WO2019196883A1 - 一种激活p21基因表达的方法 - Google Patents
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Definitions
- the present invention relates to the field of molecular biology, and in particular to the forward regulation of gene expression using a double-stranded small RNA targeting a gene promoter sequence.
- Double-stranded small nucleic acid molecules including chemically synthesized oligoribonucleotides such as small activating RNA (saRNA) and naturally occurring oligoribonucleotides such as microribonucleotides (miRNAs) have been shown to target in a sequence-specific manner
- the expression level of a gene encoding a gene, such as a promoter sequence is positively regulated at the transcriptional and epigenetic levels, and this phenomenon is called RNA activation (RNAa) (Li, Okino et al. (2006) Proc Natl Acad Sci U S A 103: 17337-17342; Janowski, Younger et al.
- RNA activation is an evolutionarily conserved endogenous molecular mechanism from C. elegans to humans (Huang, Qin et al. (2010) PLoS One 5: e8848; Seth, Shirayama et al. (2013) Dev Cell 27: 656-663; Turner, Jiao et al. (2014) Cell Cycle 13: 772-781).
- RNA activation has the advantage of being able to activate endogenous gene expression without changing the genome, and represents a new strategy for activating endogenous gene expression, which has great application value in disease treatment.
- the p21 WAF1/CIP1 also known as CDKN1A, hereinafter referred to as p21
- CDK cyclin-dependent kinase
- p21 cyclin-dependent kinase
- CDK cyclin-dependent kinase
- the present invention provides a small activating RNA characterized in that one of the small activating RNAs is in the sequence shown in SEQ ID NOs: 5, 6, 7, 8, 9, 10, 11, and 12. Any contiguous fragment of 16-35 nucleotides in length having at least 75% homology or complementarity activates or up-regulates the expression of the p21 gene by targeting the human p21 gene promoter sequence. .
- the target gene of the human p21 gene is selected from the group consisting of the sequences set forth in SEQ ID NOS: 5-12, wherein the human p21 gene promoter sequence is located at a distance from the transcription start position, respectively.
- TSS Transcription start site upstream - 893 ⁇ - 801 bp (SEQ ID NO: 5), -717 ⁇ - 632 bp (SEQ ID NO: 6), -585 ⁇ - 551 bp (SEQ ID NO: 7), -554 ⁇ -504 bp (SEQ ID NO: 8), -514 to -485 bp (SEQ ID NO: 9), -442 to -405 bp (SEQ ID NO: 10), -352 to -313 bp (SEQ ID NO: 11), -325 to -260 bp (SEQ ID NO: 12).
- the small activating RNA comprises a sense nucleic acid strand and an antisense nucleic acid strand, the sense nucleic acid strand and the antisense nucleic acid strand comprising a complementary region, wherein the complementary region is capable of forming a double stranded nucleic acid structure, wherein the sense nucleic acid strand or Any one of 16-35 nucleotides in length of the antisense nucleic acid strand and the human p21 gene promoter sequence has 75% or more, 80% or more, 90% or more, 95% or more, 99% or more, or 100%. Homology.
- the sense nucleic acid strand and the antisense nucleic acid strand are present on two different nucleic acid strands as described above; the sense nucleic acid strand and the antisense nucleic acid strand are present on the same nucleic acid strand, A sandwich-type single-stranded nucleic acid molecule in which a complementary region of a sense nucleic acid strand and an antisense nucleic acid strand forms a double-stranded nucleic acid structure.
- At least one of the small activating RNAs has a 3' overhang of 0 to 6 nucleotides in length; both of the small activating RNAs have a length of 2-3 3' overhang of nucleotides.
- the sense nucleic acid strand or the antisense nucleic acid strand is 16-35 nucleotides in length, such as 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleotides.
- the sense nucleic acid strand or the antisense nucleic acid strand is SEQ ID NOs: 13-30, 35-46, 59-62, 67-74, 77-80, 85-96, 103-108, 111-118, 121-132, 139-140, 147-180, 185-186, 189-190, 195-198, 201-202, 209-212, 215-218, 225-240, 243-246, 249- 258, 261-262, 265-270, 275-280, 283-300, 303-308, 317-320, 323-324, 329-348, 351-352, 357-358, 361-366, 371-392,
- the sequences shown at 399-400, 405-412, 415-416, 419-424, 429-432, 439-442, 447-450, 453-458, 463-468 have at least 75%, such as 80%, 85%, 90. %, 95%, 99%, 100% homo
- the sense nucleic acid strand or antisense nucleic acid strand sequence is SEQ ID NOs: 13-30, 35-46, 59-62, 67-74, 77-80, 85-96, 103-108 , 111-118, 121-132, 139-140, 147-180, 185-186, 189-190, 195-198, 201-202, 209-212, 215-218, 225-240, 243-246, 249 -258, 261-262, 265-270, 275-280, 283-300, 303-308, 317-320, 323-324, 329-348, 351-352, 357-358, 361-366, 371-392
- the nucleotide sequences of any of 399-400, 405-412, 415-416, 419-424, 429-432, 439-442, 447-450, 453-458, and 463-468 are shown.
