Patent Application
20240301409
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Aug. 18, 2023, is named “F23-UBNAG2-036_Replacement Sequence Listing_ST25.txt” and is 8040 kb in size.
The present disclosure relates to the field of biomedicine, in particular to a chemically modified small activating RNA, which is a double-stranded small RNA that up-regulates the expression of a gene by targeting the promoter sequence of the gene.
Oligonucleotides can regulate target gene expression through various molecular mechanisms such as RNAi, RNase H activity, miRNA inhibition, and RNA activation (RNAa), which are referred to as siRNA, antisense oligonucleotide (ASO), miRNA mimics or inhibitors, and small activating RNA (saRNA), respectfully. Different from siRNA and ASO, saRNA is a double-stranded RNA oligonucleotide targeting the non-coding sequence in the nucleus to stimulate the expression of target genes at the transcriptional and epigenetic levels (Li, Adv Exp Med Biol. 2007, 983:1-20).
It has been well recognized that chemical modification of oligonucleotides has played a key role in the development of oligonucleotides as therapeutic agents (Manoharan, Curr Opin Chem Biol. 2004, 8(6): 570-579; Khvorova and Watts. Nat Biotechnol. 2017, 35(3): 238-248). Chemical modification of oligonucleotide sequences can improve their in vivo activity in various ways, such as increasing resistance to nucleases, improving cellular uptake, reducing immune stimulation and off-target effects, but at the same time, it may also affect the activity of oligonucleotides by reducing a mechanism of itself such as gene knock-downing (similar to the situation in RNAi) (Khvorova and Watts. Nat Biotechnol, 2017, 35(3):238-248). Many different chemical modifications have been used in the field of siRNA and antisense oligonucleotide (ASO) drug development. The most commonly used modifications are 2′-O-methyl and 2′-fluoro (2′F) modifications to the ribose sugar group and modification by replacing phosphodiester bonds with phosphorothioate (PS) bonds (Watts, Deleavey et al. Drug Discov Today, 2008, 13(19-20):842-855). These modifications can be used alone or in combination to produce chimeric oligonucleotides. However, how to improve the pharmaceutical properties of saRNA oligonucleotides, including increasing their stability, suppressing immunostimulatory activity and mitigating off-target effects, remains to be problematic.
One object of the present disclosure is to improve the pharmaceutical properties of saRNA oligonucleotides and provide chemical modifications to nucleotides in saRNA. The inventors have surprisingly found that optimized chemical modifications can stabilize saRNA duplexes, suppress their immunostimulatory activity, and/or mitigate off-target effects. Most importantly, these modifications can also increase the potency of saRNA-induced RNA activation.
The application provides a chemically modified small activating RNA that can be used to activate target genes. The small activating RNA is composed of a sense oligonucleotide strand and an antisense oligonucleotide strand, the sense oligonucleotide strand or the antisense oligonucleotide strand being at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% homologous or complementary to the target gene promoter; the two nucleotides at the 5′ end and at the 3′ end of the sense oligonucleotide strand are all chemically modified nucleotides, and the antisense oligonucleotide strand comprises at least one chemically modified nucleotide. In a specific embodiment, the chemical modification is selected from one or more of the following modifications: (1) chemical modification of nucleotide ribose(s); (2) chemical modification to inter-nucleotide phosphodiester bond(s); (3) chemical modification of nucleotide base(s); (4) inclusion of locked nucleic acid(s); and (5) modification with vinylphosphonate at 5′-end nucleotide(s).
Another object of the present disclosure is to provide a small activating RNA for human p21WAF1/CIP1 gene (P21 gene). The p21 gene is a member of the Clp family, which is a cyclin-dependent kinase inhibitor located downstream of the p53 gene. p21 and p53 can jointly constitute the G1 checkpoint of the cell cycle. As a cell with unrepaired DNA damage cannot pass the checkpoint, the replication and accumulation of damaged DNA are reduced, and thus cancer is suppressed. p21 is not only closely related to tumor suppression, but also can coordinate the relationship between cell cycle, DNA replication and repair by inhibiting the activity of cyclin-dependent kinase (CDK) complex, so as to link between tumor suppression and cell cycle control. p21 is associated with tumor differentiation, depth of infiltration, proliferation and metastasis.
The present disclosure provides a nucleic acid molecule comprising a segment encoding the small activating RNA. The present disclosure also provides a cell comprising the small activating RNA or the nucleic acid molecule as described.
The present disclosure provides a pharmaceutical composition comprising the small activating RNA, or the nucleic acid molecule, and optionally, a pharmaceutically acceptable carrier. The present disclosure also provides a preparation comprising the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition as described. And, also provided is a kit comprising the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the preparation as described.
The present disclosure further provides a combined pharmaceutical composition, comprising, the small activating RNA, and a small molecule drug. Optionally, the small molecule drug is selected from Mitomycin C or Valrubicin.
The present disclosure further provides use of the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the preparation as described in the manufacture of a medicine or formulation for activating or up-regulating the expression of p21 gene in cells. In some embodiments, the use can be for the preparation of medicines or formulations for preventing, treating or alleviating malignant tumors or benign proliferative lesions. In some embodiments, the malignant tumor can be bladder cancer, prostate cancer, liver cancer, or colorectal cancer. In some embodiments, the bladder cancer can be non-muscle-invasive bladder cancer (NMIBC).
The present disclosure also provides a method for preventing, treating or alleviating malignant tumors or benign proliferative lesions, comprising, administering the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the preparation to an individual in need thereof. In some embodiments, the malignant tumor is bladder cancer, prostate cancer, liver cancer, or colorectal cancer. In some embodiments, the bladder cancer is non-muscle invasive bladder cancer (NMIBC).
Those skilled in the art can easily perceive other aspects and advantages of the present disclosure from the following detailed description. In the following detailed description, exemplary and illustrative embodiments of the present disclosure are shown and described. As those skilled in the art will understand, the content of the present disclosure enables those skilled in the art to make changes to the specific embodiments which are disclosed without departing from the spirit and scope of the invention. Correspondingly, the drawings and descriptions in the specification are only exemplary and illustrative rather than restrictive.
The particular features of the invention are set forth in the appended claims. The features and advantages of the invention can be better understood with reference to the exemplary embodiments described in detail hereinafter and the accompanying drawings. A brief description of the accompanying drawings is as follows.
The embodiments of the invention will be described in the following specific examples, and those skilled in the art can easily understand other advantages and effects of the invention from the content disclosed in this specification.
The application discloses a small activating RNA for activating a target gene, wherein the small activating RNA is composed of a sense oligonucleotide strand and an antisense oligonucleotide strand, and the sense oligonucleotide strand or the antisense oligonucleotide strand is at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% homologous or complementary to the target gene promoter; the two nucleotides at the 5′ end and at the 3′ end of the sense oligonucleotide strand are all chemically modified nucleotides, and the antisense oligonucleotide strand comprises at least one chemically modified nucleotide.
The chemical modification described herein can be the alteration, addition, reduction or replacement of atoms/chemical groups at different positions in an oligonucleotide strand, between single nucleotides in the oligonucleotide strand, or single nucleotide residues, or the alteration, addition, reduction or replacement of chemical bonds between atoms, or covalent attachment of groups, ligands, or conjugates to nucleotides at any position in the oligonucleotide strand. In some embodiments, the chemical modification can be selected from one or more of the following modifications:
The chemical modification of ribose described herein can be those commonly used in the art, including, for example, the modification of the hydroxyl group (2′-OH) in the pentose of a nucleotide. In some embodiments, the modification of the hydroxyl group in the pentose of a nucleotide can include 2′-fluro (2′F), 2′-O-methyl (2′-OMe), 2′-methoxyethyl (2′-MOE), 2,4′-dinitrophenol modification (2′-DNP), locked nucleic acid (LNA), 2′-amino and the like.
Alternatively, in some embodiments, the chemical modification can be substitution of the ribose 2′-OH in a nucleotide with one or more of 2′-fluoro, 2′-O-methyl, 2′-methoxyethyl, 2,4′-dinitrophenol, LNA, 2′-amino, 2′-H. Among them, the substitution of the ribose 2′-OH with 2′-H can change the chemically modified nucleotide from a ribonucleic acid (RNA) to a deoxyribonucleic acid (DNA). Some typical chemical modifications of nucleotides can include, for example, the nucleotides shown below:
In some embodiments, the modification of bases may refer to a chemical modification of nucleotide base(s), for example, may include 5′-bromouracil modification, 5′-iodouracil modification, N-methyl uracil modification and/or 2,6-diaminopurine modification. In some embodiments, the modification of phosphodiester bond can be one commonly used in the art, including but not limited to the modification of a non-bridging oxygen atom in the phosphodiester bond. For example, it can include phosphorothioate modification (PS) and/or boranophosphate modification.
