WO2020155534A1 - 寡核苷酸分子及其在肿瘤治疗中的应用 - Google Patents

寡核苷酸分子及其在肿瘤治疗中的应用 Download PDF

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WO2020155534A1
WO2020155534A1 PCT/CN2019/092720 CN2019092720W WO2020155534A1 WO 2020155534 A1 WO2020155534 A1 WO 2020155534A1 CN 2019092720 W CN2019092720 W CN 2019092720W WO 2020155534 A1 WO2020155534 A1 WO 2020155534A1
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nucleic acid
acid molecule
small
lhpp
cell
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PCT/CN2019/092720
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French (fr)
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康涛
李龙承
姜武林
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中美瑞康核酸技术(南通)研究院有限公司
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Priority to KR1020217024914A priority Critical patent/KR20210121079A/ko
Priority to EP19913370.3A priority patent/EP3919618A4/en
Priority to JP2021544868A priority patent/JP2022529562A/ja
Priority to US17/427,393 priority patent/US20220096516A1/en
Priority to CN201980067436.3A priority patent/CN112912501A/zh
Publication of WO2020155534A1 publication Critical patent/WO2020155534A1/zh
Priority to JP2023206801A priority patent/JP2024028895A/ja

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    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/12—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes
    • C12N2310/122—Hairpin
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    • C12Y306/01—Hydrolases acting on acid anhydrides (3.6) in phosphorus-containing anhydrides (3.6.1)
    • C12Y306/01001—Inorganic diphosphatase (3.6.1.1)

Definitions

  • the present invention belongs to the field of nucleic acid technology. Specifically, it relates to gene activation-related oligonucleotide molecules, such as small activation nucleic acid molecules, and applications of small activation nucleic acid molecules in activating/up-regulating histidine phosphatase LHPP gene transcription, and In the treatment of diseases related to LHPP deficiency, such as tumor treatment.
  • the histidine phosphatase LHPP (Phospholysine phosphohistidine inorganic pyrophosphate phosphatase) gene is located on chromosome 10q26.13 of the human genome. It has 7 exons and can be transcribed into 9 types of LHPP. Splice variants (Splice variants). LHPP is expressed in a variety of human tissues, including liver, kidney, and brain tissues (1-3).
  • LHPP is a risk factor for severe depression (2; 4-7) and cancer (8-10).
  • a recent study on hepatocellular carcinoma showed that LHPP was confirmed as a histidine phosphatase with tumor suppressor effect (11).
  • the present invention provides a small activating RNA that continuously activates LHPP transcription with high specificity, which increases the expression of LHPP protein by effectively activating/up-regulating the transcription of LHPP gene, and shows a significant tumor suppressive effect in in vitro and in vivo experiments. It is expected to become a specific medicine for the treatment of cancer.
  • One objective of the present invention is to provide small activating nucleic acid molecules based on the RNA activation process, which can treat diseases related to LHPP deficiency, such as tumors, by activating/up-regulating LHPP gene transcription, thereby increasing the expression of LHPP protein.
  • Another object of the present invention is to provide a composition or preparation containing small activating nucleic acid molecules with tumor suppressive activity.
  • Another object of the present invention is to provide the application of small activating nucleic acid molecules with tumor suppressor activity or compositions or preparations containing them in the preparation of drugs for activating/upregulating the expression of LHPP genes in cells.
  • Another objective of the present invention is to provide a method for activating/up-regulating the expression of LHPP gene in cells.
  • Another object of the present invention is to provide a small activating nucleic acid molecule with tumor suppressor activity or a composition or preparation containing the same for use in the preparation of a medicine for treating diseases or conditions related to LHPP deficiency or deficiency, such as tumors.
  • LHPP deficiency or deficiency related diseases or conditions such as tumor methods.
  • Another objective of the present invention is to provide an isolated LHPP gene small activating nucleic acid molecule target site, wherein the target site includes or is selected from any consecutive 16-35 nuclei on any sequence of SEQ ID NO: 500-504 The sequence of nucleotides.
  • a small activating nucleic acid molecule which activates or up-regulates the expression of the LHPP gene in a cell, and the length of a strand of the small activating nucleic acid molecule and the promoter region of the LHPP gene is 16-35 nucleotides
  • the nucleic acid sequence has at least 75% homology or complementarity, and the promoter region includes 1000 nucleotides upstream of the transcription start site, so as to activate or up-regulate the gene expression.
  • one strand of the small activation nucleic acid molecule includes or is selected from the region -917 to -844 (H1, SEQ ID NO: 500), -710 to -675 from the transcription start site in the promoter of the LHPP gene.
  • Region (H2, SEQ ID NO: 501), -198 to -168 (H3, SEQ ID NO: 502), -151 to -28 (H4, SEQ ID NO: 503), or -845 to -711 region (H5, SEQ ID NO: 504) of consecutive 16-35 nucleotides have at least 75%, for example, at least about 79%, about 80%, about 85%, about 90%, about 95%, about 99% or 100% Nucleic acid sequences of homology or complementarity.
  • one strand of the small activation nucleic acid molecule of the present invention has at least 75%, such as at least about 79%, about 80%, about 85%, and any nucleotide sequence selected from SEQ ID NO: 329-492. About 90%, about 95%, about 99%, or about 100% homology or complementarity.
  • one strand of the small activation nucleic acid molecule of the present invention includes at least 75%, such as at least about 79%, about 80%, and any nucleotide sequence selected from SEQ ID NO: 329-492. , About 85%, about 90%, about 95%, about 99%, or about 100% homology or complementarity of nucleic acid sequences.
  • a strand of the small activation nucleic acid molecule of the present invention has at least 75%, such as at least about 79%, about 80%, and any nucleotide sequence selected from SEQ ID NO: 329-492. About 85%, about 90%, about 95%, about 99%, or about 100% homology or complementarity of nucleic acid sequences are composed.
  • the small activating nucleic acid molecule of the present invention includes a double-stranded small activating nucleic acid molecule targeted to the promoter region of the LHPP gene, comprising a first nucleic acid strand and a second nucleic acid strand, and the first nucleic acid strand and the LHPP gene promoter are between the transcription start site -917 to -844 region (SEQ ID NO: 500), -710 to -675 region (SEQ ID NO: 501), -198 to -168 (SEQ ID NO: 502), -151 to -28 (SEQ ID NO: :503) or -845 to -711 region (SEQ ID NO: 504) any one of consecutive 16-35 nucleotides has at least 75% homology or complementarity, the first nucleic acid strand and the second nucleic acid strand
  • the double-stranded nucleic acid structure can be formed by complementation, and the double-stranded nucleic acid structure can activate the expression of the LHPP
  • the first nucleic acid strand and the second nucleic acid strand of the small activation nucleic acid of the present invention may exist on two different nucleic acid strands, or may exist on the same nucleic acid strand.
  • at least one strand of the small activation nucleic acid molecule may have protrusions or overhangs at the 5'end and/or 3'end, for example, it may have 0 at the 3'end. Up to 6 nucleotides overhangs, such as 0, 1, 2, 3, 4, 5 or 6 nucleotides overhangs.
  • both strands of the small activation nucleic acid molecule of the present invention have protrusions, and more preferably, the 3'ends of both strands of the small activation nucleic acid molecule may have protrusions of 0 to 6 nucleotides, for example, Overhangs of 0, 1, 2, 3, 4, 5, or 6 nucleotides, most preferably, overhangs of 2 or 3 nucleotides.
  • the nucleotide of the overhang may be dT.
  • the small activation nucleic acid molecule of the present invention may also include a small activation nucleic acid molecule that can form a double-stranded region hairpin structure, such as a single-stranded small activation RNA molecule.
  • the small activating nucleic acid molecule of the present invention includes a single-stranded small activating RNA molecule targeted to the promoter region of the LHPP gene, wherein the single-stranded small activating nucleic acid molecule can form a double-stranded hairpin structure.
  • the small activation nucleic acid molecule of the present invention may be a hairpin type single-stranded nucleic acid molecule, wherein the first nucleic acid strand and the second nucleic acid strand have A complementary region capable of forming a double-stranded nucleic acid structure that can promote the expression of the LHPP gene in a cell through, for example, an RNA activation mechanism.
  • the length of the first nucleic acid strand and the second nucleic acid strand may be 16-35 nucleotides, for example, 16, 17, 18, 19, 20, 21, 22, 23, 24 , 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleotides.
  • the first nucleic acid strand of the small activation nucleic acid molecule of the present invention has at least 75% of any nucleotide sequence selected from SEQ ID NO: 1-164, such as at least about 79%, about 80% , About 85%, about 90%, about 95%, about 99%, or about 100% identity or homology
  • the second nucleic acid strand of the small activation nucleic acid molecule is selected from SEQ ID NO: 165-328 Any nucleotide sequence of has at least 75%, for example, at least about 79%, about 80%, about 85%, about 90%, about 95%, about 99%, or about 100% identity or homology.
  • the first nucleic acid strand of the small activation nucleic acid molecule of the present invention includes at least 75%, such as at least about 79%, about 80%, and any nucleotide sequence selected from SEQ ID NO: 1-164. %, about 85%, about 90%, about 95%, about 99%, or about 100% identity or homology of a nucleic acid sequence, or composed of a nucleic acid sequence selected from SEQ ID NO: 1-164
  • the nucleotide sequence has at least 75%, for example, at least about 79%, about 80%, about 85%, about 90%, about 95%, about 99%, or about 100% identity or homology of nucleic acid sequence composition
  • the second nucleic acid strand of the small activation nucleic acid molecule of the present invention includes at least 75% of any nucleotide sequence selected from SEQ ID NO: 165-328, such as at least about 79%, about 80%, about 85% , About 90%, about 95%, about 99%, or about 100% identity or homo
  • the first nucleic acid strand of the small activation nucleic acid molecule of the present invention may include or be selected from any nucleotide sequence of SEQ ID NO: 1-164, and the second strand may include or be selected from SEQ. ID NO: any nucleotide sequence of 165-328.
  • the small activation nucleic acid molecules described herein can be synthesized, transcribed in vitro, or expressed in a vector.
  • nucleotides in the small activation nucleic acid molecules described herein can be natural non-chemically modified nucleotides, and can also include at least one modification.
  • the modification in the small activation nucleic acid molecule described herein may be a chemical modification.
  • at least one nucleotide may have a chemical modification.
  • the chemical modification used in the present invention may include or be selected from one of the following modifications One or more, or any combination:
  • At least one nucleotide in the nucleotide sequence of the small activation nucleic acid molecule is a locked nucleic acid.
  • the chemical modification is well known to those skilled in the art, and the modification of the phosphodiester bond refers to the modification of the oxygen in the phosphodiester bond, including but not limited to phosphorothioate modification and borating phosphate modification. Both modifications can stabilize the structure of saRNA and maintain the high specificity and affinity of base pairing.
  • Ribose modification refers to the modification of the 2'-OH in the nucleotide pentose, that is, the introduction of certain substituents at the hydroxyl position of the ribose sugar, for example, including but not limited to, 2'-fluoro modification, 2'-oxymethyl Group modification, 2'-oxyethylene methoxy modification, 2,4'-dinitrophenol modification, locked nucleic acid (LNA), 2'-amino modification, 2'-deoxy modification, etc.
  • Base modification refers to the modification of the base of a nucleotide, for example, including but not limited to, 5'-bromouracil modification, 5'-iodouracil modification, N-methyluracil modification, 2,6- Diaminopurine modification, etc.
  • lipophilic groups such as cholesterol can be introduced at the end of the first nucleic acid strand or the second nucleic acid strand of the small activating nucleic acid molecule to facilitate the passage of lipids.
  • the cell membrane and nuclear membrane composed of the bilayer interact with the gene promoter region in the nucleus.
  • the small activating nucleic acid molecule provided by the present invention can effectively activate or up-regulate the expression of the LHPP gene in the cell after contact with the cell, and preferably the expression is up-regulated by at least 10%.
  • nucleic acids encoding the small activation nucleic acid molecules described herein.
  • the nucleic acid may be a DNA molecule.
  • the small activation nucleic acid molecule of the present invention may be a double-stranded small activation nucleic acid molecule targeted to the promoter region of the LHPP gene, which includes a first nucleic acid strand and a second nucleic acid strand.
  • the small activating nucleic acid molecule of the present invention may be a single-stranded small activating nucleic acid molecule targeting the promoter region of the LHPP gene.
  • compositions for example, a pharmaceutical composition
  • a composition which comprises the small activation nucleic acid molecule of the present invention or the nucleic acid encoding the small activation nucleic acid molecule described herein and optionally, a pharmaceutically acceptable Accepted carrier.
  • the pharmaceutically acceptable carrier may include or be selected from liposomes, high molecular polymers or polypeptides.
  • the composition of the present invention contains 1-150nM, such as 1-100nM, such as 1-50nM, such as 10nM, 20nM, 30nM, 40nM, 50nM, 60nM, 70nM, 80nM, 90nM, 100nM, 110nM, 120nM , 130nM, 140nM or 150nM of the small activating nucleic acid molecule of the present invention.
  • the composition of the present invention may further include other compounds, such as small molecule compounds for tumor treatment.
  • the small molecule compounds used for tumor treatment may include multi-target anti-tumor drugs such as sorafenib (Sorafenib, the target is PDGFR, KIT, RAF) (SELLECK, S1040), tyrosine kinase inhibitor Agents such as Lenvatinib (Lenvatinib, targets FGFR, VEGFR2, PDGFR, KIT) (SELLECK, S1164), kinase inhibitors such as Regorafenib (Regorafenib, targets FGFR, VEGFR2, PDGFR, KIT, RAF) (SELLECK, S1178) or Cabozantini (Cabozantini, which inhibits MET, VEGFR2 and RET signal transduction) (SELLECK, S1119).