- the invention also provides a method for preparing a small activating RNA according to any one of the preceding claims, which comprises the steps of: 1) selecting a target gene promoter sequence as a template and selecting 19 bases; The sequence serves as a target site; 2) synthesizes an RNA sequence having a homology of more than 75% of the sequence of the target site obtained in step 1) to obtain a sense oligonucleotide chain; 3) the sequence and the sense oligonucleoside obtained in step 2) The acid chain is complementary; 4) the sense oligonucleotide strand obtained in step 2) is mixed with the antisense oligonucleotide strand obtained in step 3) in the same molar number in the RNA annealing buffer, heated, and then naturally cooled to At room temperature, a double-stranded small activating RNA is obtained; wherein the human p21 gene promoter sequence is selected from the group consisting of the sequences set forth in SEQ ID NOs: 5, 6, 7, 8, 9, 10, 11, 12 .
- At least one nucleotide of the small activating RNA is a chemically modified nucleotide, the chemical modification being at least one of the following modifications:
- At least one nucleotide in the nucleotide sequence of the small activating nucleic acid molecule is a locked nucleic acid.
- the activating or upregulating expression of the p21 gene is upregulated by at least 10%, such as 15%, 20%, 30%, 40%, 50%, 80%, 100%, 200% or more.
- the invention also provides the use of a small activating RNA for the preparation of a preparation for activating or upregulating the expression of the p21 gene in a cell.
- the small activating RNA is introduced directly into the cell or is produced in the cell after the nucleotide sequence encoding the small activating RNA is introduced into the cell.
- the cell is a mammalian cell, preferably a human cell, more preferably a human tumor cell.
- the human cell can be an isolated human cell line or can be present in a human body.
- the human body is a patient having a tumor caused by insufficient expression of the p21 protein, and the small activating nucleic acid molecule is administered in an amount effective to achieve treatment of a tumor, preferably a bladder cancer, Prostate cancer, liver cancer or colorectal cancer.
- the present invention provides an isolated p21 gene small activating RNA target site, wherein the target site is any consecutive 16-35 nucleosides selected from any one of SEQ ID Nos. 5-12. Acid sequence.
- the invention features a method of activating or upregulating expression of a human p21 gene in a cell, wherein the method comprises administering to the subject or cell a small activating RNA as described in any one of the preceding.
- the small activating RNA may be directly introduced into the cell, or may be produced in the cell after the nucleotide sequence encoding the small activating RNA is introduced into the cell.
- the cell is a mammalian cell, preferably a human cell, more preferably a human tumor cell, and more preferably a human bladder cancer, prostate cancer, liver cancer or colorectal cancer cell.
- the invention further discloses a composition
- a composition comprising a small activating RNA as described above and a pharmaceutically acceptable carrier.
- the pharmaceutically acceptable carrier is a liposome, a high molecular polymer or a polypeptide.
- the present invention also discloses the use of a small activating RNA as described above or a composition as described above for the preparation of a medicament for activating or upregulating the expression of the p21 gene, preferably in the preparation of an anti-tumor or benign proliferative lesion.
- the tumor is bladder cancer, prostate cancer, liver cancer or colorectal cancer.
- FIG. 1 shows the p21 gene promoter sequence from -1000 bp upstream of the transcription start site (TSS) to 3 bp downstream of the TSS.
- the TSS is indicated by a curved arrow.
- Figure 2 shows the screening of small activated RNA hotspot regions on the p21 gene promoter.
- 439 double-stranded RNA molecules were designed and chemically synthesized for the p21 promoter sequence shown in Figure 1, and transfected into PC3 human prostate cancer cells, respectively.
- the p21 gene mRNA level was analyzed after 72 hours using the QuantiGene 2.0 method.
- Figure 3 shows the activation of the p21 gene by double-stranded RNA molecules of the hotspots 1 to 8.
- Figure 4 shows the analysis of p21 gene mRNA levels by RT-qPCR method to verify the experimental results of QuantiGene 2.0.
- A 439 double-stranded RNA molecules were divided into four regions (groups) according to their activity to induce p21 mRNA expression, and 5 double-stranded RNA molecules were randomly selected from each group and transfected into PC3 cells at a concentration of 10 nM, respectively. . After 72 hours, total cellular RNA was extracted, and p21 gene mRNA levels were analyzed by RT-qPCR after reverse transcription.
- QuantiGene 2.0 (X-axis) and RT-qPCR (Y-axis) methods were used to detect the correlation of p21 gene-induced mRNA levels induced by double-stranded RNA molecules.
- Figure 5 shows the effect of small activating RNA on the induction of p21 mRNA expression and inhibition of KU-7 cell proliferation.