In some embodiments, the small activating RNA of the present disclosure can comprise a sense oligonucleotide strand, and the two nucleotides at the 5′ end and at the 3′ end of the sense oligonucleotide strand can all be chemically modified nucleotides. In some embodiments, the segment between the two nucleotides at the 5′ end and the two nucleotides at the 3′ end of the sense oligonucleotide strand may comprise no more than 40%, no more than 30%, no more than 20%, no more than 10%, no more than 5% of chemically modified nucleotides, or is completely free of chemically modified nucleotides. In some embodiments, the two nucleotides at the 5′ end and/or 3′ end of the sense oligonucleotide strand can all be chemically modified nucleotides. In certain cases, the other nucleotides of the sense oligonucleotide strand can all be nucleotides without chemical modification.
In some embodiments, one of the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand of the small activating RNA of the present disclosure can be chemically modified, or the last two phosphodiester bonds at the 3′ end can both be chemically modified. In some embodiments, the last two phosphodiester bonds at the 3′ end can be modified independently with sulfur and borane, respectively, to replace the non-bridging oxygen atoms in the phosphodiester bonds. In some embodiments, the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand can both be modified with sulfur to replace the non-bridging oxygen atom in the phosphodiester bonds, that is, phosphorothioate (PS) modification.
In some embodiments, the sense oligonucleotide strand of the small activating RNA of the present disclosure comprises at least one chemically modified nucleotide. The chemical modification may be a chemical modification of the ribose 2′-OH in nucleotide(s), a chemical modification of inter-nucleotide phosphodiester bond(s), a chemical modification of nucleotide base(s), the replacement of any nucleotide with a LNA, or modification with vinylphosphonate at 5′-end nucleotide(s) of the oligonucleotide. In some embodiments, the sense oligonucleotide strand can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, 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, at least 23, or more chemically modified nucleotides. In some embodiments, the sense oligonucleotide strand can comprise at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, 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%, at least 95%, at least 97%, or 100% of chemically modified nucleotides. In some embodiments, all nucleotides comprised in the sense oligonucleotide strand can be chemically modified nucleotides.
In some embodiments, one of the last two phosphodiester bonds at the 3′ end or 5′ end of the antisense oligonucleotide strand of the small activating RNA of the present disclosure can be chemically modified, or both of the last two phosphodiester bonds at 3′ end or 5′ end can be chemically modified. In some embodiments, the last two phosphodiester bonds at the 3′ end and/or 5′ end of the antisense oligonucleotide strand can comprise phosphorothioate modifications or boranophosphate modifications or a combination thereof. In some embodiments, both of the last two phosphodiester bonds at the 3′ end of the antisense oligonucleotide strand can be phosphorothioate modified. In some embodiments, both of the last two phosphodiester bonds at the 5′ end of the antisense oligonucleotide strand can be phosphorothioate-modified. In some embodiments, all of the last two phosphodiester bonds at the 5′ end and the 3′ end of the antisense oligonucleotide strand can be phosphorothioate modified.
In some embodiments, the antisense oligonucleotide strand of the small activating RNA of the present disclosure can comprise at least one (for example, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 at least 8, at least 9, at least 10, at least 11, 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, at least 23, or more) chemically modified nucleotides. The chemical modification can be a chemical modification of the ribose 2′-OH in nucleotide(s), including, for example, one or more of 2′-fluoro, 2′-O-methyl, 2′-methoxyethyl, 2,4′-dinitrophenol, LNA, 2′-amino; a chemical modification of inter-nucleotide phosphodiester bond(s), including, for example, phosphorothioate modification or boranophosphate modification; a chemical modification of nucleotide base(s); replacement of any nucleotide with a locked nucleic acid (LNA); or modification with vinylphosphonate at 5′-end nucleotide(s) of the oligonucleotide. In some embodiments, the antisense oligonucleotide strand can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, 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, at least 23, or more chemically modified nucleotides. In some embodiments, the antisense oligonucleotide strand can comprise at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, 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%, at least 95%, at least 97%, or 100% of chemically modified nucleotides. In some embodiments, all nucleotides comprised in the antisense oligonucleotide strand can be chemically modified nucleotides.
In some embodiments, 1-56 nucleotides at the 5′-end of the antisense oligonucleotide strand can have a certain proportion of the ribose 2′-OH modification, for example, at least 2, at least 3, at least 4, at least 5 or more 2′-fluoro modifications. In some embodiments, 1-6 nucleotides at the 3′-end of the antisense oligonucleotide strand can have a higher proportion of chemical modification of the ribose 2′-OH, for example, at least 3, at least 4, at least 5, at least 6 or more 2′-fluoro modifications. The inventors found that the 2′-fluoro modification at these positions may be critical for stability.
In some embodiments, the most central 1-5 nucleotides of the antisense oligonucleotide strand can have a higher proportion of modification of the ribose 2′-OH, for example, at least 1, at least 2, at least 3, at least 4, at least 5 or more nucleotides of the most central nucleotides can have a chemical modification of the ribose 2′-OH.
In some embodiments, the antisense oligonucleotide strand can comprise a combination of three modifications: 2′-fluoro, 2′-O-methyl and phosphorothioate (PS) modifications. In some embodiments, the sense oligonucleotide strand can comprise a combination of three modifications: 2′-fluoro, 2′-O-methyl and phosphorothioate (PS) modifications. In some embodiments, the small activating RNA duplex can comprise a combination of three modifications: 2′-fluoro, 2′-O-methyl and phosphorothioate (PS) modification.
The inventors have found that the combination of the three modifications composed of 2′-fluoro, 2′-O-methyl and phosphorothioate (PS) modifications (the combination of the three) can increase the ability of small activating RNA duplexes to induce gene expression; in some embodiments, the combination of the three can increase the ability of the small activating RNA to induce p21 gene expression; in some embodiments, the combination of the three can increase the effect of the small activating RNA of suppressing the proliferation of cancer cells; in some embodiments, the cancer cells can include bladder cancer cells.
In some embodiments, the antisense oligonucleotide strand does not comprise modifications in which ribonucleotides can be replaced with deoxyribonucleotides (DNA). The inventors have found that RNA-to-DNA modification in the oligonucleotide strand can attenuate the cellular proliferation-suppressing activity of small activating RNA duplexes. In certain cases, modifications that convert RNA to DNA in the oligonucleotide strand should be avoided.
In some embodiments, when a majority (e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%) or all of the nucleotides of the antisense oligonucleotide strand are chemically modified (for example, with 2′-fluoro and/or 2′-O-methyl), the sense oligonucleotide strand can comprise at least 1, at least 2, at least 3, at least 5 or more of 2′-O-methyl modifications. The inventors have found that chemically modifying most or all of the nucleotides in the antisense oligonucleotide strand can have a negative impact on the activity of the small activating RNA (such as p21-targeting saRNAs) to inhibit cellular proliferation. The inventors have also found that the negative impact on the suppression of cellular proliferation activity brought about by modifying most or all of the nucleotides of the antisense oligonucleotide strand can be offset or corrected by 2′OMe modifications of the sense oligonucleotide strand.
Through exploration of innumerable permutations and combinations of different types of chemical modifications at each nucleotide position of the sense and antisense oligonucleotide strands of the small activating RNA, the inventors have found, surprisingly, that the chemical modifications to the sense oligonucleotide strand and the antisense oligonucleotide strand of the small activating RNA disclosed herein can make the small activating RNA of the present disclosure exhibit better pharmaceutical properties, including, for example, stability of saRNA duplex, lower immune stimulation and less off-target effects; more importantly, these modifications can also improve the efficacy of saRNA-induced RNA activation. In some embodiments, the efficacy of saRNA-induced RNA activation of a target gene can be at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.5-fold, at least 1.6-fold, at least 1.8-fold, At least 2-fold, at least 2.5-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 8-fold, at least 10-fold, at least 12-fold, at least 15-fold, or higher, compared with a baseline level of expression of the gene in a control group or cell. In some embodiments, the target gene described in the present disclosure may be human or mouse p21WAF1/CIP1 gene (P21 gene). In some embodiments, the target gene described in the present disclosure can be human p21WAF1/CIP1 gene, and by using the small activating RNA the sense oligonucleotide strand and the antisense oligonucleotide strand of which are chemically modified as described herein, the efficacy of saRNA-induced RNA activation of the p21 gene can be at least 1.1-fold, at least 1.5-fold, at least 2-fold, at least 5-fold, at least 10-fold, or higher compared with the baseline level of expression of the gene in a control group or cell.