  • sorafenib sorafenib
  • the target is PDGFR, KIT, RAF
  • SELLECK tyrosine kinase inhibitor Agent
  • kits comprising the small activation nucleic acid molecule described above, the nucleic acid encoding the small activation nucleic acid molecule described herein, the small activation nucleic acid molecule of the present invention, or the encoding The nucleic acid cell of the small activating nucleic acid molecule of the present invention, or the composition containing the small activating nucleic acid molecule of the present invention.
  • Another aspect of the present invention relates to the small activation nucleic acid molecule of the present invention, the nucleic acid encoding the small activation nucleic acid molecule of the present invention, the cell comprising the small activation nucleic acid molecule of the present invention and the nucleic acid encoding the small activation nucleic acid molecule of the present invention, Or the application of the composition containing the small activating nucleic acid molecule of the present invention in the preparation of a medicine or preparation for activating/up-regulating the expression of LHPP gene in cells.
  • Another aspect of the present invention also relates to a method for activating/up-regulating the expression of the LHPP gene in a cell, the method comprising administering to the cell the small activating nucleic acid molecule of the present invention, the nucleic acid encoding the small activating nucleic acid molecule of the present invention, Or a composition containing the small activating nucleic acid molecule of the present invention.
  • the small activating nucleic acid molecule of the present invention can be directly introduced into a cell, or a nucleic acid sequence encoding the small activating nucleic acid molecule of the present invention can be introduced into the cell and then produced in the cell; the cell is preferably a mammalian cell, more preferably a human cell.
  • the above-mentioned cells may be in vitro, such as cell lines or cell lines, etc., or they may exist in mammals, such as humans.
  • the human body may be a patient with a disease or condition associated with insufficient or decreased expression of LHPP protein.
  • the small activating nucleic acid molecule of the present invention can be administered in a sufficient amount to achieve the treatment of diseases or conditions related to the lack of LHPP protein amount or the lack or reduction of LHPP protein expression.
  • the disease or condition related to the lack of LHPP protein or the insufficient or decreased expression of LHPP may include, for example, tumors, such as solid tumors, and the solid tumors may include, for example, liver cancer, lung cancer, bladder cancer, prostate cancer, Glioma and so on.
  • Another aspect of the present invention provides an isolated LHPP gene small activating nucleic acid molecule action site, which has any continuous 16-35 nucleotide sequence on the promoter region of the LHPP gene.
  • the action site includes or is selected from any consecutive 16-35 nucleotide sequence on any sequence of SEQ ID NO: 500-504.
  • the site of action may include or be selected from any nucleotide sequence in SEQ ID NO: 329-492.
  • Another aspect of the present invention relates to a method for treating diseases or conditions related to insufficient or decreased expression of LHPP protein in an individual, comprising administering to the individual a therapeutically effective amount of the small activation nucleic acid molecule of the present invention, encoding the small activation nucleic acid of the present invention
  • the method for treating diseases or conditions related to insufficient or decreased expression of LHPP protein in an individual of the present invention includes administering to the individual a therapeutically effective amount of the small activation nucleic acid molecule of the present invention, encoding the small activation of the present invention.
  • the individual may be a mammal, such as a human.
  • diseases or conditions related to insufficient or decreased expression of LHPP protein may include, for example, tumors, such as solid tumors, which may include, for example, liver cancer, lung cancer, bladder cancer, prostate cancer, glioma, and the like.
  • Another aspect of the present invention relates to the small activation nucleic acid molecule of the present invention, the nucleic acid encoding the small activation nucleic acid molecule of the present invention, the cell containing the small activation nucleic acid molecule of the present invention or the nucleic acid encoding the small activation nucleic acid molecule of the present invention, Or the application of the composition containing the small activating nucleic acid molecule of the present invention in the preparation of a medicine for treating diseases or conditions related to insufficient or decreased expression of LHPP protein.
  • the individual may be a mammal, such as a human.
  • the diseases associated with insufficient or decreased expression of LHPP protein may include, for example, tumors, such as solid tumors, and the solid tumors may include, for example, liver cancer, lung cancer, bladder cancer, prostate cancer, glioma, and the like.
  • the small activation nucleic acid molecule of the present invention the nucleic acid encoding the small activation nucleic acid molecule of the present invention, the cell containing the small activation nucleic acid molecule of the present invention or the nucleic acid encoding the small activation nucleic acid molecule of the present invention are provided , Or application of a composition comprising the small activating nucleic acid molecule of the present invention in the preparation of a medicament for the treatment of tumors, such as solid tumors, wherein the solid tumors may include, for example, liver cancer, lung cancer, bladder cancer, prostate cancer, and glial Tumor etc.
  • Another aspect of the present invention relates to the small activation nucleic acid molecule of the present invention, the nucleic acid encoding the small activation nucleic acid molecule of the present invention, the cell containing the small activation nucleic acid molecule of the present invention or the nucleic acid encoding the small activation nucleic acid molecule of the present invention, Or a composition containing the small activating nucleic acid molecule of the present invention and chemotherapeutics, radiotherapy, cell therapy, small molecules, polypeptides, proteins, antibodies or other anti-tumor drugs are prepared for the treatment of LHPP protein underexpression or reduction related The application of drugs or combinations of drugs for diseases or conditions.
  • the small activation nucleic acid molecule of the present invention the nucleic acid encoding the small activation nucleic acid molecule of the present invention, the cell containing the small activation nucleic acid molecule of the present invention or the nucleic acid encoding the small activation nucleic acid molecule of the present invention are provided , Or a composition containing the small activating nucleic acid molecule of the present invention and chemotherapeutics, radiotherapy, cell therapy, small molecules, polypeptides, proteins, antibodies or other anti-tumor drugs are prepared for the treatment of tumors, such as solid tumors or Application in a drug combination, wherein the solid tumor may include, for example, liver cancer, lung cancer, bladder cancer, prostate cancer, glioma and the like.
  • the chemotherapeutic agent includes or is selected from sorafenib, levatinib, regorafenib and cabozantinib.
  • the small activating nucleic acid molecules of the present invention can be used in combination with chemotherapeutic agents, radiotherapy, cell therapy, small molecules, polypeptides, proteins, antibodies or other anti-tumor drugs. It is preferably selected from sorafenib, levatinib, regorafenib and cabozantinib.
  • the small activating nucleic acid molecule capable of activating/up-regulating the expression of LHPP gene provided by the present invention can permanently activate the LHPP gene, thereby efficiently and specifically up-regulating or restoring the expression of LHPP gene and protein and at the same time has low toxicity and side effects, and can be used for preparation Drugs or preparations for diseases or disorders related to insufficient or decreased expression of LHPP protein.
  • the activating saRNA of LHPP shows a good synergistic effect when combined with other anti-tumor drugs, reflecting the synergistic effect on the anti-tumor effect.
  • Figure 1 is a schematic diagram of the LHPP gene structure. Shown in the figure is the LHPP gene structure and the 1kb promoter region used to design saRNA, in which a 449bp Alu repeat sequence is excluded.
  • FIG. 2 shows the changes in the expression of LHPP mRNA mediated by saRNA.
  • 290 saRNAs targeted to the LHPP promoter were transfected into Huh7 cells respectively, and the expression of LHPP mRNA was analyzed by one-step RT-qPCR 72 hours later.
  • the figure shows the changes in LHPP expression relative to the control treatment (control, mock), sorted according to the position of saRNA in the promoter target from -917 to -28.
  • Figure 3 shows the hot spots of saRNA on the LHPP promoter.
  • 290 saRNAs targeted to the LHPP promoter were transfected into Huh7 cells respectively, and the expression of LHPP mRNA was analyzed by one-step RT-qPCR 72 hours later.
  • the figure shows the change in LHPP expression relative to the control treatment (control, mock), sorted according to the target position of saRNA on the LHPP promoter from -917 to -28.
  • the numbers above or below indicate the boundaries of the region (relative to the LHPP transcription start site).
  • Figure 4 shows the negative correlation between LHPP mRNA expression and cell viability.
  • 290 saRNAs targeting the LHPP promoter were respectively transfected into Huh7 cells. After 72 hours, the expression of LHPP mRNA was analyzed by one-step RT-qPCR, and the cell viability was detected by the CCK8 method.
  • Thin line relative expression level of LHPP mRNA (log 2 ), thick line: cell viability.
  • Figure 5 shows that saRNA induces the expression of LHPP and inhibits AKT phosphorylation.
  • Ten saRNAs targeting the LHPP promoter were respectively transfected into Huh7 cells. 72 hours later, (A) RT-qPCR analysis of LHPP mRNA expression; (B) Western blotting method to detect LHPP, pAKT, AKT protein levels.
  • Figure 6 shows that saRNA induces LHPP mRNA expression and inhibits the proliferation of liver cancer cells.
  • the 8 small activating RNA molecules were transfected into liver cancer cells at 10 nM for 72 hours.
  • A RT-qPCR analysis of LHPP gene mRNA expression level.
  • B The CCK-8 method assesses cell viability. The viability of the saRNA-treated group is expressed as a percentage of the cell viability of the control (Mock)-treated group.
  • Figure 7 shows that saRNA induces LHPP mRNA expression and inhibits the proliferation of other cancer cells.
  • the 8 small activating RNAs shown were transfected into cancer cells at 10 nM for 72 hours.
  • A RT-qPCR analysis of LHPP gene mRNA expression level.
  • B The CCK-8 method assesses cell viability. The viability of the saRNA-treated group is expressed as a percentage of the cell viability of the control (Mock)-treated group.
  • Figure 8 shows the combination of saRNA and chemical drugs inhibiting the proliferation of HepG2 cells.
  • the small activating RNAs were transfected into cancer cells with different concentration gradients and used with different chemicals.
  • A The CCK-8 method assesses cell viability. The viability of the saRNA-treated group is expressed as a percentage of the cell viability of the control (Mock)-treated group.
  • use version 1.0software draws the joint index graph (B) and calculates the joint index value (C).
  • Figure 9 shows the combined use of saRNA and chemical drugs to inhibit U87MG cell proliferation.
  • the small activating RNAs were transfected into cancer cells with different concentration gradients and used with different chemicals.
  • the CCK-8 method assesses cell viability. The viability of the saRNA-treated group is expressed as a percentage of the cell viability of the control (Mock)-treated group.
  • use version 1.0software draws the joint index graph (B) and calculates the joint index value (C).
  • Figure 10 shows the combined use of saRNA and chemical drugs to inhibit the growth of HepG2 xenograft tumors.
  • the small activating RNA was injected intratumorally at a dose of 1 mg/kg in combination with chemical drugs, and the volume change of the transplanted tumor during the administration period was recorded.
  • Figure 11 shows the combination of saRNA and chemical drugs inhibiting the growth of U87MG transplanted tumors.
  • the small activating RNA was injected intratumorally at a dose of 1 mg/kg in combination with chemical drugs, and the volume change of the transplanted tumor during the administration period was recorded.
  • Complementary refers to the ability of two oligonucleotide strands to form base pairs with each other. Base pairs are usually formed by hydrogen bonds between nucleotides in antiparallel oligonucleotide chains.
  • Complementary oligonucleotide strands can be base paired in a Watson-Crick manner (e.g., AT, AU, CG), or in any other manner that allows duplex formation (e.g., Hoogsteen type or reverse Hoogsteen type base pairing) performs base pairing.
  • Complementarity includes two situations: complete complementarity and incomplete complementarity.
  • Complete complementarity or 100% complementarity means that each nucleotide from the first oligonucleotide strand in the double-stranded region of the double-stranded oligonucleotide molecule can correspond to the nucleoside at the corresponding position of the second oligonucleotide strand. Acids form hydrogen bonds without "mismatch”. Incomplete complementarity refers to the situation where all the nucleotide units of the two strands cannot be hydrogen bonded to each other.
  • oligonucleotide chain exhibits 10% Complementarity.
  • the oligonucleotide strand exhibits 90% complementarity.
  • Substantial complementarity refers to at least about 75%, about 79%, about 80%, about 85%, about 90%, about 95%, about 99%, or about 100% complementarity.
  • oligonucleotide refers to a polymer of nucleotides, including but not limited to single-stranded or double-stranded molecules of DNA, RNA or DNA/RNA hybrids, including regularly and irregularly alternating Oligonucleotide chains of deoxyribosyl moieties and ribosyl moieties, as well as modifications of these types of oligonucleotides, and naturally occurring or non-naturally occurring backbones.
  • the oligonucleotides used to activate transcription of target genes described in the present invention are small activating nucleic acid molecules.
  • oligonucleotide chain and “oligonucleotide sequence” are used interchangeably and refer to the general term for short-chain nucleotides of less than 35 bases (including deoxyribonucleic acid DNA or ribonucleic acid Nucleotides within RNA).
  • the length of the oligonucleotide chain can be any length from 16 to 35 nucleotides.
  • first nucleic acid strand can be either the sense strand or the antisense strand.
  • the sense strand of the small activating RNA refers to the small activating RNA duplex that contains the coding strand of the promoter DNA sequence of the target gene.
  • the antisense strand refers to the nucleic acid strand complementary to the sense strand in the small activating RNA duplex.
  • the term "second nucleic acid strand" can also be a sense strand or an antisense strand.
