OLIGOMERIC NUCLEIC ACID MOLECULE, AND APPLICATION THEREOF IN AN ACUTE INTERMITTENT PORPHYRIA TREATMENT
20220211739 · 2022-07-07
Inventors
Cpc classification
A61K31/7125
HUMAN NECESSITIES
A61K31/712
HUMAN NECESSITIES
A61P7/00
HUMAN NECESSITIES
C12N15/1034
CHEMISTRY; METALLURGY
C12N5/10
CHEMISTRY; METALLURGY
A61K31/713
HUMAN NECESSITIES
A61K31/7115
HUMAN NECESSITIES
International classification
A61K31/713
HUMAN NECESSITIES
A61P7/00
HUMAN NECESSITIES
C12N15/113
CHEMISTRY; METALLURGY
Abstract
The present invention relates to compositions of small activating nucleic acid molecules for increasing the expression of HMBS gene and a use thereof. The small activating nucleic acid molecule can be a double-stranded or single-stranded RNA molecule targeting the promoter region of the HMBS gene. The first nucleic acid strand and the second nucleic acid strand each contain a complementary region, and the complementary regions can form a double-stranded nucleic acid structure, which can promote the expression of the HMBS gene. The first nucleic acid strand or the second nucleic acid strand independently have a length of 16 to 35 nucleotides. The 3′ terminus of the two oligonucleotide strands may have an overhang of 0 to 6 nucleotides in length. The small activating nucleic acid molecule for the HMBS gene can be used to up-regulate mRNA and protein expressions of the HMBS gene in a cell and promote enzymatic activity thereof
Claims
1. A small activating nucleic acid molecule comprising: a first nucleic acid strand and a second nucleic acid strand, wherein the first nucleic acid strand has at least 75% homology or complementarity to any continuous sequence of 16 to 35 nucleotides in length in SEQ ID NO:1 or SEQ ID NO:2 in the promoter of HMBS gene, the second nucleic acid strand has at least 75% complementarity to the first nucleic acid strand, and the first nucleic acid strand and the second nucleic acid strand can complementarily form a double-stranded nucleic acid structure.
2. The small activating nucleic acid molecule of claim 1, wherein the first nucleic acid strand and the second nucleic acid strand are present on two different nucleic acid strands.
3. The small activating nucleic acid molecule of claim 1, wherein the first nucleic acid strand and the second nucleic acid strand are present on the same nucleic acid strand, wherein the small activating nucleic acid molecule is a hairpin single-stranded nucleic acid molecule, wherein complementary regions of the first nucleic acid strand and the second nucleic acid strand form a double-stranded nucleic acid structure.
4. (canceled)
5. The small activating nucleic acid molecule of claim 2, wherein both strands of the small activating nucleic acid molecule have an overhang of 2 or 3 nucleotides in length at the 3′ terminus.
6. The small activating nucleic acid molecule of claim 1, wherein the first nucleic acid strand and the second nucleic acid strand independently have a length of 16 to 35 nucleotides.
7. The small activating nucleic acid molecule of claim 5, wherein one strand of the small activating nucleic acid molecule comprises a sequence having at least 75 homology or complementarity to a nucleotide sequence selected from SEQ ID NOs:11-29.
8. The small activating nucleic acid molecule of claim 1, wherein the first nucleic acid strand has at least 75% homology to a nucleotide sequence selected from SEQ ID NOs: 30-48, and the second nucleic acid strand has at least 75% homology to a[ny] nucleotide sequence selected from SEQ ID NOs: 49-67.
9. The small activating nucleic acid molecule of claim 1, wherein said first and second strand is selected from the group consisting of: SEQ ID NO:30 and SEQ ID NO:49; SEQ ID NO:31 and SEQ ID NO:50; SEQ ID NO:32 and SEQ ID NO:51; SEQ ID NO:33 and SEQ ID NO:52; SEQ ID NO:34 and SEQ ID NO:53; SEQ ID NO:35 and SEQ ID NO:54; SEQ ID NO:36 and SEQ ID NO:55; SEQ ID NO:37 and SEQ ID NO:56; SEQ ID NO:38 and SEQ ID NO:57; SEQ ID NO:39 and SEQ ID NO:58; SEQ ID NO:40 and SEQ ID NO:59; SEQ ID NO:41 and SEQ ID NO:60; SEQ ID NO:42 and SEQ ID NO:61; SEQ ID NO:43 and SEQ ID NO:62; SEQ ID NO:44 and SEQ ID NO:63; SEQ ID NO:45 and SEQ ID NO:64; SEQ ID NO:46 and SEQ ID NO:65; SEQ ID NO:47 and SEQ ID NO:66; and SEQ ID NO:48 and SEQ ID NO:67.
