Method for the treatment of non-muscle invasive bladder cancer by oligonucleotide agents
Patent Information
- Application Number
- PCT/CN2026/079315
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2025-02-21
- Filing Date
- 2026-02-13
- Publication Date
- 2026-08-27
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Figure PCTCN2026079315-FTAPPB-I100001 
Figure PCTCN2026079315-FTAPPB-I100002 
Figure PCTCN2026079315-FTAPPB-I100003
Abstract
Description
METHOD FOR THE TREATMENT OF NON-MUSCLE INVASIVE BLADDER CANCER BY OLIGONUCLEOTIDE AGENTSTECHNICAL FIELD
[0001] The present application relates to the technical field of nucleic acids. In particular, it relates to treatment of non-muscle invasive bladder cancer (NMIBC) , especially Bacillus Calmette Guérin (BCG) failed NMIBC, by oligonucleotide agents.BACKGROUND OF THE INVENTION
[0002] Non-muscle-invasive bladder cancer (NMIBC) represents approximately 80%of the 573,000 new diagnosed bladder cancer cases worldwide in 2020 [WHO. Globocan 2020 Bladder] . Multiple factors are associated with bladder carcinogenesis; however, tobacco smoking is the most significant and common risk factor [Sam S, et al., 2016] . NMIBC, localized to the bladder's mucosal and submucosal layers without involving the detrusor muscle, is notable for its recurrence risk and potential progression to muscle-invasive disease. About 80%of bladder cancers are NMIBC, including pTa / pT1 stage and pTis stage carcinoma in situ (CIS) , and the remaining 20%are ≥ pT2 muscle-invasive bladder cancer (MIBC) [Nielsen ME SA, et al., 2014; Rodolfo Montironi, et al., 2005] .
[0003] According to the risk of progression to MIBC, NMIBC can be classified as low-, intermediate-, and high-risk, of which intermediate to high risk NMIBC accounts for 80%of the total NMIBC [Sam S, et al., 2016] . These patients receive simple transurethral resection of bladder tumors (TURBT) with tumor recurrence rates of 50%to 90%within 1 year and long-term recurrence rates close to 100%. Among them, the type with the highest recurrence rate is high-grade T1 tumor (pT1G3) , with a 29%risk of progression to MIBC within 5 years [Babjuk M BM, et al., 2013] .
[0004] Standard treatment for high-risk NMIBC is TURBT. All patients except low-risk NMIBC need to receive local intravesical chemotherapy (intermediate-risk) or BCG intravesical instillation immunotherapy (high-risk) adjuvant therapy [Sam S, et al., 2016] . Intravesical BCG instillation includes induction and maintenance therapy. BCG treatment is a mainstay for patients with CIS tumors as well as for preventing recurrence of high-risk stage Ta or T1 papillary tumors [NCCN Clinical practice guidelines in oncology: Bladder Cancer, version 3.2023] . While BCG treatment is initially effective, it eventually fails in up to 50%of patients, with 50%of those failures occurring within the first 6 months. Even with standard care, the 1-year recurrence rate in high-risk NMIBC patients is as high as 25%, and the 1-year progression rate to MIBC is 5%. If BCG treatment fails, the patient will need to receive radical cystectomy, and the quality of life will be significantly compromised [Sam S, et al., 2016; Babjuk M BM, et al., 2013] .
[0005] Therefore, reducing tumor recurrence in such patients and preventing the progression to MIBC are the significant unmet medical needs.SUMMARY OF THE INVENTION
[0006] The invention introduces a groundbreaking approach using small activating RNA (saRNA) technology to directly upregulate p21 gene expression at the transcriptional level via the RNA activation (RNAa) mechanism. This first-in-human study represents the first clinical approach of a saRNA targeting p21 in patients with NMIBC and has the potential to establish a novel therapeutic paradigm for activating tumor suppressor genes to treat cancer.
[0007] In some aspects, provided herein is a method for treatment of NMIBC in a subject in need thereof, wherein the method comprises the step of administering the subject a therapeutically effective amount of an oligonucleotide agent or a medicament comprising the oligonucleotide agent, wherein the oligonucleotide agent comprises (i) a saRNA (such as RD-13520 or RD-10773) targeting a selected region of p21 gene having a sequence of any one of SEQ ID NOs: 11-18 and capable of upregulating the expression of p21 gene; and (ii) a conjugation moiety (such as C5x5) that is covalently tethered to the saRNA to deliver the saRNA in the body of a subject.
[0008] In some embodiments, the oligonucleotide agent comprises a saRNA comprising a sense strand of SEQ ID NO: 1 and an antisense strand of SEQ ID NO: 2, or a saRNA comprising a sense strand of SEQ ID NO: 3 and an antisense strand of SEQ ID NO: 2, optionally in a powder form or solved in a pharmaceutically acceptable carrier (such as in saline or PBS) . In some embodiments, the oligonucleotide agent is administered to the subject once a week, once two weeks, once three weeks in a dose of 30 mg per dose, 100 mg per dose, 300 mg per dose or 600 mg per dose. In some embodiments, the course of treatment lasts for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks.
[0009] In some aspects, provided herein is a product for use in the treatment of NMIBC by the method of the present application. In some aspects, also provide herein is the use of the oligonucleotide agent in the preparation of a medicament for the treatment of NMIBC by the method of the present application.
[0010] In some further aspects, provide herein is a pharmaceutical composition comprising the oligonucleotide agent or medicament in the present application, and, at least one pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprises from about 30 mg to about 600 mg of the oligonucleotide agent.
[0011] In some further aspects, provide herein is a kit comprising one or more pharmaceutical compositions of the present application in dosage unit form. In some embodiments, the kit comprises 3 to 72 dosage units, 3, 12, 16, 18, 24, 36, 48, or 72 dosage units, each unit comprises 30-600 mg of the oligonucleotide agent, such as 30 mg, 100 mg, 300 mg or 600 of the oligonucleotide agent.INCORPORATION BY REFERENCE
[0012] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWING
[0013] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are employed, and the accompanying drawings (also “figure” and “FIG. ” herein) , of which:
[0014] FIGs. 1A-1B show the activity of saRNA and saRNA-C5x5 in inducing p21 mRNA expression in human bladder cell lines (KU-7 and T24 cells) . saRNA (i.e., RD-10773) and saRNA-C5x5 (i.e., RD-13520, a lipid compound C5x5 conjugated saRNA, with identical nucleotide sequences to the saRNA except for lipid compound C5x5 conjugated to the 5' end of the sense strand) , were transfected into KU-7 and T24 cells at the indicated concentrations (i.e., 0.0025, 0.005, 0.01, 0.04, 0.16, 0.64, 2.56, 5.12 and 10.24 nM) for 2 days, respectively. Cells transfected in the absence of any oligonucleotide were used as Mock treatment (not shown) . FIG. 1A and FIG. 1B show the p21 mRNA levels in KU-7 and T24 cells in Day 2, respectively. p21 mRNA levels were quantified by two step RT-qPCR using a gene specific primer set. Geometric means of the mRNA levels of HPRT1 and B2M were used as internal reference. The values (y-axis) represent p21 mRNA expression levels relative to Mock treatment after normalized to the reference of HPRT1 and B2M.
[0015] FIGs. 2A-2B show the concentration of saRNA-C5x5 in the bladder and plasma of female C57BL / 6J mice following intravesical bladder (IVB) instillation. Female C57BL / 6J mice were administered with a single dose of saRNA-C5x5 (i.e., RD-13520) at the indicated doses (i.e., 0.3, 1 or 3 mg) via IVB instillation. The mice were sacrificed at 2, 6, or 12 hours (h) , or on Day 1, 4, 7 and 12 post-dosing, and bladder, kidney and liver tissues and plasma were collected at the corresponding time points. The concentrations of RD-13520 were quantified in bladder, kidney and liver tissues and plasma samples via stem-loop RT-qPCR using a gene specific primer set (R1-40-AS-SL-RT (SEQ ID NO: 19) , R1-40-AS-SL-F1 (SEQ ID NO: 20) and SL-RT-qPCR-Uni-R2 (SEQ ID NO: 21) ) . Mean concentration of RD-13520 in mouse bladder (FIG. 2A; ng / g) , kidney and liver tissues (ng / g, not shown in the figure) and plasma (FIG. 2B; ng / mL) from 2 animals of each dose (n=2 / dose) are shown at the indicated time points (mean ± SEM) .
[0016] FIGs. 3A-3B show the expression of p21 protein following intravesical instillation of saRNA-C5x5 treatment in the bladder tissue of cynomolgus macaques (crab-eating monkeys) . One group of cynomolgus macaque monkeys was administered with RD-13520 for five doses (200 mg / dose) at the indicated time points (i.e., Day 1, Day 8, Day 15, Day 22 and Day 29) via IVB instillation. Another group of cynomolgus macaque monkeys was administered with phosphate-buffered saline (PBS) alone and served as a vehicle control. The monkeys were sacrificed at Day 30 post first dosing. p21 protein levels were tested by immunohistochemistry (IHC) using anti-p21 antibody (2947S, Cell signaling technology, US) . FIG. 3A shows the expression of p21 protein (indicated by the arrowhead) following PBS treatment in the bladder tissue of the monkeys. FIG. 3B shows the expression of p21 protein (indicated by the arrowheads) following RD-13520 treatment in the bladder tissue of the monkeys. One animal was assigned to each of the RD13520-treated and PBS-treated groups.
[0017] FIGs. 4A-4D show urinary concentration and total amounts of RD-13520 following each treatment in patients with NMIBC who have failed BCG therapy. Patients were administered with RD-13520 at 30, 100, 300 and 600 mg via IVB injection once weekly for six doses (on Days 1, 7, 14, 21, 28 and 35) Urine samples from patients were collected on both Day 1 and Day 35, with the first morning void discarded prior to sample collection. On each of these two days, sampling was performed across sequential time windows of 0-2h, 2-4h, 4-6h, 6-8h, 8-12h, 12-16h, 16-20h, 20-24h, 24-32h, 32-40h and 40-48 h post-dose, yielding 11 urine samples per patient. Urine samples were also collected prior to administration (pre-dose) as baseline controls. FIGs. 4A-4D show the urinary concentration and total amounts of RD-13520 in patients as determined by LC-MS / MS quantitative analysis.DETAILED DESCRIPTION
[0018] While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.
[0019] Targeting the p21WAF1 / CIP1 (p21) gene represents a promising yet challenging therapeutic strategy in cancer treatment. As a critical cell cycle inhibitor with profound tumor suppressive potential, p21 has remained largely "undruggable" for conventional modalities. In the present application, saRNA technology introduces a groundbreaking approach utilizing p21-targeting saRNAs, such as RD-13520, to directly upregulate p21 gene expression at the transcriptional level via the RNA activation mechanism. The present application not only substantiates preclinical efficacy through in vitro and animal studies, but also reports on first-in-human trials and subsequent clinical investigations of optimized saRNAs. Notably, this application marks the first documented clinical deployment of p21-targeting saRNA therapy in patients with NMIBC, positioning it to establish a novel therapeutic paradigm for tumor suppressor gene activation in oncology.
[0020] Hence, the present application is at least based in part on the discovery that p21-targeting saRNAs can target and upregulate the expression p21 gene in a cell, a tissue, and an animal body, including human and non-human mammals (such as mouse and Cynomolgus macaques monkey) , and thus can be effectively used in the treatment of NMIBC, especially those failed in BCG therapy.DEFINITIONS
[0021] In the present application, the related terms are defined as follows:
[0022] Every numerical range given throughout this specification will include every narrower numerical range or number that falls within such broader numerical range, as if such narrower numerical ranges or numbers were all expressly written herein.
[0023] In the present application, singular forms, such as “a” and “this” , include plural objects, unless otherwise specified clearly in the context.
[0024] The transitional terms / phrases (and any grammatical variations thereof) "comprising" , "comprises" , "comprise" , include the phrases "consisting essentially of" , "consists essentially of" , "consisting of" , and "consists of" and can be interchanged throughout the application. The open term "comprise" also includes a closed term "consisting of" as one option. As used herein, the terms "include, " "have" and "comprise" are used synonymously, which terms and variants thereof are intended to be construed as non-limiting.
[0025] The term “non-muscle invasive bladder cancer” and “NMIBC” as used herein can be used interchangeably. NMIBC, localized to the bladder's mucosal and submucosal layers without involving the detrusor muscle, is notable for its recurrence risk and potential progression to muscle-invasive disease. About 80%of bladder cancers are NMIBC, including pTa / pT1 stage and pTis stage CIS, and the remaining 20%are ≥ pT2 muscle-invasive bladder cancer (MIBC) .
[0026] The term “BCG-failure” as used herein should be interpreted broadly to encompass all possible embodiments, whether explicitly described or not. In some embodiments, BCG-failure includes BCG-unresponsive, BCG-exposed and BCG-intolerant describing as follow. “BCG-unresponsive” refers to 1) Persistent or recurrent CIS (± recurrent Ta / T1 disease) within 12 months of receiving adequate BCG (at least 5 of 6 doses of an initial induction course plus either at least 2 of 3 doses of maintenance therapy or at least 2 of 6 doses of a second induction course) ; or 2) Recurrent high-grade Ta / T1 disease within 6 months of completion of adequate BCG (at least 5 of 6 doses of an initial induction course plus either at least 2 of 3 doses of maintenance therapy or at least 2 of 6 doses of a second induction course) ; or 3) T1 high-grade disease at the first evaluation following an induction BCG course alone (at least 5 of 6 doses of an initial induction course) . “BCG-exposed” refers to the population can be summarized as having high-grade persistent or recurrent NMIBC within 24 months of the last BCG dose but not meeting the definition of BCG-unresponsive. “BCG-Intolerant” refers to disease persistence as a result of inability to receive adequate BCG because of toxicity or side effects. With current attention to abrogation of BCG adverse effects, we expect this category to represent a small portion of the BCG-treated population. In some embodiments, BCG-failure may also includes: BCG-resistance, which refers to recurrence of lesser or improving disease that resolves with further BCG; BCG-relapsing, which refers to recurrence after achieving 6 month complete response (CR , i.e., disease resolves after BCG then returns; and BCG-refractory, which refers to no CR by 6 months after BCG, not improving or worsening disease despite two courses of BCG or maintenance (cf. Nieder AM et al, Urology 66: 108-125, 2005) .
[0027] The term "oligonucleotide" refers to polymers of nucleotides, and includes, but is not limited to, single-strand or double-strand nucleic acid molecules of deoxyribonucleic acid (DNA) , ribonucleic acid (RNA) , or DNA / RNA hybrid, oligonucleotide strands containing regularly and irregularly alternating deoxyribosyl portions and ribosyl portions, as well as modified and naturally or unnaturally existing frameworks for such oligonucleotides.
[0028] The terms "oligonucleotide strand" , “strand” and "oligonucleotide sequence" as used herein can be used interchangeably, referring to a generic term for short nucleotide sequences having less than 35 bases (including nucleotides in DNA or RNA) . In a non-limiting example, the length of a strand can be any length from 16 to 35 nucleotides.
[0029] The term "complementary" as used herein refers to the capability of forming base pairs between two oligonucleotide strands. The base pairs are generally formed through hydrogen bonds between nucleotides in the antiparallel oligonucleotide strands. The bases of the complementary oligonucleotide strands can be paired in the Watson-Crick manner (such as A pairs with T, A pairs with U, and C pairs with G) or in any other manner allowing the formation of a duplex (such as Hoogsteen or reverse Hoogsteen base pairing) .
[0030] Complementarity includes complete complementarity and incomplete complementarity. "Complete complementarity" or "100%complementarity" means that each nucleotide from the first oligonucleotide strand can form a hydrogen bond with a nucleotide at a corresponding position in the second oligonucleotide strand in the double strand region of the double-stranded oligonucleotide molecule, with no base pair being "mis-paired" or “mismatched” . "Incomplete complementarity" and “mismatch” can be used interchangeably and mean that not all the nucleotide units of the two strands are bound with each other by hydrogen bonds. For example, for two oligonucleotide strands each of 20 nucleotides in length in the double strand region, if only two base pairs in this double strand 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 strand region can be formed through hydrogen bonds, the oligonucleotide strands have a complementarity of 90%. Substantial complementarity refers to at least about 75%, about 79%, about 80%, about 85%, about 90%, about 95%or 99%complementarity.
