WO2015139044A1 - Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof - Google Patents

Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof Download PDF

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Publication number
WO2015139044A1
WO2015139044A1 PCT/US2015/020776 US2015020776W WO2015139044A1 WO 2015139044 A1 WO2015139044 A1 WO 2015139044A1 US 2015020776 W US2015020776 W US 2015020776W WO 2015139044 A1 WO2015139044 A1 WO 2015139044A1
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Prior art keywords
strand
nucleotides
ras
rna molecule
duplex rna
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PCT/US2015/020776
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French (fr)
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Chiang J. Li
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Boston Biomedical, Inc.
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Priority to CA2937767A priority Critical patent/CA2937767A1/en
Priority to CN201580012331.XA priority patent/CN107428794A/en
Priority to JP2016549041A priority patent/JP2017511302A/en
Priority to US15/125,655 priority patent/US20170016001A1/en
Priority to KR1020167020509A priority patent/KR20160130986A/en
Priority to RU2016131028A priority patent/RU2016131028A/en
Priority to EP15761005.6A priority patent/EP3116890A4/en
Priority to AU2015229033A priority patent/AU2015229033A1/en
Priority to BR112016017680A priority patent/BR112016017680A2/en
Publication of WO2015139044A1 publication Critical patent/WO2015139044A1/en
Priority to HK17105685.0A priority patent/HK1232228A1/en

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    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—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
    • C12N15/1135—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 oncogenes or tumor suppressor genes
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    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57446—Specifically defined cancers of stomach or intestine
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5748—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving oncogenic proteins
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/31—Chemical structure of the backbone
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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    • G—PHYSICS
    • G01—MEASURING; TESTING
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    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/914—Hydrolases (3)

Definitions

  • the invention generally relates to compositions for use in silencing K-Ras gene expression. More particularly, the invention relates to novel asymmetrical interfering RNA molecules as inhibitors of K-Ras expression, and to pharmaceutical compositions and uses thereof in the treatment of cancer or a related disorder in a mammal.
  • RNAi-interference by use of small or short interfering RNA (siRNA) has emerged as a therapeutic tool.
  • siRNA small or short interfering RNA
  • the gene silencing efficacy by siRNA is limited to about 50% or less for majority of genes in mammalian cells.
  • the manufacture of these molecules is expensive (much more expensive than manufacturing anti sense deoxynucleotides), inefficient, and requires chemical modification.
  • the extracellular administration of synthetic siRNAs can trigger interferon-like responses has added a significant barrier for RNAi-based research and RNAi-based therapeutic development.
  • the protein K-Ras is a molecular switch that under normal conditions regulates cell growth and cell division. Mutations in this protein lead to the formation of tumors through continuous cell growth. About 30% of human cancers have a mutated Ras protein that is constitutively bound to GTP due to decreased GTPase activity and insensitivity to GAP action. Ras is also an important factor in many cancers in which it is not mutated but rather functionally activated through inappropriate activity of other signal transduction elements. Mutated K-Ras proteins are found in a large proportion of all tumour cells. K-Ras protein occupies a central position of interest.
  • aiRNA asymmetric silencing RNA technology
  • CSCs are not only addicted to activating mutations of K-Ras, or activation of the downstream regulators of the Ras pathway, but also that CSCs with amplified mutant K-Ras become highly sensitive to K-Ras silencing.
  • the present inventors made a surprising discovery that the DNA copy numbers of the mutant K-Ras directly predicts sensitivity of cancer stem cells to K-Ras silencing, which suggests that amplified mutated K-Ras is required to the maintenance of the malignancy and cancer cell sternness, which may have significant implication for understanding the connection between oncogene and cancer cell sternness and for developing cancer stem cell inhibitors.
  • aiRNA asymmetrical interfering RNAs
  • aiRNA can have RNA duplex structure of much shorter length than the other siRNA, which should reduce the cost of synthesis and abrogate/reduce the length-dependent triggering of nonspecific interferon-like responses.