Through exploration of innumerable permutations and combinations of different types of chemical modifications at each nucleotide position of the sense and antisense oligonucleotide strands of the small activating RNA, the inventors have found, more surprisingly, that in some embodiments, the small activating RNAs described herein can stimulate enhanced immune activity.
In some embodiments, the chemical modification of the sense oligonucleotide strand can be selected from the group consisting of four patterns: RAG1-SS-S6A, RAG1-SS-S6B, RAG1-SS-S6C, and RAG1-SS-S6D.
In some embodiments, the chemical modification of the antisense oligonucleotide strand can be selected from the group consisting of ten patterns: RAG1-SS-AS2A, RAG1-SS-AS2B, RAG1-SS-AS2C, RAG1-SS-AS2D, RAG1-SS-AS2E, RAG1-SS-AS2F, RAG1-SS-AS2G, RAG1-SS-AS2H, RAG1-SS-AS2I, and RAG1-SS-AS2J.
In some embodiments, the chemical modification of the sense oligonucleotide strand can be selected from the group consisting of four patterns: RAG1-SS-S6A, RAG1-SS-S6B, RAG1-SS-S6C, and RAG1-SS-S6D, and the chemical modification of the antisense oligonucleotide strand can be selected from the group consisting of ten patterns: RAG1-SS-AS2A, RAG1-SS-AS2B, RAG1-SS-AS2C, RAG1-SS-AS2D, RAG1-SS-AS2E, RAG1-SS-AS2F, RAG1-SS-AS2G, RAG1-SS-AS2H, RAG1-SS-AS2I, and RAG1-SS-AS2J.
In some embodiments, the chemical modification of the sense oligonucleotide strand can be the pattern set forth in RAG1-SS-S6D, and the chemical modification of the antisense oligonucleotide strand can be the pattern set forth in RAG1-SS-AS2G.
In some embodiments, either or both of the sense oligonucleotide strand or the antisense oligonucleotide strand of the small activating RNA of the present disclosure can have an overhang of 6, 5, 4, 3, 2, 1 or 0 nucleotides, which can be located at the respective 5′ end and/or 3′ end of the sense oligonucleotide strand and/or the antisense oligonucleotide strand. In some embodiments, the 3′ end of the antisense oligonucleotide strand can have an overhang of 0-6 nucleotides. In some embodiments, the 3′ end of the antisense oligonucleotide strand can have an overhang of 2 or 3 nucleotides. In some embodiments, the 3′ end of the sense oligonucleotide strand and the 5′ end of the antisense oligonucleotide strand do not have an overhang, or are of blunt ends. In some embodiments, the overhang can be dTdT or dTdTdT, or of nucleotide(s) identical or complementary to the nucleotide(s) at the corresponding position(s) of the target gene, or neither identical nor complementary to the nucleotide(s) at the corresponding position(s) of the target gene. In some embodiments, the overhang can be nucleotide(s) that is/are complementary to nucleotide(s) at a corresponding position(s) on the target gene.
The length of the sense oligonucleotide strand and the antisense oligonucleotide strand of the small activating RNA of the present disclosure can vary depending on different target genes, different positions of action of target genes, or different activation effects brought about by different lengths. In some embodiments, the sense oligonucleotide strand and the antisense oligonucleotide strand can each have 17-30 nucleotides in length, for example, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the sense oligonucleotide strand and the antisense oligonucleotide strand form a duplex region of base complementarity comprising at least 10, at least 11, at least 12, at least 13, at least 14, or at least 15 nucleotides in length, for example, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 base-paired nucleotide pairs.
In some embodiments, there can be 1-3 nucleotide mismatches in the sense oligonucleotide strand and the antisense oligonucleotide strand. In some embodiments, there can be 1-3 nucleoside mismatches in the 3′ or 5′ region of the sense oligonucleotide strand and the corresponding 5′ or 3′ region of the antisense oligonucleotide strand, for example, there can be 1, 2, or 3 nucleotide mismatches in the nucleotides in the 3′ region of the sense oligonucleotide strand and the nucleotides in the corresponding 5′ region of the antisense oligonucleotide strand. In some embodiments, there can be 1-3 nucleoside mismatches in the nucleotides in the corresponding middle region of the sense oligonucleotide strand and the antisense oligonucleotide strand other than the 5′ or 3′ end nucleotides.
In some embodiments, there can be 1-3 nucleotide mismatches between the 3′ or 5′ end of the sense oligonucleotide strand and the corresponding nucleotides on the target gene. In some embodiments, there can be 1-3 nucleotide mismatches between the 3′ or 5′ end of the antisense oligonucleotide strand and the corresponding nucleotides on the target gene. In some embodiments, there can be 1, 2, or 3 nucleotide mismatches between the 3′ end of the sense oligonucleotide strand and the corresponding nucleotides on the target gene.
In some embodiments, the sense oligonucleotide strand or the antisense oligonucleotide strand of the small activating RNA of the present disclosure can be conjugated with one or more groups selected from the group consisting of: lipid, fatty acids, fluorescent groups, ligands, sugars, polymers, polypeptides, antibodies, and cholesterol. The conjugation can be at the 3′ end or the 5′ end of the sense oligonucleotide strand or the antisense oligonucleotide strand, or between the 3′ end and the 5′ end. In some embodiments, the sense oligonucleotide strand or the antisense oligonucleotide strand of the small activating RNA of the present disclosure can be conjugated with at least one lipid group, at the 3′ end or 5′ end of the oligonucleotide strand. In some embodiments, the lipid group can be one or more selected from fatty acid (fatty acyl), cationic lipid, anionic lipid, ionizable lipid, saccharolipid, glycerolipid, glycerophospholipid, sterol lipid, sphingolipid, prenol lipid, and polyketide. In some embodiments, the sense oligonucleotide strand or the antisense oligonucleotide strand of the small activating RNA of the present disclosure can be conjugated with at least one cholesterol group, which, for example, can be at the 3′ end or 5′ end of the oligonucleotide strand. In some embodiments, the sense oligonucleotide strand or the antisense oligonucleotide strand of the small activating RNA of the present disclosure can be conjugated with at least one sugar group, which, for example, can be at the 3′ end or 5′ end of the oligonucleotide strand. The sugar group includes, for example, N-acetyl galactosamine (GalNAc), glucose, mannose and other suitable sugar groups. In some embodiments, the conjugation of one or more groups can make the small activating RNA of the present disclosure exhibit better ability to enter into specific organs, tissues or cells, and/or enable the small activating RNA of the present disclosure to possess desired pharmaceutical properties, such as pharmacokinetics (pK), pharmacodynamics (pD), toxicity, and the properties in terms of the body's absorption, distribution, metabolism and excretion of exogenous chemicals.
The present disclosure discloses a small activating RNA, and the target gene of the small activating RNA can be human p21WAF1/CIP1 gene. In particular, in some embodiments, the small activating RNA can specifically target the promoter region of the p21 gene. In some embodiments, the small activating RNA can specifically target the region from −1000 nucleotides upstream of the transcription start site (TSS) of the p21 gene promoter to the TSS.
In some embodiments, the sense oligonucleotide strand of the small activating RNA targeting p21 can be 17-30 nucleotides in length, and/or the antisense oligonucleotide strand can be 17-30 nucleotides in length. For example, the sense oligonucleotide strand of the small activating RNA can have 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length; and/or, the antisense oligonucleotide strand length of the small activating RNA can have 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length; the length of the sense oligonucleotide strand of the small activating RNA can be the same as or different from that of the antisense oligonucleotide strand.
In some embodiments, the sense oligonucleotide strand of the present disclosure, being p21-targeting, can have a segment of at least 15 nucleotides in length to form base complementarity with the antisense oligonucleotide strand. For example, the nucleotide segment in the sense oligonucleotide strand or the antisense oligonucleotide strand that is sequence matching with the target gene promoter can have 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 nucleotides in length. In some embodiments, the 3′ end of the antisense oligonucleotide strand can have an overhang of 2 nucleotides, at least one of which can be complementary to the target gene promoter. In some embodiments, the 3′ end of the antisense oligonucleotide strand can have an overhang of 1, 2, or 3 nucleotides, which, for example, can all be complementary to the target gene promoter. In some embodiments, there can be a mismatch of 1 nucleotide between the 3′ region of the sense oligonucleotide strand and the coding strand of the target gene promoter sequence. In some embodiments, there can be one nucleotide mismatch between the 3′ nucleotides of the sense oligonucleotide strand and the nucleotides at the corresponding positions in the coding strand of the target gene promoter. In some embodiments, there can be one nucleotide mismatch between the 3′ end nucleotides of the sense oligonucleotide strand and the 5′ end nucleotides of the antisense oligonucleotide strand. In some embodiments, there can be one nucleotide mismatch between the 5′ end nucleotides of the sense oligonucleotide strand and the 3′ end nucleotides of the antisense oligonucleotide strand.