  • the first oligonucleotide strand is the sense strand
  • the second oligonucleotide strand is the antisense strand
  • the first oligonucleotide strand is the antisense strand
  • the second oligonucleotide strand is the sense strand.
  • gene refers to the entire nucleotide sequence required to encode a polypeptide chain or transcribe a functional RNA.
  • a “gene” may be a gene endogenous to the host cell or fully or partially recombined (e.g., due to the introduction of an exogenous oligonucleotide encoding a promoter and a coding sequence or a heterologous promoter adjacent to an endogenous coding sequence Into host cells).
  • the term “gene” includes nucleic acid sequences that can be composed of exons and introns.
  • a sequence encoding a protein is, for example, a sequence contained within an exon in an open reading frame between a start codon and a stop codon.
  • gene may refer to including, for example, gene regulatory sequences such as promoters , Enhancers and all other sequences known in the art that control the transcription, expression or activity of another gene, regardless of whether the other gene contains coding or non-coding sequences.
  • gene regulatory sequences such as promoters , Enhancers and all other sequences known in the art that control the transcription, expression or activity of another gene, regardless of whether the other gene contains coding or non-coding sequences.
  • “gene” can be used to describe a functional nucleic acid containing regulatory sequences such as promoters or enhancers. The expression of recombinant genes 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, a chromosomal or extrachromosomal and/or transient or stable transfection or incorporation into a cell and/or its chromatin, naturally occurring in an organism .
  • the target gene may be a protein-coding gene or a non-protein-coding gene (for example, a microRNA gene, a long-chain non-coding RNA gene).
  • the target gene usually contains a promoter sequence, and the design of a small activating nucleic acid molecule that has the same (also called homology) with the promoter sequence can realize the positive regulation of the target gene, which is manifested as the up-regulation of the target gene expression.
  • target gene promoter sequence refers to the non-coding sequence of the target gene.
  • target gene promoter sequence is complementary to the target gene promoter sequence” refers to the coding strand of the sequence, also known as the non-template strand, It is a nucleic acid sequence that is the same sequence as the gene coding sequence.
  • Target or target sequence refers to a sequence fragment homologous or complementary to the sense oligonucleotide strand or antisense oligonucleotide of the small activating nucleic acid molecule in the promoter sequence of the target gene.
  • sense strand and “sense nucleic acid strand” are used interchangeably.
  • the sense oligonucleotide strand of the small activation nucleic acid molecule refers to the small activation nucleic acid molecule duplex containing the promoter sequence of the target gene.
  • the coding strand has the same identity as the first nucleic acid strand.
  • antisense strand and “antisense nucleic acid strand” are used interchangeably.
  • the antisense oligonucleotide strand of a small activating nucleic acid molecule refers to a small activating nucleic acid molecule duplex with a sense oligonucleotide.
  • the second nucleic acid strand that is complementary to the acid strand.
  • coding strand refers to the DNA strand that cannot be transcribed in the target gene.
  • the nucleotide sequence of this strand is consistent with the sequence of the RNA generated by transcription (in RNA, U replaces the DNA in DNA). T).
  • the coding strand of the double-stranded DNA sequence of the target gene promoter in the present invention refers to the promoter sequence on the same DNA strand as the target gene DNA coding strand.
  • template strand refers to another strand of the double-stranded DNA of the target gene that is complementary to the coding strand and can be used as a template to be transcribed into RNA. This strand is complementary to the base of the transcribed RNA (AU, GC). During the transcription process, 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 double-stranded DNA sequence of the target gene promoter in the present invention refers to the promoter sequence on the same DNA strand as the target gene DNA template strand.
  • promoter refers to a sequence that regulates the transcription of protein-encoding or RNA-encoding nucleic acid sequences by being positionally associated with them.
  • a eukaryotic gene promoter contains 100 to 5,000 base pairs, although this length range is not meant to limit the term “promoter” used herein.
  • the promoter sequence is generally located at the 5'end of the protein coding or RNA coding sequence, the promoter sequence can also be present in exon and intron sequences.
  • transcription start site refers to a nucleotide on the template strand of a gene that marks the start of transcription.
  • the transcription initiation site can appear on the template strand in the promoter region.
  • a gene can have more than one transcription start site.
  • identity refers to the coding strand between one of the oligonucleotide strands (sense strand or antisense strand) of the small activating RNA and a region of the promoter sequence of the target gene Or the similarity in the template chain.
  • 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% .
  • overhang As used herein, the terms “overhang”, “overhang”, and “overhang” are used interchangeably and refer to non-base paired nucleotides at the end (5' or 3') of an oligonucleotide chain, which are extended beyond One of the strands in a double-stranded oligonucleotide is produced by the other strand.
  • the single-stranded region that extends beyond the 3'and/or 5'end of the duplex is called an overhang.
  • gene activation or “activation of genes” or “gene up-regulation” or “up-regulation of genes” are used interchangeably and refer to the measurement of gene transcription level, mRNA level, protein level, enzyme activity, methylation State, chromatin state or configuration, translation level, or its activity or state in a cell or biological system is used to determine the increase in transcription, translation, or expression or activity of a certain nucleic acid. These activities or states can be measured directly or indirectly.
  • gene activation “activation of genes”, “gene upregulation”, and “upregulation of genes” refer to an increase in the activity associated with a nucleic acid sequence, regardless of the mechanism by which such activation occurs, for example, it acts as a regulatory sequence. It is transcribed into RNA, translated into protein and increases protein expression.
  • small activating RNA As used herein, the terms “small activating RNA”, “saRNA”, and “small activating nucleic acid molecule” are used interchangeably, and refer to nucleic acid molecules that can promote gene expression, and can be composed of non-coding nucleic acid sequences (for example, a promoter, an enhancer, etc.) a first nucleic acid fragment (an antisense nucleic acid strand, also called an antisense oligonucleotide strand) having a nucleotide sequence of sequence identity or homology, and a nucleic acid fragment that is complementary to the first nucleic acid fragment
  • the second nucleic acid fragment (sense nucleic acid strand, also called sense strand or sense oligonucleotide strand) of the nucleotide sequence of, 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 synthetic or vector-expressed single-stranded RNA molecule that can form a double-stranded region hairpin structure, wherein the first region contains a nucleotide sequence that has sequence identity with the promoter target sequence of the gene, The nucleotide sequence contained in the second region is complementary to the first region.
  • the length of the duplex region of a small activation nucleic acid molecule is generally about 10 to about 50 base pairs, about 12 to about 48 base pairs, about 14 to about 46 base pairs, and about 16 to about 44 base pairs.
  • Base pairs about 18 to about 42 base pairs, about 20 to about 40 base pairs, about 22 to about 38 base pairs, about 24 to about 36 base pairs, about 26 to about 34 base pairs, about 28 to about 32 base pairs, usually about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50 Base pairs.
  • the terms "saRNA”, “small activating RNA” and “small activating nucleic acid molecule” also contain nucleic acids other than ribonucleotides, including but not limited to modified nucleotides or the like.
  • hot spot refers to a gene promoter region with a length of at least 30 bp, where there is an aggregation of functional small activating nucleic acid molecule targets, that is, the small activating nucleic acid molecule targeting these hot spots is at least 30 bp. % Can induce target gene mRNA expression to 1.2 times or more.
  • synthetic refers to the synthesis method of oligonucleotides, including any method capable of synthesizing RNA, such as chemical synthesis, in vitro transcription, vector expression, and the like.
  • the present invention up-regulates the expression of LHPP gene by means of RNA activation, and treats related diseases, especially hepatocellular carcinoma, by increasing the expression of full-length LHPP protein.
  • the LHPP gene is sometimes referred to as a target gene.
  • the preparation method of the small activation nucleic acid molecule provided by the present invention includes sequence design and sequence synthesis.
  • the synthesis of the small activating nucleic acid molecule sequence of the present invention can adopt chemical synthesis methods, or entrust the synthesis of biotechnology companies specializing in nucleic acid synthesis.
  • the method of chemical synthesis includes the following four processes: (1) synthesis of oligoribonucleotides; (2) deprotection; (3) purification and separation; (4) desalting and annealing.
  • the first cycle connects a base to the solid support, and then in the nth cycle (19 ⁇ n ⁇ 2), in the first cycle One base is connected to the connected base in n-1 cycles, and this cycle is repeated until the synthesis of all nucleic acid sequences is completed.
  • the obtained crude saRNA product was dissolved in 2 ml of triethylamine acetate solution with a concentration of 1 mol/L, and then separated by a high-pressure liquid chromatography reverse phase C18 column to obtain a purified saRNA single-stranded product.
  • the target sequence is filtered, and the criteria for retaining the target sequence are: 1) The GC content is between 35% and 65%; 2) Does not contain 5 or more than 5 consecutive identical nucleotides; 3) No Contains more than 2 dinucleotide repeats; 4) does not contain more than 2 3-nucleotide repeats. After filtering, 290 target sequences were obtained.
  • the length of the sense and antisense strands of the double-stranded small activating RNA (saRNA) used in the experiment are both 21 nucleotides, and the length of the 5'region of the first nucleic acid strand (sense strand) of the double-stranded saRNA is 19
  • the nucleotide sequence has 100% identity with the promoter target sequence, and its 3'end contains the TT sequence; the 19 nucleotides in the 5'region of the second nucleic acid strand are completely complementary to the first ribonucleic acid strand sequence.
  • the 3'end contains the TT sequence.
  • the two strands of the aforementioned double-stranded saRNA are mixed in the same amount of moles and annealed to form a double-stranded saRNA.
  • the LHPP promoter sequence is shown below, which corresponds to SEQ ID No: 493 from position 1 to position 1000 from 5'to 3'in the sequence list:
  • the human liver cancer cell line Huh7 was cultured in DMEM medium (Gibco) containing 10% calf serum (Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco). The cells were cultured under 5% CO 2 and 37°C. Following the manufacturer's instructions, RNAiMax (Invitrogen, Carlsbad, CA) was used to transfect small activation RNA at a concentration of 10 nM (unless otherwise specified).
  • the culture medium was discarded, and 150 ⁇ l PBS was added to each well to wash once, PBS was discarded, and 50 ⁇ l cell lysate (Takara) was added to each well, and incubated at room temperature for 5 minutes. Take 1 ⁇ l of cell lysate from each well and use one-step TB Green TM PrimeScrip TM RT-PCR Kit II (Takara, RR086A) for qPCR analysis on ABI 7500 Fast Real-time PCR system (Applied Biosystems). The sample was amplified in 3 multiple wells, and the PCR reaction conditions are shown in Table 1 below.
  • stage 1 reverse transcription reaction 42°C for 5 minutes; 95°C for 10 seconds; stage 2 PCR reaction: 95°C for 5 seconds, 60°C for 20 seconds, and 45 cycles of amplification.
  • HPRT1 and TBP were used as internal reference genes.
  • the PCR primers used for LHPP, HPRT1 and TBP are shown in Table 2, where LHPP is amplified with LHPP F1/R1 primer pair.
  • CtTm is the Ct value of the target gene from the control (Mock) sample
  • CtTs is the Ct value of the target gene from the saRNA-treated sample
  • CtR1m is the Ct value of the internal reference gene 1 from the control (Mock) sample
  • CtR1s is from the saRNA
  • CtR2m is the Ct value of the internal reference gene 2 from the control (Mock) sample
  • CtR2s is the Ct value of the internal reference gene 2 from the saRNA-treated sample.
  • Huh7 cells were transfected with the above 290 saRNAs at a transfection concentration of 10 nM. After 72 hours, the cells were lysed in the same manner as described above and analyzed by one-step RT-qPCR. Relative (compared with control (Mock)) expression value of LHPP gene of saRNA-treated samples. As shown in Table 3, 164 (56.6%) and 37 (12.8%) saRNAs showed activation and inhibitory activities, respectively, and 89 (30.7%) saRNAs had no effect on the expression of LHPP. The maximum amplitude of activation is 3.46 times, and the maximum suppression amplitude is 0.49 times. These saRNAs with activating activity are called activating saRNAs, and those with inhibitory activity are called inhibitory saRNAs.
  • Figure 2 further shows the activity distribution of LHPP saRNA from highly activated to highly inhibited.
  • Hot spot H1 (5' to 3': -917 to -844) sequence, which corresponds to SEQ ID NO: 500 from 5'to 3'position 1 to position 74 in the sequence table:
  • Hot spot H2 (5' to 3': -710 to -675) sequence, which corresponds to SEQ ID NO: 501 from 5'to 3'position 1 to position 36 in the sequence table:
  • Hotspot H3 (5’ to 3’: -198 to -168) sequence, which corresponds to SEQ ID NO: 502 from 5’ to 3’ position 1 to position 31 in the sequence table:
  • Hotspot H4 (5' to 3': -151 to -28) sequence, which corresponds to SEQ ID NO: 503 from 5'to 3'position 1 to position 124 in the sequence table:
  • the hot spot HC (5' to 3': -845 to -711) sequence, which corresponds to SEQ ID NO: 504 from 5'to 3'position 1 to position 135 in the sequence table:
  • Example 3 saRNA promotes LHPP mRNA expression and inhibits tumor cell proliferation
  • 290 saRNAs targeted to the LHPP promoter were respectively transfected into Huh7 cells, 72 hours later, the expression of LHPP mRNA was analyzed by one-step RT-qPCR, and the cell viability was detected by the CCK8 method. As shown in Figure 4, when activating saRNA promotes the expression of LHPP mRNA, cell viability is reduced, and the amount of mRNA expression is negatively correlated with cell viability.