  • the asymmetry of the aiRNA structure abrogates and/or otherwise reduces the sense-strand mediated off-target effects.
  • aiRNA is more efficacious, potent, rapid-onset, and durable than siRNA in inducing gene silencing.
  • AiRNA can be used in all areas that other siRNA or shRNA are being applied or contemplated to be used, including biology research, R&D research in biotechnology and pharmaceutical industry, and RNAi-based therapies.
  • the duplex RNA molecule comprises a first strand with a length from 18-23 nucleotides and a second strand with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing in a eukaryotic cell.
  • the first strand comprises a sequence being substantially complementary to a target K-Ras mRNA sequence.
  • the first strand comprises a sequence being at least 70 percent complementary to a target K-Ras mRNA sequence.
  • the eukaryotic cell is a mammalian cell or an avian cell.
  • the target K-Ras mRNA sequence is a human K-Ras target sequence.
  • the target K-Ras mRNA sequence is a human K-Ras target sequence selected from at least a portion of the sequence shown in GenBank Accession No. NM_004985 shown below as SEQ ID NO: 1 :
  • the target K-Ras mRNA sequence is a target sequence shown in Table 1 below.
  • the RNA duplex molecule also referred to herein as an asymmetrical interfering RNA molecule or aiRNA molecule, comprises a sense strand sequence, an antisense strand sequence or a combination of a sense strand sequence and antisense strand sequence selected from those shown in Table 2 below.
  • AAAAUGACUGAAUAU 420 AAUAUAUUCAGUCAUUUUCAG 738
  • AAAGAAGUCAAAGAC 506 AAUGUCUUUGACUUCUUUUUC 824
  • AAAGUGUAAUUAU 510 AACAUAAUUACACACUUUGUC 828
  • AAAAAGAAACUGAAU 540 AAUAUUCAGUUUCUUUUUCAC 858
  • the RNA duplex molecule comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • the RNA duplex molecule comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637.
  • the RNA duplex molecule comprises an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • the RNA duplex molecule comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • At least one nucleotide of the sequence of 5' overhang is selected from the group consisting of A, U, and dT.
  • the GC content of the double stranded region is
  • the first strand has a length from 19-22 nucleotides. [0017] In some embodiments, the first strand has a length of 21 nucleotides. In a further embodiment, the second strand has a length of 14-16 nucleotides.
  • the first strand has a length of 21 nucleotides, and the second strand has a length of 15 nucleotides. In a further embodiment, the first strand has a 3'-overhang of 2-4 nucleotides. In an even further embodiment, the first strand has a 3'- overhang of 3 nucleotides.
  • the duplex RNA molecule contains at least one modified nucleotide or its analogue.
  • the at least one modified nucleotide or its analogue is sugar-, backbone-, and/or base- modified ribonucleotide.
  • the backbone-modified ribonucleotide has a modification in a phosphodiester linkage with another ribonucleotide.
  • the phosphodiester linkage is modified to include at least one of a nitrogen or a sulphur heteroatom.
  • the nucleotide analogue is a backbone-modified ribonucleotide containing a phosphothioate group.
  • the at least one modified nucleotide or its analogue is an unusual base or a modified base.
  • the at least one modified nucleotide or its analogue comprises inosine, or a tritylated base.
  • the nucleotide analogue is a sugar-modified ribonucleotide, wherein the 2'-OH group is replaced by a group selected from H, OR, R, halo, SH, SR, NH 2 , NHR, NR 2 , or CN, wherein each R is independently C1-C6 alkyl, alkenyl or alkynyl, and halo is F, CI, Br or I.
  • the first strand comprises at least one deoxynucleotide.
  • the at least one deoxynucleotides are in one or more regions selected from the group consisting of 3 '-overhang, 5 '-overhang, and double- stranded region.
  • the second strand comprises at least one deoxynucleotide.