In some embodiments, the sequence of the sense oligonucleotide strand of the small activating RNA targeting p21 can be selected from the group consisting of SEQ ID NOs: 5, 14, 15, and 16. In some embodiments, the sequence of the antisense oligonucleotide strand of the small activating RNA targeting p21 can be selected from the group consisting of SEQ ID NOs: 6, 8, 11, 12, 13, 18, and 19. In some embodiments, the sequences of the sense oligonucleotide strand and the antisense oligonucleotide strand of the small activating RNA targeting p21 can be selected from the paired sequences listed in Table 2.
The p21 gene-targeting small activating RNA provided in the present disclosure can be suitable for to all the different types of chemical modifications carried out on the small activating RNA, so that the p21 gene-targeting small activating RNA can exhibit improved pharmaceutical properties include, for example, stability of the saRNA duplex, lower immune stimulation and less off-target effects; more importantly, these modifications also improve the efficacy of saRNA-induced RNA activation. In some embodiments, the chemical modification of the p21 gene-targeting small activating RNA may need to maintain a certain immunostimulatory activity, for example, an immunostimulatory activity sufficient to cause suppression of cancer cell proliferation, such as suppression of the proliferation of bladder cancer cells.
In some embodiments, the antisense oligonucleotide strand targeting small activating RNA of p21 gene can comprise at least one chemically modified nucleotide. The chemical modification can be a chemical modification of the ribose 2′-OH in nucleotide(s), including, for example, one or more of 2′-fluoro, 2′-O-methyl, 2′-methoxyethyl, 2,4′-dinitrophenol, LNA, and 2′-amino modifications; a chemical modification of inter-nucleotide phosphodiester bond(s), including, for example, phosphorothioate modification or boranophosphate modification; a chemical modification of nucleotide base(s); the replacement of any nucleotide with a LNA; or modification with vinylphosphonate at 5′-end nucleotide(s) of the oligonucleotide. In some embodiments, the antisense oligonucleotide strand comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or more chemically modified nucleotides. In some embodiments, the antisense oligonucleotide strand comprises at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, 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%, at least 95%, at least 97%, or 100% of chemically modified nucleotides.
In some embodiments, only part of the nucleotides constituting the antisense oligonucleotide strand of the small activating RNA targeting p21 gene is chemically modified nucleotides, for example, the strand comprises no more than 80%, no more than 75%, no more than 70%, no more than 65%, no more than 60%, no more than 55%, no more than 50%, no more than 45%, no more than 40%, not more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, or no chemically modified nucleotides. The chemical modification can be a chemical modification of the ribose 2′-OH in nucleotide(s), a chemical modification of the phosphodiester bond between the nucleotides, or a chemical modification of nucleotide base(s), or replacement of any nucleotide with a locked nucleic acid (LNA), or modification with vinylphosphonate at 5′-end nucleotide(s) of the oligonucleotide. The inventors have found that when it is desired to improve the small activating RNA to possess a certain immunostimulatory activity, it is suitable to select a lower proportion of chemically modified nucleotides in the antisense oligonucleotide strand, such as lower than 80% or lower than 60%.
In some embodiments, the nucleotides constituting the sense oligonucleotide strand of the small activating RNA targeting p21 gene comprise at least one chemically modified nucleotide. The chemical modification type is the same as that of the antisense oligonucleotide strand. In some embodiments, the sense oligonucleotide strand comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, 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, at least 23 or more chemically modified nucleotides. In some embodiments, the sense oligonucleotide strand can comprise at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, 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%, at least 95%, at least 97%, or 100% of chemically modified nucleotides. In some embodiments, all nucleotides constituting the sense oligonucleotide strand are chemically modified nucleotides.
In some embodiments, the nucleotides constituting the sense oligonucleotide strand of the p21 gene-targeting small activating RNA may only partially be chemically modified nucleotides, for example, the strand can comprise no more than 80%, no more than 75%, no more than 70%, no more than 65%, no more than 60%, no more than 55%, no more than 50%, no more than 45%, no more than 40%, not more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, or no chemically modified nucleotides. The type of chemical modification is the same as for the antisense oligonucleotide strand.
Similarly, the inventors have found that when it is desired to improve the small activating RNA with a certain immunostimulatory activity, it is suitable to select a lower proportion of chemically modified nucleotides in the sense oligonucleotide strand, such as lower than 80%, or lower than 60%, or lower than 40%, or lower than 20%.
The inventors have found that the position of chemically modified nucleotides can influence the activity, stability, immunostimulatory, and/or off-target effects of the saRNA. In some embodiments, 1-5 nucleotides at the 5′-end of the antisense oligonucleotide strand can have a certain proportion of chemical modification of the ribose 2′-OH, for example, at least 2, at least 3, at least 4, or 5. In some embodiments, 1-6 nucleotides at the 3′-end of the antisense oligonucleotide strand have a higher proportion of chemical modification of the ribose 2′-OH, for example, at least 3, at least 4, at least 5, or 6. In some embodiments, the most central 1-5 nucleotides of the antisense oligonucleotide strand can have a higher proportion chemical modification of the ribose 2′-OH, for example, the most central one, two, three, four or five nucleotides can have chemical modification of the ribose 2′-OH.
In some embodiments, the small activating RNA targeting p21 comprises a chemical modification of nucleotide ribose(s), for example, a chemical modification of the ribose 2′-OH in nucleotides. In some embodiments, the ribose 2′-OH in at least one nucleotide of the small activating RNA targeting p21 can be substituted by one or more of 2′-fluoro, 2′-O-methyl, 2′-methoxyethyl, 2,4′-dinitrophenol, LNA, and 2′-amino modifications. In some embodiments, the chemical modification of at least one phosphodiester bond between the nucleotides of the small activating RNA targeting p21 can be a modification of the inter-nucleotide phosphodiester bond(s), including, for example, phosphorothioate modification, or boranophosphate modification, or combination thereof.
In some embodiments, one of the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand of the p21-targeting small activating RNA described herein is chemically modified, or both of the last two phosphodiester bonds at the 3′ end are chemically modified. The modification of the phosphodiester bond of the sense oligonucleotide strand of the small activating RNA targeting p21 is commonly used in the art, including but not limited to modifying the non-bridging oxygen atom in the phosphodiester bond, such as phosphorthioate (PS) modification and boranophosphate modification. In some embodiments, the last two phosphodiester bonds at the 3′ end can be replaced with sulfur and borane for the non-bridging oxygen atoms in the phosphodiester bonds, respectively. In some embodiments, the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand can be modified with sulfur in place of the non-bridging oxygen atom in the phosphodiester bond, that is, phosphorothioate (PS) modification. The inventors have found that the gene activation efficiency of the small activating saRNA can be improved when both of the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand comprise phosphorthioate modification, or boranophosphate modification, or combination thereof. In some embodiments, the activity of small activating RNA duplexes in suppressing cellular proliferation can be enhanced when both of the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand comprise phosphorthioate modification, or boranophosphate modification, or combination thereof. In some embodiments, the small activating RNA can target the p21 gene. In some embodiments, the cells can be cancer cells. In some embodiments, the cancer cells can include bladder cancer cells.
In some embodiments, one or both of the last two phosphodiester bonds at the 3′ end of the antisense oligonucleotide strand of the p21-targeting small activating RNA of the present disclosure is chemically modified. In some embodiments, the last two phosphodiester bonds at the 3′ end of the p21-targeting antisense oligonucleotide strand can comprise phosphorthioate modification, or boranophosphate modification, or combination thereof. In some embodiments, both of the last two phosphodiester bonds at the 3′ end of the p21-targeting antisense oligonucleotide strand can be phosphorothioate modified. In some embodiments, both of the last two phosphodiester bonds at the 5′ end and the 3′ end of the antisense oligonucleotide strand of the p21-targeting small activating RNA can comprise phosphorothioate modification. In some embodiments, the antisense oligonucleotide strand targeting p21 has a higher proportion ribose 2′-OH modification for the most central 1-3 nucleotides, for example, for the most central 1, 2, or 3 nucleotides.