[0031] The term "target gene" as used herein 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) . In some embodiments, the target gene generally contains a promoter sequence, and the positive regulation for the target gene can be achieved by designing a double-stranded oligonucleotide having sequence identity (also called homology) to the promoter sequence, characterized as the up-regulation of expression of the target gene. "Target sequence" or “target site” used interchangeably refers to a sequence fragment in the sequence of a target gene, such as, a target gene promoter, which is homologous or complementary to a sense strand or an antisense strand of a double-stranded oligonucleotide. The target gene can also include one or more regulatory elements where one or more double-stranded oligonucleotides are designed to have sequence identity to a regulatory element. Non-limiting examples of one or more regulatory elements include: a promoter, an enhancer, a silencer, an insulator, a TATA box, a GC box, a CAAT box, a transcriptional start site, a DNA binding motif of a transcription factor or other protein that regulates transcription, and a 5’ untranslated region.
[0032] The terms "sense strand" of a double-stranded oligonucleotide refers to the strand having sequence homology or sequence identity with a fragment of the coding strand of the sequence of a target gene.
[0033] The terms "antisense strand" of a double-stranded oligonucleotide refers to the strand having sequence complementary to the sense strand. Said antisense strand may interact with a target sequence to up-regulate gene expression, said target sequence may be a fragment of the coding strand of the sequence of a target gene.
[0034] The term "coding strand" as used herein refers to a DNA strand in the target gene which cannot be used for transcription, and the nucleotide sequence of this strand is the same as that of an RNA produced from transcription (in the RNA, T in DNA is replaced by U) . In some embodiments, the coding strand of the double strand DNA sequence of the target gene promoter described herein refers to a promoter sequence on the same DNA strand as the DNA coding strand of the target gene.
[0035] The term "template strand" as used herein refers to the other strand complementary to the coding strand in the double strand DNA of the target gene, i.e., the strand that, as a template, can be transcribed into RNA, and this strand is complementary to the transcribed RNA (Apairs with U and G pairs with C) .In the process of transcription, RNA polymerase binds to the template strand, moves along the 3'→5' direction of the template strand, and catalyzes the synthesis of the RNA along the 5'→3' direction. The template strand of the double strand 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.
[0036] The term "promoter" as used herein refers to a sequence which 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, a eukaryotic gene promoter contains 100 to 5000 base pairs, although 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.
[0037] The term "transcription start site (TSS) " as used herein refers to a nucleotide marking the transcription start on the template strand of a gene. The transcription start site can appear on the template strand of the promoter region. Different variants of a gene may have different TSS, but with identical upstream sequences. Conventional means can be used to find the TSS in a gene, such as cap analysis of gene expression (CAGE) , oligo-capping and robust analysis of 5'-transcipt ends (5'-RACE) .
[0038] The term “locked nucleic acid (LNA) ” refers to a locked nucleic acid in which the 2′-oxygen and 4′-carbon atoms are joined by an extra bridge. As used herein, the term “bridged nucleic acid (BNA) ” refers to a 2'-O and 4'-aminoethylene bridged nucleic acid that can contain a five-membered or six-membered bridged structure with an N-O linkage. As used herein, the term “peptide nucleic acid (PNA) ” refers to a nucleic acid mimic with a pseudopeptide backbone composed of N- (2-aminoethyl) glycine units with the nucleobases attached to the glycine nitrogen via carbonyl methylene linkers.
[0039] The term "identity" or "homology" as used herein means that one oligonucleotide strand (sense or antisense strand) of a double-stranded oligonucleotide has sequence similarity with a coding strand or template strand in a region of a target gene. As used herein, the "identity" or "homology" may be at least about 75%, about 79%, about 80%, about 85%, about 90%, about 95%or 99%. In some embodiments, the double-stranded oligonucleotide has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 residues that are different from a reference sequence. To determine the percent identity of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes) . The nucleotides at corresponding nucleotide positions are then compared. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm, such as using the Needleman and Wunsch ( (1970) J. Mol. Biol. 48: 444-453) algorithm which has been incorporated into the GAP program in the GCG software package (available at www. gcg. com) . The percent identity between two nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller ( (1989) CABIOS, 4: 11-17) which has been incorporated into the ALIGN program (version 2.0) , using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. It is understood that the molecules described herein may have additional conservative or non-essential nucleic acid substitutions, which do not have a substantial effect on their functions.
[0040] The term “sequence specific mode” as used herein means a binding or hybridization way of two nucleic acid fragments according to their nucleotide sequence, e.g., a Watson-Crick manner (such as A pairs with T, A pairs with U, and C pairs with G) or any other manner allowing the formation of a duplex (such as Hoogsteen or reverse Hoogsteen base pairing) .
[0041] The term "overhang" as used herein 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-strand region extending out of the 3' terminus and / or 5' terminus of a duplex is referred to as an overhang.
[0042] The term “natural overhang” as used herein refers to an overhang which consists of one or more nucleotides identical to or complementary to the corresponding position on the target sequence. A natural overhang on a sense strand consists of one or more nucleotides identical to the corresponding position on the DNA target. A natural overhang on a sense strand consists of one or more nucleotides identical to the corresponding position on the DNA target. A natural overhang on an antisense strand consists of one or more nucleotides complementary to the corresponding position on the DNA target.
[0043] The term “isolated” refers to material that is removed from its original or native environment (e.g., the natural environment if it is naturally occurring) . For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated by human intervention from some or all of the co-existing materials in the natural system, is isolated. Such polynucleotide could be part of a vector and / or such polynucleotide or polypeptide could be part of a composition, and still be isolated in that such vector or composition is not part of the environment in which it is found in nature. An isolated molecule may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid, or by chemically synthesizing the molecule. For example, the term "isolated RNA" refers to RNA molecules which are substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. In some embodiments, the materials of the present application, such as the polynucleotides, oligonucleotides and / or double-stranded oligonucleotides of the present application, are isolated.
[0044] The terms "gene activation" or "activating gene expression" and "gene up-regulation" or "up-regulating gene expression" can be used interchangeably, and mean an increase in transcription, translation, expression or activity of a certain nucleic acid as determined 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 expression" , "gene up-regulation" or "up-regulating gene expression" refers to an increase in activity associated with a nucleic acid sequence, regardless of the mechanism of such activation. For example, gene activation occurs at the transcriptional level to increase transcription into RNA and the RNA is translated into a protein, thereby increasing the expression of the protein.
[0045] The terms "small activating RNA" , "saRNA" , and "small activating nucleic acid molecule" can be used interchangeably, and refer to a nucleic acid molecule that can up-regulate target gene expression and can be composed of a first nucleic acid fragment (sense strand) containing a nucleotide sequence having high sequence identity to the non-coding nucleic acid sequence (e.g., a promoter or an enhancer) of a target gene and a second nucleic acid fragment (antisense strand) containing a nucleotide sequence complementary to the first nucleic acid fragment, wherein the first nucleic acid fragment and the second nucleic acid fragment form a duplex. The saRNA can also be comprised of a synthesized or vector-expressed single-strand RNA molecule that can form a hairpin structure by two complementary 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 to the first region. The length of the duplex region of the saRNA is typically about 15 to about 35, about 16 to about 32, about 17 to about 30, about 18 to about 28, about 19 to about 26, about 20 to about 24, and about 21 to about 22 base pairs, and typically about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22 or about 23 base pairs. In addition, the terms "saRNA" , "small activating RNA" , and "small activating nucleic acid molecule" also contain nucleic acids other than the ribonucleotide, including, but not limited to, modified nucleotides or analogues.
[0046] The terms “oligonucleotide modulator” and “oligonucleotide agent” are used interchangeably, and refer to an oligonucleotide-containing substance which at least comprises or consists of one or more double-stranded oligonucleotide of the invention and has the activity of modulating target gene expression, and further comprises other oligonucleotide moieties / components or non-oligonucleotide moieties / components (such as lipid) conjugated with the double-stranded oligonucleotide (s) . In certain embodiments, the oligonucleotide modulator comprises an RNA (such as the saRNA of the invention) , a DNA, a BNA, an LNA, a PNA or a mixture thereof.
[0047] The term “isolated target site” , “target site” and “isolated polynucleotide" can be used interchangeably, herein means a target site which a saRNA has complementarity or hybridizes to. For example, an oligonucleotide of a target site can include a nucleic acid sequence which a region of saRNAs have complementarity or hybridize to. The term “a polynucleotide” in the context of saRNA means a polynucleotide which encodes a saRNA, for example a DNA.
[0048] The terms “p21” , “p21 gene” , “CDKN1A” , or “CDKN1A gene” refers to a human gene. The term “p21” and “CDKN1A” can be used interchangeably. The term "CDKN1A mRNA" refers to a message RNA (mRNA) generated from the expression of CDKN1A gene, or the transcription of CDKN1A gene. The cell cycle inhibitor p21 (CDKN1A) encoded by CDKN1A gene is a protein playing multiple roles not only in the DNA damage response, but also in many cellular processes during unperturbed cell growth.
[0049] The terms "baseline expression of p21 refers to the expression of p21 gene of a parallel reference (such as a cell or an individual) without or before the treatment of the saRNA.
[0050] The terms “subject” and “individual” are used interchangeably herein to mean any living organism that may be treated with agents of the present application. The term “patient” means a human subject or individual, including infants, children, and adults.
[0051] The terms “therapeutically effective amount” of a composition is an amount sufficient to achieve a desired therapeutic effect, and therefore does not require cure or complete remission. In embodiments of the present application, therapeutic efficacy is an improvement in any of the disease indicators, and a therapeutically effective amount is sufficient to cause an improvement in a clinically significant condition / symptom in the treated individual. The phrases “therapeutically effective amount” and “effective amount” are used herein to mean an amount sufficient to reduce by at least about 15 percent, preferably by at least 50 percent, more preferably by at least 90 percent, or to decrease at least about 50 percent, at least about 100 percent, at least about 200 percent, more preferable at least about 500 percent and most preferably prevent, a clinically significant deficit in the activity, function and response of the individual being treated.
[0052] The effective amount may vary depending on such factors as the size and weight of the subject, the type of illness, or the particular agents of the application. For example, the choice of the agent of the application could affect what constitutes an “effective amount. ” One of the ordinary skills in the art would be able to study the factors contained herein and make the determination regarding the effective amount of the agents of the application without undue experimentation.
[0053] The regime of administration may affect what constitutes an effective amount. The agent of the application can be administered to the subject either prior to or after the disease diagnosis or condition. Further, several divided dosages, as well as staggered dosages, can be administered daily, weekly, monthly, quarterly or sequentially, or the dose can be continuously infused, or can be a bolus injection. Further, the dosages of the agent (s) of the application could be proportionally increased or decreased as indicated by the exigencies of the therapeutic or prophylactic situation.
[0054] The terms “treat, ” “treated, ” “treating” , or “treatment” as used herein have the meanings commonly understood in the medical arts, and therefore do not require cure or complete remission, and include any beneficial or desired clinical results. Non-limiting examples of such beneficial or desired clinical results are prolonging survival as compared to expected survival without treatment, reduced symptoms including one or more of the followings: weakness and atrophy of proximal skeletal muscles, inability to sit or walk independently, difficulties in swallowing, breathing, etc.
[0055] As used herein, “preventing” or “delaying” a disease refers to inhibiting the full development of a disease.
[0056] The term “biological sample” refers to any tissue, cell, fluid, or other material derived from an organism (e.g., human subject) . In some embodiments, the biological sample is obtained from serum, urine and blood.
[0057] The term “synthetic” refers to the manner in which oligonucleotides are synthesized, including any means capable of synthesizing or chemically modifying RNA, such as chemical synthesis, in vitro transcription, vector expression, and the like.
[0058] The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm, such as using the Needleman and Wunsch ( (1970) J. Mol. Biol. 48: 444-453) algorithm which has been incorporated into the GAP program in the GCG software package (available at www. gcg. com) . The percent identity between two nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller ( (1989) CABIOS, 4: 11-17) which has been incorporated into the ALIGN program (version 2.0) , using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. It is understood that the molecules described herein may have additional conservative or non-essential nucleic acid substitutions, which do not have a substantial effect on their functions.
[0059] saRNAs may contain natural nucleotides or chemically modified nucleotides. The modifications can impart increased nuclease stability and / or increased cellular potency. Examples of chemical modifications include phosphorothioate backbone modification, 2'-deoxynucleotide, 2'-OCH3-containing ribonucleotides, 2'-F-ribonucleotides, 2'-methoxyethyl ribonucleotides, combinations thereof and the like. The saRNA can have varying lengths (e.g., 10-200 bps) and structures (e.g., hairpins, single / double strands, bulges, nicks / gaps, mismatches) and are processed in cells to knock down target mRNA. A double-stranded saRNA can have the same number of nucleotides on each strand (blunt ends) or asymmetric ends (overhangs) . An overhang of 1-2 nucleotides, for example, can be present on the sense and / or the antisense strand, as well as present on the 5'-and / or the 3'-ends of a given strand.
[0060] The length of the saRNA molecule is typically about 10 to about 60, about 10 to about 50, about 15 to about 30, about 17 to about 29, about 18 to about 28, about 19 to about 27, about 20 to about 26, about 21 to about 25, and about 22 to about 24 base pairs, and typically about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 23, about 25, about 30, about 40, or about 50 base pairs. In addition, the terms “small activating RNA” and “saRNA” also contain nucleic acids other than the ribonucleotide, including, but not limited to, modified nucleotides or analogues.
[0061] Unless otherwise defined, all the technological and scientific terms used therein have the same meanings as those generally understood by those of ordinary skill in the art covering the present application.saRNA
[0062] In some embodiments of the present application, saRNA is capable of upregulating or increasing the expression of a target gene associated with a bladder cancer (such as NMIBC) . In particular, the saRNA comprises a sense strand and an antisense strand forming a double strand which comprises 0, 1, 2 or 3 mismatches, wherein the antisense strand comprises a region of complementarity to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of a target gene, and / or wherein the sense strand comprises a region of homology to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of the target gene.
[0063] As a beneficial consequence, a target sequence (e.g., a nucleic acid sequence on the promoter region of the target gene which the saRNA can complement to) , upon interacting with the saRNA, can activate / upregulate the mRNA transcript by at least 10%, for example, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, or about 250%, as compared to a baseline level of the mRNA transcript in a cell. In one embodiment, mRNA transcript of the target gene is increased by at least 50%. Based at least in part on these discoveries, the present application relates to saRNA, compositions, and pharmaceutical compositions for activating / upregulating the target mRNA transcript by at least 10%as compared to baseline levels of the mRNA transcript. Also provided herein are methods for preventing or treating a bladder cancer (such as NMIBC) caused by low expression of the corresponding target protein, a target gene mutation, and / or low or abnormal target mRNA level in an individual comprising administering to the individual any of the saRNA, compositions, and / or pharmaceutical compositions described herein.
[0064] In some embodiments, the target sequence for designing the saRNA is a region in the promoter of p21 gene, from -1000 bp upstream of a TSS to +3 bp downstream of the TSS. The TSS is represented by a curved arrow. Putative human p21 promoter sequence (5'-3') (SEQ ID NO: 10) :
[0065] In some embodiments, the functional saRNAs capable of activating / up-regulating the level of p21 mRNA were not randomly distributed on the target sequence but clustered in specific hotspot regions. Only some regions on the promoter of p21 gene are in favor of gene activation by saRNAs. A hotspot region herein is defined by a nucleic acid region (such as in the promoter) on the target gene of the saRNAs, where the full-length target sequences of a plurality of the functional saRNAs are located and enriched. The hotspot region of the p21 gene is selected from a group consisting of SEQ ID NO: 11-18, wherein the sequence of the target region in the p21 promoter is from -893 bp to -801 bp (SEQ ID NO: 11) , -717 bp to -632 bp (SEQ ID NO: 12) , -585 bp to -551 bp (SEQ ID NO: 13) , -554 bp to -504 bp (SEQ ID NO: 14) , -514 bp to -485 bp (SEQ ID NO: 15) , -442 bp to -405 bp (SEQ ID NO: 16) , -352 bp to -313 bp (SEQ ID NO: 17) , or -325 bp to -260 bp (SEQ ID NO: 18) , respectively. The hotspot regions are listed in Table A1. In some embodiments, the saRNA (1) has a GC content of 35-65%; (2) does not contain 5 or more consecutive identical nucleotides; and (3) does not contain 3 or more duplicated or triplicated nucleotides. Table A1. Target sequences of hotspot regions of p21 promoter
[0066] The saRNAs of the oligonucleotide agent described herein include a RNA strand (the antisense strand) having a region which is 60 nucleotides or less in length, i.e., 15-40 nucleotides in length, generally 19-25 nucleotides in length, which region is substantially complementary to at least part of a promoter of a p21 gene differing by 0, 1, 2 or 3 nucleotides from the selected region of p21 gene.