  • CCK8 method to detect cell viability The cells are plated in a 96-well plate at 3-5 ⁇ 10 3 cells/well, cultured overnight, and transfected with oligonucleotide duplexes. After 72 hours of transfection, 10uL CCK8 solution (Dojindo Molecular Technologies) was added to each well, incubated at 37°C for 1 hour, and then the absorbance at 450nm was measured using a microplate reader.
  • Example 4 saRNA promotes LHPP protein expression
  • the cells were plated in a 96-well plate at 3-5 ⁇ 10 3 cells/well, cultured overnight, and transfected with 10 randomly selected oligonucleotide duplexes. The cells were collected 72 hours after transfection and lysed with a cell lysate containing protease inhibitor (1 ⁇ RIPA buffer, CST). BCA method (Thermo) for protein quantification, followed by polyacrylamide gel electrophoresis separation and transfer to 0.45 ⁇ m PVDF membrane.
  • the primary antibodies used are: mouse monoclonal anti-LHPP (Invitrogen) or rabbit polyclonal anti-AKT (Cell Signaling Technology), pAKT (Cell Signaling Technology), ⁇ / ⁇ -tubulin antibody (Cell Signaling Technology) to detect the blot;
  • the secondary antibodies were respectively used: anti-mouse IgG, HRP-linked antibody (Cell Signaling Technology) or anti-rabbit IgG, HRP-linked antibody (Cell Signaling Technology).
  • Use Image Lab BIO-RAD, Chemistry Doctm MP imaging System
  • these 10 randomly selected saRNAs promoted or increased LHPP mRNA and protein expression levels while at the same time lowering the phosphorylation level of AKT.
  • Example 5 saRNA inhibits the proliferation of various tumor cells
  • the 8 saRNAs were transfected into the liver cancer cell lines Huh7 (Tohoku University Medical Cell Resource Bank), HepG2 (ATCC), Hep3B (ATCC), Li-7 (Tohoku University Medical Cell Resource Bank), SK- HEP-1 (ATCC); lung cancer cell line A549 (ATCC), bladder cancer cell line T24 (ATCC), prostate cancer cell line PC3 (ATCC) and glioma cell line U87MG (ATCC) and measure its mRNA expression and cell vitality.
  • RAG7-133 can induce LHPP gene expression to varying degrees and inhibit cell proliferation in 5 liver cancer cell lines; RAG7-694 can be used in 4 liver cancer cell lines except Li-7 Induce LHPP gene expression to varying degrees and inhibit cell proliferation.
  • the above 8 saRNAs can induce LHPP gene expression to varying degrees and inhibit cell proliferation.
  • RAG7-133 can induce LHPP gene expression in T24, PC3 and U87MG cell lines to varying degrees, and inhibit cell proliferation
  • RAG7-694 can be in A549, T24 and PC3 cell lines to varying degrees Induces LHPP gene expression and inhibits cell proliferation
  • RAG7-177 can induce LHPP gene expression and inhibit cell proliferation in A549, T24 and U87MG cell lines to varying degrees:
  • Example 6 saRNA combined with chemical drugs to inhibit cell proliferation
  • the compounds used include: Sorafenib (Sora) (SELLECK, S1040), Levatinib (Lenv) (SELLECK, S1164), Rego (SELLECK, S1178) and Cabozantinib (Cabo) (SELLECK, S1119).
  • Sorafenib Sora
  • Levatinib Lenv
  • Rego SELLECK, S1178
  • Cabozantinib Cabo
  • RAG7-133 and regorafenib have a strong synergistic effect (CI ⁇ 0.3), while low doses (1.0nM ⁇ 10nM) also have a synergistic effect (0.3 ⁇ CI ⁇ 0.7);
  • RAG7-133 has a synergistic effect with sorafenib and cabozantinib (CI ⁇ 1), but has no synergistic effect with levatinib (CI>1).
  • RAG7-133 has a synergistic effect with the four compounds (CI ⁇ 1); especially in combination with levatinib or cabotinib, RAG7-133 has a wider dose Within the range (1.0nM ⁇ 100nM), it has a strong synergistic effect (CI ⁇ 0.1).
  • Example 7 Combination medication inhibits the growth of human HepG2 transplanted tumors in mice
  • saRNA preparation preparation saRNA delivery system adopts in vivo-jetPEI (201-10G, Polyplus-transfection, France). The preparation process is briefly described as follows: first dilute saRNA in a 10% glucose solution to obtain solution A; according to the manufacturer's instructions, dilute the required amount of in vivo-jetPEI in a 10% glucose solution to obtain solution B; then mix solution A in equal volumes And solution B (the nitrogen to phosphorus ratio is 8, the final concentration of glucose is 5%), mix well and let stand at room temperature for 15 minutes.
  • saRNA 1 mg ⁇ kg -1 was injected intratumorally on days 1, 4, 7, and 10; for the regorafenib group and saRNA+regorafenib group, within 1-12 days ,According to the dose of 3mg ⁇ kg -1 Regorafenib is administered daily.
  • V (l ⁇ w 2 )/2, where l represents the longest diameter of the tumor mass; w represents The diameter parallel to the surface of the tumor and perpendicular to the major diameter.
  • the tumor growth curve during the administration period and the tumor size and shape after anatomy were recorded.
  • the saRNA group administered RAG7-133 alone
  • the tumor volume increased by 34% compared with that of the carrier control group by 34%, while the tumor volume of the carrier control group increased by 118%.
  • the saRNA and regorafenib combination group (RAG7-133+Rego) showed a trend of slow tumor growth since the 4th day, and the tumor shrank from the 7th day, and the tumor volume was the same as the tumor volume at the beginning of the treatment on the 13th day Compared with an increase of only 4%, the tumor volume of the single-use chemical drug Regofenib (Rego) group increased by 70% compared with the tumor volume at the beginning of treatment on the 13th day of treatment. There is a significant difference between the two (P ⁇ 0.01), indicating that the combination of saRNA and chemical drugs synergistically enhances the anticancer effect of chemical drugs.
  • Example 8 Combination medication inhibits the growth of human U87MG transplanted tumors in mice
  • saRNA preparation preparation saRNA delivery system adopts in vivo-jetPEI (201-10G, Polyplus-transfection, France), the preparation process is briefly described as follows: first dilute saRNA in a 10% glucose solution to obtain solution A; dilute the required amount in vivo- JetPEI in 10% glucose solution to obtain solution B; then equal volume of solution A and solution B (nitrogen to phosphorus ratio is 8, the final concentration of glucose is 5%), mix well and stand at room temperature for 15 minutes.
  • in vivo-jetPEI 201-10G, Polyplus-transfection, France
  • the tumor growth curve during the administration period and the tumor size and shape after anatomy were recorded.
  • the tumor volume of the saRNA group administered RAG7-133 alone
  • the control group The tumor volume increased by 406%, and there was a significant difference in tumor volume changes between the two (P ⁇ 0.05), indicating that LHPP saRNA can significantly inhibit tumor growth in mice.