- the three small activating RNAs shown were transfected with KU-7 cells at 10 nM for 72 hours.
- A RT-qPCR analysis of p21 gene mRNA expression levels.
- B CCK-8 method to assess cell viability. The viability of the cells in the saRNA-treated group was expressed as a percentage of the cell viability relative to the control-treated group (Mock).
- C Representative cell image at the end of transfection (100 x).
- Figure 6 shows the effect of small activating RNA on the induction of p21 mRNA expression and inhibition of HCT116 cell proliferation.
- the three small activating RNAs shown were transfected with HCT116 cells at 10 nM for 72 hours.
- A RT-qPCR analysis of p21 gene mRNA expression levels.
- B CCK-8 method was used to evaluate cell viability, and the viability of cells in the saRNA-treated group was expressed as a percentage of cell viability relative to the control-treated group (Mock).
- C Representative cell image at the end of transfection (100 x).
- Figure 7 shows the effect of small activating RNA on the induction of p21 mRNA expression and inhibition of HepG2 cell proliferation.
- the three small activating RNAs shown were transfected with HepG2 cells at 10 nM for 72 hours.
- A RT-qPCR analysis of p21 gene mRNA expression levels.
- B CCK-8 method was used to evaluate cell viability, and the viability of cells in the saRNA-treated group was expressed as a percentage of cell viability relative to the control-treated group (Mock).
- C Representative cell image at the end of transfection (100 x).
- complementary refers to the ability of two oligonucleotide strands to form base pairs with each other.
- Base pairs are typically formed by hydrogen bonds between nucleotide units in an antiparallel oligonucleotide chain.
- the complementary oligonucleotide strand can be base paired in Watson-Crick mode (eg, AT, AU, CG), or in any other manner that allows for the formation of a duplex (eg, Hoogsteen type or reverse Hoogsteen type base pairing).
- Base pairing “100% pairing" or “completely complementary” means having 100% complementarity, ie, the nucleotide units of both strands are all hydrogen bonded to each other.
- Fully complementary or 100% paired means that each nucleotide unit from the first oligonucleotide strand in the double stranded region of the double stranded oligonucleotide molecule can form a hydrogen bond with the second oligonucleotide strand There is no "mismatch" situation. Incomplete complementarity refers to the case where the nucleotide units of both strands cannot all be hydrogen bonded to each other. For example, for an oligonucleotide strand of 20 nucleotides in length with two double stranded regions, if only two base pairs on each strand can hydrogen bond to each other, the oligonucleotide strand exhibits 10% Complementarity.
- the oligonucleotide strand exhibits 90% complementarity.
- Substantial complementarity refers to about 79%, about 80%, about 85%, about 90%, and about 95% complementarity.
- oligonucleotide refers to a polymer of nucleotides and includes, but is not limited to, single or double stranded molecules of DNA, RNA, or DNA/RNA hybrids, including regularly and irregularly. Alternate deoxyribosyl moieties and oligonucleotide moieties, as well as modifications of these classes of oligonucleotides and to naturally occurring or non-naturally occurring backbones.
- oligonucleotide refers to an oligonucleotide comprising two or more modified or unmodified ribonucleotides and/or analogs thereof.
- oligonucleotide strand and "oligonucleotide sequence” as used herein are used interchangeably and refer to a generic term for short-chain nucleotides of less than 50 bases (nucleotides may be deoxyribonucleic acid DNA or RNA RNA).
- the length of the oligonucleotide strand may be any length of 17 to 30 nucleotides.
- gene refers to all nucleotide sequences required to encode a polypeptide chain or to transcribe a functional RNA.
- a “gene” can be a gene that is endogenous or fully or partially recombined for a host cell (eg, due to the introduction of an exogenous oligonucleotide encoding a promoter and a coding sequence or a heterologous promoter that will be adjacent to an endogenous coding sequence). Introduced into the host cell).
- the term “gene” includes nucleic acid sequences that can be composed of exons and introns.
- the sequence encoding the protein is, for example, a sequence contained within an exon of an open reading frame between the initiation codon and the stop codon, and as used herein, "gene” may be taken to include, for example, a gene regulatory sequence such as a promoter.
- a gene regulatory sequence such as a promoter.
- a "gene” can be used to describe a functional nucleic acid comprising a regulatory sequence, such as a promoter or enhancer. Expression of the recombinant gene can be controlled by one or more heterologous regulatory sequences.
- target gene may be a nucleic acid sequence, a transgene, a viral or bacterial sequence naturally occurring in an organism, a chromosomal or extrachromosomal and/or transient or stable transfection or incorporation into a cell and/or its chromatin.
- the target gene may be a protein-coding gene or a non-protein-encoding gene (for example, a microRNA gene or a long-chain non-coding RNA gene).