In some embodiments, the last two phosphodiester bonds at the 3′ end of the sense oligonucleotide strand of the small activating RNA targeting p21 can be substituted by phosphorothioate bonds, and the two nucleotides at the 5′ end and at 3′ end of the sense oligonucleotide strand of the small activating RNA can be chemically modified with 2′-fluoro.
In some embodiments, one of the last two phosphodiester bonds at the 3′ end of the antisense oligonucleotide strand of the small activating RNA targeting p21 can be substituted with a phosphorothioate bond, and the one of the last two phosphodiester bonds at the 5′ end can be substituted by a phosphorothioate bond, and three of the five nucleotides at the 5′ end can be chemically modified with 2′-fluoro or 2′-O-methyl, and three of six nucleotides at the 3′ end can be chemically modified with 2′-fluoro or 2′-O-methyl.
In some embodiments, the last two phosphodiester bonds at the 3′ end of the antisense oligonucleotide strand of the small activating RNA targeting p21 can both be substituted with phosphorothioate bonds, and both of the last two phosphodiester bonds at the 5′ end can be substituted with phosphorothioate bonds, and three of five nucleotides at the 5′ end can be chemically modified with 2′-fluoro, and three of six nucleotides at the 3′ end can be chemically modified with 2′-fluoro. In some embodiments, the 3rd, 4th, and 5th nucleotides at the 5′ end are chemically modified with 2′-fluoro, and the 2nd, 5th, and 6th nucleotides at the 3′ end can be chemically modified with 2′-fluoro.
In some embodiments, the chemical modification pattern of the sense oligonucleotide strand of the p21-targeting small activating RNA described in the present disclosure can be selected from
The method for preparing the small activating RNA of the present disclosure can be modified or improved on the basis of the conventional methods in the art. In some embodiments of preparing small activating RNAs, the method can substantially include the following steps: 1) using the coding strand of the target gene promoter sequence as a template, selecting a sequence comprising 17 to 28 bases as the target site; 2) synthesizing an RNA sequence corresponding to the target site sequence obtained in step 1) as a basic sequence to obtain a sense oligonucleotide strand; 3) synthesizing an antisense oligonucleotide strand with a length of 17 to 30 nucleotides, so that the antisense oligonucleotide strand comprises a segment of at least 15 nucleotides that is complementary to the sense oligonucleotide strand obtained in step 2); 4) mixing the sense oligonucleotide strand obtained in step 2) with the same mole number of the antisense oligonucleotide strand obtained in step 3) in an RNA annealing buffer, before heating and then being naturally cooling to room temperature to obtain a double-stranded small activated RNA.
The present disclosure also provides a nucleic acid molecule comprising a fragment encoding the small activating RNA. Also provided is a cell comprising the small activating RNA or the nucleic acid molecule.
Optionally, the present disclosure also provides a nucleic acid molecule comprising a segment encoding the small activating RNA targeting p21 gene. Also provided is a cell comprising the small activating RNA targeting p21 gene or the nucleic acid molecule.
The present disclosure further provides a pharmaceutical composition comprising: the small activating RNA, or the nucleic acid molecule, and optionally, a pharmaceutically acceptable carrier. Likewise, provided herein is a preparation comprising the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition described herein. And, also provided is a kit comprising the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the preparation described herein.
Optionally, the pharmaceutical composition can be a p21 gene-targeting pharmaceutical composition, comprising a p21 gene-targeting small activating RNA, a nucleic acid molecule, and optionally, a pharmaceutically acceptable carrier. Optionally, the preparation can be a p21 gene-targeting preparation, comprising the p21 gene-targeting small activating RNA, the nucleic acid molecule, the cell, or the pharmaceutical composition described herein. Optionally, the kit can comprise the p21 gene-targeting small activating RNA, nucleic acid molecule, cell, pharmaceutical composition, or preparation described herein.
The pharmaceutically acceptable carriers described herein may include lipid-based encapsulation systems used in the field of small nucleic acid active molecules such as lipid nanoparticles (LNP), carbohydrate receptor-targeting conjugates comprising, for example, N-acetylgalactosamine (GalNAc), glucose, mannose, and other suitable carbohydrate moieties, covalent conjugates with different lipid or polypeptide moieties as ligands. Choosing a suitable carrier can not only assist small nucleic acid molecules to access the organ or tissue of interest, but also assist small nucleic acid molecules to enter target cells and even subcellular structures, such as assisting double-stranded siRNA or antisense oligonucleotides strand (ASO) to enter the cytoplasm, or saRNA molecules to enter the nucleus, and then achieve the biological regulation with the corresponding small nucleic acid molecules.
Among various delivery technologies, lipid nanoparticles (LNPs), which can generally be composed of four components: ionizable lipids, cholesterol, phospholipids, and PEG, can be used to efficiently encapsulate oligonucleotides and protect them from nuclease digestion. Using ionizable lipids DLin-MC3-DMA (one of the most commonly used cationic lipids for making LNPs) or DLin-KC2-DMA, lipid nanoparticles can successfully deliver oligonucleotides to liver after intravenous injection. However, the LNP formulation, process and limited target organs (liver is specific, and the delivery efficiency is in the order of liver>spleen>kidney, only negligible accumulation in duodenum, lung, heart, and brain) can limit the application of LNP in pharmaceutical compositions.
The p21 gene-targeting small activating RNA described herein can form a preparation or a pharmaceutical composition with lipid nanoparticle (LNP) as needed. The p21 gene-targeting small activating RNA carried by LNP can be delivered to liver to treat liver cancer, or delivered to colorectum, prostate, or bladder by systemic or local administration to treat colorectal cancer, prostate or bladder cancer. For the composition of RNA molecule and LNP, its formulation, and its preparation method, reference can be made to the existing publications in this field, for example, US20190240354A1, US20190336452A1, US20160038612A1, etc. In some embodiments, the present disclosure provides a preparation comprising the p21 gene-targeting small activating RNA and LNP, which can be administered locally in bladder to treat bladder cancer. In some embodiments, the present disclosure provides a preparation comprising the p21 gene-targeting small activating RNA and LNP, which can be used to treat bladder cancer by intravesical infusion. In some embodiments, the present disclosure provides a preparation comprising the p21 gene-targeting small activating RNA and a DLin-KC2-DMA-based LNP, which can be used to treat bladder cancer by intravesical infusion. In some embodiments, the present disclosure provides a preparation comprising the p21 gene-targeting small activating RNA and a DLin-KC2-DMA-based LNP, which can be used to treat non-muscle-invasive bladder cancer (NMIBC) by intravesical infusion.
The present disclosure also provides a pharmaceutical composition of combined agents, comprising: the small activating RNA, and a small molecule drug. Optionally, the small molecule drug is selected from Mitomycin C or Valrubicin. At a certain concentration, the small activating RNA described in the present disclosure can produce a synergistic effect with the described small molecule drug such as Mitomycin C or Valrubicin, showing a stronger suppression on proliferation of bladder cancer cells.
The present disclosure also provides use of the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the pharmaceutical composition of combined agents, or the preparation in the manufacture of a medication or formulation for activating or up-regulating the expression of p21 gene in cells. In some embodiments, the use can be for the manufacture of the medication or formulation for preventing, treating or alleviating malignant tumors or benign proliferative lesions. In some embodiments, the malignancy may include bladder cancer, prostate cancer, liver cancer, or colorectal cancer. In some embodiments, the bladder cancer may comprise non-muscle invasive bladder cancer.
The present disclosure also provides the use of the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the pharmaceutical composition of combined agents, or the preparation in the manufacture of a medicament with immunostimulatory activity.
The present disclosure also provides a method for preventing, treating or alleviating malignant tumors or benign proliferative lesions, comprising administering the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the pharmaceutical composition of combined agents, or the preparation, to an individual in need thereof. In some embodiments, the malignancy may include bladder cancer, prostate cancer, liver cancer, or colorectal cancer. In some embodiments, the bladder cancer may comprise non-muscle invasive bladder cancer (NMIBC). In some embodiments, the small activating RNA, or the nucleic acid molecule, or the cell, or the pharmaceutical composition, or the pharmaceutical composition of combined agents, or the preparation can all be p21 gene-targeting.