  • the tumor volume of the saRNA combined with regorafenib (RAG7-133+Rego) on the 13th day of treatment increased by 132% compared with the tumor volume at the beginning of the treatment.
  • the tumor volume at 13 days increased by 251% compared with the tumor volume at the beginning of the treatment. There was also a significant difference between the two (P ⁇ 0.05), indicating that the combination of saRNA and chemical drugs synergistically enhanced the tumor suppressor effect of chemical drugs.
  • the applicant through high-throughput screening of saRNA targeting the LHPP gene promoter, found a number of saRNAs that can significantly activate the expression of the LHPP gene. These saRNAs inhibit tumor cell proliferation in vitro or in vivo by up-regulating the expression of LHPP genes and proteins, and down-regulating phosphorylated AKT levels. These results clearly indicate that the use of saRNA targeting the LHPP gene promoter will be a promising strategy for tumor treatment.

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Abstract

提供了用于治疗肿瘤的寡聚核酸，其可以为小激活核酸分子，所述小激活核酸分子可以是靶向LHPP基因启动子区的双链或单链RNA分子，包含第一核酸链和第二核酸链。还提供了包含所述小激活核酸分子和可选的药学上可接受的载体的药物组合物及其应用。使用所述小激活核酸分子以及使用所述药物组合物可以上调LHPP基因在细胞中的表达及治疗与LHPP基因表达不足或减少相关的疾病或状况。

Description

寡核苷酸分子及其在肿瘤治疗中的应用 技术领域
本发明属于核酸技术领域，具体来讲，涉及基因激活相关的寡聚核酸分子，例如小激活核酸分子，和小激活核酸分子在激活/上调组氨酸磷酸酶LHPP基因转录中的应用，以及其在与LHPP缺乏相关的疾病，如肿瘤治疗中的应用。
背景技术
组氨酸磷酸酶LHPP(磷酸赖氨酸磷酸组氨酸无机焦磷酸磷酸酶，Phospholysine phosphohistidine inorganic pyrophosphate phosphatase)基因定位在人类基因组10q26.13染色体，有7个外显子，可转录生成9种LHPP剪接异构体(Splice variants)。LHPP在人类多种组织中表达，包括肝脏、肾、脑组织等(1-3)。
多项GWAS(全基因组关联分析，Genome-wide association study)研究显示，LHPP是严重抑郁(2；4-7)和癌症(8-10)的风险因子。最近一项关于肝细胞癌的研究显示，LHPP被证实为具有肿瘤抑制作用的组氨酸磷酸酶(11)。该项研究借助肝细胞癌小鼠模型(mTOR-驱动的)，显示在肿瘤发生的同时，肿瘤组织中整体组氨酸磷酸化水平显著升高。蛋白质组分析则发现肿瘤组织中组氨酸激酶NME1(核苷二磷酸激酶A，Nucleoside diphosphate kinase A)和NME2(核苷二磷酸激酶B，Nucleoside diphosphate kinase B)的表达水平升高，而组氨酸磷酸酶LHPP的表达水平降低。更为鼓舞人心的是，在将LHPP基因导入肝细胞癌小鼠模型后，瘤重降低，肝功能获得保护。另外，根据病人肝癌样本LHPP表达量的分析结果，LHPP表达量与患者肿瘤严重程度成负相关，与总体生存率成正相关(11)。因此，LHPP具有成为肝细胞癌治疗靶点的潜质。
中国是肝癌大国，全世界50％以上的新发和死亡肝癌患者发生在中国(12)，但肝癌治疗手段不多，疗效有限，急需创新药物。本发明提供了一种高度特异性持续激活LHPP转录的小激活RNA，其通过有效激活/上调LHPP基因转录，而提高LHPP蛋白的表达量，在体外和体内实验中显示了显著的肿瘤抑制效果，有望成为治疗癌症的特效药。
发明内容
公开内容
本发明的一个目标是提供基于RNA激活过程的小激活核酸分子，其通过激活/上调LHPP基因转录，从而提高LHPP蛋白的表达量来治疗与LHPP缺乏相关的疾病，如肿瘤。
本发明的另一目标是提供包含具有肿瘤抑制活性的小激活核酸分子的组合物或制剂。
本发明的又一目标为提供具有肿瘤抑制活性的小激活核酸分子或包含其的组合物或制剂在制备用于激活/上调LHPP基因在细胞中的表达的药物中的应用。
本发明的又一目标为提供激活/上调LHPP基因在细胞中的表达方法。本发明的还一目标为提供具有肿瘤抑制活性的小激活核酸分子或包含其的组合物或制剂在制备用于治疗与LHPP缺乏或不足相关的疾病或状况如肿瘤的药物中的应用或治疗与LHPP缺乏或不足相关的疾病或状况如肿瘤的方法。
本发明的另一目标为提供分离的LHPP基因小激活核酸分子靶位点，其中所述靶位点包括或选自SEQ ID NO:500-504的任一条序列上的任意连续16-35个核苷酸的序列。
技术方案
在本发明的一个方面，提供了小激活核酸分子，其激活或者上调细胞中LHPP基因的表达，所述小激活核酸分子的一条链与LHPP基因启动子区的长度为16-35个核苷酸的核酸序列具有至少75％的同源性或互补性，启动子区是指包括转录起始位点上游的1000个核苷酸，从而实现所述基因表达的激活或者上调。具体地，所述小激活核酸分子的一条链包括或选自与LHPP基因启动子中距转录起始位点的-917至-844区域(H1，SEQ ID NO:500)、-710至-675区域(H2,SEQ ID NO:501)、-198至-168(H3,SEQ ID NO:502)、-151至-28(H4,SEQ ID NO:503)或-845至-711区域(H5,SEQ ID NO:504)中的连续16-35个核苷酸具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％或100％的同源性或互补性的核酸序列。更具体地，本发明的小激活核酸分子的一条链与选自SEQ ID NO:329-492的任一核苷酸序列具有至少75％、例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同源性或互补性。在一个具体的实施方式中，本发明的小激活核酸分子的一条链包括与选自SEQ ID NO:329-492的任一核苷酸序列具有至少75％、例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同源性或互补性的核酸序列。在另一实施方式中，本发明的小激活核酸分子的一条链由与选自SEQ ID NO:329-492的任一核苷酸序列具有至少75％、例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同源性或互补性的核酸序列组成。
本发明的小激活核酸分子包括靶向LHPP基因启动子区的双链小激活核酸分子，包含第一核酸链和第二核酸链，第一核酸链与LHPP基因启动子中距转录起始位点-917至-844区域(SEQ ID NO:500)、-710至-675区域(SEQ ID NO:501)、-198至-168(SEQ ID NO:502)、-151至-28(SEQ ID NO:503)或-845至-711区域(SEQ ID NO:504)中的任一连续16-35个核苷酸具 有至少75％的同源性或互补性，第一核酸链和第二核酸链能通过互补形成双链核酸结构，双链核酸结构能够激活LHPP基因在细胞中的表达。
本发明的小激活核酸的第一核酸链和第二核酸链可以存在于两条不同的核酸链上，也可以存在于同一条核酸链上。当第一核酸链和第二核酸链分别位于两条链上时，小激活核酸分子的至少一条链可以在5’端和/或3’端具有突出或悬垂，例如在3’端可以具有0至6个核苷酸的突出，如，0、1、2、3、4、5或6个核苷酸的突出。优选地，本发明的小激活核酸分子的两条链都具有突出，更优选地，小激活核酸分子的两条链的3’端均可以具有0至6个核苷酸的突出，例如，具有0、1、2、3、4、5或6个核苷酸的突出，最优选地，具有2个或3个核苷酸的突出。优选地，突出端的核苷酸可以是dT。
本发明的小激活核酸分子也可以包括可形成双链区发夹结构的小激活核酸分子，例如单链小激活RNA分子。在一个实施方式中，本发明的小激活核酸分子包括靶向LHPP基因启动子区的单链小激活RNA分子，其中所述单链小激活核酸分子可形成双链区发夹结构。当第一核酸链和第二核酸链存在于同一条核酸链上时，优选地，本发明的小激活核酸分子可以为发夹型单链核酸分子，其中第一核酸链和第二核酸链具有能形成双链核酸结构的互补区域，所述双链核酸结构可以通过例如RNA激活机制促进LHPP基因在细胞中的表达。
上述小激活核酸分子中，第一核酸链和第二核酸链的长度可以分别为16-35个核苷酸，例如，可以为16、17、18、19、20、21、22、23、24、25、26、27、28、29、30、31、32、33、34或35个核苷酸。
在一个实施方式中，本发明的小激活核酸分子的第一核酸链与选自SEQ ID NO:1-164中的任一核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性，并且小激活核酸分子的第二核酸链与选自SEQ ID NO:165-328中的任一核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性。在一个实施方式中，本发明的小激活核酸分子的第一核酸链包括与选自SEQ ID NO:1-164中的任一核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性的核酸序列，或者由与选自SEQ ID NO:1-164中的任一核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性的核酸序列组成，并且本发明的小激活核酸分子的第二核酸链包括与选自SEQ ID NO:165-328中的任一核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性的核酸序列，或者由与选自SEQ ID NO:165-328中的任一 核苷酸序列具有至少75％，例如至少约79％、约80％、约85％、约90％、约95％、约99％、或约100％的同一性或同源性的核酸序列组成。在具体的实施方式中，本发明的小激活核酸分子的第一核酸链可以包括或选自SEQ ID NO:1-164的任一核苷酸序列，并且其第二链可以包括或选自SEQ ID NO:165-328的任一核苷酸序列。在一个实施方式中，本文所述的小激活核酸分子可以是合成的、体外转录的或者载体表达的。
本文所述小激活核酸分子中所有的核苷酸都可以为天然的未经化学修饰的核苷酸，也可以包括至少一种修饰。在一个实施方式中，本文所述的小激活核酸分子中的修饰可以是化学修饰，如在至少一个核苷酸可以具有化学修饰，本发明使用的化学修饰可以包括或选自如下修饰中的一种或多种，或其任意组合：
(1)对所述小激活核酸分子的核苷酸序列中核苷酸的磷酸二酯键的修饰；
(2)对所述小激活核酸分子的核苷酸序列中的核糖的2’-OH的修饰；
(3)对所述小激活核酸分子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。
所述化学修饰为本领域技术人员所公知，所述磷酸二酯键的修饰是指对磷酸二酯键中的氧进行修饰，包括但不限于，硫代磷酸修饰和硼烷化磷酸盐修饰。两种修饰都能稳定saRNA结构，保持碱基配对的高特异性和高亲和力。
核糖修饰是指对核苷酸戊糖中2’-OH的修饰，即，在核糖的羟基位置引入某些取代基，例如，包括但不限于，2’-氟代修饰、2’-氧甲基修饰、2’-氧亚乙基甲氧基修饰、2,4’-二硝基苯酚修饰、锁核酸(LNA)、2’-氨基修饰、2’-脱氧修饰等。
碱基修饰是指对核苷酸的碱基进行修饰，例如，包括但不限于，5′-溴尿嘧啶修饰、5′-碘尿嘧啶修饰、N-甲基脲嘧啶修饰、2,6－二氨基嘌呤修饰等。
这些修饰可以增加小激活核酸分子的生物可利用性，提高与靶序列的亲和性，增强在细胞内抵抗核酸酶水解的能力。
此外，为了促进小激活核酸分子进入细胞，可以在以上修饰的基础上，在小激活核酸分子的第一核酸链或第二核酸链的末端引入例如胆固醇等亲脂性基团以利于通过由脂质双分子层构成的细胞膜及核膜与细胞核内的基因启动子区发生作用。
本发明提供的小激活核酸分子在与细胞接触后可有效激活或上调细胞中LHPP基因的表达，优选情况下表达至少上调10％。
本发明的另一方面还涉及编码本文所述的小激活核酸分子的核酸。在一个实施方式中，所述核酸可以是DNA分子。
在本发明的另一方面，提供了包含上文所述的小激活核酸分子或编码本文所述的小激活核酸分子的核酸的细胞。在一个实施方式中，本发明的小激活核酸分子可以是靶向LHPP基因启动子区的双链小激活核酸分子，其包括第一核酸链和第二核酸链。在另一实施方式中，本发明的小激活核酸分子可以是靶向LHPP基因启动子区的单链小激活核酸分子。
本发明的另一方面提供了组合物(例如药物组合物)，该组合物包含本发明所述的小激活核酸分子或编码本文所述的小激活核酸分子的核酸和任选地，药学上可接受的载体。在一个实施方式中，所述药学上可接受的载体可以包括或选自脂质体、高分子聚合物或多肽。在一个实施方式中，本发明的组合物含有1-150nM，例如1-100nM，例如1-50nM，例如10nM、20nM、30nM、40nM、50nM、60nM、70nM、80nM、90nM、100nM、110nM、120nM、130nM、140nM或150nM的本发明的小激活核酸分子。在另一个实施方式中，本发明的组合物可以进一步包括其他化合物，例如用于肿瘤治疗的小分子化合物。在一个实施方式中，用于肿瘤治疗的小分子化合物可以包括多靶点抗肿瘤药物如索拉非尼(Sorafenib，靶点为PDGFR,KIT,RAF)(SELLECK，S1040)、酪氨酸激酶抑制剂如乐伐替尼(Lenvatinib,靶点为FGFR、VEGFR2、PDGFR、KIT)(SELLECK，S1164)、激酶抑制剂如瑞戈非尼(Regorafenib，靶点为FGFR、VEGFR2、PDGFR、KIT、RAF)(SELLECK，S1178)或卡博替尼(Cabozantini，其抑制MET、VEGFR2和RET信号转导)(SELLECK，S1119)。