10. (canceled)
11. The small activating nucleic acid molecule of claim 1, wherein the the small activating nucleic acid molecule comprises at least one chemical modification selected from the group consisting of: (1) modification of a phosphodiester bond connecting nucleotides in the nucleotide sequence of the small activating nucleic acid molecule; (2) modification of 2′-OH of a ribose in the nucleotide sequence of the small activating nucleic acid molecule; and (3) modification of a base in the nucleotide sequence of the small activating nucleic acid molecule; and (4) at least one nucleotide in the nucleotide sequence of the small activating nucleic acid molecule being a locked nucleic acid.
12. The small activating nucleic acid molecule of claim 11, wherein the at least one chemical modification is one or more modification selected from the group consisting of: 2′-fluoro modification, 2′-oxymethyl modification, 2′-oxyethylidene methoxy modification, 2,4′-dinitrophenol modification, locked nucleic acid (LNA), 2′-amino modification, 2′-deoxy modification, 5′-bromouracil modification, 5′-iodouracil modification, N-methyluracil modification, 2,6-diaminopurine modification, phosphorothioate modification, and boranophosphate modification.
13. A nucleic acid coding the small activating nucleic acid molecule of claim 1.
14. The nucleic acid of claim 13, wherein the nucleic acid is a DNA molecule.
15. (canceled)
16. (canceled)
17. The small activating nucleic acid molecule of claim 1, wherein the small activating nucleic acid molecule can activate /upregulate the expression of the HMBS gene by at least 10%.
18. The small activating nucleic acid molecule of claim 8, wherein said first nucleic acid strand is a first DNA, RNA or DNA/RNA hybrid and second nucleic acid strand is a second DNA, RNA or a DNA/RNA hybrid.
19-25. (canceled)
26. A method for activating/upregulating the expression of HMBS gene in a cell, comprising administering the small activating nucleic acid molecule of claim 1 to the cell.
27-30. (canceled)
31. The method of claim 26, wherein the cell is present in a human body.
32. The method of claim 26, wherein the small activating nucleic acid molecule is administered to the cell at a final concentration of 1 nM to 150 nM.
33. (canceled)
34. A method of treating a human patient having a disease or symptom caused by a decreased protein expression of HMBS comprising the step of administering to said patient the small activating nucleic acid of claim 1.
35. The method of claim 34, wherein said human patient has acute intermittent porphyria.
36. The method of claim 35, wherein the small activating nucleic acid molecule is administered at a final concentration of 1 nM to 150 nM.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION
[0049] In the present invention, the related terms are defined as follows.
[0050] The term “complementarity” 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 to T, A to U, and C to G) or in any other manner allowing the formation of a duplex (such as Hoogsteen or reverse Hoogsteen base pairing).
[0051] 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-stranded region of the double-stranded oligonucleotide molecule without “mispairing”. “Incomplete complementarity” means that not all the nucleotide units of the two strands are bonded with each other by hydrogen bonds. For example, for two oligonucleotide strands each of 20 nucleotides in length in the double-stranded region, if only two base pairs in this double-stranded region can be formed through hydrogen bonds, the oligonucleotide strands have a complementarity of 10%. In the same example, if 18 base pairs in this double-stranded region can be formed through hydrogen bonds, the oligonucleotide strands have a complementarity of 90%. Substantial complementarity refers to at least about 75%, about 79%, about 80%, about 85%, about 90%, about 95%, about 99% or about 100% complementarity.
[0052] The term “oligonucleotide” or “small nucleic acid molecule” as used herein refers to polymers of nucleotides, and includes, but is not limited to, single-stranded or double-stranded molecules of DNA, RNA, or DNA/RNA hybrid, oligonucleotide strands containing regularly and irregularly alternating deoxyribosyl portions and ribosyl portions, as well as modified and naturally or nonnaturally existing frameworks for such oligonucleotides. The oligonucleotide for activating target gene transcription described herein is a small activating nucleic acid molecule.