  • the present invention also provides a method of modulating K-Ras expression, e.g., silencing K-Ras expression or otherwise reducing K-Ras expression, in a cell or an organism comprising the steps of contacting said cell or organism with an asymmetrical duplex RNA molecule of the disclosure under conditions wherein selective K-Ras gene silencing can occur, and mediating a selective K-Ras gene silencing effected by the duplex RNA molecule towards K-Ras or nucleic acid having a sequence portion substantially corresponding to the double-stranded RNA.
  • a method of modulating K-Ras expression e.g., silencing K-Ras expression or otherwise reducing K-Ras expression
  • said contacting step comprises the step of introducing said duplex RNA molecule into a target cell in culture or in an organism in which the selective K-Ras silencing can occur.
  • the introducing step is selected from the group consisting of transfection, lipofection, electroporation, infection, injection, oral administration, inhalation, topical and regional administration.
  • the introducing step comprises using a pharmaceutically acceptable excipient, carrier, or diluent selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a nanoemulsion, a lipid, and a lipoid.
  • the modulating method is used for determining the function or utility of a gene in a cell or an organism.
  • the modulating method is used for treating or preventing a disease or an undesirable condition.
  • the disease or undesirable condition is a cancer, for example, gastric cancer.
  • the disclosure provides compositions and methods for targeting K-Ras in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer.
  • the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure.
  • the subject is human.
  • the subject is suffering from gastric cancer.
  • the subject is diagnosed with gastric cancer.
  • the subject is predisposed to gastric cancer.
  • the disclosure also provides compositions and methods for targeting K-Ras to inhibit the survival and/or proliferation of cancer stem cells.
  • the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure.
  • the subject is human.
  • the subject is suffering from gastric cancer.
  • the subject is diagnosed with gastric cancer.
  • the subject is predisposed to gastric cancer.
  • the disclosure also provides compositions and methods for targeting K-Ras in the inhibition of to inhibit the survival and/or proliferation of CSCs in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer.
  • the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure.
  • the subject is human.
  • the subject is suffering from gastric cancer.
  • the subject is diagnosed with gastric cancer.
  • the subject is predisposed to gastric cancer.
  • the disclosure also provides a method for treating cancer in a selected patient population, the method comprising the steps of: (a) measuring a level of mutant K-Ras gene amplification in a biological sample obtained from a patient candidate diagnosed of a cancer; (b) confirming that the patient candidate's mutant K-Ras gene amplification level is above a benchmark level; and (c) administering to the patient candidate a duplex RNA molecule comprising a first strand comprising a nucleotide sequence with a length from 18- 23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleot
  • the steps (a), (b), and (c) may be performed by one actor or several actors.
  • a patient candidate's mutant K-Ras gene amplification level is considered to be above a benchmark level if it is at least, e.g., 2-fold greater relative to that of a control patient who would not respond favorably to the claimed treatment method according to the present invention.
  • a skilled physician may determine that the optimal benchmark level of the DNA copy number is, e.g., about 3-fold or 4-fold greater relative to that of a non-responsive patient, based on the data presented in the present disclosure.
  • the disclosure also provides a method for treating cancer in a selected patient population, the method comprising the steps of: (a) measuring an expression level of mutant K-Ras protein in a biological sample obtained from a patient candidate diagnosed of a cancer; (b) confirming that the patient candidate's mutant K-Ras protein expression level is above a benchmark level; and (c) administering to the patient candidate a duplex RNA molecule comprising a first strand comprising a nucleotide sequence with a length from 18- 23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a
  • the steps (a), (b), and (c) may be performed by one actor or several actors.
  • a patient candidate's mutant K-Ras protein expression level is considered to be above a benchmark level if it is at least, e.g., 2-fold greater relative to that of a control patient who would not respond favorably to the claimed treatment method according to the present invention.
  • a skilled physician may determine that the optimal benchmark level of the mutant K-Ras protein expression is, e.g., about 3-fold or 4- fold greater relative to that of a non-responsive patient, based on the data presented in the present disclosure.
  • the present invention further provides a kit.