[0067] In some embodiments, the continuous oligonucleotide sequence of the saRNA has five or less, i.e., 5, 4, 3, 2, 1, or 0 nucleotide differences or mismatches relative to the equal length portion of p21 promoter. In some embodiments, the continuous oligonucleotide sequence of the sense strand of saRNA has three or less, i.e., 3, 2, 1, or 0 nucleotide differences or mismatches relative to the equal length portion of p21 promoter. In some embodiments, the continuous oligonucleotide sequence of the antisense strand of saRNA has three or less, i.e., 3, 2, 1, or 0 nucleotide differences or mismatches relative to the equal length portion of p21 promoter. In some embodiments, the equal length region of p21 gene is located in a region of SEQ ID NO: 10. In some embodiments, the equal length region of p21 gene is located in a region selected from a group consisting of SEQ ID NO: 11-18.
[0068] In some embodiments, the differences or mismatches are located in the middle or 3’ terminus of the oligonucleotide sequence of the saRNA. Methods and principles of saRNA molecule design are well known to those skilled in the art and are described in detail in, for example, Place et. al., Molecular Therapy-Nucleic Acids (2012) 1, e15; and Li et. al., PNAS, 2006, vol. 103, no. 46, 17337–17342, which are herein incorporated by reference in their entireties.
[0069] In some embodiments, the saRNA disclosed herein comprises a sense strand and an antisense strand. The sense strand and / or the antisense strand comprise complementary regions capable of forming a double-stranded nucleic acid structure that increases the p21 transcript level in a cell via the RNAa (RNA activation) mechanism. The sense strand and the antisense strand of the saRNA can exist either on two different nucleic acid strands or on one nucleic acid strand (e.g., a contiguous nucleic acid sequence) . When the sense strand and the antisense strand are located on two different strands, at least one strand of the saRNA has a 3' overhang of 0 to 6 nucleotides in length, such that the overhangs of 0, 1, 2, 3, 4, 5 or 6 nucleotides in length, and in some cases, both strands have a 3' overhang of 2 or 3 nucleotides in length. The nucleotide of the overhang is, in some cases thymine deoxyribonucleotide (dT) , or in some cases, natural overhangs which are nucleotides selected from or complementary to the corresponding position on the DNA target. When the sense strand and the antisense strand are located on one nucleic acid strand, in some cases, the saRNA is a hairpin single-stranded nucleic acid molecule, where the complementary regions of the sense strand and the antisense strand form a double-stranded nucleic acid structure with each other.
[0070] In the saRNA disclosed herein, in some embodiments, the sense strand has a length ranging from 10 to 60 nucleotides. For example, in some embodiments, the sense strand and the antisense strand, independently comprise a length of 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleotides. In some embodiments, the antisense strand has a length ranging from 10 to 60 nucleotides. For example, in some embodiments, the sense strand and the antisense strand, independently comprise a length of 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleotides.
[0071] In some embodiments, the antisense strand and / or the sense strand disclosed herein is capable of interacting with a target nucleic acid sequence in the promoter of p21 gene in a sequence specific manner, meaning that the antisense strand and / or the sense strand is capable of undergoing hybridization to a target nucleic acid through hydrogen bonding. In some embodiments, an antisense strand and / or a sense strand has a nucleotide sequence that, when written in the 5' to 3' direction, comprises the reverse complement of the target portion of a target nucleic acid to which it is targeted, e.g., the target portion in a fragment of a p21 gene promoter.
[0072] In some embodiments, the sense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 1, and / or the antisense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 2. In some embodiments, the saRNA has a nucleotide sequence that is at least 60%(e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%or 100%) identical to the nucleotide sequences of RD-10773 whose antisense strand has a nucleotide sequence of SEQ ID NO: 2 that has complementarity with a fragment the of the sense strand of SEQ ID NO: 1.
[0073] In some embodiments, the sense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 3, and / or the antisense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 2. In some embodiments, the saRNA has a nucleotide sequence that is at least 60%(e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%or 100%) identical to the nucleotide sequences of RD-13520 whose antisense strand has a nucleotide sequence of SEQ ID NO: 2 that has complementarity with a fragment of the C5x5 (alipid compound) conjugated sense strand of SEQ ID NO: 3.
[0074] saRNAs targeting p21 gene are also selected as described in WO2019196883A1 and WO2022166815A1 which are hereby incorporated by reference in their entirety.Chemical modification
[0075] In the saRNAs disclosed herein, all nucleotides may be natural or non-chemically modified nucleotides, or at least one nucleotide is a chemically modified nucleotide. Non-limiting examples of the chemical modification include one or more of a combination of the following: 1) modification of a phosphodiester bond of nucleotides in the nucleotide sequence of the saRNA; 2) modification of 2'-OH of the ribose in the nucleotide sequence of the saRNA; 3) modification of a base in the nucleotide of the saRNA;
[0076] The chemical modification described herein is well-known to those skilled in the art, and the modification of the phosphodiester bond refers to the modification of oxygen in the phosphodiester bond, including phosphorothioate modification and boranophosphate modification. The modifications disclosed herein stabilize the saRNA structure, maintaining high specificity and high affinity for base pairing.
[0077] In some embodiments, the chemical modification is to substitute the phosphodiester bond with phosphorothioate (PS) bond on the backbone of the nucleotide sequence of the oligonucleotide agent disclosed herein. In some embodiments, the oligonucleotide agent disclosed herein comprises at least one PS backbone modification.
[0078] In some embodiments, the saRNA of the present application includes at least one chemically modified nucleotide which is modified at 2'-OH in pentose of a nucleotide, i.e., the introduction of certain substituents at the hydroxyl position of the ribose, such as 2'-fluoro modification, 2'-oxymethyl modification, 2'-oxyethylidene methoxy modification, 2, 4'-dinitrophenol modification, locked nucleic acid, 2'-amino modification or 2'-deoxy modification, e.g., a 2’ -deoxy-2’ -fluoro modified nucleotide, a 2’-deoxy-modified nucleotide.
[0079] In some embodiments, the saRNA of the present application includes at least one chemically modified nucleotide which is modified at the base of the nucleotide, e.g., 5-bromouracil modification, 5-iodouracil modification, N-methyluracil modification, or 2, 6-diaminopurine modification.
[0080] In some embodiments, the chemical modification of the saRNA is an addition of a (E) ‐vinylphosphonate moiety at the 5’ end of the sense or antisense sequence. In some embodiments, the chemical modification of the at least one chemically modified nucleotide is an addition of a 5-methyl cytosine moiety at the 5’ end of the sense or antisense sequence.
[0081] In some embodiments, the saRNA of the present application includes at least one nucleotide in the nucleotide sequence of the saRNA being a chemically modified nucleic acid, e.g., a locked nucleotide, an abasic nucleotide, a glycerol nucleic acid, a morpholino nucleotide, a phosphoramidate, and a non-natural base comprising nucleotide. In some embodiments, the saRNA disclosed herein includes an “endo-light” modification with 2’ -O-methyl modified nucleotides and nucleotides comprising a 5’ -phosphorothioate group.
[0082] In some embodiments, the saRNA of the present application is chemically modified to enhance stability or other beneficial characteristics. The nucleic acids featured in the present application may be synthesized and / or modified by conventional methods, such as those described in “Current protocols in nucleic acid chemistry, ” Beaucage, S. L. et al. (Edrs. ) , John Wiley &Sons, Inc., New York, N.Y., USA, which is hereby incorporated herein by reference. Modifications include, for example, (a) end modifications, e.g., 5’ end modifications (phosphorylation, conjugation, inverted linkages, etc. ) 3’ end modifications (conjugation, DNA nucleotides, inverted linkages, etc. ) , (b) base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides) , or conjugated bases, (c) sugar modifications (e.g., at the 2’ position or 4’ position) or replacement of the sugar, as well as (d) backbone modifications, including modification or replacement of the phosphodiester linkages. Specific examples of saRNA molecules that can be used in this present application include but are not limited to RNAs containing modified backbones or no natural internucleoside linkages. In some embodiments, RNAs having modified backbones include, among others, those that do not have a phosphorus atom in the backbone. In some embodiments, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be oligonucleosides. In some embodiments, the modified oligonucleotide will have a phosphorus atom in its internucleoside backbone.
[0083] Modified oligonucleotide backbones include, for example, phosphorothioates (PSs) , chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3’ -alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3’ -amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3’ -5’ linkages, 2’ -5’ linked analogs of these, and those) having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3’ -5’ to 5’ -3’ or 2’ -5’ to 5’ -2’ . Various salts, mixed salts and free acid forms are also included.Conjugate agent and delivery moieties
[0084] In addition, to facilitate entry of the saRNA into a cell, chemical delivery moieties may be introduced at the ends of the sense or antisense strands of the saRNA on the basis of the above modifications to facilitate action through a cell membrane composed of lipid bilayers and gene promoter regions within the nuclear membrane and nucleus. Therefore, the current disclosure also provides an oligonucleotide agent comprising the oligonucleotide and at least one delivery moiety.
[0085] In certain embodiments, saRNAs disclosed in the present application are covalently attached to one or more conjugate moieties. In certain embodiments, delivery moieties modify one or more properties of the attached oligonucleotide, including but not limited to pharmacodynamics (PD) , pharmacokinetics (PK) , stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge and clearance. In certain embodiments, delivery moieties impart a new property on the attached oligonucleotide, e.g., fluorophores or reporter groups that enable detection of the oligonucleotide. Certain delivery moieties and conjugate moieties have been described previously, for example: an accessory oligonucleotide (WO2023280190A1 and WO2024199445A1) , lipid (fatty acid, WO2024002046A1) , cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556) , cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053-1060) , a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N. Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Lett., 1993, 3, 2765-2770) , a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538) , an aliphatic chain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al., EMBO 1, 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54) , a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1, 2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783) , a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides &Nucleotides, 1995, 14, 969-973) , or adamantane acetic acid, a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237) , an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937) , a tocopherol group (Nishina et al., Molecular Therapy Nucleic Acids, 2015, 4, e220; and Nishina et al., Molecular Therapy, 2008, 16, 734-740) , or a GalNAc cluster (e.g., WO2024002046A1) .
[0086] In some embodiments, the saRNA of the present application relates to the sense strand or the antisense strand of the double-stranded oligonucleotide that is conjugated to one or more delivery moieties selected from: lipid, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates, vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins, fluorophores, and dyes.
[0087] In some embodiments, a delivery moiety comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S) - (+) -pranoprofen, carprofen, dansylsarcosine, 2, 3, 5-triiodobenzoic acid, fingolimod, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
[0088] In some embodiments, the saRNA of the present application is conjugated to one or more delivery moieties selected from: an oligonucleotide, a lipid, a fatty acid, a fluorophore, a ligand, a saccharide, a peptide, and an antibody.
[0089] In some embodiments, the sense strand or the antisense strand of the oligonucleotide agent is conjugated to one or more delivery moieties selected from a single-stranded oligonucleotide, a cell-penetrating peptide, polyethylene glycol, an alkaloid, a tryptamine, a benzimidazole, a quinolone, an amino acid, a cholesterol, glucose and N-acetylgalactosamine.
[0090] In certain embodiments, the double-stranded oligonucleotide is conjugated to a lipid selected from C4-30 fatty acid. In certain embodiments, the delivery moiety is a lipid / fatty acid having a saturated or unsaturated, linear or branched C2-16 carbon chain. In certain embodiments, said delivery moiety is fatty acid comprising a carbon chain length of 16, 18 or 22 carbon atoms. In certain embodiments, the delivery moiety is selected from lipophilic moieties as described in WO2024002046A1. In certain embodiments, the double-stranded oligonucleotide may comprise 1, 2, 3, 4, or even more oligonucleotides separately conjugated to 1, 2, 3, 4 or even more of the delivery moieties via 1, 2, 3, 4 or even more linking moieties.
[0091] According to another embodiment, the double-stranded oligonucleotide agents further comprise at least one ACO conjugated with the oligonucleotide (s) . The term “accessory oligonucleotide” herein means a non-targeting single-stranded oligonucleotide having at least 6 nucleotides with or without one or more linking components conjugated to another oligonucleotide. The ACO component is not designed to specifically target any complementary nucleic acid sequence in the subject to be administered to. The ACO component can be chemically-modified on its backbone, nucleoside, base or other positions, e.g., a phosphorothioate, mesyl phosphoramidate or boranophosphate backbone, a 2′-fluoro-2′-deoxynucleoside (2′-F) , a 2′-O-methyl (2′-O-Me) , a 2′-O- (2-methoxyethyl) (2′-O-MOE) , LNA, BNA, PNA, 5’ - (E) ‐vinylphosphonate moiety, 5-methyl uracil, 5-methyl cytosine moiety, etc., to impart physiochemical properties conducive to improve the oligonucleotide (s) ’ bioavailability and delivery. Covalent linking components can be natural or unnatural nucleotides, ethylglycol, carbohydrates, alkyl chains, or any other linker used to covalently connect any two oligonucleotides positioned on the 3’ -or 5’-terminus of one or both of the strands within the oligonucleotide agent. ACO and its conjugation with dsRNA may be described and prepared according to those disclosed in WO2023280190A1, which is herein incorporated by reference in its entirety. In certain embodiments, ACO conjugates to the 3' end of sense strand of the double-stranded oligonucleotide.
[0092] In some embodiments, the sense strand or the antisense strand of the double-stranded oligonucleotide is conjugated to lipid compound C5x5, as shown below:
[0093] In some embodiments, the conjugation group derived from C5x5 has a structure as shown below: wherein the asterisk represents the site where the conjugation group is attached to the strand, either directly or via a linking moiety.
[0094] In certain embodiments, C5x5 conjugates to the 5' end of sense strand and / or antisense strand of the double-stranded oligonucleotide. In certain embodiments, the 5' end of the sense strand and / or antisense strand of the double-stranded oligonucleotide conjugates to one or more C5x5. In some embodiments, the 5' end of the sense strand of the saRNA conjugates to a C5x5. In certain embodiments, the conjugation group conjugated to the saRNA is derived from C5x5. In certain embodiments, the saRNA attached with a conjugation group has a structure as shown below:
[0095] The delivery moieties can be purchased or can be synthesized via procedures known in the art, for example WO2024002046A1 is fully incorporated herein for synthetic process of C5x5.