[0053] The terms “oligonucleotide 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 deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)). In the present invention, an oligonucleotide strand may have any of 16 to 35 nucleotides in length.
[0054] As used herein, the term “first nucleic acid strand” may be a sense strand or an antisense strand. The sense strand of a small activating RNA refers to a nucleic acid strand contained in a small activating RNA duplex which has identity to the coding strand of the promoter DNA sequence of a target gene, and the antisense strand refers to a nucleic acid strand in the small activating RNA duplex which is complementary to the sense strand.
[0055] As used herein, the term “second nucleic acid strand” may also be a sense strand or an antisense strand. If the first oligonucleotide strand is a sense strand, the second oligonucleotide strand is an antisense strand; and if the first oligonucleotide strand is an antisense strand, the second oligonucleotide strand is a sense strand.
[0056] The term “gene” as used herein refers to all nucleotide sequences required to encode a polypeptide chain or to transcribe a functional RNA. “Gene” can be an endogenous or fully or partially recombinant gene for a host cell (for example, because an exogenous oligonucleotide and a coding sequence for encoding a promoter are introduced into a host cell, or a heterogeneous promoter adjacent to an endogenous coding sequence is introduced into a host cell). For example, the term “gene” comprises a nucleic acid sequence consisting of exons and introns. Protein-coding sequences are, for example, sequences contained within exons in an open reading frame between an initiation codon and a termination codon, and as used herein, “gene” can comprise such as a gene regulatory sequence, such as a promoter, an enhancer, and all other sequences known in the art for controlling the transcription, expression or activity of another gene, no matter whether the gene comprises a coding sequence or a non-coding sequence. In one case, for example, “gene” can be used to describe a functional nucleic acid comprising a regulatory sequence such as a promoter or an enhancer. The expression of a recombinant gene can be controlled by one or more types of heterogeneous regulatory sequences.
[0057] The term “target gene” as used herein can refer to nucleic acid sequences naturally present in organisms, transgenes, viral or bacterial sequences, can be chromosomes or extrachromosomal genes, and/or can be transiently or stably transfected or incorporated into cells and/or chromatins thereof. The target gene can be a protein-coding gene or a non-protein-coding gene (such as a microRNA gene and a long non-coding RNA gene). The target gene generally contains a promoter sequence, and the positive regulation for the target gene can be achieved by designing a small activating nucleic acid molecule having sequence identity (also called homology) to the promoter sequence, characterized as the up-regulation of expression of the target gene. “Sequence of a target gene promoter” refers to a non-coding sequence of the target gene, and the reference of the sequence of a target gene promoter in the phrase “complementary to the sequence of a target gene promoter” of the present invention refers to a coding strand of the sequence, also known as a non-template strand, i.e., a nucleic acid sequence having the same sequence as the coding sequence of the gene. “Target sequence” refers to a sequence fragment in the sequence of a target gene promoter, which is homologous or complementary to a sense oligonucleotide strand or an antisense oligonucleotide strand of a small activating nucleic acid molecule.
[0058] As used herein, the terms “sense strand” and “sense oligonucleotide strand” can be used interchangeably, and the sense oligonucleotide strand of a small activating nucleic acid molecule refers to the first nucleic acid strand having sequence homology with the coding strand of the sequence of a target gene promoter in the small activating nucleic acid molecule duplex.
[0059] As used herein, the terms “antisense strand” and “antisense oligonucleotide strand” can be used interchangeably, and the antisense oligonucleotide strand of a small activating nucleic acid molecule refers to the second nucleic acid strand which is complementary to the sense oligonucleotide strand in the small activating nucleic acid molecule duplex.
[0060] 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). The coding strand of the double-stranded DNA sequence of the target gene promoter described herein refers to a promoter sequence on the same DNA strand as the DNA coding strand of the target gene.
[0061] The term “template strand” as used herein refers to the other strand complementary with the coding strand in the double-stranded DNA of the target gene, i.e., the strand that, as a template, can be transcribed into RNA, and this strand is complementary with the transcribed RNA (A to U and G to C). In the process of transcription, RNA polymerase binds to the template strand, moves along the 3′.fwdarw.5′ direction of the template strand, and catalyzes the synthesis of the RNA along the 5′.fwdarw.3′ direction. The template strand of the double-stranded DNA sequence of the target gene promoter described herein refers to a promoter sequence on the same DNA strand as the DNA template strand of the target gene.