  • the kit comprises a first RNA strand with a length from 18-23 nucleotides and a second RNA strand with a length from 12- 17 nucleotides, wherein the second strand is substantially complementary to the first strand, and capable of forming a duplex RNA molecule with the first strand, wherein the duplex RNA molecule has a 3 '-overhang from 1-9 nucleotides, and a 5 '-overhang from 0-8 nucleotides, wherein said duplex RNA molecule is capable of effecting K-Ras specific gene silencing.
  • the present invention also provides a method of preparing the duplex RNA molecule.
  • the method comprises the steps of synthesizing the first strand and the second strand, and combining the synthesized strands under conditions, wherein the duplex RNA molecule is formed, which is capable of effecting sequence-specific gene silencing.
  • the method further comprises a step of introducing at least one modified nucleotide or its analogue into the duplex RNA molecule during the synthesizing step, after the synthesizing and before the combining step, or after the combining step.
  • the RNA strands are chemically synthesized, or biologically synthesized.
  • the present invention provides an expression vector.
  • the vector comprises a nucleic acid or nucleic acids encoding the duplex RNA molecule operably linked to at least one expression-control sequence.
  • the vector comprises a first nucleic acid encoding the first strand operably linked to a first expression-control sequence, and a second nucleic acid encoding the second strand operably linked to a second expression-control sequence.
  • the vector is a viral, eukaryotic, or bacterial expression vector.
  • the present invention also provides a cell.
  • the cell comprises the vector.
  • the cell comprises the duplex RNA molecule.
  • the cell is a mammalian, avian, or bacterial cell.
  • the modulating method can also be used for studying drug target in vitro or in vivo.
  • the present invention provides a reagent comprising the duplex RNA molecule.
  • the present invention also provides a method of preparing a duplex RNA molecule of the disclosure comprising the steps of synthesizing the first strand and the second strand, and combining the synthesized strands under conditions, wherein the duplex RNA molecule is formed, which is capable of effecting K-Ras sequence-specific gene silencing.
  • the RNA strands are chemically synthesized, or biologically synthesized.
  • the first strand and the second strand are synthesized separately or simultaneously.
  • the method further comprises a step of introducing at least one modified nucleotide or its analogue into the duplex RNA molecule during the synthesizing step, after the synthesizing and before the combining step, or after the combining step.
  • the present invention further provides a pharmaceutical composition.
  • the pharmaceutical composition comprises as an active agent at least one duplex RNA molecule and one or more carriers selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a cholesterol, a lipid, and a lipoid.
  • Figure 1(A) shows an in vitro study in which aiRNA ID NO: 21 ("aiK-Ras
  • Figure 1(B) shows an in vitro study in which aiRNA ID NO: 142 ("aiK-Ras
  • Figure 2(A) shows detection of siRNA and aiR A loading to RISC by northern blot analysis.
  • Figure 2(B) shows detection of TLR3/aiRNA or siRNA binding.
  • FIG. 1 shows that TLR3/RNA complexes were immunoprecipitated with anti-HA antibody.
  • Figure 3(A) shows colony formation assay in AGS and DLD1 transfected with aiK-Ras #1 or aiK-Ras #2.
  • Figure 3(B) shows western blot analysis of lysate from AGS and DLD1.
  • Figure 3(C) shows colony formation assay results in large cell panel.
  • Figure 4 shows western blot analysis of K-Ras and EGFR-RAS pathway molecules.
  • Figure 5(A) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel.
  • Figure 5(B) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel.
  • Figure 6(A) shows sternness gene expression in CSC culture.
  • Figure 6(B) shows the results of sphere formation assay in various cell lines.
  • Figure 6(C) shows depletion of CD44-high population in AGS and DLD1 cells with aiK-Ras #1 and aiK-Ras #2.
  • Figure 7(A) shows heat map of CSC-related genes in cancer cells transfected with aiK-Ras.
  • Figure 7(B) shows confirmation of down-regulated Notch signaling by western blot.