- the target gene usually contains a promoter sequence, and a small activating RNA designed to have identity (also referred to as homology) with the promoter sequence can achieve positive regulation of the target gene, which is manifested by up-regulation of target gene expression.
- Target gene promoter sequence refers to a non-coding sequence of a target gene
- a target gene promoter sequence in “complementary to a target gene promoter sequence” refers to a coding strand of the sequence, also referred to as a non-template strand, That is, a nucleic acid sequence which is the same sequence as the coding sequence of the gene.
- a “target sequence” refers to a sequence fragment to which a sense oligonucleotide strand or an antisense oligonucleotide of a small activating RNA in a target gene promoter sequence is homologous or complementary.
- sense strand As used herein, the terms “sense strand”, “sense oligonucleotide strand” are interchangeable, and a sense oligonucleotide strand of a small activating RNA refers to a promoter sequence containing a target gene in a small activating RNA duplex. A first ribonucleic acid strand having the identity of the coding strand.
- antisense strand As used herein, the terms “antisense strand”, “antisense oligonucleotide strand” are interchangeable, and an antisense oligonucleotide strand of a small activating RNA refers to a small activating RNA duplex and a sense oligonucleotide. A second ribonucleic acid strand complementary to the strand.
- coding strand refers to a DNA strand in a target gene that is not transcribed, and the nucleotide sequence of the strand is identical to the sequence of the RNA produced by transcription (in the RNA, the DNA is substituted with U). T).
- the coding strand of the target gene promoter double-stranded DNA sequence described in the present invention refers to a promoter sequence on the same DNA strand as the target gene DNA coding strand.
- template strand refers to another strand of a double-stranded DNA of a target gene that is complementary to the coding strand, which can be transcribed as a template for RNA, which is complementary to the transcribed RNA base (AU, GC).
- RNA polymerase binds to the template strand and moves along the 3' ⁇ 5' direction of the template strand, catalyzing the synthesis of RNA in the 5' ⁇ 3' direction.
- the template strand of the target gene promoter double-stranded DNA sequence described in the present invention refers to a promoter sequence on the same DNA strand as the target gene DNA template strand.
- promoter refers to a nucleic acid sequence that does not encode a protein, which exerts a regulatory effect on their transcription by positional association with protein encoding or RNA encoding nucleic acid sequences.
- a eukaryotic promoter comprises 100-5,000 base pairs, although this range of lengths is not meant to limit the term “promoter” as used herein.
- the promoter sequence is typically located at the 5' end of the protein coding or RNA coding sequence, in some cases the promoter sequence is also present in the exon and intron sequences.
- transcription initiation site refers to a nucleotide that marks the initiation of transcription on a template strand of a gene.
- a transcription initiation site can occur on the template strand of the promoter region.
- a gene can have more than one transcription initiation site.
- identity refers to a coding strand of a region of a promoter sequence of a promoter gene of a small activation RNA (sense strand or antisense strand). Or the template chain has at least 75% similarity.
- overhang refers to an oligonucleotide (5' or 3') non-base pairing nucleotide that is extended beyond the double strand. Another strand of one of the strands within the oligonucleotide is produced. A single-stranded region that extends beyond the 3' and/or 5' ends of the duplex is referred to as a protrusion.
- gene activation or “activation gene” are used interchangeably to refer to measurement of gene transcription levels, mRNA levels, protein levels, enzymatic activity, methylation status, chromatin status or conformation, translation levels, Or its activity or state in a cell or biological system to determine the increase in transcription, translation or expression or activity of a nucleic acid. These activities or states can be determined directly or indirectly.
- gene activation and activation gene refer to an increase in activity associated with a nucleic acid sequence, regardless of the mechanism by which such activation occurs, for example, it acts as a regulatory sequence, is transcribed into RNA, is translated into a protein and Increase protein expression.
- small activating RNA As used herein, the terms “small activating RNA,” “saRNA,” “small activating nucleic acid molecule” are used interchangeably to refer to a ribonucleic acid molecule capable of promoting gene expression, and may be comprised of a non-coding nucleic acid sequence comprising a target gene (eg, Promoter, enhancer, etc.) a first ribonucleic acid strand of a ribonucleotide sequence having sequence identity (antisense strand, also referred to as an antisense oligonucleotide strand) and a nucleotide sequence complementary to the first strand A second ribonucleic acid chain (sense strand, also referred to as a sense strand or a sense oligonucleotide strand), wherein the first strand and the second strand form a duplex.
- a target gene eg, Promoter, enhancer, etc.
- antisense strand also referred to as an anti
- Small activating RNAs can also be composed of synthetic or vector-expressed single-stranded RNA molecules that form a double-stranded region hairpin structure, wherein the first region comprises a nucleic acid sequence having sequence identity to the promoter sequence of the gene, and the second region comprises The nucleic acid sequence is complementary to the first region.