[0062] 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.
[0063] The term “transcription start site” as used herein refers to a nucleotide marking the transcription start on the template strand of a gene. The transcription start site may appear on the template strand of the promoter region. A gene can have more than one transcription start site.
[0064] The term “identity” or “homology” as used herein means that one oligonucleotide strand (a sense or an antisense strand) of a small activating RNA has sequence similarity to a coding strand or a template strand in a region of the promoter sequence 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%, about 99% or about 100%.
[0065] 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-stranded region extending out of the 3′ terminus and/or 5′ terminus of a duplex is referred to as an overhang.
[0066] As used herein, the terms “gene activation”, “activating gene expression”, “gene up-regulation” and “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, the nucleic acid sequence plays a regulatory role as a regulatory sequence, the nucleic acid sequence is transcribed into RNA and the RNA is translated into a protein, thereby increasing the expression of the protein. Preferably, the small activating RNA molecule provided by the present invention can up-regulate gene or protein expression or increase activity by at least 10%.
[0067] As used herein, 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 upregulate target gene expression and can be composed of a first nucleic acid fragment (antisense strand, also referred to as antisense oligonucleotide strand) containing a nucleotide sequence having sequence homology or identity to the non-coding nucleic acid sequence (e.g., a promoter and an enhancer) of a target gene and a second nucleic acid fragment (sense strand, also referred to as sense oligonucleotide 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 small activating nucleic acid molecule can also be composed of a synthesized or vector-expressed single-stranded RNA molecule that can form a hairpin structure by two complementary regions within the molecule, wherein the first region comprises a nucleotide sequence having sequence identity to the target sequence of a promoter of a gene, and the second region comprises a nucleotide sequence which is complementary to the first region. The length of the duplex region of the small activating nucleic acid molecule is typically about 10 to about 50, about 12 to about 48, about 14 to about 46, about 16 to about 44, about 18 to about 42, about 20 to about 40, about 22 to about 38, about 24 to about 36, about 26 to about 34, and about 28 to about 32 base pairs, and typically about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, or about 50 base pairs. In addition, the terms “saRNA”, “small activating RNA”, and “small activating nucleic acid molecule” also comprise nucleic acids other than the ribonucleotide, including, but not limited to, modified nucleotides or analogues.
[0068] As used herein, the term “hot spot” refers to a gene promoter region of at least 30 bp in length where functional small activating nucleic acid molecules are enriched, i.e., at least 30% of the small activating nucleic acid molecules designed to target this region is functional and can induce a 1.2-fold or more change in the mRNA expression of the target gene.
[0069] As used herein, the term “synthesis” refers to a method for synthesis of an oligonucleotide, including any method allowing RNA synthesis, such as chemical synthesis, in vitro transcription, and/or vector-based expression.
[0070] According to the present invention, the expression of HMBS gene is up-regulated by an RNA activation method, and the production of heme is promoted by increasing the expression protein of HMBS. The HMBS gene in the present invention is sometimes also called a target gene.
[0071] The method for preparing the small activating nucleic acid molecule provided by the present invention comprises sequence design and synthesis.
[0072] Small activating nucleic acid molecule can be chemically synthesized or can be obtained from a biotechnology company specialized in nucleic acid synthesis.
[0073] Generally speaking, chemical synthesis of nucleic acids comprises the following four steps: (1) synthesis of oligomeric ribonucleotides; (2) deprotection; (3) purification and isolation; and (4) desalination and annealing.