  • the present invention relates to asymmetric duplex RNA molecules that are capable of effecting selective K-Ras gene silencing in a eukaryotic cell.
  • the duplex RNA molecule comprises a first strand and a second strand.
  • the first strand is longer than the second strand.
  • the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand.
  • the protein K-Ras is a molecular switch that under normal conditions regulates cell growth and cell division. Mutations in this protein lead to the formation of tumors through continuous cell growth. About 30% of human cancers have a mutated Ras protein that is constitutively bound to GTP due to decreased GTPase activity and insensitivity to GAP action. Ras is also an important factor in many cancers in which it is not mutated but rather functionally activated through inappropriate activity of other signal transduction elements. Mutated K-Ras proteins are found in a large proportion of all tumor cells. K-Ras protein occupies a central position of interest. The identification of oncogenically mutated K- Ras in many human cancers led to major efforts to target this constitutively activated protein as a rational and selective treatment. Despite decades of active agent research, significant challenges still remain to develop therapeutic inhibitors of K-Ras.
  • compositions and methods provided herein are useful in elucidating the function of K-Ras in the cancer development and maintenance.
  • the compositions and methods use asymmetric interfering RNAs (aiRNAs) that are able to silence target genes with high potency leading to long-lasting knockdown, and reducing off-target effects, and investigated the dependency of K-Ras on cell survival in several types of human cancer cell lines.
  • aiRNA-induced silencing of K-Ras was found to inhibit the cell proliferation of gastric cancer cells and the ability of gastric cancer cells to form colonies compared to other cancer types.
  • CSCs cancer stem cells
  • K-Ras inhibition decreased the colonies derived from gastric CSCs and altered the gene expression patterns of several genes involved in "sternness" compared to other cancer types.
  • the results of these studies suggest that gastric cancer and gastric CSCs are affected by the K-Ras oncogene and that Kras aiRNAs are promising therapeutic candidates for the treatment of gastric cancer.
  • the disclosure provides compositions and methods for targeting K-Ras in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer.
  • the disclosure also provides compositions and methods for targeting K-Ras to inhibit the survival and/or proliferation of CSCs, as well as compositions and methods for targeting K-Ras in the inhibition of to inhibit the survival and/or proliferation of CSCs in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer.
  • the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure.
  • the subject is human.
  • the subject is suffering from gastric cancer.
  • the subject is diagnosed with gastric cancer. In some embodiments, the subject is predisposed to gastric cancer.
  • the duplex RNA molecule used in the compositions and methods of the disclosure has a 3'-overhang from 1-8 nucleotides and a 5'-overhang from 1 -8 nucleotides, a 3 '-overhang from 1-10 nucleotides and a blunt end, or a 5'- overhang from 1- 10 nucleotides and a blunt end. In another embodiment, the duplex RNA molecule has two 5'-overhangs from 1-8 nucleotides or two 3'-overhangs from 1- 10 nucleotides.
  • the first strand has a 3 '-overhang from 1-8 nucleotides and a 5'-overhang from 1 -8 nucleotides.
  • the duplex RNA molecule is an isolated duplex RNA molecule.
  • the first strand has a 3'-overhang from 1-10 nucleotides, and a 5'-overhang from 1-10 nucleotides or a 5'-blunt end. In another embodiment, the first strand has a 3 ⁇ overhang from 1-10 nucleotides, and a 5 ⁇ overhang from 1-10 nucleotides. In an alternative embodiment, the first strand has a 3 '-overhang from 1-10 nucleotides, and a 5 '-blunt end.
  • the first strand has a length from 5-100 nucleotides, from 12-30 nucleotides, from 15-28 nucleotides, from 18-27 nucleotides, from 19-23 nucleotides, from 20-22 nucleotides, or 21 nucleotides.
  • the second strand has a length from 3-30 nucleotides, from 12-26 nucleotides, from 13-20 nucleotides, from 14-23 nucleotides, 14 or 15 nucleotides.