在本发明的另一方面，提供了试剂盒，所述试剂盒包含上文所述的小激活核酸分子、编码本文所述的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物。
本发明的另一方面涉及本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子和编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物在制备用于激活/上调LHPP基因在细胞中表达的药物或制剂中的应用。
本发明的另一方面还涉及激活/上调LHPP基因在细胞中的表达的方法，该方法包括给所述细胞施用本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、或包含本发明的小激活核酸分子的组合物。
本发明的小激活核酸分子可以被直接导入细胞中，也可以是将编码本发明的小激活核酸分子的核酸序列导入细胞后在细胞内产生；所述细胞优选为哺乳动物细胞，更优选为人类细胞。上述细胞可以是离体的，如细胞系或细胞株等，也可以存在于哺乳动物体中，如人体中。该人体可以是具有与LHPP蛋白表达不足或减少相关的疾病或状况的患者。本发明所述的小 激活核酸分子可以被施以足够的量以实现对与LHPP蛋白量的缺乏或与LHPP蛋白表达不足或减少相关的疾病或状况的治疗。具体情况下，所述与LHPP蛋白量的缺乏或与LHPP表达不足或减少相关的疾病或状况可以包括例如肿瘤，如实体瘤，所述实体瘤可以包括例如肝癌、肺癌、膀胱癌、前列腺癌、神经胶质瘤等。
本发明另一方面提供了分离的LHPP基因小激活核酸分子作用位点，该位点具有LHPP基因的启动子区上任意连续的16-35个核苷酸的序列，优选情况下，所述作用位点包括或选自SEQ ID NO:500-504的任一条序列上的任意连续16-35个核苷酸的序列。具体地，所述作用位点可以包括或选自SEQ ID NO:329-492中的任一核苷酸序列。
本发明的另一方面涉及治疗个体中与LHPP蛋白表达不足或减少相关的疾病或状况的方法，包括给所述个体施用治疗有效量的本发明的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物。在一个实施方式中，本发明的治疗个体中与LHPP蛋白表达不足或减少相关的疾病或状况的方法包括给个体施用治疗有效量的本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物和治疗有效量的小分子化合物、抗体、多肽、蛋白等。所述个体可以是哺乳动物，例如人。在一个实施方案中，与LHPP蛋白表达不足或减少相关的疾病或状况可以包括例如肿瘤，如实体瘤，所述实体瘤可以包括例如肝癌、肺癌、膀胱癌、前列腺癌、神经胶质瘤等。
本发明的另一方面涉及本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物在制备用于治疗与LHPP蛋白表达不足或减少相关的疾病或状况的药物中的应用。所述个体可以是哺乳动物，例如人。在一个实施方案中，所述与LHPP蛋白表达不足或减少相关的疾病可以包括例如肿瘤，如实体瘤，所述实体瘤可以包括例如肝癌、肺癌、膀胱癌、前列腺癌、神经胶质瘤等。
在一个实施方式中，提供了本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物在制备用于治疗肿瘤，如实体瘤的药物中的应用，其中所述实体瘤可以包括例如肝癌、肺癌、膀胱癌、前列腺癌、神经胶质瘤等。
本发明的另一方面涉及本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含 本发明的小激活核酸分子的组合物与化学治疗剂、放射治疗、细胞治疗、小分子、多肽、蛋白、抗体或其他抗肿瘤药物在制备用于治疗与LHPP蛋白表达不足或减少相关的疾病或状况的药物或药物组合组合中的应用。
在一个实施方式中，提供了本发明所述的小激活核酸分子、编码本发明的小激活核酸分子的核酸、包含本发明的小激活核酸分子或编码本发明的小激活核酸分子的核酸的细胞、或包含本发明的小激活核酸分子的组合物与化学治疗剂、放射治疗、细胞治疗、小分子、多肽、蛋白、抗体或其他抗肿瘤药物在制备用于治疗肿瘤，如实体瘤的药物或药物组合中的应用，其中所述实体瘤可以包括例如肝癌、肺癌、膀胱癌、前列腺癌、神经胶质瘤等。在一个实施方式中，所述化学治疗剂包括或选自索拉非尼、乐伐替尼、瑞戈非尼和卡博替尼。
在所述方法和用途中，本发明所述的小激活核酸分子可以与化学治疗剂、放射治疗、细胞治疗、小分子、多肽、蛋白、抗体或其他抗肿瘤药物组合使用，所述化学治疗剂优选地选自索拉非尼、乐伐替尼、瑞戈非尼和卡博替尼。
本发明的有益效果
本发明提供的能够激活/上调LHPP基因表达的小激活核酸分子，能够持久地激活LHPP基因，因而高效、特异地上调或恢复LHPP基因和蛋白的表达并同时具有较低的毒副作用，可用于制备与LHPP蛋白表达不足或减少相关的疾病或病症的药物或制剂。而且，LHPP的激活性saRNA在与其他抗肿瘤药物联用时显示了很好的协同效果，体现了在抗肿瘤效果上的协同作用。
附图说明
图1为LHPP基因结构示意图。图中所示为LHPP基因结构及用于设计saRNA的长度为1kb的启动子区域，其中一段449bp的Alu重复序列被排除在外。
图2为saRNA介导的LHPP mRNA表达改变。靶向LHPP启动子的290个saRNA分别转染Huh7细胞，72小时后用一步法RT-qPCR分析LHPP mRNA表达。图示为相对于对照处理(对照，mock)的LHPP表达改变，按照saRNA在启动子靶点位置从-917到-28排序。
图3为发现saRNA在LHPP启动子上的热点区域。靶向LHPP启动子的290个saRNA分别转染Huh7细胞，72小时后用一步法RT-qPCR分析LHPP mRNA表达。图示为相对于对照处理(对照，mock)的LHPP表达改变，按照saRNA在LHPP启动子上的靶点位置从-917到-28排序。上方或者下方的数字表示区域的界限(相对于LHPP转录起始位点)。
图4为LHPP mRNA表达量与细胞活力呈现负相关性。靶向LHPP启动子的290个saRNA分别转染Huh7细胞，72小时后用一步法RT-qPCR分析LHPP mRNA表达，使用CCK8法检测细胞活力。细线:LHPP mRNA相对表达水平(log 2)，粗线：细胞活力。
图5为saRNA诱导LHPP的表达并抑制AKT磷酸化。靶向LHPP启动子的10个saRNA分别转染Huh7细胞，72小时后,(A)RT-qPCR分析LHPP mRNA表达；(B)蛋白质印迹方法检测LHPP、pAKT、AKT蛋白水平。
图6为saRNA诱导LHPP mRNA表达并抑制肝癌细胞增殖。所示8个小激活RNA分子分别以10nM转染肝癌细胞72小时。(A)RT-qPCR分析LHPP基因mRNA表达水平。(B)CCK-8方法评估细胞活力，saRNA处理组细胞的活力表示为相对于对照(Mock)处理组细胞活力的百分比。
图7为saRNA诱导LHPP mRNA表达并抑制其他多种癌细胞增殖。所示8个小激活RNA分别以10nM转染癌细胞72小时。(A)RT-qPCR分析LHPP基因mRNA表达水平。(B)CCK-8方法评估细胞活力，saRNA处理组细胞的活力表示为相对于对照(Mock)处理组细胞活力的百分比。
图8为saRNA与化学药物联用抑制HepG2细胞增殖。所示小激活RNA分别以不同浓度梯度转染癌细胞并联用不同的化学药物。(A)CCK-8方法评估细胞活力，saRNA处理组细胞的活力表示为相对于对照(Mock)处理组细胞活力的百分比。采用
Figure PCTCN2019092720-appb-000001
version 1.0software绘制联合指数图(B)并计算联合指数值(C)。
图9为saRNA与化学药物联用抑制U87MG细胞增殖。所示小激活RNA分别以不同浓度梯度转染癌细胞并联用不同的化学药物。(A)CCK-8方法评估细胞活力，saRNA处理组细胞的活力表示为相对于对照(Mock)处理组细胞活力的百分比。采用
Figure PCTCN2019092720-appb-000002
version 1.0software绘制联合指数图(B)并计算联合指数值(C)。
图10为saRNA与化学药物联用抑制HepG2移植瘤生长。所示小激活RNA以1mg/kg的剂量瘤内注射并联用化药，记录给药期间的移植瘤体积变化。
图11为saRNA与化学药物联用抑制U87MG移植瘤生长。所示小激活RNA以1mg/kg的剂量瘤内注射并联用化药，记录给药期间的移植瘤体积变化。
具体实施方式
在本发明中，相关术语采用如下定义：
如本文所用的术语“互补”是指两条寡核苷酸链彼此形成碱基对的能力。碱基对通常由 反向平行的寡核苷酸链中的核苷酸之间通过氢键形成。互补寡核苷酸链可以沃森-克里克(Watson-Crick)方式碱基配对(例如，A-T，A-U，C-G)，或以允许形成双链体的任何其他方式(例如Hoogsteen型或者反向Hoogsteen型碱基配对)进行碱基配对。
互补包括完全互补和不完全互补两种情况。完全互补或100％互补是指双链寡核苷酸分子的双链区中来自第一条寡核苷酸链的每个核苷酸可以与第二条寡核苷酸链相应位置的核苷酸形成氢键而没有“错配”的情况。不完全互补是指两条链的核苷酸单元不能全部互相氢键结合的情况。例如，对于两条双链区为20个核苷酸长度的寡核苷酸链，如果每条链上只有两个碱基对可以彼此氢键结合，则寡核苷酸链展现出10％的互补性。在同一实例中，如果每条链上的18个碱基对可以彼此氢键结合，则寡核苷酸链展现出90％的互补性。实质互补是指至少约75％、约79％、约80％、约85％、约90％、约95％、约99％、或约100％的互补。
如本文所用的术语“寡核苷酸”是指核苷酸的聚合物，包括但不限于DNA，RNA或DNA/RNA杂交体的单链或双链分子，包括规则地和不规则地交替的脱氧核糖基部分和核糖基部分的寡核苷酸链，以及这些种类的寡核苷酸的修饰和以及天然存在的或非天然存在的骨架。本发明中所述的用于激活靶基因转录的寡核苷酸为小激活核酸分子。
如本文所用的术语“寡核苷酸链”和“寡核苷酸序列”可互换地使用，是指35个以下碱基的短链核苷酸的总称(包括脱氧核糖核酸DNA或核糖核酸RNA内的核苷酸)。在本发明中，寡核苷酸链的长度可以是16至35个核苷酸的任一长度。
如本文所用，术语“第一核酸链”可以是正义链也可以是反义链，小激活RNA的正义链是指小激活RNA双链体中含与靶基因的启动子DNA序列的编码链具有同一性的核酸链，反义链是指小激活RNA双链体中与正义链互补的核酸链。
如本文所用，术语“第二核酸链”也可以是正义链或者反义链。当第一寡核酸链为正义链时，第二寡核酸链为反义链，当第一寡核酸链为反义链时，第二寡核酸链为正义链。
如本文所用的术语“基因”是指编码一条多肽链或转录一条功能RNA所需的全部核苷酸序列。“基因”可以是对于宿主细胞而言内源的或完全或部分重组的基因(例如，由于引入编码启动子的外源寡核苷酸和编码序列或将邻近内源编码序列的异源启动子导入宿主细胞)。例如，术语“基因”包括可以由外显子和内含子组成的核酸序列。编码蛋白质的序列是，例如，包含在起始密码子和终止密码子之间的开放阅读框中的外显子内的序列，如本文所用，“基因”可以指包括例如基因调控序列例如启动子，增强子和本领域已知的控制另一基因的转录，表达或活性的所有其他序列，无论另一基因是否包含编码序列或非编码序列。在一种情况下，例如，“基因”可以用于描述包含调控序列例如启动子或增强子的功能性核酸。重组基因的表 达可以通过一种或多种异源调节序列来控制。
如本文所用的术语“靶基因”可以是天然存在于生物体中的核酸序列、转基因、病毒或细菌序列、染色体或染色体外和/或瞬时或稳定转染或掺入细胞和/或其染色质。靶基因可以为蛋白质编码基因，也可为非蛋白编码基因(例如微小RNA基因、长链非编码RNA基因)。靶基因通常含有启动子序列，设计与启动子序列具有同一性(也称同源性)的小激活核酸分子可以实现对靶基因的正向调控，表现为靶基因表达的上调。“靶基因启动子序列”是指靶基因的非编码序列，在本发明中涉及“与靶基因启动子序列互补”中靶基因启动子序列是指该序列的编码链，亦称非模板链，即为与该基因编码序列为同一序列的核酸序列。“靶点”或“靶点序列”是指靶基因启动子序列中小激活核酸分子的正义寡核苷酸链或反义寡核苷酸与之同源或互补的序列片段。
如本文所用，术语“正义链”、“正义核酸链”可互换地使用，小激活核酸分子的正义寡核苷酸链是指小激活核酸分子双链体中含与靶基因的启动子序列的编码链具有同一性的第一核酸链。
如本文所用，术语“反义链”、“反义核酸链”可互换地使用，小激活核酸分子的反义寡核苷酸链是指小激活核酸分子双链体中与正义寡核苷酸链互补的第二核酸链。
如本文所用的术语“编码链”是指靶基因中不能进行转录的那一条DNA链，该链的核苷酸序列与转录生成的RNA的序列一致(在RNA中是以U取代了DNA中的T)。本发明中所述的靶基因启动子双链DNA序列的编码链是指与靶基因DNA编码链在同一条DNA链上的启动子序列。
如本文所用的术语“模板链”是指靶基因的双链DNA中与编码链互补的另一条链，可作为模板转录为RNA的那条链，该链与转录的RNA碱基互补(A-U，G-C)。在转录过程中，RNA聚合酶与模板链结合，并沿着模板链的3'→5'方向移动，按照5'→3'方向催化RNA的合成。本发明中所述的靶基因启动子双链DNA序列的模板链是指与靶基因DNA模板链在同一条DNA链上的启动子序列。
如本文所用的术语“启动子”是指通过与蛋白质编码或RNA编码核酸序列在位置上关联而对它们的转录发挥调控作用的序列。通常，真核基因启动子包含100～5,000个碱基对，尽管此长度范围并不意味着限制本文所用的术语“启动子”。虽然启动子序列一般位于蛋白质编码或者RNA编码序列的5'端，但启动子序列也可存在于外显子及内含子序列中。
如本文所用的术语“转录起始位点”是指在基因的模板链上标志转录起始的核苷酸。转录起始位点可出现于启动子区的模板链上。一个基因可以有多于一个的转录起始位点。
如本文所用的术语“同一性”或“同源性”是指小激活RNA的其中一条寡核苷酸链(正义链或者反义链)与靶基因的启动子序列的某一区域的编码链或者模板链存在的相似性。在本文中，所述“同一性”或“同源性”可以是至少约75％、约79％、约80％、约85％、约90％、约95％、约99％或约100％。
如本文所用的术语“突出”、“overhang”、“悬垂”可互换地使用，是指寡核苷酸链末端(5'或3')非碱基配对核苷酸，其是由延伸超出双链寡核苷酸内的其中一条链的另一条链产生的。延伸超出双链体3'和/或5'端的单链区域被称为突出。
如本文所用，术语“基因激活”或“激活基因”或“基因上调”或“上调基因”可互换地使用，是指通过测量基因转录水平、mRNA水平、蛋白水平、酶活性、甲基化状态、染色质状态或构型、翻译水平、或其在细胞或生物系统中的活性或状态来测定某一核酸转录、翻译或表达或活性的增加。这些活动或状态可以直接或间接的测定。此外，“基因激活”、“激活基因”、“基因上调”、“上调基因”是指与核酸序列相关的活性增加，而不管发生这种激活的机制如何，例如其作为调节序列发挥调控作用、被转录成RNA，被翻译为蛋白质并增加蛋白质的表达。