[0074] For example, the specific steps for chemically synthesizing the oligomeric nucleic acid molecules of the present invention are as follows. [0075] (1) Synthesis of Oligomeric Nucleic Acid Molecule
[0076] Synthesis of 1 μM RNA was set in an automatic DNA/RNA synthesizer (e.g., Applied Biosystems EXPEDITE8909), and the coupling time of each cycle was also set as 10 to 15 min. With a solid phase-bonded 5′-O-p-dimethoxytriphenylmethyl-thymidine substrate as an initiator, one base was bonded to the solid phase substrate in the first cycle, and then, in the n.sup.th (19≥n≥2) cycle, one base was bonded to the base bonded in the n-1.sup.th cycle. This process was repeated until the synthesis of the whole nucleic acid sequence was completed. [0077] (2) Deprotection
[0078] The solid phase substrate bonded with the oligomeric nucleic acid molecule was put into a test tube, and 1 mL of a mixed solution of ethanol and ammonium hydroxide (volume ratio: 1:3) was added to the test tube. The test tube was then sealed and placed in an incubator, and the mixture was incubated at 25-70 ° C. for 2 to 30 h. The solution containing the solid phase substrate bonded with the oligomeric nucleic acid molecule was filtered, and the filtrate was collected. The solid phase substrate was rinsed with double distilled water twice (1 mL each time), and the filtrate was collected. The collected eluent was combined and dried under vacuum for 1 to 12 h. Then the solution was added with 1 mL of a solution of tetrabutylammonium fluoride in tetrahydrofuran (1 M), let stand at room temperature for 4 to 12 h, followed by addition of 2 mL of n-butanol. Precipitate was collected to give a single-stranded crude product of saRNA by high-speed centrifugation. [0079] (3) Purification and Isolation
[0080] The resulting crude product of saRNA was dissolved in 2 mL of aqueous ammonium acetate solution with a concentration of 1 mol/mL, and the solution was separated by a reversed-phase C18 column of high pressure liquid chromatography to give a purified single-stranded product containing the oligomeric nucleic acid molecule. [0081] (4) Desalination and Annealing
[0082] Salts were removed by gel filtration (size exclusion chromatography). A single sense oligomeric ribonucleic acid strand and a single antisense oligomeric ribonucleic acid strand were mixed in a 1 to 2 mL of buffer (10 mM Tris, pH=7.5-8.0, 50 mM NaCl) at a molar ratio of 1:1. The solution was heated to 95° C., and was then slowly cooled to room temperature to give a solution containing the oligomeric nucleic acid molecule.
[0083] The present invention will be further illustrated with reference to specific examples and drawings below. It should be understood that these examples are merely intended to illustrate the present invention rather than limit the scope of the present invention. In the following examples, study methods without specific conditions were generally in accordance with conventional conditions, such as conditions described in Sambrook, et al., Molecular Cloning: Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989), or conditions recommended by the manufacturer.
EXAMPLES
Example 1: Design and Synthesis of Small Activating Nucleic Acid Molecule Targeting HMBS Promoter
[0084] The sense sequence of HMBS gene promoter from the transcription start site (TSS) to upstream −395 bp was retrieved from the UCSC genome database with a repeat sequence (−350 to −180) being excluded from targets. With the remaining two sequences (region 1 with a length of 45 bp: −395 to −351; and region 2 with a length of 179 bp: −179 to −1) as templates, targets with a size of 19 bp were selected by moving downstream from the most upstream, a total of 27 targets were obtained in region 1 and a total of 161 targets were obtained in region 2 (
Example 2: Screening of saRNAs Targeting HMBS Promoter
(1) Cell Culture and Transfection
[0085] Human hepatocarcinoma cell lines Huh7 and HepG2 were cultured in DMEM media (Gibco). Human embryonic liver cells CCC-HEL-1 and human hepatocarcinoma cells Li-7 were cultured in RPMI-1640 media (Gibco), which all contained 10% of calf serum (Sigma-Aldrich) and 1% of penicillin/streptomycin (Gibco). The cells were cultured at 5% CO.sub.2 and 37° C. According to the instructions of the manufacturer, RNAiMax (Invitrogen, Carlsbad, Calif.) was used to transfect double-stranded oligomeric nucleic acid molecule at a concentration of 10 nM (unless otherwise specified) by reverse transfection.
(2) One-step RT-qPCR
[0086] At the end of transfection, the media were discarded, and each well was washed with 150 μL of PBS once. After discarding PBS, 50 μL of cell lysis buffer was added into each well, and incubated at room temperature for 5 minutes. 1 μl of the resulted cell lysis was taken from each well and subjected to qPCR analysis on a LightCycler® 480 system (Roche) by using a one-step TB Green™ PrimeScrip™ RT-PCR kit II (Takara,RR086A).Each transfection sample was amplified in 3 repeat wells. PCR reaction conditions are shown in Table 1.