[0096] In certain embodiments, saRNAs disclosed in the present application are covalently attached to one or more conjugate moieties through linking moieties. The linking moieties, when present, can be selected from the group consisting of -O-, -S-, -C (O) -, -NH-, -N ( (C1-C12) alkyl) -, -N ( (C1-C12) alkyl) -C (O) -O-, -O-C (O) -, -C (O) -O-, -O-C (O) -O-, -C (O) -NH-, -OP (O) 2O-, -P (O) (O-) O-, -OP (O) O-, -OP (O) (S) O-, -O-S (O) 2-O-, -S (O) 2-O-, -S (O) -O-, - (C1-C22) alkylene-, - (C1-C22) alkylene-NH-, -NH- (C1-C22) alkylene-, - (C1-C22) alkylene-NH-C (O) -, - (C1-C22) alkylene-C (O) -, - (C1-C22) alkylene-C (O) -O-, -C (O) - (C1-C22) alkylene-, -NH-C (O) - (C1-C22) alkylene-, -C (O) -NH- (C1-C22) alkylene-, -C (O) - (C1-C22) alkylene-NH-, -NH- (C1-C22) alkylene-C (O) -, -C (O) - (C1-C22) alkylene-C (O) -, -NH- (C1-C22) alkylene-NH-, -C (O) - (C1-C22) alkylene-C (O) O-, -O-C (O) - (C1-C22) alkylene-C (O) -O-, -C (O) -O- (C1-C22) alkylene-O-C (O) -, -C (O) - (C1-C22) alkylene-NH-C (O) -, -NH-C (O) - (C1-C22) alkylene-C (O) -, -NH-C (O) - (C1-C22) alkylene-C (O) -NH-, -C (O) -NH- (C1-C22) alkylene-NH-C (O) -, - (C1-C22) alkylene-OP (O) 2O-, - (C1-C22) alkylene-OP (O) (O-) O-, - (C1-C22) alkylene-OP (O) (O-) O- (C1-C22) alkylene-, - (C1-C22) alkylene-OP (O) O-, - (C1-C22) alkylene-OP (O) (S) O-, - (C1-C22) alkylene-O-S (O) 2-O-, - (C1-C22) alkylene-S (O) 2-O-, - (C1-C22) alkylene-S (O) -O-, -O-P (O) 2-O- (C1-C22) alkylene-OP (O) 2O-, -O-P (O) -O- (C1-C22) alkylene-OP (O) O-, -OP (O) (S) O- (C1-C22) alkylene-OP (O) (S) O-, -O-S (O) 2-O- (C1-C22) alkylene-O-S (O) 2-O-, -S (O) 2-O- (C1-C22) alkylene-S (O) 2-O-and -O-S (O) - (C1-C22) alkylene-S (O) -O-; wherein the - (C1-C22) alkylene-contained in the linking moiety can be an alkylene group comprising from 1 to 22 carbon atoms, such as from 2 to 20 carbon atoms, or from 3 to 18 carbon atoms, or from 4 to 16 carbon atoms, or from 5 to 12 carbon atoms, or from 6 to 10 carbon atoms. In one embodiment, the delivery moiety is directly linked with the oligonucleotide when the linking moiety is a direct bond.
[0097] In some embodiments, the saRNA conjugated to one or more delivery moieties disclosed in the embodiments, e.g., C5x5. In some embodiments, the saRNA is directly contacted, transferred, delivered or administrated to a cell or a patient.DNA encoding saRNA
[0098] In certain embodiments, the present application relates to a nucleic acid or polynucleotide encoding the saRNA which can activate or up-regulate the expression of a target gene, e.g., p21 gene in a cell, preferably by at least 10% (e.g., as compared to baseline expression of the p21 gene) . In certain embodiments, the nucleic acid is a DNA encoding a saRNA. The vectors disclosed herein comprise a fragment of DNA that encodes a saRNA of the present application.Cell comprising saRNA
[0099] After contacting a cell, the saRNA disclosed herein can effectively activate or up-regulate the expression of p21 gene in a cell, preferably up-regulate the expression by at least 10% (e.g., as compared to baseline expression of the p21 gene) . In certain embodiments, the present application relates to a cell comprising the saRNA disclosed herein. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a human cell (e.g., KU-7 or T24 cell) . The cell disclosed herein may be in vitro, or ex vivo, such as a cell line or a cell strain, or may exist in a mammalian body, such as a human body.Composition comprising saRNA
[0100] In certain embodiments, the present application relates to a composition or pharmaceutical composition comprising the saRNA of the present application. In some embodiments, the composition comprises at least one pharmaceutically acceptable carrier. In some embodiments, the composition comprising at least one pharmaceutically acceptable carrier selected from an aqueous carrier, liposome or LNP, polymer, micelle, colloid, metal nanoparticle, non-metallic nanoparticle, bioconjugate (e.g., C5x5 or GalNAc) , polypeptide and antibody. In one embodiment, the aqueous carrier may be, for example, RNase-free water, or RNase-free buffer. In some embodiments, the composition may contain 0.001-1600 nM (e.g., 0.001-1000 nM, 0.001-500 nM, 0.001-400 nM, 10-100 nM, 10-50 nM, 20-50 nM, 20-100 nM, 50-150 nM, 50-400 nM, 50-1000 nM or 400-1600 nM) of the saRNA or polynucleotide as described herein. In some embodiments, the composition includes 25 nM of the saRNA or polynucleotide as described herein. In some embodiments, the composition may contain 0.001-150 nM (e.g., 0.01-100 nM, 0.1-50 nM, 1-150 nM, 1-20 nM, 0.001-1 nM, 1-10 nM, 10-100 nM, 10-50 nM, 20-50 nM, 20-100 nM) of the saRNA or polynucleotide as described herein.
[0101] In some embodiments, the composition includes 25 nM of the saRNA or polynucleotide as described herein.Methods of using saRNA
[0102] Another aspect of the present application relates to a method of using saRNA for activating / up-regulating the p21 gene expression. The saRNA activates / up-regulates the expression of the p21 gene, such as by at least 10% (e.g., at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 300%, at least 500%, at least 800%, at least 1000%, at least 2000%, or at least 5000%as compared to baseline expression of the p21 gene) . In certain embodiments, the expression of p21 gene is activated / up-regulated by administering the saRNA disclosed in the embodiments to a cell at a concentration of at least 0.01 nM, e.g., 0.02 nM, 0.05 nM, 0.08 nM, 0.1 nM, 0.2 nM, 0.3 nM, 0.4 nM, 0.5 nM, 0.6 nM, 0.8 nM, 1 nM, 5 nM, 10 nM, 25 nM, 50 nM, 75 nM, 100 nM, 150 nM, 200 nM, 400 nM, 800 nM, 1000 nM, or 1600 nM. In certain embodiments, the induction of p21 protein is activated / up-regulated by administering the saRNA disclosed in the embodiments to a cell at a concentration of at least 0.01 nM, e.g., 0.02 nM, 0.05 nM, 0.08 nM, 0.1 nM, 0.2 nM, 0.3 nM, 0.4 nM, 0.5 nM, 0.6 nM, 0.8 nM, 1 nM, 2 nM, 3 nM, 4nM, 5 nM, 10 nM, 25 nM, 50 nM, 75 nM, 100 nM, or 150 nM.
[0103] Another aspect of the present application relates to a method for preventing or treating p21-related disorder or condition, such as NMIBC, comprising administering an effective amount of the saRNA, the nucleic acid or polynucleotide encoding the saRNA, or the composition comprising the saRNA disclosed herein to the individual. In certain embodiments, the effective amount of the saRNA disclosed herein can be a concentration ranging from 0.001 nM to 10000 nM, e.g., 0.001 nM, 0.005 nM, 0.01 nM, 0.02 nM, 0.05 nM, 0.08 nM, 0.1 nM, 0.2 nM, 0.3 nM, 0.4 nM, 0.5 nM, 0.6 nM, 0.8 nM, 1 nM, 5 nM, 10 nM, 25 nM, 50 nM, 75 nM, 100 nM, 150 nM, 200 nM, 400 nM, 800 nM, 1000 nM, 1600 nM, 3000 nM, 5000 nM, 8000 nM, or 10000 nM. In certain embodiments, the effective amount of the saRNA disclosed herein can be a concentration ranging from 0.01 nM to 150 nM, e.g., 0.01 nM, 0.02 nM, 0.05 nM, 0.08 nM, 0.1 nM, 0.2 nM, 0.3 nM, 0.4 nM, 0.5 nM, 0.6 nM, 0.8 nM, 1 nM, 5 nM, 10 nM, 25 nM, 50 nM, 75 nM, 100 nM, or 150 nM. In some embodiments, the disorder or condition is NMIBC. In some embodiments, the individual is a mammal. In some embodiments, the individual is a human.
[0104] In any of the embodiments provided herein, such saRNA, nucleic acids encoding the saRNA of the present application, or compositions comprising such saRNA of the present application may be introduced directly into a cell, or may be produced intracellularly upon introduction of a nucleotide sequence encoding the saRNA into a cell, for example a mammalian cell including or a human cell. Such cells may be ex vivo, such as cell lines, and the like, or may be present in mammalian bodies, such as humans. In certain embodiments, a nucleic acid or a polynucleotide encoding a saRNA or a composition comprising the aforementioned saRNA as described herein, in respective amounts sufficient to treat NMIBC.
[0105] Another aspect of the present application relates administering an effective amount of the saRNA or the composition to an individual using administration pathway as described herein. In some embodiments, the administration pathway is selected from one or more of: intravesical instillation, parenteral infusions, vaginal administration, and rectal administration.
[0106] In certain embodiments, pharmaceutical compositions comprise one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes and / or coated with a tissue-specific antibody.
[0107] A typical formulation of the oligonucleotide modulator in the present application is prepared by mixing a saRNA of the present application and a carrier or excipient. Suitable carriers and excipients are well known to those skilled in the art and are described in detail in, e.g., Ansel H. C. et al., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems (2004) Lippincott, Williams &Wilkins, Philadelphia; Gennaro A. R. et al., Remington: The Science and Practice of Pharmacy (2000) Lippincott, Williams &Wilkins, Philadelphia; and Rowe R. C, Handbook of Pharmaceutical Excipients (2005) Pharmaceutical Press, Chicago. The formulations may also include one or more buffers, stabilizing agents, surfactants, wetting agents, lubricating agents, emulsifiers, suspending agents, preservatives, antioxidants, opaquing agents, glidants, processing aids, colorants, sweeteners, perfuming agents, flavoring agents, diluents and other known additives to provide an elegant presentation of the drug (i.e., a double-stranded oligonucleotide of the present application or pharmaceutical composition thereof) or aid in the manufacturing of the pharmaceutical product (i.e., medicament) .Method of treatment
[0108] Another aspect of the present application relates to the oligonucleotide agents of the present application being used in therapeutic approaches to treating NMIBC.
[0109] By non-limiting embodiments, the present application provides a method of increasing the expression level of p21 gene, comprising administering to a subject a pharmaceutical composition disclosed herein. In some embodiments, the present application relates to a method for treating or delaying the onset or progression of NMIBC in a subject, the method comprising: administering to the subject a pharmaceutical composition disclosed herein. In some embodiments, the subject has NMIBC. In some embodiments, the subject has BCG-failure NMIBC.
[0110] In some embodiments, the conjugation moiety attached to the saRNA (such as C5x5) in the pharmaceutical composition improves the stability, bioavailability, biodistribution, and / or cellular uptake of the saRNA as compared to an oligonucleotide agent without the conjugation moiety. In some embodiments, the conjugation moiety of the oligonucleotide agent increases the biodistribution of saRNA within one or more target tissues (such as papillary and CIS of NMIBC, urothelium, lamina propria, muscle, fat and peritoneum of the bladder, and the ureter) as compared to an oligonucleotide agent without the conjugation moiety. In some embodiments, the conjugation moiety of the oligonucleotide agent increases the biodistribution of saRNA within two or more target tissues as compared to an oligonucleotide agent without the conjugation moiety.
[0111] Specifically, the method and oligonucleotide agent of the present application activate / up-regulate the p21 mRNA transcript by at least 10% (e.g., at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or about 100%as compared to baseline p21 mRNA transcript) . In some embodiments, upon administering the oligonucleotide agent disclosed in the embodiments, e.g., to a cell or a subject, the p21 mRNA transcript is activated / upregulated by at least 50%, 60%, 70%, 77%, 79%, 81%, 84%, 85%, and 88%at about 10 nM treatment compared to baseline p21 mRNA transcript in control group) in an in vitro cell line. In some embodiments, an oligonucleotide agent activates or upregulates the p21 mRNA transcript by over 50%. In some embodiments, the change in the p21 mRNA transcript is measured by an in vitro activation assay. In particular, in the in vitro activation assay, KU-7 cells or T24 cells are transfected with the saRNA agent at a saRNA concentration of 0.0025, 0.005, 0.01, 0.04, 0.16, 0.64, 2.56, 5.12 and 10.24 nM for 48 hours, the p21 mRNA levels in the cells are measured, and the percentage changes of the p21 mRNA levels after treatment are calculated comparing to the baseline level of p21 mRNA in untreated cells to assess the function or activity of the saRNA agent in activating / upregulating p21 mRNA.
[0112] In some embodiments, the oligonucleotide agents disclosed in the embodiments have a dose-dependent treatment effect. In some embodiments, the oligonucleotide agent increases the p21 mRNA transcript in cells with an IC50 of less than 10 nM, 5 nM, 4 nM, 3 nM, 2 nM, 1 nM, 0.8 nM, 0.6 nM, 0.5 nM, 0.4 nM, 0.3 nM, 0.2 nM 0.1 nM, 0.08 nM, 0.06 nM, 0.04 nM, 0.02 nM, 0.01 nM, 0.008 nM, or 0.005 nM.
[0113] In any of the embodiments provided herein, such cells may be ex vivo, such as cell lines, and the like, or may be present in mammalian bodies, such as humans.
[0114] Another aspect of the present application relates administering an effective amount of the oligonucleotide agent or the composition to an individual using administration pathway as described herein. In some embodiments, the administration pathway is selected from one or more of: intravesical instillation, parenteral infusions, vaginal administration, and rectal administration.Dose regiments and route of administration
[0115] Aspects of the present application relate to a pharmaceutical composition comprising the oligonucleotide agent of the present application and a method for treatment of NMIBC by administering the same. In some embodiments, the pharmaceutical composition comprises the oligonucleotide agent of the present application and a pharmaceutically acceptable carrier, a therapeutically inert carrier, diluent or pharmaceutically acceptable excipient. The pharmaceutical composition disclosed herein is to be developed into a medicament for preventing or treating NMIBC.
[0116] Aspects of the present application also relate to methods of treating NMIBC by administering the oligonucleotide agents or any product of the present application. Another aspect of the present application relates to use of the oligonucleotide agent of the present application in manufacturing the pharmaceutical composition for treating NMIBC disclosed herein.
[0117] The dosage at which the oligonucleotide agents or compositions of the present application can be administered can vary within wide limits and will be fitted to the individual requirements in each case. In some embodiments, the oligonucleotide agent according to the present application is administered at a low starting dose and then at gradually increased dose (s) until reaching a maximum tolerant dose. In some embodiments, the oligonucleotide agent according to the present application is administered at a high loading / starting dose which not exceeding the MTD and then at gradually increased dose (s) until reaching a maximum tolerant dose.
[0118] In some embodiments, the single dose is administered to the subject once per week for at least 3 weeks, such as at least 6 weeks. In certain embodiments, the single dose in one week is the same amount as the single dose administered in a different week. In various embodiments, first single dose is administered for 6 weeks, followed by administration of a second single dose for the next at least 3 weeks, wherein the first single dose and the second single dose are different. In certain such embodiments, the second single dose is greater than the first single dose. In other embodiments, the second single dose is less than the first single dose.
[0119] During the treatment, more than one treatment periods can be applied to the subject according to the need in practice. For example, the treatment may comprise an initial treatment course, a second treatment course, or even a third treatment course or more, each may last for 3 weeks, 6 weeks, 12 weeks, 24 weeks, 36 weeks, 48 weeks or even longer. In a typical embodiment, the treatment comprises a dose-quantity-fixed multiple dose treatment course without the initial treatment course. Each of the multiple dose treatment courses may independently last for 3 weeks, 6 weeks, 12 weeks, 24 weeks, 36 weeks, 48 weeks or even longer.
[0120] The single dose of the oligonucleotide agent can be a single dose to a subject (e.g., a patient suffering from NMIBC) ranging from 10 mg / dose to a saturated solution of the saRNA or the oligonucleotide agent of the present application, for example, about 10, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 450, 500, 550, or 600 mg / dose. The doses described herein may contain two or more of any of the oligonucleotide agent sequences described herein.
[0121] The single dose of the oligonucleotide agent can be a single dose to a subject (e.g., a patient suffering from NMIBC) ranging from 30 mg to 600 mg, for example, about 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 450, 500, 550, 600 mg oligonucleotide agent per dose or any subrange or points. The doses described herein may contain two or more of any of the oligonucleotide agent sequences described herein.
[0122] The multiple dose treatment with the oligonucleotide agent can be a fixed dose to a subject (e.g., a patient suffering from NMIBC) ranging from 10 mg / dose to a saturated solution of the saRNA or the oligonucleotide agent of the present application, for example, about 10, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 450, 500, 550, or 600 mg / dose. The doses described herein may contain two or more of any of the oligonucleotide agent sequences described herein.
[0123] The multiple dose treatment with the oligonucleotide agent can be a escalated dose regime or a dose-fixed regime to a subject (e.g., a patient suffering from NMIBC) ranging from 30 mg to 600 mg, for example, about 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 450, 500, 550, 600 mg oligonucleotide agent per dose or any subrange or points. The doses described herein may contain two or more of any of the oligonucleotide agent sequences described herein.
[0124] In some embodiments, the oligonucleotide agent is administered at fixed intervals or unequaled intervals, such as once 7 days, once 14 days, once 21 days, once 28 days, once 35 days, once 42 days, once 56 days, once a week, once two weeks, once three weeks, once 1 month, once 2 months, once 3 months, once 4 months, once 5 months or once 6 months, or any combinations thereof.
[0125] To facilitate the administration, doses of the oligonucleotide agent are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder, or water-free concentrate, in a hermetically sealed container, such as an ampoule or sachet, indicating the quantity of active agent.
[0126] In some embodiments, the proposed dose frequency is approximate and may be adjusted according to need. For example, in some embodiments, if the proposed dose frequency is a dose on Day 1 and a second dose at Day 15, an NMIBC patient may receive a second dose 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 days after receipt of the first dose. In some embodiments, the dose and / or the volume of the injection will be adjusted based on the subject's age, the subject's body weight, and / or other factors that may require adjustment of the parameters of the injection. In some embodiments, the volume of the injection can range from 30 to 150 mL, such as 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150 mL, particularly, 50 mL as commonly used in intravesical instillations.
[0127] Examples of other compositions or components associated with the oligonucleotide agent, compositions, pharmaceutical compositions, and methods described herein include, but are not limited to:diluents, salts, buffers, chelating agents, preservatives, drying agents, antimicrobics, needles, syringes, packaging materials, tubes, bottles, flasks, beakers, and the like, for example, for using, modifying, assembling, storing, packaging, preparing, mixing, diluting, and / or preserving the components for a particular use. In embodiments where liquid forms of any of the components are used, the liquid form may be concentrated or ready-to-use.
[0128] In some embodiments, lipid moieties used in nucleic acid therapies can be applied in the present application for delivery of the oligonucleotide agent molecules disclosed herein. In such methods, the nucleic acid (e.g., one or more oligonucleotide agents described herein) may be introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, oligonucleotide agent complexes with mono-or poly-cationic lipids are formed without the presence of a neutral lipid. In some embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In some embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In some embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.
[0129] In some embodiments, pharmaceutical compositions comprise a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In some embodiments, certain organic solvents such as dimethylsulfoxide are used.
[0130] In some embodiments, pharmaceutical compositions comprise one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present application to specific tissues or cell types.
[0131] Preparations, pharmaceutical compositions, or medicaments of the present disclosure are formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual subject, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners.
[0132] A typical formulation of the oligonucleotide modulator in the present disclosure is prepared by mixing a saRNA of the present disclosure and a carrier or excipient. Suitable carriers and excipients are well known to those skilled in the art and are described in detail in, e.g., Ansel H. C. et al., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems (2004) Lippincott, Williams &Wilkins, Philadelphia; Gennaro A. R. et al., Remington: The Science and Practice of Pharmacy (2000) Lippincott, Williams &Wilkins, Philadelphia; and Rowe R. C, Handbook of Pharmaceutical Excipients (2005) Pharmaceutical Press, Chicago. The formulations may NMIBC include one or more buffers, stabilizing agents, surfactants, wetting agents, lubricating agents, emulsifiers, suspending agents, preservatives, antioxidants, opaquing agents, glidants, processing aids, colorants, sweeteners, perfuming agents, flavoring agents, diluents and other known additives to provide an elegant presentation of the drug (i.e., a saRNA of the present disclosure or pharmaceutical composition thereof) or aid in the manufacturing of the pharmaceutical product (i.e., medicament) .
[0133] In some embodiments, the subject suffering from NMIBC to be treated with the method, administration routes and / or the regimens disclosed herein is a mammal, such as a human, a non-human, such as a primate, a livestock or a pet. In some embodiments, the subject is suffering from BCG-failure NMIBC. In some embodiments, the subject suffering from NMIBC has a p21 mutant characterized in one or more mutations in p21 gene which lead to the NMIBC. In some embodiments, the subject suffering from NMIBC does not have any mutation in p21 gene or is not caused by p21 gene mutation (s) .Pharmaceutical composition and Kits
[0134] Another aspect of the present application relates to a pharmaceutical composition comprising the saRNA or oligonucleotide agent of the present application. In some embodiments, the pharmaceutical composition comprising the saRNA or oligonucleotide agent and, at least one pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprises from about 30 mg to about 600 mg of the oligonucleotide agent, such as comprises about 30 mg, 100 mg, 300 mg or about 600 mg of the oligonucleotide agent.
[0135] Another aspect of the present application relates to a kit for performing the method for increasing a level of p21 protein in a cell or a level of functional p21 protein, comprising the saRNA or oligonucleotide agent disclosed herein. In certain embodiments, the kit further comprises means for administering said saRNA to an individual. In certain embodiments, the kit is in a labeled package and the label on said package indicates that the saRNA or the composition can be used in preventing or treating p21-related disease or condition or disorder, such as NMIBC.
[0136] A "kit" as used herein, typically defines a package, assembly, or container (such as an insulated container) including one or more of the components or embodiments of the application, and / or other components associated with the application, for example, as previously described. Any of the agents or components of the kit may be provided in liquid form (e.g., in solution) , or in solid form (e.g., a dried powder, lyophilized powder, etc. ) .
[0137] A kit may comprise the pharmaceutical composition of the present application in unit dose form. As used herein, the term “unit dose” or “dosage unit” refers to a unit of pharmaceutical composition comprising the active ingredient (i.e., the saRNA or oligonucleotide agent) in an amount suitable and sufficient for producing a therapeutic effect in a single dosing. The kit may conveniently be presented in unit dose form for dispatching and use. In some embodiments, the kit comprises more than one unit dose sufficient for a course of treatment. In some embodiments, the kit comprises 3 to 72 dosage units, 3, 12, 16, 18, 24, 36, 48, or 72 dosage units. In some embodiments, the kit comprises dosage units sufficient for once per week treatment for at least 3 weeks, such as for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks. In some embodiments, each unit dose independently comprises 30-600 mg of the oligonucleotide agent, such as 30 mg, 100 mg, 300 mg or 600 of the oligonucleotide agent.Particular embodiments
[0138] The present application provides the following particular embodiments: 1. A method for the treatment of non-muscle invasive bladder cancer (NMIBC) in a subject in need thereof, wherein the method comprises the step of administering the subject a therapeutically effective amount of an oligonucleotide agent or a medicament comprising the oligonucleotide agent, wherein the oligonucleotide agent comprises (i) a small activating RNA (saRNA) targeting a selected region of p21 gene having a sequence of any one of SEQ ID NOs: 11-18 and capable of upregulating the expression of p21 gene; and (ii) a conjugation moiety that is covalently tethered to the saRNA to deliver the saRNA in the body of a subject. 2. The method of embodiment 1, wherein the saRNA comprises a sense strand and an antisense strand forming a double stranded structure which comprises 0, 1, 2 or 3 mismatches; and / or wherein the antisense strand comprises a region of complementarity to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of p21 gene; and / or wherein the sense strand comprises a region of homology to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of p21 gene; and / or wherein the length of the sense strand and the antisense strand is independently about 16-25 nucleotides, preferably 18-24 nucleotides, more preferably 20-23, such as 20, 21, 22 or 23 nucleotides. 3. The method of embodiment 1 or 2, wherein the sense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 1 or 3; and / or the antisense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 2; and / or wherein the sense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 1 and the antisense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 2; or the sense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 3 and the antisense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 2. 4. The method of any one of embodiments 1-3, wherein the conjugation moiety is selected from a lipid, an oligonucleotide, a fluorophore, a ligand, a saccharide, a peptide, and an antibody; and / or wherein the lipid comprises at least one C4-30 fatty acid, having a saturated or unsaturated, linear or branched C4-30, C10-24, C12-22, C14-20, or C16-18 carbon chain; and / or wherein the lipid comprises a carbon chain of 16, 18, 20 or 22 carbon atoms; and / or 5. The method of any one of embodiments 1-4, wherein the conjugation moiety is derived from a lipid compound C5x5: and / or wherein the conjugation group comprises *-C5x5: wherein *represents the site where the conjugation group is attached to the strand, either directly or via a linking moiety; and / or wherein the saRNA conjugated with C5x5 is saRNA-C5x5: 6. The method any one of embodiments 1-5, wherein the conjugation moiety is conjugated to the sense strand or the antisense strand of the saRNA directly or indirectly via a linking component; and / or the conjugation moiety is conjugated to the 5’ end and / or 3’ end and / or the internal nucleotide (s) of the sense strand or the antisense strand of the saRNA; and / or wherein at least one nucleotide, such as at least 50%, at least 60%, at least 70%, at least 80%, at least 90%or all the nucleotides of the sense strand and / or the antisense strand of the saRNA are chemically modified nucleotides, for example, one or more nucleotide are modified by 2’ -fluoro; and / or wherein at least one backbone bond, such as at least 50%, at least 60%, at least 70%, at least 80%, at least 90%or all the backbone bonds of the saRNA are selected from the group consisting of PS,mesyl phosphoramidate andboranophosphate bond. 7. The method of embodiment 6, wherein the linking component is one or more selected from the group consisting of ethylene glycol chain, an alkyl chain, an alkenyl chain, an alkynyl chain, a peptide, RNA, DNA, carbohydrates, thiol linkage, a phosphodiester, a PS, a phosphoramidate, an amide, a carbamate, a tetrazole linkage, and a benzimidazole linkage; and / or wherein the linking component is one or more selected from the group consisting of: a) Spacer phosphoramidite 18: 1, 1-bis (4-methoxyphenyl) -1-phenyl-2, 5, 8, 11, 14, 17-hexaoxanonadecan-19-yl 2-cyanoethyl N, N-diisopropylphosphoramidite; b) Spacer-9: 3- [2- [2- [2- [bis (4-methoxyphenyl) -phenylmethoxy] ethoxy] ethoxy] ethoxy- [di (propan-2-yl) amino] phosphanyl] oxypropanenitrile; c) Spacer phosphoramidite C3: 6- (4, 4'-Dimethoxytrityl) hexyl-1- [ (2-cyanoethyl) - (N, N-diisopropyl) ] -phosphoramidite; d) Spacer-C6 Phosphoramidite: 6- (4, 4'-Dimethoxytrityl) hexyl-1- [ (2-cyanoethyl) - (N, N-diisopropyl) ] -phosphoramidite; and e) Divalent linker (DIO) : 16- ( (bis (4-methoxyphenyl) (phenyl) methoxy) methyl) -1, 1-bis (4-methoxyphenyl) -18-oxo-1-phenyl-2, 5, 8, 11, 14, 17-hexaoxahenicosan-CPG. 8. The method of embodiment 6 or 7, wherein the chemical modification of the at least one chemically modified nucleotide is independently selected from the group consisting of: a 2’ sugar modification, preferably a 2’ sugar modification selected from one or more of: 2’ -fluoro-2’ -deoxynucleoside (2’ -F) modification, 2’ -O-methyl (2’ -O-Me) , modification, and 2’ -O- (2-methoxyethyl) (2’ -O-MOE) modification; a base modification; a PS backbone modification, such as 6 to 17 PS backbone modifications; an addition of an (E) -vinylphosphonate moiety at the 5’ end of the nucleotide sequence, such as at the 5’ end of the antisense strand; and an addition of a 5-methyl cytosine moiety at the 5’ end of the nucleotide sequence. 9. The method any one of embodiments 1-8, wherein the oligonucleotide agent comprises a sense strand has a nucleotide sequence of SEQ ID NO: 1 and an antisense strand has a nucleotide sequence of SEQ ID NO: 2; or the oligonucleotide agent comprises a sense strand has a nucleotide sequence of SEQ ID NO: 3 and an antisense strand has a nucleotide sequence of SEQ ID NO: 2. 10. The method any one of embodiments 1-9, wherein the subject is a mammal, such as a human, a non-human primate, a livestock or a pet; and / or wherein the subject suffering from NMIBC has one or more mutations in the p21 gene which lead to the NMIBC; or, wherein the subject suffering from NMIBC does not comprise any mutation in p21 gene or is not caused by p21 gene mutation (s) ; and / or wherein the subject is a patient with NMIBC who has failed Bacillus Calmette Guérin (BCG) therapy (BCG-failed NMIBC) . 11. The method of any one of embodiments 1-10, wherein the subject: (a) has NMIBC at a stage up to T1, including papillary Ta, papillary T1, or CIS, or CIS with papillary tumor; and / or (b) has BCG-failed NMIBC, wherein the BCG-failed NMIBC is selected from the group consisting of BCG-unresponsive, BCG-exposed, BCG-intolerant, BCG-resistant, BCG-refractory, and BCG-relapsing. 12. The method of any one of embodiments 1-11, wherein the administration of the oligonucleotide agent, as compared to without the administration, is capable of: (a) increasing the disease-free rate and disease-free survival in papillary-only NMIBC patients; and / or (b) improving the complete response rate and duration of complete responses in NMIBC patients for CIS; and / or (c) prolonging the overall survival of NMIBC patients; and / or (d) reducing the time to MIBC progression; and / or (e) avoiding cystectomy after BCG-unresponsive; and / or (f) upregulating the expression of the p21 gene, as evidenced by an increase in p21 mRNA levels of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%compared to baseline. 13. The method of any one of embodiments 1-12, wherein the oligonucleotide agent is administered in a dose of 30-600 mg per dose, such as 30-300 mg per dose, 30-100 mg per dose, 100-300 mg per dose, 100-600 mg per dose, 300-600 mg per dose, 30 mg per dose, 100 mg per dose, 300 mg per dose and 600 mg per dose; and / or wherein the oligonucleotide agent is administered at fixed interval or unequaled interval, such as once 7 days, once 14 days, once 28 days, once 35 days, once 42 days, once 56 days, once a week, once two weeks, once three weeks, once 1 month, once 2 months, once 3 months, once 4 months, once 5 months or once 6 months, or any combinations thereof; and / or wherein the oligonucleotide agent is administered for 3-6 weeks, 3-12 weeks, 3-18 weeks, 3-24 weeks, 3-36 weeks, 3-48 weeks, 3-72 weeks per treatment course, such as for 3, 6, 9, 12, 15, 18, 24, 36, 48 or 72 weeks per treatment course. 14. The method of any one of embodiments 1-13, wherein the method comprises the steps of: administering the subject a starting single dose of the oligonucleotide agent; administering the subject one or more escalated doses of the oligonucleotide agent until reaching a maximum tolerated dose (MTD) ; administering the subject one or more sustaining doses of the oligonucleotide agent at the MTD or at a dose between the starting dose and the MTD, preferably an optimal dose; optionally, the method is used in determining the subject-tailored dosage regimen. 