- the duplex region of the small activating RNA molecule typically has a length of from about 10 to about 50 base pairs, from about 12 to about 48 base pairs, from about 14 to about 46 base pairs, from about 16 to about 44.
- Base pairs about 18 to about 42 base pairs, about 20 and about 40 base pairs, about 22 and about 38 base pairs, about 24 and about 36 base pairs, about 26 and about 34 base pairs, about 28 and about 32 base pairs, typically about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50 base pairs.
- saRNA and small activating RNA small activating nucleic acid molecule
- nucleic acids other than ribonucleotide moieties, including but not limited to modified nucleotides or analogs.
- hot spot refers to a gene promoter region of at least 30 bp in length, in which aggregation of functional small activation nucleic acid molecule targets, ie, small activation nucleic acid molecules targeting these hotspot regions, are at least 60 % can induce target gene mRNA expression to be 1.5 times or more.
- p21 refers to the p21 WAF1/CIP1 gene, also known as the CDKN1A gene, is a cyclin-dependent kinase (CDK) inhibitor and an important tumor suppressor gene, sometimes referred to as a "target. gene".
- CDK cyclin-dependent kinase
- target. gene an important tumor suppressor gene
- the term "synthetic” refers to the manner in which an oligonucleotide is synthesized, including any means by which RNA can be synthesized, such as chemical synthesis, in vitro transcription, vector expression, and the like.
- the preparation methods of the small activating nucleic acid molecules provided by the present invention include sequence design and sequence synthesis.
- the synthesis of the small activating nucleic acid molecule sequence can be carried out by chemical synthesis or by a biotechnology company specializing in nucleic acid synthesis.
- the method of chemical synthesis includes the following four processes: (1) synthesis of oligoribonucleotides; (2) deprotection; (3) purification separation; (4) desalting and annealing.
- the specific steps of chemical synthesis of the double-stranded RNA molecules of the present invention, such as saRNA are as follows:
- RNA was synthesized on an automated DNA/RNA synthesizer (for example, Applied Biosystems EXPEDITE 8909) while setting the coupling time for each cycle to 10-15 minutes, and the starting material was 5' for solid phase attachment.
- -O-p-dimethoxytrityl-thymidine support the first cycle is linked to a base on a solid support, and then in the nth (19 ⁇ n ⁇ 2) cycle, at One base is ligated to the base to which the n-1 cycle is ligated, and this cycle is repeated until the synthesis of all nucleic acid sequences is completed.
- the obtained crude product of saRNA was dissolved in 2 ml of an aqueous solution of ammonium acetate having a concentration of 1 mol/ml, and then separated by a high pressure liquid chromatography reverse phase C18 column to obtain a purified saRNA single-chain product.
- Cell lines RT4, KU-7, T24, J82, TCCSUP and HT-1197 were cultured in modified McCoy's 5A medium (Gibco); cell lines 5637, PC3 and Bel-7402 were cultured in RPMI 1640 medium (Gibco); The UM-UC-3 cell line was cultured in basal medium (Gibco). All media contained 10% calf serum (Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco). The cells were cultured at 5% CO 2 at 37 °C. The double-stranded RNA molecules designed in the experiments were transfected with RNAiMax (Invitrogen, Carlsbad, CA) at a concentration of 10 nM (unless otherwise stated) according to the manufacturer's instructions.
- RNAiMax Invitrogen, Carlsbad, CA
- RNA (1 ⁇ g) was reverse transcribed into cDNA using a PrimeScript RT kit containing gDNA Eraser (Takara, Shlga, Japan).
- qPCR was performed using ABI 7500 Fast Real-time PCR System (Applied Biosystems) and SYBR Premix Ex Taq II (Takara, Shlga, Japan) reagents under the conditions of 95 ° C for 3 seconds, 60 ° C for 30 seconds, and amplification for 40 cycles. Take GAPDH as an internal reference. All primer sequences are listed in Table 1.
- the cells were plated at 2-4 x 10 3 cells/well in 96-well plates, cultured overnight, and transfected with oligonucleotide duplexes. Three days after transfection, cell proliferation assay was performed using CCK8 (Dojindo) according to the instructions. The experimental procedure is briefly described as follows: 10 ⁇ L of CCK8 solution was added to each well, and incubated at 37 ° C for 1 hour, after which the absorbance at 450 nm was measured using a microplate reader.
- the cells were plated in 96-well plates and transfected with oligonucleotide duplexes. After transfection for 72 hours, the mRNA level of the target gene was quantitatively detected using the QuantiGene 2.0 kit (AffyMetrix).
- the QuantiGene 2.0 kit is a hybridization-based method that directly quantifies mRNA levels using gene-specific probes. The experimental procedure is briefly described as follows: The lysate was added to lyse the transfected cells, and the cell lysate was loaded into a capture well plate containing CDKN1A (p21) and HPRT1 (housekeeping gene) probes, and hybridized overnight at 55 °C.