TABLE-US-00001 TABLE 1 PCR reaction preparation Reagent Volume/Reaction 2 × One-step TB Green RT-PCR buffer 4 2.5 μL PrimeScript 1 step enzyme mixture 2 0.2 μL Mixture of forward and reverse primers (5 μM) 0.4 μL No RNase dH.sub.2O 1.4 μL Crude lysate (RNA) 0.5 μL Sum 5 μL
[0087] Reaction conditions were as follows: reverse transcription reaction (stage 1): 5 min at 42° C., 10 s at 95° C.; PCR reaction (stage 2): 5 s at 95° C., 20 s at 60° C., 45 cycles of amplification. HPRT1 and TBP were used as internal reference genes. PCR primers used for amplifying HMBS, HPRT1 and TBP genes are shown in Table 2, wherein HMBS was amplified using the HMBS F1/R1 primer pair.
TABLE-US-00002 TABLE 2 Primer sequences for RT-qPCR analysis Sequence Primer No. Sequence (5′-3′) HMBS F1 SEQ ID NO: 5 ACAGCTATGAAGGATGGGCAA HMBS R1 SEQ ID NO: 6 ATCTTCATGCTGGGCAGGGA HPRT1 F SEQ ID NO: 7 ATGGACAGGACTGAACGTCTT HPRT1 R SEQ ID NO: 8 TCCAGCAGGTCAGCAAAGAA TBP F SEQ ID NO: 9 ATAATCCCAAGCGGTTTGCT TBP R SEQ ID NO: 10 CTGCCAGTCTGGACTGTTCT
[0088] In order to calculate the expression value (E.sub.rel) of HMBS (target gene) of 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 1 for calculation.
E.sub.rel=2.sup.(CtT.sup.
wherein CtT.sub.m was the Ct value of the target gene from the Mock sample; CtTs was the Ct value of the target gene from the saRNA-treated sample; CtR1.sub.m 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; CtR2.sub.m was the Ct value of the internal reference gene 2 from the Mock-treated sample; and CtR2.sub.s was the Ct value of the internal reference gene 2 from the saRNA-treated sample.
(3) Screening of Functional saRNAs
[0089] In order to obtain saRNAs capable of activating HMBS transcription, 180 double-stranded oligonucleotide molecules were transfected into Huh7 cells at a concentration of 10 nM. 72 hours later, and according to the same method as described above, cells were lysed and subjected to one-step RT-qPCR analysis to obtain the relative expression value of HMBS gene for each saRNA-treated sample when compared with Mock treatment. The results indicated that 19 saRNAs exhibited activating activity. These double-stranded oligomeric nucleic acid molecules with activating activity are referred to as functional saRNAs.
[0090]
TABLE-US-00003 TABLE 4 Active saRNA Sequences, Active Target Sequences Thereof and Changes in mRNA Expression of HMBS Fold of change in mRNA expre- ssion Functional target Sense sequence Antisense sequence of saRNA sequence (5′-3′) (5′-3′) (5′-3′) HMBS RAG5-124 CCATAGAAGCTGCACTACT CCAUAGAAGCUGCACUACUTT AGUAGUGCAGCUUCUAUGGTT 1.59 (SEQ ID No: 11) (SEQ ID No. 30) (SEQ ID No. 49) RAG5-126 CGCCATAGAAGCTGCACTA CGCCAUAGAAGCUGCACUATT UAGUGCAGCUUCUAUGGCGTT 1.49 (SEQ ID No: 12) (SEQ ID No. 31) (SEQ ID No. 50) RAG5-383 CATAGTGAGGCCACCTCCC CAUAGUGAGGCCACCUCCCTT GGGAGGUGGCCUCACUAUGTT 1.35 (SEQ ID No: 13) (SEQ ID No. 32) (SEQ ID No. 51) RAG5-373 CCACCTCCCCGCTGTCTCT CCACCUCCCCGCUGUCUCUTT AGAGACAGCGGGGAGGUGGTT 1.34 (SEQ ID No: 14) (SEQ ID No: 33) (SEQ ID No: 52) RAG5-179 TGCTGCCTATTTCAAGGTT UGCUGCCUAUUUCAAGGUUTT AACCUUGAAAUAGGCAGCATT 1.33 (SEQ ID No: 15) (SEQ ID No: 34) (SEQ ID No: 53) RAG5-21 CCTCCCCTTCGAGGGAGGG CCUCCCCUUCGAGGGAGGGTT CCCUCCCUCGAAGGGGAGGTT 1.33 (SEQ ID No: 16) (SEQ ID No: 35) (SEQ ID No: 54) RAG5-32 AGAGGGAGGGACCTCCCCT AGAGGGAGGGACCUCCCCUTT AGGGGAGGUCCCUCCCUCUTT 1.30 (SEQ ID No: 17) (SEQ ID No: 36) (SEQ ID No: 55) RAG5-20 CTCCCCTTCGAGGGAGGGC CUCCCCUUCGAGGGAGGGCTT GCCCUCCCUCGAAGGGGAGTT 1.26 (SEQ ID No: 18) (SEQ ID No: 37) (SEQ ID No: 56) RAG5-386 CAACATAGTGAGGCCACCT CAACAUAGUGAGGCCACCUTT AGGUGGCCUCACUAUGUUGTT 1.26 (SEQ ID No: 19) (SEQ ID No: 38) (SEQ ID No: 57) RAG5-374 GCCACCTCCCCGCTGTCTC GCCACCUCCCCGCUGUCUCTT GAGACAGCGGGGAGGUGGCTT 1.26 (SEQ ID No: 20) (SEQ ID No: 39) (SEQ ID No: 58) RAG5-91 CTGGGGAATGGGGTGGTCG CUGGGGAAUGGGGUGGUCGTT CGACCACCCCAUUCCCCAGTT 1.22 (SEQ ID No: 21) (SEQ ID No: 40) (SEQ ID No: 59) RAG5-168 TCAAGGTTGTAGCAAAGCT UCAAGGUUGUAGCAAAGCUTT AGCUUUGCUACAACCUUGATT 1.19 (SEQ ID No: 22) (SEQ ID No: 41) (SEQ ID No: 60) RAG5-79 GTGGTCGAATGGGGAGGTC GUGGUCGAAUGGGGAGGUCTT GACCUCCCCAUUCGACCACTT 1.18 (SEQ ID No: 23) (SEQ ID No: 42) (SEQ ID No: 61) RAG5-371 ACCTCCCCGCTGTCTCTAT ACCUCCCCGCUGUCUCUAUTT AUAGAGACAGCGGGGAGGUTT 1.18 (SEQ ID No: 24) (SEQ ID No: 43) (SEQ ID No: 62) RAG5-153 AGCTAAGTTTGAACAGAGC AGCUAAGUUUGAACAGAGCTT GCUCUGUUCAAACUUAGCUTT 1.16 (SEQ ID No: 25) (SEQ ID No: 44) (SEQ ID No: 63) RAG5-382 ATAGTGAGGCCACCTCCCC AUAGUGAGGCCACCUCCCCTT GGGGAGGUGGCCUCACUAUTT 1.16 (SEQ ID No: 26) (SEQ ID No: 45) (SEQ ID No: 64) RAG5-97 TCACAGCTGGGGAATGGGG UCACAGCUGGGGAAUGGGGTT CCCCAUUCCCCAGCUGUGATT 1.13 (SEQ ID No: 27) (SEQ ID No: 46) (SEQ ID No: 65) RAG5-88 GGGAATGGGGTGGTCGAAT GGGAAUGGGGUGGUCGAAUTT AUUCGACCACCCCAUUCCCTT 1.13 (SEQ ID No: 28) (SEQ ID No: 47) (SEQ ID No: 66) RAG5-125 GCCATAGAAGCTGCACTAC GCCAUAGAAGCUGCACUACTT GUAGUGCAGCUUCUAUGGCTT 1.13 (SEQ ID No: 29) (SEQ ID No: 48) (SEQ ID No: 67)
Example 3: saRNAs Induced Expression of HMBS Gene in Different Cell Lines
[0091] The saRNAs (n=13, final concentrations: 20 nM) shown in Table 4 were transfected into human hepatocellular carcinoma cells Huh.sup.7 and HepG2, and human embryonic liver cells CCC-HEL-1 according to the method described in Example 2. 72 hours after the transfection, the cells were collected, and RNAs were extracted using a Qiagen RNeasy kit. After reverse transcription, a 7500FAST real-time PCR system was used to perform qPCR amplification on the HMBS gene. At the same time, HPRT1 and TBP genes were amplified as internal references. Mock, dsCon2 and siHMBS represent blank and a control dsRNA transfection, and a small interference RNA control transfection, respectively. The PCR result was analyzed according to the method described in Example 2. As shown in
Example 4: saRNAs Induced Protein Expression of HMBS
[0092] The saRNAs (final concentration: 20 nM) shown in
Example 5: saRNAs Enhanced HMBS Enzymatic Activity
[0093] AIP is a disease caused by the in vivo accumulation of δ-aminolevulinic acid (ALA) and PBG (porphobilinogen), and insufficient heme synthesis as a result of the defect or insufficient activity of the third enzyme (hydroxymethylbilane synthase (HMBS)) in the heme synthesis pathway. ALA is a simple endogenous five-carbon chemical substance, and it participates in the biosynthesis of heme in vivo. As a precursor of heme, ALA produces proto-porphyrin IX (abbreviated as PPIX) with a strong photosensitive effect in mitochondria under the action of a series of enzymes such