15. The method of embodiment 14, wherein the starting dose of the oligonucleotide agent is about 30-300 mg per dose, such as about 30 mg per dose, about 100 mg per dose or about 300 mg per dose; and / or the escalated dosage reaches to about 300-600 mg per dose; and / or the escalated dose of the oligonucleotide agent is administered once a week, once every two weeks, or once every three weeks; and / or, the sustaining dose of the oligonucleotide agent is administered once a week, once every two weeks, or once every three weeks. 16. The method of any one of embodiments 1-15, wherein oligonucleotide agent is in a form of solution, powder, suspension, spray, or gel; and / or wherein the oligonucleotide agent is solved in a pharmaceutically acceptable carrier, such as in saline, PBS, Ringer’s buffer, or water for injection. 17. The method of any one of embodiments 1-16, wherein the administration pathway is one or more selected from the group consisting of: intravesical instillation, parenteral infusions, vaginal administration, and rectal administration. 18. The method of any one of embodiments 1-16, wherein the oligonucleotide agent comprises a saRNA comprising a sense strand of SEQ ID NO: 1 and an antisense strand of SEQ ID NO: 2, or a saRNA comprising a sense strand of SEQ ID NO: 3 and an antisense strand of SEQ ID NO: 2, optionally in a powder form or solved in a pharmaceutically acceptable carrier (such as in saline) ; wherein the subject is a patient with BCG-failure NMIBC papillary, and / or CIS in phase Ta, T1 or Tis; wherein the oligonucleotide agent is administered to the subject once a week, once two weeks, once three weeks in a dose of 30 mg per dose, 100 mg per dose, 300 mg per dose or 600 mg per dose; and / or wherein the course of treatment lasts for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks per treatment course. 19. A product for use in the treatment of NMIBC by the method of any one of embodiments 1-18. 20. Use of an oligonucleotide agent in the preparation of a medicament for the treatment of NMIBC by the method of any one of embodiments 1-18. 21. A pharmaceutical composition comprising the oligonucleotide agent or medicament in any one of embodiments 1-9, and, at least one pharmaceutically acceptable carrier, wherein the pharmaceutical composition comprises from about 30 mg to about 600 mg of the oligonucleotide agent. 22. The pharmaceutical composition of embodiment 21, wherein the pharmaceutical composition comprises about 30 mg, 100 mg, 300 mg or about 600 mg of the oligonucleotide agent; and / or wherein the pharmaceutically acceptable carrier is saline, PBS, Ringer’s buffer, or water for injection. 23. The pharmaceutical composition of embodiment 21 or 22, wherein the pharmaceutical composition is in a form for intravesical instillation, parenteral infusions, vaginal administration, and rectal administration. 24. A kit comprising one or more pharmaceutical compositions of any one or embodiments 21-23 in dosage unit form. 25. The kit of embodiment 24, wherein the amount of the dosage units in the kit is sufficient for a course of treatment; and / or wherein the kit comprises 3 to 72 dosage units, 3, 12, 16, 18, 24, 36, 48, or 72 dosage units; and / or wherein the kit comprises dosage units sufficient for once per week treatment for at least 3 weeks, such as for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks; and / or wherein each dosage unit independently comprises 30-600 mg of the oligonucleotide agent, such as 30 mg, 100 mg, 300 mg or 600 of the oligonucleotide agent.EXAMPLES
[0139] The following examples are set forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc. ) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair (s) ; kb, kilobase (s) ; pl, picoliter (s) ; s or sec, second (s) ; min, minute (s) ; h or hr, hour (s) ; aa, amino acid (s) ; nt, nucleotide (s) ; i. m., intramuscular (ly) ; i. p., intraperitoneal (ly) ; s. c., subcutaneous (ly) ; i. c. v. or ICV, intracerebroventricular and the like. Example 1. Preparation of compound C5x5
[0140] Compound C5x5 was prepared in this Example by using the following procedures. 1) The preparation of compound 3
[0141] To a solution of methyl methyl 2- (4-fluoro-3-nitrophenyl) acetate compound 2 (17.3 g, 81 mmol, 1.0 eq) and K2CO3 (11.2 g, 81 mmol) in anhydrous DMF (200 mL) , under nitrogen atmosphere, was added compound 1 (19.56 g, 81 mmol, 1.0 eq) . The reaction mixture was stirred at 55 ℃ for 6 h, and then cold water (100 mL) was added. The mixture was extracted three times by ethyl acetate, and then the organic phase was washed three times by saturated LiCl solution and one time by brine and then dried by anhydrous Na2SO4 and concentrated under reduced pressure to form yellow oil compound 3 which was directly used in the next step without further purification. 2) The preparation of compound 4
[0142] To a solution of compound 3 (35.18 g, 81 mmol, 1.0 eq) in THF / H2O (9: 1, 280 mL) , under ice bath, was added HCOONH4 (30.67 g, 486 mmol, 6.0 eq) and Zn powder (31.78 g, 486 mmol, 6.0 eq) . After 10 minutes, the reaction mixture was moved to room temperature and stirred overnight. Then, the reaction mixture was filtered and concentrated under reduced pressure. After that, water (200 mL) was added into the mixture, and then extracted three times by ethyl acetate, the organic phase was washed one time by brine. After dried by anhydrous Na2SO4 and concentrated under reduced pressure, the compound 4 was formed and then was directly used in the next step without further purification. The compound 4 was characterized with mass spectrometry. MW calc. : 404.34; MW. Found: 405.3 [M+H] +. 3) The preparation of compound 6
[0143] To a solution of compound 4 (19.36 g, 48 mmol, 1.0 eq) in EtOH (200 mL) under nitrogen atmosphere, was added 3- ( (tert-butyldimethylsilyl) oxy) propanal compound 5 (9.0 g, 48 mmol, 1.0 eq) and AcOH (11 mL, 192 mmol, 4.0 eq) . The reaction mixture was stirred at 80℃ overnight, and then concentrated under reduced pressure. Then, a saturated NaHCO3 solution (100 mL) was added, the mixture was extracted three times by ethyl acetate, then the organic phase was combined and washed by brine, dried over Na2SO4, and concentrated. The resultant residue compound 6 was directly used in the next step without further purification. 4) The preparation of compound 7
[0144] To a solution of compound 6 (10 g, 17.5 mmol, 1.0 eq) in anhydrous THF (50 mL) under nitrogen atmosphere, was added 1 M TBAF THF solution (26.3 mL, 26.3 mmol, 1.5 eq) . The reaction mixture was stirred at room temperature for 1 h, and then concentrated under reduced pressure. Then, water (100 mL) was added, the mixture was extracted three times with DCM, then the organic phase was combined and washed with brine, dried over Na2SO4, and concentrated. The resultant residue was dissolved in 50 mL pyridine, and DMTrCl (7.12 g, 21 mmol, 1.2 eq) was added therein. The reaction mixture was stirred at room temperature for 6 h, after which it was concentrated under reduced pressure. The resultant residue was purified with flash chromatography (silica gel, gradient eluent: 1-3%of MeOH / DCM) to provide compound 7 (8.1 g, 61%yield) as yellow solid. The product was characterized with mass spectrometry and 1H NMR. MW calc. : 760.48; MW. Found: 761.8 [M + H] +. 1H NMR (400 MHz, CDCl3) δ 7.59 –7.53 (m, 1H) , 7.38 –7.31 (m, 2H) , 7.23 -7.19 (m, 6H) , 7.18 –7.14 (m, 3H) , 6.76 (dd, J = 7.8, 5.6 Hz, 4H) , 4.17 –4.02 (m, 2H) , 3.76 (s, 6H) , 3.73 (s, 2H) , 3.67 (s, 3H) , 3.59 (t, J = 7.0 Hz, 2H) , 3.19 –3.05 (m, 2H) , 1.29 –1.25 (m, 28H) , 0.88 (t, J = 6.5 Hz, 3H) . 5) The preparation of compound C5x5
[0145] To a solution of compound 7 (2.7 g, 3.55 mmol, 1.0 eq) in anhydrous THF (20 mL) under nitrogen atmosphere and ice bath, was added LiAlH4 (202 mg, 5.33 mmol, 1.5 eq) . The mixture was moved to room temperature after 10 minutes and stirred for 1 h. Then the reaction was moved to ice bath, saturated potassium sodium tartrate solution (20 mL) was added slowly into the mixture. After 30 minutes, the reaction was extracted three times with Et2O, then the organic phase was combined and washed by brine, dried over Na2SO4, and concentrated. The crude product (300 mg, 0.41 mmol, 1.0 eq) was dissolved in anhydrous DCM (5 mL) then DIPEA (204 μL, 1.23 mmol, 3.0 eq) , 3-( (chloro (diisopropylamino) phosphanyl) oxy) propanenitrile (274 μL, 1.23 mmol, 3.0 eq. ) were added under nitrogen atmosphere at 25℃. The reaction mixture was stirred for 1 h. The mixture was extracted two times with DCM, then washed with brine and dried with anhydrous Na2SO4. The organic layer was concentrated under reduced pressure and the resultant residue was purified with flash chromatography (silica gel, gradient eluent: 1-5%of MeOH / DCM, 1%Et3N) to provide compound C5x5 (299 mg, 78%yield) as colorless oil. The product was characterized with mass spectrometry and 1H NMR. 1H NMR (400 MHz, CDCl3) δ 7.62 (s, 1H) , 7.32 (dd, J = 7.6, 4.1 Hz, 2H) , 7.27 –7.11 (m, 9H) , 6.73 (dd, J = 7.9, 5.6 Hz, 4H) , 4.34 –4.31 (m, 2H) , 4.10 –4.06 (m, 2H) , 3.75 (s, 6H) , 3.64 –3.61 (m, 2H) , 3.58 (dd, J =11.8, 5.1 Hz, 2H) , 3.24 –3.18 (m, 2H) , 3.09 –2.88 (m, 4H) , 2.65 –2.55 (m, 4H) , 1.37 –1.28 (m, 28H) , 1.22 (dd, J = 6.8, 3.2 Hz, 12H) , 0.88 (t, J = 6.5 Hz, 3H) . Example 2. Preparation of conjugated saRNA linked with the conjugation group derived from compound C5x5
[0146] saRNA conjugate with C5x5 was generated by using a conjugation group derived from the compound C5x5 as terminus amidite according to the methods of saRNA synthesis in “oligonucleotide synthesis” section.
[0147] Exemplary structure of the lipid-conjugated oligonucleotide is C5x5-saRNA as illustrated below:
[0148] It can be seen that in the structures of C5x5-saRNA, the conjugation derived from the delivery enhancing compound C5x5 is linked with saRNA duplexes at the 5’ -end of the sense strand (S) via a linking moiety, such as –OP (O) 2O-, –OP (O) (S) O-or –P (O) -O-, wherein (S) is the sense strand and (AS) is the antisense strand. Example 3. Design and synthesis of saRNAs targeting human p21 promoter
[0149] All oligonucleotides were synthesized as described in the “Materials and Methods” section. Lyophilized oligonucleotides are stored at -20℃ and shipped via a continuous -20℃ cold chain. Oligonucleotide sequences used for cell, animal or human treatments in the following examples are listed in Table 1. Table 1. Oligonucleotide sequences and duplex compositions Note: *, phosphorothioate (PS) backbone modification; f, 2'-fluoro; C5x5, as described in Examples 1-2 of the present application. Example 4. In vitro activity of saRNA and saRNA-C5x5 in inducing p21 mRNA expression in KU-7 and T24 cells
[0150] To assess in vitro activity of saRNA and saRNA-C5x5 in inducing p21 mRNA expression, the indicated saRNA (i.e., RD-10773) and saRNA-C5x5 (i.e., RD-13520) were transfected into KU-7 and T24 cells at the indicated concentrations (i.e., 0.0025, 0.005, 0.01, 0.04, 0.16, 0.64, 2.56, 5.12 and 10.24 nM) for 2 days. Cells transfected in the absence of any oligonucleotide were used as Mock treatment (not shown) . FIG. 1A and FIG. 1B show the p21 mRNA levels as quantified by two step RT-qPCR in KU-7 and T24 cells, respectively. p21 mRNA levels and half-maximal effective concentration (EC50) values are summarized in Table 2. The results indicate that saRNA-C5x5 can be successfully delivered into the cells, effectively induce p21 mRNA expression, and activate p21 mRNA maximal expression in the cells by more than 4.0-fold as compared to baseline expression (Mock) . Table 2. p21 mRNA levels and EC50 values following saRNA and saRNA-C5x5 treatments in KU-7 and T24 cells Note: SEM represents Standard Error of the Mean. Example 5. Tissue and plasma accumulation of RD-13520 in female C57BL / 6J mice following IVB instillation
[0151] To evaluate the tissue and plasma accumulation of RD-13520, female C57BL / 6J mice were administered with a single dose of RD-13520 at the indicated doses (i.e., 0.3, 1 or 3 mg) via IVB instillation. The mice were sacrificed at 2, 6, or 12 hours, and on Days 1, 4, 7, and 12 post-dosing, and bladder, kidney and liver tissues and plasma were collected at the corresponding time points. The concentration of RD-13520 was quantified in bladder, kidney and liver tissues and plasma via stem-loop RT-qPCR. The change curve of RD-13520 at 0.3, 1 and 3 mg at the indicated time points in bladder and plasma are plotted in FIGs. 2A-2B. The concentrations of RD-13520 in bladder, kidney and liver tissues are summarized in Table 3. The concentrations of RD-13520 in plasma are summarized in Table 4. Table 3. RD-13520 concentration in mice tissues following RD-13520 treatment Table 4. RD-13520 concentration in mice plasma following RD-13520 treatment
[0152] As depicted in Table 3 and Table 4, the concentrations of RD-13520 in bladder tissue and plasma exhibited a dose-dependent decrease from 2 h to Day 1 post-dosing, with the compound nearly undetectable in plasma by Day 1 and in bladder tissue by Day 12. Concurrently, minimal accumulation was detected in the kidney and liver only at 2 h post-dosing, indicating negligible systemic exposure. Example 6. Effect of saRNA-C5x5 in inducing p21 protein expression in bladder tissue of cynomolgus macaques following IVB instillation
[0153] To assess the activation of saRNA-C5x5 inducing the p21 protein expression, one group of cynomolgus macaque monkeys was administered with RD-13520 for five doses (200 mg / dose) at the indicated time points (i.e., Day 1, Day 8, Day 15, Day 22 and Day 29) via IVB instillation. Another group of cynomolgus macaque monkeys received PBS alone and served as a vehicle control. The monkeys were sacrificed on Day 30 post first dosing. p21 protein levels were tested by IHC using anti-p21 antibody. As shown in FIG. 3A and FIG. 3B, RD-13520 treatment group showed more pronounced p21 protein (indicated by the arrowheads) compared to PBS treatment group. The results indicate that saRNA-C5x5 can engage with its target to induce p21 protein expression in non-human primate (NHP) . Example 7. Human study of RD-13520 treatment in patients with NMIBC
[0154] A phase I, open label, multi-center study to evaluate the safety, tolerability, pharmacokinetics, pharmacodynamics and preliminary efficacy of RD-13520 in patients with NMIBC who have failed BCG therapy were carried out in compliance with the guidelines of the Good Clinical Practice (GCP) (E6 R2) of the International Conference on 9 November 2016 and the regulations issued by the national drug regulatory (FDA / NMPA) . The investigational product RD-13520 used in the clinical trials was synthesized by Asymchem Life Science (Tianjin) Co., Ltd (Batch No. : 130690101, Asymchem, Tianjin, China) . The major relevant personnel responsible for conducting the study all completed the ICH GCP training.
[0155] The formulation used in the study was a colorless to yellow clear solution for injection prepared in normal saline at the designated concentration, and was administered via IVB instillation. Example 8. Urine pharmacokinetics and pharmacodynamic of RD-13520 in NMIBC patients following RD-13520 treatment via IVB injection
[0156] Patients with NMIBC who have failed BCG therapy were administered with RD-13520 at 30, 100, 300 and 600 mg via IVB injection once weekly for six doses (on Day 1, 7, 14, 21, 28 and 35) . Three patients were enrolled in each of the 30 mg, 100 mg, and 300 mg cohorts, with four patients enrolled in the 600 mg cohort.
[0157] To evaluate the urinary and plasma PK of RD-13520, urine samples from patients were collected on both Day 1 and Day 35, with the first morning void discarded prior to sample collection, and plasma samples from patients also were collected on both Day 1 and Day 35. On each of these two days, sampling was performed across sequential time windows of 0-2, 2-4, 4-6, 6-8, 8-12, 12-16, 16-20, 20-24, 24-32, 32-40 and 40-48 h post-dose, yielding 11 urine and 11 plasma samples per patient. Urine and plasma samples were also collected prior to administration (pre-dose) as baseline controls. Urinary and plasma concentration and total amounts of RD-13520 in patients were determined by LC-MS / MS quantitative analysis. Systemic plasma concentrations of RD-13520 were nearly undetectable across all cohorts and time points. Urinary concentrations and total amounts of RD-13520 are plotted in FIGs. 4A-4D.Urinary maximum concentrations (Cmax) , time to maximum concentration (Tmax) , urine volume at Tmax and cumulative RD-13520 amounts are summarized in Table 5.