如本文所用，术语“小激活RNA”、“saRNA”、“小激活核酸分子”可互换地使用，是指能够促进基因表达的核酸分子，并且可以由包含与靶基因的非编码核酸序列(例如启动子、增强子等)具有序列同一性或同源性的核苷酸序列的第一核酸片段(反义核酸链，也称反义寡核苷酸链)和包含与第一核酸片段互补的核苷酸序列的第二核酸片段(正义核酸链，也称有义链或正义寡核苷酸链)组成，其中所述第一核酸片段和第二核酸片段形成双链体。小激活核酸分子也可以由合成的或者载体表达的可形成双链区发夹结构的单链RNA分子组成，其中第一区域包含与基因的启动子靶序列具有序列同一性的核苷酸序列，第二区域包含的核苷酸序列与第一区域互补。小激活核酸分子的双链体区域长度通常为约10至约50个碱基对、约12个至约48个碱基对、约14个至约46个碱基对、约16个至约44个碱基对、约18个至约42个碱基对、约20个至约40个碱基对、约22个至约38个碱基对、约24个至约36个碱基对、约26个至约34个碱基对、约28个至约32个碱基对、通常约10个、约15个、约20、约25、约30、约35、约40、约45、约50个碱基对。此外，术语“saRNA”、“小激活RNA”和“小激活核酸分子”还含有除核糖核苷酸部分之外的核酸，包括但不限于修饰的核苷酸或类似物。
如本文所用，术语“热点”是指长度至少为30bp的基因启动子区域，在这些区域，呈现出功能性小激活核酸分子靶点的聚集，即靶向这些热点区域的小激活核酸分子至少30％能 够诱导靶基因mRNA表达达到1.2倍或以上。
如本文所用，术语“合成”是指寡核苷酸的合成方式，包括任何能够合成RNA的方式，例如化学合成、体外转录、载体表达等。
本发明通过RNA激活方式上调LHPP基因的表达，通过增加全长LHPP蛋白的表达量来治疗相关疾病，尤其是肝细胞癌。本发明中LHPP基因有时也称为靶基因。
本发明提供的小激活核酸分子的制备方法包括序列设计和序列合成。
本发明的小激活核酸分子序列的合成可以采用化学合成的方法，或者委托专门从事核酸合成的生物技术公司合成。
一般来说，化学合成的方法包括以下四个过程：(1)寡聚核糖核苷酸的合成；(2)脱保护；(3)纯化分离；(4)脱盐及退火。
例如，本发明所述saRNA化学合成的具体步骤如下：
(1)寡聚核糖核苷酸的合成
在自动DNA/RNA合成仪(例如，Applied Biosystems EXPEDITE8909)上设定合成1微摩尔的RNA，同时设定每个循环的偶联时间为10-15分钟，起始物为固相连接的5’-O-对二甲氧基三苯甲基-胸苷支持物，第一个循环在固相支持物上连接一个碱基，然后在第n次(19≥n≥2)循环中，在第n-1次循环所连接的碱基上连接一个碱基，重复此循环直至完成全部核酸序列的合成。
(2)脱保护
将连接有saRNA的固相支持物加入到试管中，并在此试管中加入1毫升的乙醇/氨水溶液(体积比为1：3)，然后密封，置于25-70℃温箱中，孵育2-30小时，过滤含有saRNA的固相支持物的溶液并收集滤液，用双蒸水淋洗固相支持物2次(每次1毫升)并收集滤液，合并收集洗脱液，在真空条件下干燥1-12小时。然后，加入1毫升四丁基氟化铵的四氢呋喃溶液(1M)，室温放置4-12小时，再加入2毫升正丁醇，高速离心收集沉淀即得到saRNA单链的粗产物。
(3)纯化分离
将得到的saRNA的粗产物溶解于2毫升浓度为1摩尔/升的三乙胺乙酸盐溶液中，然后通过高压液相色谱反相C18柱进行分离，得到纯化的saRNA单链产物。
(4)脱盐及退火
用体积排阻凝胶过滤法去除盐份，将正义链和反义链的寡聚核糖核酸单链按相同摩尔比 混合在1-2毫升的缓冲液中(10mM Tris，pH＝7.5-8.0，50mM NaCl)，将此溶液加热至95℃，然后缓缓将此溶液冷却至室温，得到含有saRNA的溶液。
本研究发现，将上述saRNA导入细胞后，能够有效提高全长LHPP mRNA和蛋白的表达。
下面结合具体实施例及附图，进一步阐述本发明。应理解，这些实施例仅用于说明本发明而不用于限制本发明的范围。下列实施例中未注明具体条件的实验方法，通常按照常规条件，例如Sambrook等人，分子克隆：实验室手册(New York:Cold Spring Harbor Laboratory Press，1989)中所述的条件，或按照制造厂商所建议的条件。
实施例1 靶向LHPP启动子的小激活核酸分子的设计与合成
以LHPP启动子从-1kb到-1bp的1kb的序列(SEQ ID No:493)为靶序列,但排除从-647bp到-198bp的Alu重复序列(图1)，以19个核苷酸为saRNA靶点，每次移动一个碱基得到下一个靶点，共获得453个靶点。对靶点序列进行过滤处理，保留靶点序列的标准为：1)GC含量在35％至65％之间；2)不含有5个或者多于5个的连续同一核苷酸；3)不含多于2个的二核苷酸重复序列；4)不含多于2个的3核苷酸重复序列。过滤后得到290个靶点序列。
其中，实验中使用的双链小激活RNA(saRNA)的正义和反义链的长度均为21个核苷酸，所述双链saRNA的第一核酸链(正义链)的5’区域的19个核苷酸与启动子靶点序列具有100％的同一性，其3’末端含有TT序列；第二核酸链的5’区域的19个核苷酸与第一核糖核酸链序列完全互补，其3’末端含有TT序列。将前述双链saRNA的两条链以同等量的摩尔数混合，退火后形成双链saRNA。
LHPP启动子序列如下所示，其对应于序列表中SEQ ID No:493从5’至3’的位置1至位置1000：
Figure PCTCN2019092720-appb-000003
Figure PCTCN2019092720-appb-000004
实施例2 靶向LHPP启动子的saRNA的高通量筛选
(1)细胞培养和转染
人肝癌细胞系Huh7培养在DMEM培养基(Gibco)中，所述培养基含有10％小牛血清(Sigma-Aldrich)和1％青霉素/链霉素(Gibco)。细胞在5％CO 2，37℃条件下培养。依照制造商的说明，使用RNAiMax(Invitrogen,Carlsbad,CA)以10nM(除非另有说明)浓度转染小激活RNA。
(2)一步法RT-qPCR
转染结束后，弃掉培养基，每孔加入150μl PBS清洗一次，弃掉PBS，每孔加入50μl细胞裂解液(Takara)，室温孵育5分钟。每孔取1μl细胞裂解液使用一步法TB Green TM PrimeScrip TM RT-PCR试剂盒II(Takara,RR086A)在ABI 7500快速实时(Fast Real-time)PCR系统(Applied Biosystems)上进行qPCR分析，每个样本重复3个复孔扩增，PCR反应条件见下表1。
表1.PCR反应制备
Figure PCTCN2019092720-appb-000005
反应条件为阶段1反转录反应：42℃，5分钟；95℃10秒；阶段2PCR反应：95℃5秒，60℃20秒，扩增45个循环。以HPRT1及TBP为内参基因。LHPP、HPRT1及TBP所用PCR引物见表2，其中LHPP用LHPP F1/R1引物对扩增。
表2.qRT-PCR分析的引物序列
Figure PCTCN2019092720-appb-000006
为了计算某个saRNA转染样本的LHPP(目的基因)的相对于对照处理(Mock)的表达值(E rel)，用公式1代入目的基因及2个内参基因的Ct值计算。
E rel＝2 (CtTm-CtTs)/((2 (CtR1m-CtR1s)*2 (CtR2m-CtR2s)) (1/2))     (公式1)
其中，CtTm为来自对照(Mock)样本的目的基因的Ct值，CtTs为来自saRNA处理样本的目的基因的Ct值，CtR1m为来自对照(Mock)样本的内参基因1的Ct值,CtR1s为来自saRNA处理样本的内参基因1的Ct值,CtR2m为来自对照(Mock)样本的内参基因2的Ct值,CtR2s为来自saRNA处理样本的内参基因2的Ct值。
(3)功能性saRNA筛选
为了获得能够激活LHPP转录的saRNA，用上述290个saRNA分别转染Huh7细胞，转染浓度为10nM，72小时后以如上所述相同的方法，裂解细胞并进行一步法RT-qPCR分析得到每个saRNA处理样本的LHPP基因的相对(与对照(Mock)比较)表达值。如表3所示，分别有164(56.6％)和37(12.8％)个saRNA显示出激活和抑制活性，89(30.7％)个saRNA对LHPP的表达不产生影响。激活的最大幅度为3.46倍，最大抑制幅度为0.49倍。这些具有激活活性的saRNA被称为激活性saRNA，具有抑制活性的被称为抑制性saRNA。
表3.LHPP高通量筛选结果统计
Figure PCTCN2019092720-appb-000007
图2进一步显示了LHPP saRNA从高度激活到高度抑制的活性分布。
Figure PCTCN2019092720-appb-000008
Figure PCTCN2019092720-appb-000009
Figure PCTCN2019092720-appb-000010
Figure PCTCN2019092720-appb-000011
Figure PCTCN2019092720-appb-000012
Figure PCTCN2019092720-appb-000013
Figure PCTCN2019092720-appb-000014
Figure PCTCN2019092720-appb-000015
Figure PCTCN2019092720-appb-000016
Figure PCTCN2019092720-appb-000017
对290个saRNA的活性按照其在LHPP启动子上的位置排列，很明确地看到功能性saRNA的分布呈现聚集现象，即在某些启动子区域，激活性或者抑制性saRNA聚集在特定的“热点(hot spot)”区域(图3)。如图3所示，在启动子的-917/-844区域(H1)、-710/-675区域(H2)、-198/-168(H3)、-151/-28(H4)和-845/-711区域(H5)分别出现5个热点区域，表现为激活性saRNA的高度聚集。该分析结果表明，激活性saRNA在启动子上并非随机分布，而是存在特定的热点区域。
热点H1(5’至3’：-917至-844)序列，其对应于序列表中SEQ ID NO:500从5’至3’的位置1至位置74：
Figure PCTCN2019092720-appb-000018
热点H2(5’至3’：-710至-675)序列，其对应于序列表中SEQ ID NO:501从5’至3’的位置1至位置36：
Figure PCTCN2019092720-appb-000019
热点H3(5’至3’：-198至-168)序列，其对应于序列表中SEQ ID NO:502从5’至3’的位置1至位置31：
Figure PCTCN2019092720-appb-000020
热点H4(5’至3’：-151至-28)序列，其对应于序列表中SEQ ID NO:503从5’至3’的位置1至位置124：
Figure PCTCN2019092720-appb-000021
热点HC(5’至3’：-845至-711)序列，其对应于序列表中SEQ ID NO:504从5’至3’的位置1至位置135：
Figure PCTCN2019092720-appb-000022
实施例3 saRNA促进LHPP mRNA表达并抑制肿瘤细胞增殖
将靶向LHPP启动子的290个saRNA分别转染Huh7细胞，72小时后用一步法RT-qPCR分析LHPP mRNA表达，使用CCK8法检测细胞活力。如图4所示，当激活性saRNA促进LHPP mRNA表达时，细胞活力降低，mRNA表达量与细胞活力具有负相关性。
CCK8法检测细胞活力：将细胞以3-5×10 3个细胞/孔铺板于96孔板中，培养过夜，转染寡核苷酸双链体。转染72小时后，将10uL CCK8溶液(Dojindo Molecular Technologies)加入到每孔中，37℃孵育1小时，后使用酶标仪测定450nm处吸光值。
实施例4 saRNA促进LHPP蛋白表达
将细胞以3-5×10 3个细胞/孔铺板于96孔板中，培养过夜，转染10个随机选择的寡核苷酸双链体。转染72小时后收集细胞，使用含有蛋白酶抑制剂的细胞裂解液(1×RIPA缓冲液,CST)裂解。BCA法(Thermo)进行蛋白质定量，随后进行聚丙烯酰胺凝胶电泳分离并转至0.45μm的PVDF膜。所用一抗为：鼠单克隆抗LHPP(Invitrogen)或兔多克隆抗AKT(Cell Signaling Technology)、pAKT(Cell Signaling Technology)、α/β-微管蛋白抗体(Cell Signaling Technology)对印迹进行检测；二抗分别用：抗鼠IgG,HRP-连接的抗体(Cell Signaling Technology)或抗兔IgG,HRP-连接的抗体(Cell Signaling Technology)。采用Image Lab(BIO-RAD,Chemistry Doctm MP imaging System)扫描检测信号。
表5.作为实验对照的双链RNA序列
Figure PCTCN2019092720-appb-000023
如图5所示，这10个随机选择的saRNA在促进或增加LHPP mRNA和蛋白表达水平增加的同时，使AKT的磷酸化水平下调。
实施例5 saRNA抑制多种肿瘤细胞的增殖
为了进一步评估LHPP saRNA诱导LHPP基因mRNA表达和抑制癌细胞增殖的作用，将筛选得到的8个saRNA(RAG7-132、RAG7-133、RAG7-139、RAG7-177、RAG7-178、RAG7-694、RAG7-707和RAG7-892)分别转染肝癌细胞系Huh7(日本东北大学医用细胞资源库)、HepG2(ATCC)、Hep3B(ATCC)、Li-7(日本东北大学医用细胞资源库)、SK-HEP-1(ATCC)；肺癌细胞系A549(ATCC)、膀胱癌细胞系T24(ATCC)、前列腺癌细胞系PC3(ATCC)以及神经胶质瘤细胞系U87MG(ATCC)并且测量其mRNA表达以及细胞活力。如图6所示， RAG7-133在5种肝癌细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖；RAG7-694在除了Li-7之外的4种肝癌细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖。从另一个角度看，在细胞系HepG2和SK-HEP-1中，上述8个saRNA均可不同程度地诱导LHPP基因表达，并抑制细胞增殖。如图7所示，RAG7-133在T24、PC3以及U87MG细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖；RAG7-694在A549、T24以及PC3细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖；RAG7-177在A549、T24以及U87MG细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖：RAG7-178在A549、PC3以及U87MG细胞系中均可不同程度地诱导LHPP基因表达，并抑制细胞增殖。
实施例6 saRNA联合化学药物抑制细胞增殖
所用化合物包括：索拉非尼(Sora)(SELLECK，S1040)、乐伐替尼(Lenv)(SELLECK，S1164)、瑞戈非尼(Rego)(SELLECK，S1178)和卡博替尼(Cabo)(SELLECK，S1119)。在将候选saRNA分别以不同浓度梯度转染细胞24小时后，分别加入上述化合物(浓度分别为5μM)并继续孵育细胞48小时，采用CCK8法检测细胞活力。使用
Figure PCTCN2019092720-appb-000024
version 1.0软件(ComboSyn,Inc.Paramus,NJ,USA)分析药物联用指数(CI)，CI<1为协同作用，CI＝1为相加作用，CI>1为拮抗作用。