  • the first strand has a length from 5-100 nucleotides, and the second strand has a length from 3-30 nucleotides; or the first strand has a length from 10-30 nucleotides, and the second strand has a length from 3-29 nucleotides; or the first strand has a length from 12-30 nucleotides and the second strand has a length from 10-26 nucleotides; or the first strand has a length from 15-28 nucleotides and the second strand has a length from 12-26 nucleotides; or the first strand has a length from 19-27 nucleotides and the second strand has a length from 14-23 nucleotides; or the first strand has a length from 20-22 nucleotides and the second strand has a length from 14-15 nucleotides.
  • the first strand has a length of 21 nucleotides and the second strand has a length of 13-20 nucleotides, 14-19 nucleotides, 14-17 nucleotides, 14 or 15 nucleotides.
  • the first strand is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides longer than the second strand.
  • the duplex RNA molecule further comprises 1 -10 unmatched or mismatched nucleotides.
  • the unmatched or mismatched nucleotides are at or near the 3' recessed end.
  • the unmatched or mismatched nucleotides are at or near the 5' recessed end.
  • the unmatched or mismatched nucleotides are at the double- stranded region.
  • the unmatched or mismatched nucleotide sequence has a length from 1-5 nucleotides.
  • the unmatched or mismatched nucleotides form a loop structure.
  • the first strand or the second strand contains at least one nick, or formed by two nucleotide fragments.
  • the gene silencing is achieved through one or two, or all of RNA interference, modulation of translation, and DNA epigenetic modulations.
  • the target K-Ras mRNA sequence to be silenced is a target sequence shown in Table 1.
  • the RNA duplex molecule also referred to herein as an asymmetrical interfering RNA molecule or aiRNA molecule, comprises a sense strand sequence, an antisense strand sequence or a combination of a sense strand sequence and antisense strand sequence selected from those shown in Table 2.
  • the RNA duplex molecule comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • the RNA duplex molecule comprises a sense strand sequence that is at least, e.g, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637.
  • the RNA duplex molecule comprises an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • the RNA duplex molecule comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955.
  • the singular form "a”, “an”, and “the” include plural references unless the context clearly dictate otherwise.
  • the term "a cell” includes a plurality of cells including mixtures thereof.
  • a double stranded RNA refers to an RNA of two strands and with at least one double-stranded region, and includes RNA molecules that have at least one gap, nick, bulge, and/or bubble either within a double-stranded region or between two neighboring double-stranded regions. If one strand has a gap or a single-stranded region of unmatched nucleotides between two double-stranded regions, that strand is considered as having multiple fragments.
  • a double- stranded RNA as used here can have terminal overhangs on either end or both ends..
  • the two strands of the duplex RNA can be linked through certain chemical linker.
  • an "antisense strand” refers to an RNA strand that has substantial sequence complementarity against a target messenger RNA.
  • isolated or “purified” as used herein refers to a material that is substantially or essentially free from components that normally accompany it in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography.
  • modulating and its grammatical equivalents refer to either increasing or decreasing (e.g., silencing), in other words, either up-regulating or down- regulating.
  • gene silencing refers to reduction of gene expression, and may refer to a reduction of gene expression about, e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the targeted gene.
  • the term “subject” refers to any animal (e.g., a mammal), including, but not limited to humans, non-human primates, rodents, and the like, which is to be the recipient of a particular treatment. Under some circumstances, the terms “subject” and “patient” are used interchangeably herein in reference to a human subject.
  • Terms such as “treating” or “treatment” or “to treat” or “alleviating” or “to alleviate” as used herein refer to both (1) therapeutic measures that cure, slow down, lessen symptoms of, and/or halt progression of a diagnosed pathologic condition or disorder and (2) prophylactic or preventative measures that prevent or slow the development of a targeted pathologic condition or disorder.
  • those in need of treatment include those already with the disorder; those prone to have the disorder; and those in whom the disorder is to be prevented.