[0158] As presented in FIGs. 4A-4D and Table 5, urinary Cmax was 104-3113.8 μg / mL (0-2 h, Day 1) for the 30-600 mg cohorts and 184-1521.1 μg / mL (0-2 h, Day 35) for the 30-300 mg cohorts. The results showed that RD-13520 exhibited minimal systemic exposure, with dose-dependent increases in urinary Cmax and area under the curve (AUC) 0-24h across all dose cohorts.
[0159] To assess the urinary PD of RD-13520, morning urine sediments from patients in 30 mg, 100 mg and 300 mg per dose cohorts (patients in the cohorts shown in Table 5) , were collected within 2 h before dosing on Day 0, 7 and 35. p21 protein expression levels in urothelial cells were quantified by IHC (described in “Materials and Method” section) .
[0160] Weak p21 staining level was observed in 30 mg per dose cohort, while moderate p21 staining level was noted in 100 mg per dose cohort and sustained in 300 mg per dose cohort. These assessments of weak and moderate staining were determined by specialized and experienced clinical pathologists. As shown by the results, p21 protein expression exhibited a dose-dependent trend. The results revealed a progressive elevation in p21-positive urothelial cells with increasing dose, indicative of p21 protein induction in urothelial cells and thus confirming target engagement. Example 9. Safety and efficacy assessment of NMIBC patients following RD-13520 treatment
[0161] The safety and efficacy of RD-13520 were also evaluated using the identical dosing regimen as employed in the aforementioned PK and PD studies. All patients completed the observation and assessment of dose-limiting toxicities (DLTs) , with no DLTs observed.
[0162] For safety evaluation, all adverse events (AEs) , serious adverse events (SAEs) and treatment-emergent adverse events (TEAEs) occurring from first instillation to the end of study or maximum 30 days from the last administration, initiation of subsequent other anti-tumor therapy, withdrawal from study, death, or loss to follow-up, whichever occurs earlier, were collected and graded accordingly, and the relationship with the investigational product, i.e., treatment-related adverse events (TRAEs) , were judged by the experienced investigator.
[0163] A total of 56 TEAEs were reported in 12 patients (92.3%, 12 / 13) , all of which were classified as Grade 1-2; the most common TEAE was identified as urinary tract infection. SAEs were observed in only 2 patients (15.4%, 2 / 13) , including lower respiratory tract infection (Grade 2) and urinary retention (Grade 2) , and neither of these events was considered to be associated with RD-13520. No treatment discontinuations or deaths were reported due to AEs. Among these TEAEs, TRAEs were reported in only 3 patients (23.1%, 3 / 13) , no TRAEs of Grade ≥3 were documented, and no treatment-related SAEs were observed. The reported TRAEs included: urinary urgency, urinary frequency, urinary tract infection, dyspnea, fatigue, nausea, and decreased appetite. The results demonstrated that RD-13520 exhibited a favorable safety profile across four escalating dose cohorts (30, 100, 300, and 600 mg) , with only minimal AEs reported.
[0164] Efficacy was evaluated according to routine cystoscopy, urine cytology and imaging to rule out potential muscular invasion. The endpoints of efficacy assessment included disease free rate (DFR) and disease-free survival (DFS) for papillary-only disease; complete response (CR) rate and duration of complete response (DOR) for CIS; and, incidence of and time to MIBC progression.
[0165] Efficacy data demonstrated that 33.3% (3 / 9) patients with CIS at baseline achieved a CR, and 75%(3 / 4) patients with papillary-only tumors had no high-grade recurrence at the 3-month tumor assessment.
[0166] In summary, these results demonstrate that RD-13520 constitutes a novel therapeutic approach for NMIBC with high efficacy and safety.MATERIALS AND METHODSOligonucleotide synthesis (1) Single-stranded oligonucleotide synthesis
[0167] Single-stranded oligonucleotides were synthesized on a K&A DNA synthesizer (K&A Laborgeraete GbR, chaafheim, Germany) by a solid phase synthesis technique.
[0168] The starting material was universal solid support or special solid support commercially available or synthesis as disclosure in previous context. In general, phosphoramidite monomers including various linkers and conjugates (0.1M in acetonitrile or dichloromethane) , were added sequentially onto a solid support in the DNA synthesizer to generate the desired full-length oligonucleotides.
[0169] Amidite addition: each cycle of amidite addition consisted of four chemical reactions including detritylation, coupling, oxidation / thiolation and capping. In the first step, the detritylation was performed by using 3%dichloroacetic acid (DCA) in DCM for 45 seconds. In the second step, phosphoramidite coupling was conducted for 6 minutes for all amidites by 12 eq. In the third step, oxidation was performed by using 0.02 M iodine in THF: pyridine: water (70: 20: 10, v / v / v) for 1 minute; if phosphorothioate modification was needed then replace oxidation by thiolation which was carried out with 0.1 M solution of xanthane hydride in pyridine: ACN (50: 50, v / v) for 3 minutes. In the fourth step, the capping was performed by using a THF: acetic anhydride: pyridine (80: 10: 10, v / v / v) (CAP A) and N-methylimidazole: THF (10: 90, v / v) , (CAP B) for 20 seconds. The cycles of four chemical reactions were depended by the length of single oligonucleotide.
[0170] Deprotection I (Nucleobase Deprotection) : after completion of the synthesis, the solid support was transferred to a screw-cap microcentrifuge tube. For a 1 μmol synthesis scale, 1 ml of a mixture of methylamine and ammonium hydroxide was added. The tube containing the solid support was then heated in an oven at 60℃ to 65℃ for 15 min and then allowed to cool to room temperature. The cleavage solution was collected and evaporated to dryness in a speedvac to provide crude single strand of oligonucleotide.
[0171] Deprotection II (Removal of 2’ -TBDMS Group) : if the crude RNA oligonucleotide still carrying the 2’ -TBDMS groups, then dissolved it in 0.1 ml of DMSO. After adding 1 ml of triethylamine trihydrofluoride, the tube was capped, and the mixture was shaken vigorously to ensure complete dissolution and then heated in an oven at 65℃ for 15 minutes. The tube was removed from the oven and cooled down to room temperature. The solution containing the completely desilylated oligonucleotide was cooled on dry ice. Two ml of ice-cold n-butanol (-20℃) were carefully added in 0.5 ml portions to precipitate the oligonucleotides. The precipitate was filtered, washed with 1 ml ice-cold n-butanol, and subsequently dissolved in 0.01 M Tris (hydroxymethyl) aminomethanol hydrochloride buffer. (2) Single-stranded oligonucleotide purification
[0172] The purification of oligonucleotides was performed on an AKTA explorer 10 equipped with a Source 15Q 4.6 / 100 PE column using the following conditions: buffer A: (10 mM Tris-HCl, 1 mM EDTA, pH 7.5) , B: (10 mM Tris-HCl, 1 mM EDTA, 2M NaCl, pH 7.5) , gradient: 10%B to 60%B in 25 min, flow rate: 1 ml / min. The pure oligonucleotides were collected and desalted by a HiPrep 26 / 10 Desalting column. (3) Annealing of single-stranded oligonucleotides to form duplex
[0173] For duplex, after the generation of desalted purified single-stranded solutions, sense strand and antisense strand were mixed by equal volumes at equimolar concentration in the tube. The tube was placed in a heat block at 95℃ for 5 min and then cooled to room temperature. Then, the thus obtained duplex was subsequently lyophilized to powder which can be stored at -20 ℃.Cell culture and treatment
[0174] KU-7 cells (ATCC) and T24 cells (ATCC) were maintained in McCoy’s 5A (Gibco) medium supplemented with 10%fetal bovine serum (FBS) (Gibco) , 1%NEAA (Gibco) , sodium pyruvate (1 mM) (Gibco) , penicillin (100 U / ml) (Gibco) and streptomycin (100 μg / ml) (Gibco) . Both cell lines were cultured in a humidified atmosphere of 5%CO2 at 37℃. Transfections were carried out using Lipofectamine RNAiMax (ThermoFisher, Waltham, MA, USA) in growth media without antibiotics according to the manufacture’s protocol.Animal study
[0175] Cynomolgus macaque monkeys (crab-eating monkeys, male) aged from 3 to 4 years were purchased from WuXi AppTec (Suzhou) Co., Ltd. C57BL / 6J mice (4-6 weeks old female) were purchased from SPF Biotechnology Co., LTD (B204, Beijing, China) . All animal procedures were conducted by certified laboratory personnel following protocols consistent with local and state regulations and approved by the Institutional Animal Care and Use Committee (IACUC) . Formulations of RD-13520 for animal treatments were prepared fresh prior to use by dissolving allotments of lyophilized oligonucleotide into saline (for the administration to the mice) or PBS (for the administration to the monkeys) to create stock solutions for dilution to the intended treatment concentrations.Intravesical bladder (IVB) instillation
[0176] Mice were anesthetized and placed on a temperature-controlled pad at 28-31℃. Each mouse had its excreted urine from the bladder collected by urinary catheterization and had its bladder washed with saline before IVB instillation. A 2 cm catheter attached to a 1 ml syringe containing compound solution was intubated into bladder via urinary meatus. A total of 50 μL solution was injected into the bladder through an indwelling urinary catheterization within about 1.5 hours.
[0177] Cynomolgus macaque monkeys were anesthetized using ketamine and xylazine and kept on a warm water bath heating pad during the intravesical instillation procedure. The test article solution was administered to the monkey via IVB instillation at a dose of 200 mg / dose. The initial dose was administered on Day 1, followed by weekly administration for a total of five doses at the indicated time points (i.e., Day 1, Day 8, Day 15, Day 22, and Day 29) . A volume of 10 mL of the test article was administered within 3-5 minutes and allowed to dwell for at least 90 minutes.Inclusion and exclusion criteria for human patients with NMIBC enrolled in the clinical study
[0178] Patients with NMIBC were enrolled in the clinical study in accordance with the following inclusion criteria: 1. Ability to understand the study and have signed the informed consent form; 2. Any adult ≥ 18 years old; 3. Pathologically confirmed non-muscle invasive bladder cancer (NMIBC) of the transitional cell carcinoma high-grade subtype (mixed histology tumors allowed if transitional cell histology is predominant histology) ; 4. Expected survival ≥ 6 months; 5. ECOG PS ≤2; 6. Subject must refuse or being deemed clinically inappropriate for radical cystectomy. Subject must be diagnosed as BCG failure after standard intravesical BCG instillation recommended by NCCN guideline; 7. Subject must be confirmed as absence of resectable disease by cystoscopy within 28 days before start of study treatment: ● Patients with Ta and / or T1 disease should have complete resection before study treatment; ● Residual CIS acceptable, but obvious areas of CIS should also be fulgurated; ● Patients with T1 tumors must undergo repeat resection and biopsy (inclusive of muscularis propria) of the T1 tumor site if initial biopsy did not include muscularis propria; 8. Sufficient organ functions, as defined below: 9. Subject must be able to tolerate catheterization; 10. Female subject of childbearing potential and her spouse must use adopt effective contraception (non-pharmacological contraception required) from signing informed consent to within 6 months after the last instillation.
[0179] The exclusion criteria for patients were as follows: 1. Subject who has allergy to RD-13520 or similar products; 2. Except for TURBT, the subject received other anti-tumor treatments, and the last administration date is within ≤ 21 days or 5 half-lives whichever is shorter from the date of signing ICF; 3. History of or evidence of muscle-invasive, locally advanced, metastatic and / or extravesical bladder cancer (inclusive of the prostatic urethra) ; 4. Subject has other malignancies within the past 3 years, except for adequately treated carcinoma of the cervix, basal or squamous cell carcinomas of the skin, or adenocarcinoma of the prostate that has been surgically treated with a post-treatment PSA that is non-detectable; 5. The following illnesses have not been improved to CTCAE v5 grade ≤1: a. Uncontrolled acute and chronic infections, such as pneumonia, biliary tract infection, hepatitis B virus infection and hepatitis C virus infection; b. Dyspnea; c. Acute and chronic kidney injury, and inflammation; d. Urinary incontinence; e. Urinary frequency; f. Urinary tract obstruction (except benign prostatic hypertrophy) ; 6. Subject could not hold the urine for at least 90 mins due to any reason; 7. New York Heart Association (NYHA) 3 or 4 grade; 8. Coronary heart disease related symptoms have not been improved to CTCAE v5 grade≤ 1, including: myocardial infarction, unstable angina pectoris, congestive heart failure and arrhythmia; 9. Subject with QTc prolongation (QTc >450 msec for male; QTc >480 msec for female) . 10. Cerebrovascular accidents have not been improved to CTCAE v5 grade≤ 1; 11. HIV positive; Active hepatitis B or C. For active HBV, it’s defined as HBsAg positive with HBV DNA ≥ ULN, for active HCV, it’s defined as HCV antibody positive with HCV RNA ≥ ULN, respectively. 12. Subject is pregnant or lactating during the treatment period; 13. Subjects with severe or unstable central nervous system or psychiatric disorders, as determined by the investigator, which could potentially impact their compliance or increase their risk as study participants; 14. Other severe systemic diseases which might compromise the subject’s compliance to the study, e.g., uncontrolled diabetes, gastrointestinal disorders, and renal diseases; 15. Any other situations which are judged by the investigator, would exposure the subject to unnecessary risk, therefore he / she is not eligible.Reverse transcription-quantitative polymerase chain reaction (RT-qPCR)Two-step RT-qPCR
[0180] RNA from cell culture was extracted using the Auto-Pure 96A (Allsheng) nucleic acid extraction system. Reverse transcription (RT) reactions were performed with 1 μg total RNA using the PrimeScript RT kit with gDNA Eraser (Takara, Shlga, Japan) . The resulting cDNA was amplified in triplicate on the Roche LightCycler 480 Multiwell Plate 384 (Roche, ref: 4729749001, US) using SYBR Premix Ex Taq II (Takara, Shlga, Japan) in conjunction with primer sets specific to human p21 and an internal control for either human (i.e., HPRT1 and B2M) samples. Melting curves were made after amplification to confirm primer specificity. Reaction conditions were as follows: reverse transcription reaction (stage 1) : 42℃ for 5 min, 95℃ for 10 sec; PCR reaction (stage 2) : 95℃ for 5 sec, 60℃ for 30 sec, 72℃ for 10 sec; 40 cycles of amplification; Melting curve (stage 3) . PCR reaction conditions are shown in Table 6 and Table 7. Primer sequences are listed in Table 8. Table 6. RT reaction Table 7. RT-qPCR reaction Table 8. Primer sequences for RT-qPCR assay Two reference genes
[0181] To calculate the relative expression level (Erel) of target gene mRNA in a saRNA-transfected sample relative to control treatment (Mock) , the Ct values of the target gene and the two internal reference genes were substituted into Formula I, Erel=2 (CtTm-CtTs) / ( (2 (CtR1m-CtR1s) *2 (CtR2m-CtR2s) ) (1 / 2) ) (Formula I) wherein CtTm was the Ct value of the target gene from the mock-treated sample; CtTs was the Ct value of the target gene from the saRNA-treated sample; CtR1m was the Ct value of the internal reference gene 1 from the mock-treated sample; CtR1s was the Ct value of the internal reference gene 1 from the saRNA-treated sample; CtR2m was the Ct value of the internal reference gene 2 from the mock-treated sample; and CtR2s was the Ct value of the internal reference gene 2 from the dsRNA treated sample.Stem-loop RT-qPCR
[0182] To quantify oligonucleotides in biological samples, animal tissues were harvested using Heat-Lysis method and stored lysate at -80℃. Duplex, antisense strand and formulated saRNAs were used for the preparation of serial 10-fold dilutions into 95℃ boiled tissue (100 mg / mL) or into plasma (1: 10 diluted) in 1× lysis buffer. saRNA concentrations in nM were converted to ng / g using the corresponding molecular weights. Two non-template controls were included in all experiments. The first control contains the water used to prepare the transcription master mix and the second contains the lysis buffer used as diluent for samples and standards.