- hybridization was performed sequentially with 2.0 PreAMP, 2.0 AMP and 2.0 Lable Probe in 100 ⁇ L of the corresponding buffer (provided by the Quantigene 2.0 kit). All hybridizations were shaken for 1 hour at 50-55 °C. After the final wash, 2.0 Substrate was added and incubated for 5 minutes at room temperature. The optical signal was then detected using an Infinite 200PRO plate reader (Tecan, Switzerland).
- Results are expressed as mean ⁇ standard deviation.
- One-way analysis of variance was performed using GraphPad Prism software (GraphPad Software) followed by Tukey's t-test for statistical analysis. The criteria for statistical significance were set to *p ⁇ 0.05, **p ⁇ 0.01 and ***p ⁇ 0.001.
- Example 1 Screening for functional small activator RNA (saRNA) targeting the promoter region of the p21 gene
- a 1 kb promoter sequence of the p21 gene was obtained from the UCSC Genome database (Fig. 1).
- a target of 19 bp in size was selected from the upstream of the transcription start site (TSS) at -1 kb, and moved to the TSS site by moving 1 bp each time to obtain a total of 982 target sequences.
- the target sequence is subjected to a filtration treatment to exclude a GC sequence containing more than 65% or less than 35%, and a target sequence containing 5 or more than 5 consecutive identical nucleotides. After filtering, the remaining 439 target sequences entered the screening process as candidates.
- the corresponding double-stranded double-stranded RNA molecules are chemically synthesized.
- the length of the sense and antisense strands of the double-stranded RNA molecule used in the experiment are both 21 nucleotides, and the double-stranded RNA molecule, for example, the 5' of the first ribonucleic acid strand (sense strand) of the double-stranded saRNA
- the 19 nucleotides of the region are 100% identical to the promoter target sequence, and the 3' end contains a dTdT overhang; the 19 nucleotide of the 5' region of the second ribonucleic acid strand is aligned with the first ribonucleic acid strand
- the 19 nucleotides of the 3' region sequence are fully complementary and contain a dTdT overhang at the 3' end.
- the aforementioned double-stranded RNA molecule was transfected into PC3 prostate cancer cells at a final concentration of 10 nM, and 72 hours later, p21 gene mRNA levels were detected using the QuantiGene 2.0 kit.
- the fold change in p21 mRNA levels of each double-stranded RNA molecule relative to the blank control treatment was calculated and plotted in Figure 2.
- the fold change in p21 gene mRNA caused by all double-stranded RNA molecules in this study ranged from 0.66 (inhibition) to 8.12 (induction) (Fig. 2B).
- RNA molecules screened 132 double-stranded RNA molecules (30.1%) were able to induce p21 mRNA at least 2-fold; 229 (52.4%) double-stranded RNA molecules induced p21 mRNA at least 1.5-fold, and these induced p21 The mRNA expression increased by more than 10%.
- the double-stranded RNA molecule is a saRNA, a functional saRNA. These functional saRNAs are dispersed throughout the p21 promoter region.
- the hotspot region is defined as a region containing at least 10 corresponding small activating RNAs, wherein at least 60% of the small activating RNAs are capable of inducing p21 mRNA expression of 1.5-fold or more (Fig. 2A and Fig. 3).
- the target sequences of the hotspots 1 to 8 and the corresponding small activating RNA sequences are listed in Tables 2 and 3, respectively.
- hotspots include hotspot region 1, the corresponding target sequence is -893 bp to -801 bp of the p21 promoter sequence, and the sequence is as shown in SEQ ID NO: 93, and 44 functional saRNAs were found in this region (Table 3, Figure 3A).
- the corresponding target sequence of the hot spot region 2 (Table 3, Figure 3B) is -71 to -632 bp of the p21 promoter sequence, and the sequence is as shown in SEQ ID NO: 94.
- 31 functional saRNAs were found in this region, respectively, RAG -693, RAG-692, RAG-688, RAG-696, RAG-694, RAG-687, RAG-691, RAG-690, RAG-689, RAG-682, RAG-686, RAG-662, RAG-695 , RAG-654, RAG-658, RAG-685, RAG-704, RAG-714, RAG-705, RAG-661, RAG-656, RAG-698, RAG-697, RAG-657, RAG-715, RAG -652, RAG-651, RAG-650, RAG-716, RAG-717, RAG-711;
- Hot spot 3 (Table 3, Figure 3C), the corresponding target sequence is -585 bp to -551 bp of the p21 promoter sequence, the sequence is shown as SEQ ID NO: 95, and it is found in this region that it contains 9 functional saRNAs, respectively RAG-580, RAG-577, RAG-569, RAG-576, RAG-570, RAG-574, RAG-585, RAG-579, RAG-584;
- Hot spot 4 (Table 3, Figure 3D), the corresponding target sequence is -554 bp to -505 bp of the p21 promoter sequence, and the sequence is shown as SEQ ID NO: 96.