In summary, chemical modifications can improve the pharmaceutical properties of saRNA oligonucleotides. Optimized chemical modifications can increase the stability of saRNA duplexes, suppress their immune stimulation, and mitigate off-target effects. Most importantly, these modifications also increase the efficacy of saRNA-induced RNA activation. The combination of chemically modified small activating RNA and other small molecule chemotherapeutic drugs can exhibit stronger anti-tumor activity.
The invention is further illustrated through specific description. Unless otherwise expressly defined, all technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art.
As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise.
The term “complementarity” or “complementary” as used herein refers to the capability of forming base pairs between two oligonucleotide strands. The base pairs are generally formed through inter-nucleotide hydrogen bonds in the antiparallel oligonucleotide strands. The bases of the complementary oligonucleotide strands can be paired in the Watson-Crick manner (such as A to T, A to U, and C to G) or in any other manner allowing the formation of a duplex (such as Hoogsteen or reverse Hoogsteen base pairing). “100% complementary (complementarity)” means 100% complementarity, i.e. all nucleotide units of the two strands are hydrogen bonded to each other.
“Complete complementarity”, “completely complementary”, “100% complementarity” or “100% complementary” means that each nucleotide from the first oligonucleotide strand can form a hydrogen bond with the second oligonucleotide strand in the double-stranded region of the double-stranded oligonucleotide molecule, with no base pair being “mismatched”. “Incomplete complementarity” or “incompletely complementary” means that not all of the nucleotides of the two strands are bound to each other pairwise by a hydrogen bond. For example, for two oligonucleotide strands with each of 20 nucleotides in length in the double stranded region, if only two base pairs in this double-stranded region can be formed through hydrogen bonds, the oligonucleotide strands have a complementarity of 10%. In the same example, if 18 base pairs in this double-stranded region can be formed through hydrogen bonds, the oligonucleotide strands have a complementarity of 90%. Substantial complementarity or substantially complementary refers to more than about 79%, about 80%, about 85%, about 90%, about 95% or a higher complementarity.
The term “polynucleotide” refers to nucleotide polymers, and includes but is not limited to single-stranded or double-stranded molecules of DNA, RNA, DNA/RNA hybrids that include polynucleotide chains of deoxyribosyl portions and ribosyl portions that alternate regularly and/or irregularly (i.e., where the alternate nucleotide units have an —OH, then an —H, then an —OH, then a —H, and so on at the 2′ position of a sugar portion), and modifications of these types of oligonucleotides, in which various entities or moieties are substituted or linked with nucleotide units at any position and naturally occurring or non-naturally occurring linkages. The oligonucleotide for activating the transcription of a target gene described herein is a small activating nucleic acid molecule (saRNA).
As used herein, the terms “oligonucleotide strand”, and “oligonucleotide sequence” can be used interchangeably, referring to a generic term for short nucleotide sequences having less than 30 bases (including nucleotides in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)). In the present disclosure, the length of the oligonucleotide strand can be any length from 17 to 30 nucleotides.
As used herein, the term “gene” refers to the entire nucleotide sequence required to produce a polypeptide chain or functional RNA. A “gene” can be a gene that is endogenous to the host cell or fully or partially recombinant (e.g., due to the introduction of an exogenous oligonucleotide encoding a promoter and coding sequence or a heterologous promoter adjacent to an endogenous coding sequence into host cells). For example, the term “gene” includes a nucleic acid sequence that can be composed of exons and introns. A protein-encoding sequence is, for example, a sequence comprised of exons in an open reading frame between a start codon and a stop codon. As used herein, a “gene” may include, for example, a promoter sequence such as a promoter, an enhancer and all other sequences known in the art that control the transcription, expression or activity of another gene, whether or not another gene comprises coding or non-coding sequences. In some cases, for example, “gene” can be used to describe a functional nucleic acid comprising regulatory sequences such as a promoter or an enhancer. Expression of a recombinant gene can be controlled by one or more heterologous regulatory sequences.
As used herein, the term “target gene” can refer to nucleic acid sequences, transgenes, viral or bacterial sequences, chromosomes or extrachromosomal genes that are naturally present in organisms, and/or can be transiently or stably transfected or incorporated into cells and/or chromatins thereof. The target gene can be a protein-coding gene or a non-protein-coding gene (such as a microRNA gene and a long non-coding RNA gene). The target gene generally contains a promoter sequence, and the positive regulation for the target gene can be achieved by designing an saRNA having sequence identity (also called homology) to the promoter sequence, characterized as the up-regulation of expression of the target gene. “Target gene promoter” refers to a non-coding sequence of the target gene. The target gene promoter in the expression “complementary to target gene promoter” refers to the coding strand of the sequence, also referred to as a non-template strand, that is, a nucleic acid sequence having the same sequence as the coding strand of the gene.
As used herein, the term “coding strand” refers to a DNA strand which cannot be used for transcription, and the nucleotide sequence of this strand is the same as that of the RNA produced from transcription (in the RNA, T in DNA is replaced by U). Coding strand is also referred to as sense strand. The coding strand of the double-stranded DNA sequence of the target gene promoter described herein refers to a promoter sequence in the same DNA strand as the DNA coding strand of the target gene.
As used herein, the term “template strand” refers to the other strand complementary with the coding strand in the double-stranded DNA of the target gene, i.e., the strand that, as a template, can be transcribed into RNA, and this strand is complementary with the transcribed RNA (A to U and G to C). In the process of transcription, RNA polymerase binds to the template strand, moves in the 3′-5′ direction along the template strand, and catalyzes the synthesis of the RNA in the 5′-3′ direction. Template strand is also referred to as antisense strand, or negative strand. The template strand of the double-stranded DNA sequence of the target gene promoter described herein refers to a promoter sequence on the same DNA strand as the DNA template strand of the target gene.
As used herein, the term “identity” or “homology” means that one oligonucleotide strand (sense or antisense strand) of an saRNA has at least about 60% sequence similarity with the coding strand or template strand in a region of the promoter sequence of a target gene.
As used herein, the term “promoter” refers to a nucleic acid sequence that does not encode a protein, and that is spatially associated with a protein-coding or RNA-coding nucleic acid sequence and plays a regulatory role for the transcription of the protein-coding or RNA-coding nucleic acid sequence. Generally, an eukaryotic promoter contains 100 to 5000 base pairs, though this length range is not intended to limit the term “promoter” as used herein. Although the promoter sequence is generally located at the 5′ terminus of a protein-coding or RNA-coding sequence, it may also exist in exon and intron sequences.
As used herein, the term “transcription start site” refers to a nucleotide marking the transcription start on the template strand of a gene. A gene can have more than one transcription start site.
As used herein, the term “overhang” refers to non-base-paired nucleotides at the terminus (5′ or 3′) of an oligonucleotide strand, which is formed by one strand extending out of the other strand in a double-stranded oligonucleotide. A single-stranded region extending out of the 3′ terminus and/or 5′ terminus of a duplex is referred to as an overhang.
As used herein, the terms “gene activation” or “activating gene” can be used interchangeably, and mean an increase in transcription, translation, expression or activity of a certain nucleic acid, as measured by measuring the transcriptional level, mRNA level, protein level, enzymatic activity, methylation state, chromatin state or configuration, translation level or the activity or state in a cell or biological system of a gene. These activities or states can be determined directly or indirectly. In addition, “gene activation”, “activating gene” refers to an increase in activity associated with a nucleic acid sequence, regardless of the mechanism of such activation, for example, such as being regulated by a regulatory sequence, transcribed into RNA, translated into protein, resulting in increased protein expression.
As used herein, the terms “small activating RNA” and “saRNA” can be used interchangeably, and refer to a nucleic acid molecule that can facilitate gene expression and can be composed of a first ribonucleic acid strand (antisense strand, also called antisense oligonucleotide strand) containing a nucleotide sequence having sequence identity to the non-coding nucleic acid sequence (e.g., a promoter or an enhancer) of a target gene and a second ribonucleic acid strand (sense strand, also called sense oligonucleotide strand) containing a nucleotide sequence complementary to the first strand, wherein the first strand and the second strand form a duplex. A small activating RNA can also be composed of a single-stranded RNA molecule that can form a hairpin structure by two complementary regions (first and second regions) within the molecule, wherein the first region contains a nucleotide sequence having sequence identity to the target sequence of a promoter of a gene, and the second region contains a nucleotide sequence which is complementary with the first region. The length of the duplex region of the saRNA molecule is typically about 10 to about 50, about 12 to about 48, about 14 to about 46, about 16 to about 44, about 18 to about 42, about 20 to about 40, about 22 to about 38, about 24 to about 36, about 26 to about 34, and about 28 to about 32 base pairs, and typically about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45 or about 50 base pairs. In addition, the terms “saRNA” and “small activating RNA” also contain nucleic acids other than ribonucleotide portions, including, but not limited to, modified nucleotides or analogues.