[0183] Reverse transcription reactions were performed using a Takara Reverse Transcription kit (Takara, RR037A) . A total of 4 μL of cDNA (1: 40 dilution) from the previous step was added into the PCR amplification reaction mix (0.5 μM forward primer, 0.5 μM reverse primer, 2 × TG Green premix Ex Taq II) . The qPCR reaction was run with the option ‘Standard Curve’ in a Light cycler 480. Stem-loop RT-qPCR reaction conditions are shown in Table 9 and Table 10. Stem-loop primer sequences are listed in Table 11. Table 9. Stem-loop RT reaction Table 10. Stem-loop RT-qPCR reaction Table 11. Primer sequences for stem-loop RT-qPCR assay Immunohistochemistry (IHC)
[0184] Bladder was removed and immediately placed in fixative (10%formalin solution, HT501128, Sigma, Darmstadt, Germany) . Histological sections (2-4 μm) were cut from formalin-fixed, paraffin-embedded tissue blocks and four slides were selected for IHC assay. The slides were baked at 60℃and then underwent retrieval at 60℃. After cooling, all slides were incubated with 3%H2O2 solution (Catalog No. : GT100535, Genetech) to inactivate endogenous peroxidases in the tissue, followed by incubation with 10%normal goat serum (005-000-121, Jackson Immuno Research, West Grove, PA, USA) to block nonspecific staining. The sections were then incubated with a primary anti-p21 antibody (2947S, Cell signaling technology, US) for 2 hours. Subsequently, secondary antibody Goat Anti-Rabbit IgG (H+L) (Catalog No. : 111-035-003, Jackson ImmunoResearch) was applied, and all slides were visualized using 3, 3'-diaminobenzidine (DAB) substrate kit (Catalog No. : 8059S, cell signaling technology) as the chromogen and counterstained with hematoxylin. Sections were observed under an Olympus microscope (BX53, Shinjuku-ku, Tokyo, Japan) . For each animal, 3 to 5 areas were analyzed, and a representative image was shown.Liquid Chromatography-Tandem Mass Spectrometry (LC-MS / MS) quantitative analysis
[0185] Urine samples from patients were collected on both Day 1 and Day 35, with the first morning void discarded prior to sample collection. Plasma samples from patients were also collected on both Day 1 and Day 35. On each of these two days, sampling was performed across sequential time windows of 0-2, 2-4, 4-6, 6-8, 8-12, 12-16, 16-20, 20-24, 24-32, 32-40 and 40-48 h post-dose, yielding 11 urine and 11 plasma samples per patient. Urine samples and plasma samples were also collected prior to administration (pre-dose) as baseline controls. The concentrations of RD-13520 in urine and plasma samples from NMIBC patients were quantified at the indicated time windows using LC-MS / MS analysis conducted by Resolian Bioanalytics (Australia) .Statistical analysis
[0186] Differences between groups of continuous variables were compared using one-way analysis of variance (ANOVA) followed by Dunnett’s multiple comparisons. A P value of less than 0.05 was considered statistically significant between the two groups. *represents p < 0.05, **represents p <0.01, ***represents p < 0.001, ****represents p < 0.0001.EQUIVALENTS
[0187] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. It is not intended that the invention be limited by the specific examples provided within the specification. While the invention has been described with reference to the aforementioned specification, the descriptions and illustrations of the embodiments herein are not meant to be construed in a limiting sense. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. Furthermore, it should be understood that all aspects of the invention are not limited to the specific depictions, configurations or relative proportions set forth herein which depend upon a variety of conditions and variables. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is therefore contemplated that the invention shall also cover any such alternatives, modifications, variations or equivalents. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.REFERENCE 1. WHO. Globocan 2020 Bladder. https: / / gco. iarc. fr 2. Sam S. Chang, Stephen A. Boorjian, Roger Chou, et al. Diagnosis and Treatment of Non-Muscle Invasive Bladder Cancer: AUA / SUO Guideline. The Journal of Urology. Vol. 196, 1021-1029, October 2016 3. Nielsen ME SA, Meyer AM: Trends in stage-specific incidence rates for urothelial carcinoma of the bladder in the United States: 1988-2006. Cancer 120: 86-95, 2014 4. Babjuk M BM, Zigeuner R: EAU guidelines on non-muscle-invasive urothelial carcinoma of the bladder: update 2013. Eur Urol 64: 639-653, 2013 5. Rodolfo Montironi and Antonio Lopez-Beltran, The 2004 WHO Classification of Bladder Tumors: A Summary and Commentary. INT J SURG PATHOL 2005 13: 143 6. NCCN Clinical practice guidelines in oncology:Bladder Cancer, version 3.2023
Claims
1.A method for the treatment of non-muscle invasive bladder cancer (NMIBC) in a subject in need thereof, wherein the method comprises the step of administering the subject a therapeutically effective amount of an oligonucleotide agent or a medicament comprising the oligonucleotide agent,wherein the oligonucleotide agent comprises (i) a small activating RNA (saRNA) targeting a selected region of p21 gene having a sequence of any one of SEQ ID NOs: 11-18 and capable of upregulating the expression of p21 gene; and (ii) a conjugation moiety that is covalently tethered to the saRNA to deliver the saRNA in the body of a subject.2.The method of claim 1, wherein the saRNA comprises a sense strand and an antisense strand forming a double stranded structure which comprises 0, 1, 2 or 3 mismatches; and / orwherein the antisense strand comprises a region of complementarity to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of p21 gene; and / orwherein the sense strand comprises a region of homology to at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from the selected region of p21 gene; and / orwherein the length of the sense strand and the antisense strand is independently about 16-25 nucleotides, preferably 18-24 nucleotides, more preferably 20-23, such as 20, 21, 22 or 23 nucleotides.3.The method of claim 1 or 2, wherein the sense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 1 or 3; and / orthe antisense strand of the saRNA comprises at least 15 contiguous nucleotides differing by 0, 1, 2 or 3 nucleotides from a sequence of SEQ ID NO: 2; and / orwherein the sense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 1 and the antisense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 2; or the sense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 3 and the antisense strand of the saRNA has a nucleotide sequence of SEQ ID NO: 2.4.The method of any one of claims 1-3, wherein the conjugation moiety is selected from a lipid, an oligonucleotide, a fluorophore, a ligand, a saccharide, a peptide, and an antibody; and / orwherein the lipid comprises at least one C4-30 fatty acid, having a saturated or unsaturated, linear or branched C4-30, C10-24, C12-22, C14-20, or C16-18 carbon chain; and / orwherein the lipid comprises a carbon chain of 16, 18, 20 or 22 carbon atoms; and / or5.The method of any one of claims 1-4, wherein the conjugation moiety is derived from a lipid compound C5x5:and / orwherein the conjugation group comprises *-C5x5:wherein * represents the site where the conjugation group is attached to the strand, either directly or via a linking moiety; and / orwherein the saRNA conjugated with C5x5 is saRNA-C5x5:6.The method any one of claims 1-5, wherein the conjugation moiety is conjugated to the sense strand or the antisense strand of the saRNA directly or indirectly via a linking component; and / orthe conjugation moiety is conjugated to the 5’ end and / or 3’ end and / or the internal nucleotide (s) of the sense strand or the antisense strand of the saRNA; and / orwherein at least one nucleotide, such as at least 50%, at least 60%, at least 70%, at least 80%, at least 90%or all the nucleotides of the sense strand and / or the antisense strand of the saRNA are chemically modified nucleotides, for example, one or more nucleotide are modified by 2’-fluoro; and / orwherein at least one backbone bond, such as at least 50%, at least 60%, at least 70%, at least 80%, at least 90%or all the backbone bonds of the saRNA are selected from the group consisting of PS, mesyl phosphoramidate and boranophosphate bond.7.The method of claim 6, wherein the linking component is one or more selected from the group consisting of ethylene glycol chain, an alkyl chain, an alkenyl chain, an alkynyl chain, a peptide, RNA, DNA, carbohydrates, thiol linkage, a phosphodiester, a PS, a phosphoramidate, an amide, a carbamate, a tetrazole linkage, and a benzimidazole linkage; and / orwherein the linking component is one or more selected from the group consisting of:a) Spacer phosphoramidite 18: 1, 1-bis (4-methoxyphenyl) -1-phenyl-2, 5, 8, 11, 14, 17-hexaoxanonadecan-19-yl 2-cyanoethyl N, N-diisopropylphosphoramidite;b) Spacer-9: 3- [2- [2- [2- [bis (4-methoxyphenyl) -phenylmethoxy] ethoxy] ethoxy] ethoxy- [di (propan-2-yl) amino] phosphanyl] oxypropanenitrile;c) Spacer phosphoramidite C3: 6- (4, 4'-Dimethoxytrityl) hexyl-1- [ (2-cyanoethyl) - (N, N-diisopropyl) ] -phosphoramidite;d) Spacer-C6 Phosphoramidite: 6- (4, 4'-Dimethoxytrityl) hexyl-1- [ (2-cyanoethyl) - (N, N-diisopropyl) ] -phosphoramidite; ande) Divalent linker (DIO) : 16- ( (bis (4-methoxyphenyl) (phenyl) methoxy) methyl) -1, 1-bis (4-methoxyphenyl) -18-oxo-1-phenyl-2, 5, 8, 11, 14, 17-hexaoxahenicosan-CPG.8.The method of claim 6 or 7, wherein the chemical modification of the at least one chemically modified nucleotide is independently selected from the group consisting of:a 2’ sugar modification, preferably a 2’ sugar modification selected from one or more of: 2’-fluoro-2’-deoxynucleoside (2’-F) modification, 2’-O-methyl (2’-O-Me) , modification, and 2’-O- (2-methoxyethyl) (2’-O-MOE) modification;a base modification;a PS backbone modification, such as 6 to 17 PS backbone modifications;an addition of an (E) -vinylphosphonate moiety at the 5’ end of the nucleotide sequence, such as at the 5’ end of the antisense strand; andan addition of a 5-methyl cytosine moiety at the 5’ end of the nucleotide sequence.9.The method any one of claims 1-8, wherein the oligonucleotide agent comprises a sense strand has a nucleotide sequence of SEQ ID NO: 1 and an antisense strand has a nucleotide sequence of SEQ ID NO: 2; orthe oligonucleotide agent comprises a sense strand has a nucleotide sequence of SEQ ID NO: 3 and an antisense strand has a nucleotide sequence of SEQ ID NO: 2.10.The method any one of claims 1-9, wherein the subject is a mammal, such as a human, a non-human primate, a livestock or a pet; and / orwherein the subject suffering from NMIBC has one or more mutations in the p21 gene which lead to the NMIBC; or, wherein the subject suffering from NMIBC does not comprise any mutation in p21 gene or is not caused by p21 gene mutation (s) ; and / orwherein the subject is a patient with NMIBC who has failed Bacillus Calmette Guérin (BCG) therapy (BCG-failed NMIBC) .11.The method of any one of claims 1-10, wherein the subject:(a) has NMIBC at a stage up to T1, including papillary Ta, papillary T1, or CIS, or CIS with papillary tumor; and / or(b) has BCG-failed NMIBC, wherein the BCG-failed NMIBC is selected from the group consisting of BCG-unresponsive, BCG-exposed, BCG-intolerant, BCG-resistant, BCG-refractory, and BCG-relapsing.12.The method of any one of claims 1-11, wherein the administration of the oligonucleotide agent, as compared to without the administration, is capable of:(a) increasing the disease-free rate and disease-free survival in papillary-only NMIBC patients; and / or(b) improving the complete response rate and duration of complete responses in NMIBC patients for CIS; and / or(c) prolonging the overall survival of NMIBC patients; and / or(d) reducing the time to MIBC progression; and / or(e) avoiding cystectomy after BCG-unresponsive; and / or(f) upregulating the expression of the p21 gene, as evidenced by an increase in p21 mRNA levels of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%compared to baseline.13.The method of any one of claims 1-12, wherein the oligonucleotide agent is administered in a dose of 30-600 mg per dose, such as 30-300 mg per dose, 30-100 mg per dose, 100-300 mg per dose, 100-600 mg per dose, 300-600 mg per dose, 30 mg per dose, 100 mg per dose, 300 mg per dose and 600 mg per dose; and / orwherein the oligonucleotide agent is administered at fixed interval or unequaled interval, such as once 7 days, once 14 days, once 28 days, once 35 days, once 42 days, once 56 days, once a week, once two weeks, once three weeks, once 1 month, once 2 months, once 3 months, once 4 months, once 5 months or once 6 months, or any combinations thereof; and / orwherein the oligonucleotide agent is administered for 3-6 weeks, 3-12 weeks, 3-18 weeks, 3-24 weeks, 3-36 weeks, 3-48 weeks, 3-72 weeks per treatment course, such as for 3, 6, 9, 12, 15, 18, 24, 36, 48 or 72 weeks per treatment course.14.The method of any one of claims 1-13, wherein the method comprises the steps of:administering the subject a starting single dose of the oligonucleotide agent;administering the subject one or more escalated doses of the oligonucleotide agent until reaching a maximum tolerated dose (MTD) ;administering the subject one or more sustaining doses of the oligonucleotide agent at the MTD or at a dose between the starting dose and the MTD, preferably an optimal dose;optionally, the method is used in determining the subject-tailored dosage regimen.15.The method of claim 14, wherein the starting dose of the oligonucleotide agent is about 30-300 mg per dose, such as about 30 mg per dose, about 100 mg per dose or about 300 mg per dose; and / orthe escalated dosage reaches to about 300-600 mg per dose; and / orthe escalated dose of the oligonucleotide agent is administered once a week, once every two weeks, or once every three weeks; and / or,the sustaining dose of the oligonucleotide agent is administered once a week, once every two weeks, or once every three weeks.16.The method of any one of claims 1-15, wherein oligonucleotide agent is in a form of solution, powder, suspension, spray, or gel; and / orwherein the oligonucleotide agent is solved in a pharmaceutically acceptable carrier, such as in saline, PBS, Ringer’s buffer, or water for injection.17.The method of any one of claims 1-16, wherein the administration pathway is one or more selected from the group consisting of: intravesical instillation, parenteral infusions, vaginal administration, and rectal administration.18.The method of any one of claims 1-16, wherein the oligonucleotide agent comprises a saRNA comprising a sense strand of SEQ ID NO: 1 and an antisense strand of SEQ ID NO: 2, or a saRNA comprising a sense strand of SEQ ID NO: 3 and an antisense strand of SEQ ID NO: 2, optionally in a powder form or solved in a pharmaceutically acceptable carrier (such as in saline) ;wherein the subject is a patient with BCG-failure NMIBC papillary, and / or CIS in phase Ta, T1 or Tis;wherein the oligonucleotide agent is administered to the subject once a week, once two weeks, once three weeks in a dose of 30 mg per dose, 100 mg per dose, 300 mg per dose or 600 mg per dose; and / orwherein the course of treatment lasts for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks per treatment course.19.A product for use in the treatment of NMIBC by the method of any one of claims 1-18.20.Use of an oligonucleotide agent in the preparation of a medicament for the treatment of NMIBC by the method of any one of claims 1-18.21.A pharmaceutical composition comprising the oligonucleotide agent or medicament in any one of claims 1-9, and, at least one pharmaceutically acceptable carriers, wherein the pharmaceutical composition comprises from about 30 mg to about 600 mg of the oligonucleotide agent.22.The pharmaceutical composition of claim 21, wherein the pharmaceutical composition comprises about 30 mg, 100 mg, 300 mg or about 600 mg of the oligonucleotide agent; and / orwherein the pharmaceutically acceptable carrier is saline, PBS, Ringer’s buffer, or water for injection.23.The pharmaceutical composition of claim 21 or 22, wherein the pharmaceutical composition is in a form for intravesical instillation, parenteral infusions, vaginal administration, and rectal administration.24.A kit comprising one or more pharmaceutical compositions of any one or claims 21-23 in dosage unit form.25.The kit of claim 24, wherein the amount of the dosage units in the kit is sufficient for a course of treatment; and / orwherein the kit comprises 3 to 72 dosage units, 3, 12, 16, 18, 24, 36, 48, or 72 dosage units; and / orwherein the kit comprises dosage units sufficient for once per week treatment for at least 3 weeks, such as for about 3 weeks, 6 weeks, 12 weeks, 16 weeks, 18 weeks, 24 weeks, 36 weeks, 48 weeks or 72 weeks; and / orwherein each dosage unit independently comprises 30-600 mg of the oligonucleotide agent, such as 30 mg, 100 mg, 300 mg or 600 of the oligonucleotide agent.