Applied Biosystems). Thereafter, the efficiency of the T cells treated as above to inhibit PD-1 expression was evaluated through qRT-PCR at the mRNA level.
[0145] Then, using an effector cell (T cell) that has been genetically engineered to express luciferase, to quantitatively confirm the effect of inhibiting the activity or reducing the expression of PD-1, Promega bioassay kit (Catalogue No: J4011) was used to perform PD-1 blockade assay.
[0146] As a result, as shown in
[0147] As described above, specific parts of the present invention have been described in detail, and it will be apparent to of ordinary skill in the art that this specific description is only a preferred embodiment, and the scope of the present invention is not limited thereto. Accordingly, it will be said that the substantial scope of the present invention is defined by the appended claims and their equivalents.