As used herein, the terms “sense strand” and “sense oligonucleotide strand” are interchangeably used and refer to the first ribonucleic acid strand having sequence identity with the coding strand containing the promoter sequence of a target gene in the small activating RNA duplex.
As used in the application, the terms “antisense strand” and “antisense oligonucleotide strand” are interchangeably used and refer to the second ribonucleic acid strand complementary to the sense oligonucleotide strand in the small activating RNA duplex.
As used herein, the term “basic sequence” refers to an RNA sequence generated in a process of preparing a small activating RNA, in which the coding strand of the double-stranded DNA sequence of the target gene promoter is taken as a template, and a sequence comprising 17-30 (e.g., 19) bases is selected as the target site, based on which the RNA sequence synthesized corresponding to the target site sequence is a basic sequence. The basic sequence can be completely consistent with the sequence on the coding strand of the double-stranded DNA sequence of the target gene promoter, and can also have more than 60% homology therewith.
As used in this application, the term “synthesis” refers to the synthesis method of RNA, including any method capable of synthesizing RNA, such as chemical synthesis, in vitro transcription, etc.
As used in this application, the term “derived sequence” refers to an oligonucleotide sequence obtained after a specific oligonucleotide sequence is chemically modified.
Double-stranded saRNA and transfection: Double-stranded saRNA was chemically synthesized by GenePharm (Shanghai, China) or GeneScript (Nanjing, China).
Human bladder cancer cells Ku-7-LG (ATCC), J82 (ATCC) and T24 (ATCC) were cultured in McCoy medium (Gibco) comprising 10% calf serum (Sigma-Aldrich) and 1% penicillin/Streptomycin (Gibco). Cells were cultured at 37° C. under 5% CO2. Ku-7-LG, J82 and T24 cells were plated into 12-well plates at 10×104 cells per well, transfected with the small RNA at a concentration of 10 nM (unless otherwise specified) for three days, using RNAiMax (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. Two replicate wells were set for each treatment. All saRNA sequences are listed in Table 2.
After transfection, the medium was discarded and to each well 500 μl cell lysate was added and incubated at room temperature for 5 minutes. RNA was extracted with the Qiagen RNeasy kit, and after reverse transcription, qPCR analysis was performed on the ABI 7500 Fast Real-time PCR system (Applied Biosystems). Each sample was amplified in 3 replicate wells. The PCR reaction conditions are shown in Table 5.
The PCR reaction conditions are: 95° C. for 30 seconds, 95° C. for 5 seconds, 60° C. for 30 seconds, and 40 cycles of amplification. The GAPDH gene was amplified as an internal reference at the same time. p21 was amplified with the p21F1/R1 primer pair, and the specific sequences of the amplification primers are shown in Table 1.
In order to calculate the expression value (Erel) of p21 (target gene) of a saRNA transfection sample relative to the control treatment, Formula 1 is used to input the Ct values of the target gene and the internal reference gene for calculation.
wherein, CtTm is the Ct value of the target gene from the control treatment sample; CtTs is the Ct value of the target gene from the saRNA treated sample; CtRm is the Ct value of the internal reference gene from the control treatment sample; and CtRs is the Ct value of the internal reference gene from the saRNA treated sample.
J82 cells were transfected with RAG1-40-31 at 0.1, 1, 10 and 25 nM. After 24 hours of transfection, the cells were refreshed with PBMC cell-containing fresh medium. The PBMC and J82 cells were co-cultured for 48 hours, and then the supernatant was discarded and the cells were collected. 500 μL PBS was added to each well for washing and then discarded, before the addition of 100 μL trypsin/well. 900 μL medium was added to stop digestion and the content was transferred to a 1.5 mL centrifuge tube. All the cells were collected through centrifugation (400 rcf, 5 min) and counted (1˜2×105 cells/100 μL Binding Buffer). 100 μL of 1× Binding Buffer (B&D Systems, 51-66121E), 5 μL FITC Annexin V (B&D Systems, 51-65874X) and 5 μL PI (B&D Systems, 51-66211E) were added before incubation in dark at room temperature for 15 minutes. After the incubation, 100 μL of 1× binding buffer was added before blending and transferring to a 96-well plate for analysis with flow cytometer (Beckman Coulter). The sample should be analyzed within 1 hour.
After transfection, the supernatant was discarded to collect cells. To each well 500 μL PBS was added for one wash and then discarded. To each well 100 μL trypsin was further added. 900 μL medium was added to stop digestion before transferring to a 1.5 mL centrifuge tube. All the cells were collected through centrifugation (400 rcf, 5 min) and counted (2×105 cells/200 μL PBS). Cold 70% absolute ethanol was added before incubation overnight at 4° C. After washing twice with PBS, 200 μL Krishan buffer was added before incubation at 4° C. for 1 hour. After washing twice with PBS, the supernatant was discarded and 200 μL PBS was added for cell re-suspension, then the cells were transferred to a 96-well plate and analyzed by flow cytometer. The collected data were analyzed with MotFit software.
Cells were plated in a 96-well plate at 2˜4×103 cells/well, cultured overnight, and transfected with the oligonucleotide duplexes. Three days after transfection, CCK8 (Dojindo) was used to detect cellular proliferation following manufacturer's instructions. The experimental steps are briefly described as follows: 10 μL of CCK8 solution was added to each well, incubated at 37° C. for 1 hour, and then the absorbance at 450 nm was measured using a microplate reader.
saRNA Stability Analysis
saRNA (1.5 μL, 10 μM) was incubated at a final concentration of 0.02 mg/mL in PBS in the presence of RNase A (Amresco, OH, USA) at 37° C. for different durations. At the end of the incubation, the mixture was snap frozen in liquid nitrogen to stop nuclease activity. Samples were analyzed on a 4% agarose gel and examined for duplex degradation.
A 26 bp fragment comprising the Rag1-40 target sequence was cloned in the antisense orientation into a multiple cloning site (MCS) of the 3′ untranslated region of firefly luciferase of the pmirGLO dual luciferase vector (Promega, Fitchburg, WI), to obtain pOff-Target plasmid. All oligonucleotide sequences used to generate the inserts are listed in Table 4. Following E. coli transformation and overnight incubation, plasmids for each construct were prepared by standard method. Each plasmid was transfected into COS-1 monkey kidney epithelial cells using Lipofectamine 3000 (Invitrogen, Carlsbad, CA). Subsequently, saRNA was transfected using RNAiMAX. After 24 hours of incubation, COS-1 cells were lysed with 1× lysis buffer, and luciferase activity was measured using dual luciferase reporter gene assay system (Promega, WI, USA) following manufacturer's instructions.
Human peripheral blood mononuclear cells (Allcells, Alameda, CA) were seeded in a 96-well microplate at a density of approximately 10×104 cells/well. Transfection of dsRNA was performed using RNAiMAX (Invitrogen, Carlsbad, CA) following manufacturer's instructions. Supernatants were collected 24 hours after transfection and immediately assayed for IFN-α and TNF-α production using ELISA kit (R&D Systems). Each treatment group was analyzed in triplicate.
Results are expressed as mean±standard deviation. GraphPad Prism software (GraphPad Software) was used for one-way analysis of variance followed by Tukey's t test for statistical analysis. The criteria for statistical significance were set as *p<0.05, **p<0.01 and ***p<0.001.
Without wishing to be bound by any particular theory, the following examples are only for illustrating and explaining the fusion protein, preparation method and use of the invention, and the present invention is not limited to the following examples.
The present disclosure is further illustrated by the following examples. It should be understood that the following examples are for illustrative purpose only and are not to be construed as limiting this invention in any manner.
As shown in Table 2,
aNucleotides in lower-case letters = DNA
bm = 2′OMe;
cf = 2′F;
d* = phosphorothioate (PS)
The antisense oligonucleotide strands are:
Each sense oligonucleotide strand-derived sequence was annealed to the first eight antisense oligonucleotide strand-derived sequences (RAG1-SS-AS2A-RAG1-SS-AS2H), resulting in a total of 32 duplexes, each duplex comprising a unique modification pattern (
To assess the stability of the saRNA RAG1-40-38 duplex in the presence of nucleases, the duplex was incubated in 0.02 μg/L of RNase A solution for various durations of 0-1 hour.