as ALA dehydratase. As an intermediate for the last step of heme biosynthesis, PPIX is bonded with Fe ions to produce heme. Normally, the heme biosynthesis pathway is regulated by a negative feedback mechanism, that is the synthesis of ALA is regulated by the amount of heme in cells, so there is no excessive ALA accumulated in the body. When exogenous ALA is added into cells, the heme synthesis pathway in the cells can convert ALA into PPIX. The content of PPIX can be detected by a fluorescence method. Therefore, the activity of HMBS and the amount of biosynthesized heme can be indirectly reflected by detecting the fluorescence intensity of PPIX (Sassa, et al., J Exp Med 1975; 142:722-731, Divaris, et al., Am J Pathol 1990; 136:891-897, Kennedy, et al., J Photochem Photobiol. 1992; 14:275-292). This detection method is called ALA conversion analysis.
[0094] Human embryonic liver cells CCC-HEL-1 were inoculated into 6-well plates at a concentration of 2×10.sup.5 cells/well. RNAiMax (Invitrogen, Carlsbad, Calif.) and the saRNAs shown in
[0095] As shown in
Example 6: saRNAs Dose-Dependently Induced mRNA and Protein Expressions of HMBS Gene and Increased HMBS Enzynmatic Activity
[0096] Cells were cultured as described in Example 2. Human hepatocarcinoma cells (Li-7) were inoculated into 6-well plates at 2×10.sup.5 cells/well. saRNAs (RAG5-386) as shown in
[0097] As shown in
Example 7: saRNAs Induced mRNA and Protein Expressions of HMBS Gene AIP Patients' Cells GM01623
[0098] GM01623, GM01624 and GM01625 cells (purchased from Coriell Institute, Camden, N.J., USA) were cultured in MEM media (Gibco), all of which contained 15% of calf serum (Sigma-Aldrich), 1% of NEAA (non-essential amino acids, purchased from Thermo Fisher; Item No. 11140050), and 1% of penicillin/streptomycin (Gibco). The cells were cultured at 5% CO.sub.2 and 37° C. The cells GM01623 were inoculated into 6-well plates at 1×10.sup.5 cells/well and transfected using RNAiMax at a final transfection concentration of 20 nM. 72 hours after the transfection, the cells were collected. The cell mRNA extraction and protein lysis quantification method are as described in Example 3 and Example 4.
[0099] As shown in
Example 8: saRNAs Induced mRNA and Protein Expressions of HMBS Gene in AIP Patients' Cells GM01624
[0100] The conditions for culturing and transfecting cells GM01624 are as described in Example 7, and cell mRNA extraction and protein lysis quantification method are as described in Example 3 and Example 4. As shown in
Example 9: saRNAs Induced mRNA and Protein Expressions of HMBS Gene in AIP Patient Cells GM01625
[0101] The conditions for culturing and transfecting cells GM01625 are as described in Example 7 and cell mRNA extraction and protein lysis quantification method are as described in Example 3 and Example 4. As shown in
[0102] Altogether, a plurality of saRNAs capable of activating the expression of HMBS gene were identified through high-throughput screening of saRNAs targeting the HMBS gene promoter. These saRNAs promote heme production by upregulating the expression of HMBS mRNA and HMBS protein. These results suggest that the saRNAs targeting the HMBS gene promoter can be a therapeutic strategy for AIP treatment.