- 17 functional saRNAs were found, respectively RAG-524, RAG-553, RAG-537, RAG-526, RAG-554, RAG-523, RAG-534, RAG-543, RAG-525, RAG-535, RAG-546, RAG-545, RAG- 542, RAG-531, RAG-522, RAG-529, RAG-552;
- Hot spot 5 (Table 3, Figure 3E), the corresponding target sequence is -514 bp to -485 bp of the p21 promoter sequence, and the sequence is shown as SEQ ID NO: 97.
- 9 functional saRNAs were found, respectively RAG-503, RAG-504, RAG-505, RAG-506, RAG-507, RAG-508, RAG-509, RAG-510, RAG-511, RAG-512, RAG-513, RAG-514;
- Hot spot 6 (Table 3, Figure 3F), the corresponding target sequence is -442 bp to -405 bp of the p21 promoter sequence, and the sequence is shown as SEQ ID NO: 98. In this region, 12 functional saRNAs were found, respectively.
- Hot spot 7 (Table 3, Figure 3G), the corresponding target sequence is -352 bp to -313 bp of the p21 promoter sequence, the sequence is shown as SEQ ID NO: 99, and 13 functional saRNAs were found in this region, respectively RAG-335, RAG-351, RAG-352, RAG-331, RAG-344, RAG-342, RAG-341, RAG-333, RAG-345, RAG-346, RAG-336, RAG-332, RAG- 343;
- Hot spot 8 (Table 3, Figure 3H), the corresponding target sequence is -325 bp to -260 bp of the p21 promoter sequence, the sequence is shown as SEQ ID NO: 100, and 18 functional saRNAs were found in this region, respectively RAG-294, RAG-285, RAG-286, RAG-292, RAG-291, RAG-284, RAG-279, RAG-280, RAG-325, RAG-293, RAG-322, RAG-321, RAG- 281, RAG-289, RAG-278, RAG-283, RAG-282, RAG-295.
- Example 2 saRNA induces p21 gene mRNA expression and inhibits cancer cell proliferation
- the saRNA (RAG1-431, RAG1-553, RAG1-688) screened by QuantiGene 2.0 was transfected into the cancer cell line KU-7 (bladder cancer), HCT116 (colon cancer) and HepG2 (hepatocellular carcinoma). The results showed that in all of the above cell lines, saRNA induced at least twice the expression level of p21 gene mRNA and inhibited cell proliferation, revealing the efficacy of saRNA-mediated p21 induction.
- RAG1-431, RAG1-553, and RAG1-688 were transfected into KU7 cells, respectively, to induce p21 mRNA expression of 14.0, 36.9, and 31.9 fold, respectively, and the survival rate relative to blank treatment was 71.7%, 60.7%, 67.4% (Figure 5).
- RAG1-431, RAG1-553, and RAG1-688 were transfected into HCT116 cells, respectively, to induce p21 mRNA expression of 2.3, 3.5, and 2.4 fold, respectively, and the survival rates relative to blank treatment were 45.3%, 22.5%, and 38.5% ( Figure 6).
- RAG1-431, RAG1-553, and RAG1-688 were transfected into HepG2 cells, respectively, to induce p21 mRNA expression of 2.2, 3.3, and 2.0 fold, respectively, and the survival rate of the corresponding blank treatment was 76.7%, 64.9%, and 79.9% (Fig. 7).
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Abstract
Description
Claims (23)
- 一种小激活RNA,其特征在于,所述小激活RNA中的一条链与SEQ ID NO:5、6、7、8、9、10、11、12所示的序列中的任一长度为16-35个核苷酸的连续片段具有至少75%的同源性或互补性,所述小激活RNA通过靶向人p21基因启动子序列激活或上调p21基因的表达。