如图8所示，对于HepG2细胞，高剂量(25nM～100nM)的RAG7-133与瑞戈非尼具有强的协同效应(CI<0.3)，而低剂量(1.0nM～10nM)也具有协同效应(0.3<CI<0.7)；RAG7-133分别与索拉非尼、卡博替尼具有协同效应(CI<1)，而与乐伐替尼没有协同效应(CI>1)。如图9所示，在U87MG细胞中，RAG7-133与四种化合物分别具有协同效应(CI<1)；尤其与乐伐替尼或卡博替尼联用，RAG7-133在较宽的剂量范围内(1.0nM～100nM)具有极强的协同效应(CI<0.1)。
实施例7 联合用药在小鼠体内抑制人HepG2移植瘤生长
saRNA制剂配制：saRNA递送系统采用体内-jetPEI(201-10G,Polyplus-transfection，法国)。配制过程简述如下：首先稀释saRNA于10％葡萄糖溶液中，得到溶液A；按照制造商的说明，稀释所需量体内-jetPEI于10％葡萄糖溶液中，得到溶液B；然后等体积混合溶液A和溶液B(氮磷比为8，葡萄糖终浓度为5％)，混合均匀后室温静置15分钟备用。
取对数生长期HepG2细胞,计数后,将细胞悬液调至每毫升5×10 7个,以每只0.1mL接种于BALB/c裸鼠右腋皮下。肿瘤长至约100mm 3,将荷瘤裸鼠随机分为4组(载体对照(Vehicle) 组、saRNA组、瑞戈非尼组以及saRNA和瑞戈非尼联用组(saRNA+瑞戈非尼组)),每组6只。对于saRNA组和saRNA+瑞戈非尼组，在1、4、7、10天按saRNA 1mg·kg -1瘤内注射；对于瑞戈非尼组和saRNA+瑞戈非尼组，在1-12天，按瑞戈非尼3mg·kg -1的剂量每天灌胃给药。从第1次给药开始,每2天用游标卡尺测量肿瘤的长径和短径,按公式:V＝(l×w 2)/2计算肿瘤体积,其中l表示瘤块最长直径；w表示与瘤块表面平行且垂直于长径的直径。记录给药期间肿瘤生长曲线及解剖后肿瘤大小与形态。如图10所示，与载体对照组(Vehicle)相比，saRNA组(单独给药RAG7-133)自第7天开始肿瘤增长出现减缓和缩小趋势，至第13天saRNA组肿瘤体积与治疗开始时的肿瘤体积相比增加了34％，而载体对照组肿瘤体积增加了118％，两者的肿瘤体积变化有显著差异(P<0.05)，说明LHPP saRNA可显著抑制小鼠体内肿瘤生长。saRNA与瑞戈非尼联用组(RAG7-133+Rego)自第4天开始即出现肿瘤增长缓慢的趋势，自第7天开始肿瘤缩小，至第13天肿瘤体积与治疗开始时的肿瘤体积相比仅增加了4％，单用化药瑞戈非尼(Rego)组在治疗第13天肿瘤体积与治疗开始时的肿瘤体积相比增加70％，两者相比具有显著性差异(P<0.01)，说明saRNA与化药联用协同地增强了化药的抑癌作用。
实施例8 联合用药在小鼠体内抑制人U87MG移植瘤生长
saRNA制剂配制：saRNA递送系统采用体内-jetPEI(201-10G,Polyplus-transfection，法国),配制过程简述如下：首先稀释saRNA于10％葡萄糖溶液中，得到溶液A；稀释所需量in vivo-jetPEI于10％葡萄糖溶液中，得到溶液B；然后等体积混合溶液A和溶液B(氮磷比为8，葡萄糖终浓度为5％)，混合均匀后室温静置15分钟备用。
取对数生长期神经胶质瘤细胞系U87MG细胞,计数后,将细胞悬液调至每毫升9×10 7个,以每只0.1mL接种于BALB/c裸鼠右腋皮下。肿瘤长至约100mm 3,将荷瘤裸鼠随机分为4组(载体对照组、saRNA组、瑞戈非尼组以及saRNA和瑞戈非尼的联用组(RAG7-133+Rego组)),每组7只。对于saRNA组和saRNA+瑞戈非尼组，在1、4、7、10天按saRNA 1mg·kg -1瘤内注射；对于瑞戈非尼组和saRNA+瑞戈非尼组，在1-12天，按瑞戈非尼3mg·kg -1的剂量每天灌胃给药。从第1次给药开始,每2天用游标卡尺测量肿瘤的长径和短径,按公式:V＝(l×w 2)/2计算肿瘤体积,其中l表示瘤块最长直径：w表示与瘤块表面平行且垂直于长径的直径。记录给药期间肿瘤生长曲线及解剖后肿瘤大小与形态。如图11所示，与载体对照组(Vehicle)相比，saRNA组(单独给药RAG7-133)在治疗第13天肿瘤体积与治疗开始时的肿瘤体积相比增加了167％，而对照组肿瘤体积增加了406％，两者的肿瘤体积变化有显著差异(P<0.05)， 说明LHPP saRNA可显著抑制小鼠体内肿瘤生长。saRNA与瑞戈非尼联用组(RAG7-133+Rego)在治疗第13天肿瘤体积与治疗开始时的肿瘤体积相比增加了132％，单用瑞戈非尼(Rego)组在治疗第13天肿瘤体积与治疗开始时的肿瘤体积相比增加251％，两者相比也有显著性差异(P<0.05)，说明saRNA与化药联用协同地增强了化药的抑癌作用。
综合上述结果，申请人通过高通量筛选靶向LHPP基因启动子的saRNA，发现了多个能够显著激活LHPP基因表达的saRNA。这些saRNA通过上调LHPP基因和蛋白的表达，下调磷酸化AKT水平进而在体外或体内抑制肿瘤细胞增殖。这些结果明确提示用靶向LHPP基因启动子的saRNA将是一种很有前景的治疗肿瘤的策略。
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Claims (52)

  1. 小激活核酸分子，包含第一核酸链和第二核酸链，其中第一核酸链与LHPP基因启动子中距转录起始位点-917至-844区域(SEQ ID NO:500)、-710至-675区域(SEQ ID NO:501)、-198至-168(SEQ ID NO:502)、-151至-28(SEQ ID NO:503)或-845至-711区域(SEQ ID NO:504)中的任一连续16-35个核苷酸具有至少75％的同源性或互补性，所述第一核酸链和所述第二核酸链能通过互补形成双链核酸结构，所述双链核酸结构能够激活LHPP基因在细胞中的表达。
  2. 根据权利要求1所述的小激活核酸分子，其中所述第一核酸链和所述第二核酸链存在于两条不同的核酸链上。
  3. 根据权利要求1所述的小激活核酸分子，其中所述第一核酸链和所述第二核酸链存在于同一条核酸链上，优选地，所述小激活核酸分子为发夹型单链核酸分子，其中所述第一核酸链和所述第二核酸链包含形成双链核酸结构的互补区域。
  4. 根据权利要求2所述的小激活核酸分子，其特征在于所述小激活核酸分子的至少一条链在3’端具有0至6个核苷酸的突出。
  5. 根据权利要求4所述的小激活核酸分子，其特征在于所述小激活核酸分子的两条链在3’端都具有0至6个核苷酸的突出，优选地具有2-3个核苷酸的突出。
  6. 根据权利要求1-5任一项所述的小激活核酸分子，其特征在于所述第一核酸链和所述第二核酸链的长度分别为16至35个核苷酸。
  7. 根据权利要求1-6任一项所述的小激活核酸分子，其特征在于所述小激活核酸分子的一条链包括与选自SEQ ID NO:SEQ ID NO:329-492中的任一核苷酸序列具有至少75％的同源性或互补性的核酸序列，或由与选自SEQ ID NO:SEQ ID NO:329-492中的任一核苷酸序列具有至少75％的同源性或互补性的核酸序列组成。
  8. 根据权利要求1-7所述的小激活核酸分子，其特征在于所述第一核酸链与选自SEQ ID NO:1-164的任一核苷酸序列具有至少75％的同源性，并且所述第二核酸链与选自SEQ ID NO:165-328的任一核苷酸序列具有至少75％的同源性。
  9. 权利要求1-8所述的小激活核酸分子，其特征在于所述第一核酸链包括选自SEQ ID NO:1-164的任一核苷酸序列或由选自SEQ ID NO:1-164的任一核苷酸序列组成，并且所述第二核酸链包括选自SEQ ID NO:165-328的任一核苷酸序列或由选自SEQ ID NO:165-328的任一核苷酸序列组成。
  10. 根据权利要求1-9任一项所述的小激活核酸分子，其中所述小激活核酸分子包括至少一个修饰，优选地，所述修饰为化学修饰。
  11. 根据权利要求10所述的小激活核酸分子，其中所述化学修饰包括或选自如下修饰中的至少一种或多种：
    (1)对所述小激活核酸分子的核苷酸序列中连接核苷酸的磷酸二酯键的修饰；
    (2)对所述小激活核酸分子的核苷酸序列中的核糖的2’-OH的修饰；
    (3)对所述小激活核酸分子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。
  12. 根据权利要求10所述的小激活核酸分子，其中所述化学修饰包括或选自如下修饰中的一种或多种：2’-氟代修饰、2’-氧甲基修饰、2’-氧亚乙基甲氧基修饰、2,4’-二硝基苯酚修饰、锁核酸(LNA)、2’-氨基修饰、2’-脱氧修饰、5′-溴尿嘧啶修饰、5′-碘尿嘧啶修饰、N-甲基脲嘧啶修饰、2,6－二氨基嘌呤修饰、硫代磷酸修饰和硼烷化磷酸盐修饰。
  13. 权利要求1-12任一项所述的小激活核酸分子，其激活/上调LHPP基因表达至少10％。
  14. 编码权利要求1-9任一项所述的小激活核酸分子的核酸。
  15. 权利要求14所述的核酸，其中所述核酸是DNA分子。
  16. 包含权利要求1-13任一项所述的小激活核酸分子或权利要求14或15所述的核酸的细胞。
  17. 包含权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸或权利要求16所述的细胞，和任选地药学上可接受的载体的组合物。
  18. 权利要求17所述的组合物，其特征在于所述药学上可接受的载体包括或选自脂质体、高分子聚合物或多肽。
  19. 权利要求17或18所述的组合物，其中所述组合物含有1-150nM的所述小激活核酸分子。
  20. 试剂盒，其包含权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸、权利要求16所述的细胞或权利要求17-19中任一项所述的组合物。
  21. 权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸或权利要求17-19任一项所述的组合物在制备用于在细胞中激活/上调LHPP基因表达的制剂中的应用。
  22. 根据权利要求21所述的应用，其中所述小激活核酸分子被直接导入所述细胞中。
  23. 根据权利要求21所述的应用，其中所述小激活核酸分子是在编码该小激活核酸分子的核苷酸序列导入所述细胞后在细胞内产生的。
  24. 根据权利要求21-23的任一项所述的应用，其中所述细胞包括哺乳动物细胞。
  25. 根据权利要求21所述的应用，其中所述细胞是人类细胞。
  26. 根据权利要求25所述的应用，其中所述细胞存在于人体中。
  27. 根据权利要求26所述的应用，其中所述人体是患有与LHPP蛋白表达不足或减少相关的疾病或状况的患者，并且所述小激活核酸分子被施用足够的量以实现对所述疾病或状况的治疗。
  28. 根据权利要求27所述的应用，其中所述与LHPP蛋白表达不足或减少相关的疾病或状况包括肿瘤，优选包括实体瘤，更优选地，包括肝癌、肺癌、膀胱癌、前列腺癌和神经胶质瘤。
  29. 分离的LHPP基因小激活核酸分子靶位点，其中所述靶位点包括或选自SEQ ID NO:500-504的任一条序列上的任意连续16-35个核苷酸序列。
  30. 根据权利要求29所述的小激活核酸分子靶位点，其中所述靶位点包括或选自SEQ ID NO:329-492中所示的任一核苷酸序列。
  31. 激活/上调LHPP基因在细胞中的表达的方法，该方法包括给所述细胞施用权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸或权利要求17-19中任一项所述的组合物。
  32. 根据权利要求31所述的方法，其中所述小激活核酸分子被直接导入所述细胞中。
  33. 根据权利要求31所述的方法，其中所述小激活核酸分子是在编码所述小激活核酸分子的所述核酸导入所述细胞后在细胞内产生的。
  34. 根据权利要求31-33任一项所述的方法，其中所述细胞包括哺乳动物细胞。
  35. 根据权利要求31所述的方法，其中所述细胞是人类细胞。
  36. 根据权利要求35所述的方法，其中所述细胞存在于人体中。
  37. 根据权利要求36所述的方法，其中所述人体是患有与LHPP蛋白表达不足或减少相关的疾病或状况的患者，并且所述小激活核酸分子被施用足够的量以实现对所述疾病或状况的治疗。
  38. 根据权利要求36所述的方法，其中所述与LHPP蛋白表达不足或减少相关的疾病或状况包括肿瘤，优选包括实体瘤，更优选地，包括肝癌、肺癌、膀胱癌、前列腺癌和神经胶质瘤。
  39. 治疗个体中与LHPP蛋白表达不足或减少相关的疾病或状况的方法，包括给所述个体施用治疗有效量的权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸、权利要求16所述的细胞或权利要求17-19任一项所述的组合物。
  40. 权利要求39的方法，其中所述与LHPP蛋白表达不足或减少相关的疾病或状况包括肿瘤，优选地包括实体瘤，更优选地，包括肝癌、肺癌、膀胱癌、前列腺癌和神经胶质瘤。
  41. 权利要求39或40所述的方法，其中所述个体是哺乳动物。
  42. 权利要求39所述的方法，其中所述个体是人。
  43. 权利要求39-42任一项所述的方法，其特征在于还可以给所述个体施用化学治疗剂、放射治疗、细胞治疗、小分子、多肽、蛋白、抗体或其他抗肿瘤药物，所述化学治疗剂优选地包括或选自索拉非尼、乐伐替尼、瑞戈非尼和卡博替尼。
  44. 权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸、权利要求16所述的细胞或权利要求17-19任一项所述的组合物在制备用于治疗与LHPP蛋白表达不足或减少相关的疾病或状况的药物中的应用。
  45. 权利要求44所述的应用，其中所述与LHPP蛋白表达不足或减少相关的疾病或状况包括肿瘤，优选地包括实体瘤，更优选地包括或选自肝癌、肺癌、膀胱癌、前列腺癌和神经胶质瘤。
  46. 权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸、权利要求16所述的细胞或权利要求17-19任一项所述的组合物在制备用于治疗由LHPP蛋白表达不足引发的疾病的药物中的应用。
  47. 权利要求44-46任一项所述的应用，其中所述个体是哺乳动物。
  48. 权利要求44-46任一项所述的应用，其中所述个体是人。
  49. 权利要求1-13任一项所述的小激活核酸分子、权利要求14或15所述的核酸、权利要求16所述的细胞或权利要求17-19任一项所述的组合物与化学治疗剂在制备用于治疗与LHPP蛋白表达不足或减少相关的疾病或状况的药物或药物组合中的应用，所述化学治疗剂优选地包括或选自索拉非尼、乐伐替尼、瑞戈非尼和卡博替尼。
  50. 权利要求49所述的应用，其中所述与LHPP蛋白表达不足或减少相关的疾病或状况包括肿瘤，优选为包括实体瘤，更优选地包括或选自肝癌、肺癌、膀胱癌、前列腺癌或神经胶质瘤。
  51. 权利要求49或50所述的应用，其中所述个体是哺乳动物。
  52. 权利要求49或50所述的应用，其中所述个体是人。
PCT/CN2019/092720 2019-01-30 2019-06-25 寡核苷酸分子及其在肿瘤治疗中的应用 WO2020155534A1 (zh)

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