As shown in
All chemically modified duplexes (Rag1-40-1 to Rag1-40-32) were incubated with 0.02 μg/L of RNase A for different durations (0 to 96 hours). At the end of the incubation, the size and amount of duplexes were detected by agarose gel electrophoresis. As shown in
Further analysis of the data in
To further test the stability of the chemically modified double-stranded saRNA in human urine, the duplexes were incubated in urine for different durations ranging from 0 to 48 hours. As shown in
RAG1-0 is the target sequence of CDKN1A (p21), based on which the structure was optimized to obtain 16 saRNAs: RAG1-29, RAG1-30, RAG1-31, RAG1-32, RAG1-33, RAG1-34, RAG1-35, RAG1-36, RAG1-37, RAG1-38, RAG1-39, RAG1-40, RAG1-41, RAG1-42, RAG1-43, RAG1-44.
The main purpose of introducing chemical modifications to regulatory oligonucleotides of a gene is to improve their pharmaceutical properties, including enhancing in vivo stability and mitigating off-target effects (e.g., sequence-dependent targeting of unrelated genes, sequence-dependent or independent immune stimulation), while maintaining their gene regulatory capacity (gene knockdown or activation). To assess the effect of chemical modification on the RNAa activity of saRNA on the p21 gene, 10 nM unmodified (Rag1-40) and modified (Rag1-40-1 to Rag1-40-34) duplexes were transfected into Ku-7-LG and T24 cells, respectively. After 72 hours, the mRNA expression level of p21 was assessed by RT-qPCR. All duplexes induced p21 mRNA expression in all 3 cell lines at least double that of the control.
In chemically modified duplexes Rag1-40-32, Rag1-40-33, and Rag1-40-34, the region of positions 2 to 4 from the 5′ end of the antisense oligonucleotide strand was replaced with deoxynucleotide. All cell lines tested showed attenuated activity (
It is known that p21 induction by saRNA is that a variety of tumor suppressor factors such as p21 protein suppress the proliferation of cancer cells. To evaluate the effect of chemically modified saRNAs on the function of cancer cells, cells (Ku-7-LG and T24) were transfected with 10 nM unmodified and modified saRNAs for 72 hours, and the cellular proliferation was determined by CCK8. As shown in
Based on the proliferation suppressing activity of the saRNA duplex, it is suggested that:
Oligonucleotides are used in the treatment of diseases by interfering with gene expression, and the immunostimulatory effect of oligonucleotides is an undesirable side effect in some cases. To assess the immunostimulatory effect of chemically modified saRNAs, human peripheral blood mononuclear cells (PBMC) from healthy donors were incubated with the double-stranded saRNAs, and INF-α and TNF-α levels in the supernatant of treated cells after 24 hours were measured.
As shown in
These data suggest that most of the various combinations of chemical modifications of saRNA duplexes suppress the immunostimulatory effects of the duplexes, but specific modification permutations promote the immunostimulatory activity of dsRNAs. This immune-enhancing effect is valuable for the treatment of certain diseases, for example, intravesical infusion administration in the treatment of non-muscle invasive bladder cancer (NMIBC), because such saRNAs not only directly act on the target genes, but also activate the immune system to achieve tumor suppression.
In RNA activation, the strand identical to the sequence of the promoter's sense DNA strand is called the sense oligonucleotide strand, and its targeting activity should be inhibited to mitigate potential off-target effects. To assess the off-target effects of unmodified and modified saRNAs, a sequence complementary to the sense oligonucleotide strand of Rag1-40 was cloned into the 3′UTR region of the luciferase gene in a pmirGLO dual luciferase vector. The vector plasmid was co-transfected with the saRNA into COS-1 cells. Cells were lysed 48 hours after transfection and the resulting lysates were assessed for luciferase activity. See Table 4 for primer sequences.
As shown in
This result indicates that chemical modifications and their combinations used in the disclosure can mitigate the off-target effect of saRNA oligonucleotides, and one possible mechanism is to prevent Ago from loading the sense strand as the guide strand. For the 3 saRNA duplexes that showed increased off-target effects, two of them (Rag1-40-16 and Rag1-40-32) had DNA modification in the antisense oligonucleotide strand and 2′F modification in the sense oligonucleotide strand, indicating that DNA modification, especially when combined with 2′F modification in the sense oligonucleotide strand, should be avoided.
In order to further evaluate the expression level of p21 mRNA after the different durations of treatment by the chemically modified saRNA duplexes, two saRNAs (RAG1-40-31 and RAG1-40-53) were randomly selected from the above chemically modified saRNA duplexes for detection. RAG1-40-31 and RAG1-40-53 were transfected into Ku-7-LG and T24 cells at a final concentration of 10 nM, for 1, 2, 3, 4, 7 and 9 days, respectively. Each treatment was set up in duplicate. Two-step RT-qPCR was performed as described in the general protocol above.
This suggests that the randomly selected saRNAs RAG1-40-31 and RAG1-40-53 gradually increased the expression level of p21 mRNA with increasing treatment duration, reached the peak after 2 and 3 days of treatment, respectively, and then the expression began to decline but the activation activity was remained.
Example 5 above shows that the chemically modified saRNA duplexes can suppress cellular proliferation. In order to study the mechanism of cellular proliferation suppression, change in cell cycle was analyzed using flow cytometry in this example. Randomly selected saRNAs RAG1-40-31 and RAG1-40-53 were transfected into Ku-7-LG cells at final concentrations of 0.1, 1, 10 and 50 nM, respectively, for 48 hours. Each treatment was set in duplicate. Cell cycle was detected and analyzed as described in the general protocol above.
This suggests that the randomly selected chemically modified saRNAs RAG1-40-31 and RAG1-40-53 suppress cellular proliferation by blocking replication in the S phase of the cell cycle.
Peripheral blood mononuclear cells (PBMC) are cells with a single nucleus in peripheral blood, including lymphocytes, monocytes and dendritic cells. PBMC cells can activate immune stimulation by secreting inflammatory factors, thereby inhibiting the growth and reproduction of tumor cells.
Given that chemically modified RAG1-40-31 exhibited stronger immunostimulatory activity (Example 6), we speculated that this property could be exploited to promote tumor cell suppression. In order to verify this hypothesis, in this example, RAG1-40-31 duplex was selected to transfect J82 cells, and after 24 hours of transfection, the cells were refreshed with fresh medium and PBMC cells at a certain ratio (J82 cells:PBMC cells=1:4) were added, or cells free of PBMC were replaced as control. After 48 hours of co-culture, FITC Annexin V kit was used to detect the apoptosis of tumor cells on a flow cytometer. As shown in
In this example, chemically modified saRNA RAG1-40-31 was used in combination with clinical chemical agents to evaluate the suppressing effect of the combined agents on cancer cells.
Mitomycin C (MMC) is a chemical agent clinically used to treat tumors. It mainly inhibits DNA synthesis by generating DNA cross-links (adherence to cancer cell DNA), making cells unable to divide and eventually causing cell death.
Valrubicin is a chemotherapy drug for the clinical treatment of bladder cancer. It mainly interacts with DNA topoisomerase II to affect the normal break between DNA and enzyme compounds, thereby inhibiting the incorporation of nucleosides into nucleic acids, causing chromosomal damage and arresting cell cycle entry into G2 phase.
The above results indicate that the combined use of chemically modified RAG1-40-31, Mitomycin C or valrubicin has a synergistic effect, and the combined use can provide a better inhibitory effect on J82 tumor cells.
The information of compound drugs is as described in Example 10.
The above results indicated that the combined use of chemically modified RAG1-40-31, Mitomycin C or valrubicin had a synergistic effect, and the combined use can achieve a better suppressing effect on T24 tumor cells.
The entire disclosure of each patent document and scientific document cited in the present disclosure is hereby incorporated by reference for all purposes.
The present disclosure can be implemented in other specific forms without departing from its essential characteristics. Accordingly, the foregoing embodiments are considered to be illustrative and not limiting of the invention described herein. The scope of the invention is indicated by the appended claims rather than the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.
| Number | Date | Country | Kind |
|---|---|---|---|
| 202110175652.9 | Feb 2021 | CN | national |
| PCT/CN2021/075958 | Feb 2021 | WO | international |
This application is a National Stage Application under 35 U.S.C. 371 of co-pending PCT application PCT/CN2022/074635 designating the United States and filed Jan. 28, 2022; which claims the benefit of PCT application number PCT/CN2021/075958 and filed Feb. 8, 2021 and CN Application No. 202110175652.9 and filed Feb. 7, 2021, each of which are hereby incorporated by reference in their entireties.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2022/074635 | 1/28/2022 | WO |