  • a subject is successfully "treated” according to the methods of the present invention if the patient shows one or more of the following: a reduction in the number of or complete absence of cancer cells; a reduction in the tumor size; inhibition of or an absence of cancer cell infiltration into peripheral organs including the spread of cancer into soft tissue and bone; inhibition of or an absence of tumor metastasis; inhibition or an absence of tumor growth; relief of one or more symptoms associated with the specific cancer; reduced morbidity and mortality; and improvement in quality of life.
  • the terms “inhibiting”, “to inhibit” and their grammatical equivalents, when used in the context of a bioactivity, refer to a down-regulation of the bioactivity, which may reduce or eliminate the targeted function, such as the production of a protein or the phosphorylation of a molecule.
  • the terms refer to a down-regulation of a bioactivity of the organism, which may reduce or eliminate a targeted function, such as the production of a protein or the phosphorylation of a molecule.
  • inhibition may refer to a reduction of about, e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the targeted activity.
  • the terms refer to success at preventing the onset of symptoms, alleviating symptoms, or eliminating the disease, condition or disorder.
  • the term “substantially complementary” refers to complementarity in a base-paired, double-stranded region between two nucleic acids and not any single-stranded region such as a terminal overhang or a gap region between two double- stranded regions.
  • the complementarity does not need to be perfect; there may be any number of base pair mismatches, for example, between the two nucleic acids. However, if the number of mismatches is so great that no hybridization can occur under even the least stringent hybridization conditions, the sequence is not a substantially complementary sequence.
  • substantially complementary it means that the sequences are sufficiently complementary to each other to hybridize under the selected reaction conditions.
  • substantially complementary sequences can be, for example, perfectly complementary or can contain from 1 to many mismatches so long as the hybridization conditions are sufficient to allow, for example discrimination between a pairing sequence and a non-pairing sequence. Accordingly, substantially complementary sequences can refer to sequences with base- pair complementarity of, e.g., 100%, 95%, 90%, 80%, 75%, 70%, 60%, 50% or less, or any number in between, in a double-stranded region.
  • RNA interference is a cellular process for the targeted destruction of single-stranded RNA (ssRNA) induced by double-stranded RNA (dsRNA).
  • ssRNA single-stranded RNA
  • dsRNA double-stranded RNA
  • mRNA messenger RNA
  • RNAi is a form of post-transcriptional gene silencing in which the dsRNA can specifically interfere with the expression of genes with sequences that are complementary to the dsRNA.
  • the antisense RNA strand of the dsRNA targets a complementary gene transcript such as a messenger RNA (mRNA) for cleavage by a ribonuclease.
  • mRNA messenger RNA
  • RNAi process long dsRNA is processed by a ribonuclease protein Dicer to short forms called small interfering RNA (siRNA).
  • siRNA small interfering RNA
  • the siRNA is separated into guide (or antisense) strand and passenger (or sense) strand.
  • the guide strand is integrated into RNA- induced-silencing-complex (RISC), which is a ribonuclease-containing multi-protein complex.
  • RISC RNA- induced-silencing-complex
  • RNAi has been shown to be a common cellular process in many eukaryotes.
  • RISC as well as Dicer, is conserved across the eukaryotic domain. RNAi is believed to play a role in the immune response to virus and other foreign genetic material.
  • siRNAs are a class of short double-stranded RNA
  • siRNA RNA interference molecules
  • RNAi RNA interference pathway
  • siRNAs also play roles in the processes such as an antiviral mechanism or shaping the chromatin structure of a genome.
  • siRNA has a short (19-21 nt) double- strand RNA (dsRNA) region with 2-3 nucleotide 3' overhangs with 5 '-phosphate and 3'-hydroxyl termini.
  • Dicer is a member of RNase III ribonuclease family. Dicer cleaves long, double-stranded RNA (dsRNA), pre-microRNA (miRNA), and short hairpin RNA (shRNA) into short double-stranded RNA fragments called small interfering RNA (siRNA) about 20- 25 nucleotides long, usually with a two-base overhang on the 3' end.