- 如权利要求1所述的小激活RNA,其中所述小激活RNA包含正义核酸链和反义核酸链,所述正义核酸链和反义核酸链含有互补区域,互补区域能形成双链核酸结构,其中的正义核酸链或反义核酸链与人p21基因启动子序列中的任一长度为16-35个核苷酸的连续片段具有75%以上、80%以上、90%以上、95%以上、99%以上或100%的同源性。
- 如权利要求2所述的小激活RNA,其中所述正义核酸链和反义核酸链存在于两条不同的核酸链上。
- 如权利要求2所述的小激活RNA,其中所述正义核酸链和反义核酸链存在于同一条核酸链上,为发夹型单链核酸分子,其中正义核酸链和反义核酸链的互补区域形成双链核酸结构。
- 如权利要求3所述的小激活RNA,其中所述小激活RNA中的至少一条链具有长度为0至6个核苷酸的3’突出端。
- 如权利要求5所述的小激活RNA,其中所述小激活RNA中的两条链都具有长度为2-3个核苷酸的3’突出端。
- 如权利要求2至6任一项所述的小激活RNA,其中所述正义核酸链或反义核酸链的长度为16-35个核苷酸。
- 如权利要求1所述的小激活RNA,其中所述正义核酸链或反义核酸链与SEQ ID NO:13-30、35-46、59-62、67-74、77-80、85-96、103-108、111-118、121-132、139-140、147-180、185-186、189-190、195-198、201-202、209-212、215-218、225-240、243-246、249-258、261-262、265-270、275-280、283-300、303-308、317-320、323-324、329-348、351-352、357-358、361-366、371-392、399-400、405-412、415-416、419-424、429-432、439-442、447-450、453-458、463-468所示序列具有至少75%的同源性。
- 如权利要求8所述的小激活RNA,其中所述正义核酸链或反义核酸链序列如SEQ ID NO:13-30、35-46、59-62、67-74、77-80、85-96、103-108、111-118、121-132、 139-140、147-180、185-186、189-190、195-198、201-202、209-212、215-218、225-240、243-246、249-258、261-262、265-270、275-280、283-300、303-308、317-320、323-324、329-348、351-352、357-358、361-366、371-392、399-400、405-412、415-416、419-424、429-432、439-442、447-450、453-458、463-468任一核苷酸序列所示。
- 如权利要求1至9任一项所述的小激活RNA,其中所述小激活RNA中的至少一个核苷酸为化学修饰的核苷酸,所述化学修饰为如下修饰中的至少一种:(1)对所述小激活RNA的核苷酸序列中连接核苷酸的磷酸二酯键的修饰;(2)对所述小激活RNA的核苷酸序列中的核糖的2’-OH的修饰;(3)对所述小激活RNA的核苷酸序列中的碱基的修饰;(4)所述小激活核酸分子的核苷酸序列中的至少一个核苷酸为锁核酸。
- 如权利要求1至10任一项所述的小激活RNA,所述激活或上调p21基因的表达为上调至少10%。
- 如权利要求1至11任一项所述的小激活RNA在制备用于激活或上调p21基因在细胞中表达的制剂中的应用。
- 如权利要求12所述的应用,其中所述的小激活RNA被直接导入所述细胞中。
- 如权利要求13所述的应用,其中所述的细胞是哺乳动物细胞,优选为人类细胞,更优选为人类肿瘤细胞。
- 如权利要求14所述的应用,其中所述的细胞存在于人体中。
- 如权利要求15所述的应用,其中所述的人体是患有由p21蛋白表达不足引发的肿瘤患者,并且所述小激活核酸分子被施用以有效量以实现对肿瘤的治疗,所述肿瘤优选为膀胱癌、前列腺癌、肝癌或结直肠癌。
- 一种分离的p21基因小激活RNA靶位点,其中所述靶位点为选自SEQ ID No5-12的任一条序列上的任意连续16-35个核苷酸序列。
- 一种激活或上调p21基因在细胞中表达的方法,其中所述方法包括向所述细胞施用如权利要求1至11任一项所述的小激活RNA。
- 如权利要求18所述的方法,其中所述的小激活RNA被直接导入所述细胞中。
- 如权利要求18或19所述的方法,其中所述的细胞是哺乳动物细胞,优选为人类细胞,更优选为人类肿瘤细胞,再优选为人膀胱癌、前列腺癌、肝癌或结直肠癌细胞。
- 一种包含如权利要求1至11任一项所述的小激活RNA和药学上可接受的载 体的组合物。
- 如权利要求21所述的组合物,其特征在用于药学上可接受的载体为脂质体、高分子聚合物或多肽。
- 如权利要求1至11任一项小激活RNA或如权利要求21或22所述的组合物在制备用于激活或上调p21基因表达的药物中的应用,优选为在制备抗肿瘤或良性增殖性病变中的药物中的应用,更优选地,所述肿瘤为膀胱癌、前列腺癌、肝癌或结直肠癌。
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WO2022166849A1 (en) * | 2021-02-08 | 2022-08-11 | Ractigen Therapeutics | Multi-valent oligonucleotide agent and methods of use thereof |
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WO2022166815A1 (zh) * | 2021-02-07 | 2022-08-11 | 中美瑞康核酸技术(南通)研究院有限公司 | 用于治疗增殖性玻璃体视网膜病变的双链核酸分子及其应用 |
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WO2022166814A1 (zh) * | 2021-02-07 | 2022-08-11 | 中美瑞康核酸技术(南通)研究院有限公司 | 一种化学修饰的小激活rna |
WO2022166815A1 (zh) * | 2021-02-07 | 2022-08-11 | 中美瑞康核酸技术(南通)研究院有限公司 | 用于治疗增殖性玻璃体视网膜病变的双链核酸分子及其应用 |
WO2022166849A1 (en) * | 2021-02-08 | 2022-08-11 | Ractigen Therapeutics | Multi-valent oligonucleotide agent and methods of use thereof |
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US20210024915A1 (en) | 2021-01-28 |
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