  • dsRNA double-stranded RNA
  • miRNA pre-microRNA
  • shRNA short hairpin RNA
  • siRNA small interfering RNA
  • Dicer catalyzes the first step in the RNA interference pathway and initiates formation of the RNA-induced silencing complex (RISC), whose catalytic component argonaute is an endonuclease capable of degrading messenger RNA (mRNA) whose sequence is complementary to that of the siRNA guide strand.
  • RISC RNA-induced silencing complex
  • an effective siRNA sequence is a siRNA that is effective in triggering RNAi to degrade the transcripts of a target gene. Not every siRNA complementary to the target gene is effective in triggering RNAi to degrade the transcripts of the gene. Indeed, time-consuming screening is usually necessary to identify an effective siRNA sequence.
  • the effective siRNA sequence is capable of reducing the expression of the target gene by more than 90%, more than 80%, more than 70%, more than 60%, more than 50%, more than 40%, or more than 30%.
  • the present invention uses a structural scaffold called asymmetric interfering
  • RNA that can be used to effect siRNA-like results, and also to modulate miRNA pathway activities, initially described in detail PCT Publications WO 2009/029688 and WO 2009/029690, the contents of which are hereby incorporated by reference in their entirety.
  • aiRNA can have RNA duplex structure of much shorter length than the current siRNA constructs, which should reduce the cost of synthesis and abrogate or reduce length-dependent triggering of nonspecific interferon-like immune responses from host cells.
  • the shorter length of the passenger strand in aiRNA should also eliminate or reduce the passenger strand's unintended incorporation in RISC, and in turn, reduce off-target effects observed in miRNA-mediated gene silencing.
  • AiRNA can be used in all areas that current miRNA-based technologies are being applied or contemplated to be applied, including biology research, R&D in biotechnology and pharmaceutical industries, and miRNA-based diagnostics and therapies.
  • the first strand comprises a sequence being substantially complimentary to a target K-Ras mRNA sequence.
  • the second strand comprises a sequence being substantially complimentary to a target K-Ras mRNA sequence.
  • an RNA molecule of the present invention comprises a first strand and a second strand, wherein the second strand is substantially complementary, or partially complementary to the first strand, and the first strand and the second strand form at least one double-stranded region, wherein the first strand is longer than the second strand (length asymmetry).
  • the RNA molecule of the present invention has at least one double-stranded region, and two ends independently selected from the group consisting of a 5 '-overhang, a 3'-overhang, and a blunt.
  • RNA strands of the invention can be stabilized against degradation, either through chemical modification or secondary structure.
  • the RNA strands can have unmatched or imperfectly matched nucleotides.
  • Each strand may have one or more nicks (a cut in the nucleic acid backbone), gaps (a fragmented strand with one or more missing nucleotides), and modified nucleotides or nucleotide analogues.
  • each strand may be conjugated with one or more moieties to enhance its functionality, for example, with moieties such as one or more peptides, antibodies, antibody fragments, aptamers, polymers and so on.
  • the first strand is at least 1 nt longer than the second strand. In a further embodiment, the first strand is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, or 20 nt longer than the second strand. In another embodiment, the first strand is 20-100 nt longer than the second strand. In a further embodiment, the first strand is 2-12 nt longer than the second strand. In an even further embodiment, the first strand is 3-10 nt longer than the second strand.
  • the first strand, or the long strand has a length of 5-100 nt, or preferably 10-30 or 12-30 nt, or more preferably 15-28 nt. In one embodiment, the first strand is 21 nucleotides in length. In some embodiments, the second strand, or the short strand, has a length of 3-30 nt, or preferably 3-29 nt or 10-26 nt, or more preferably 12-26 nt. In some embodiments, the second strand has a length of 15 nucleotides.
  • the double-stranded region has a length of 3-98 basepairs (bp). In a further embodiment, the double-stranded region has a length of 5-28 bp. In an even further embodiment, the double-stranded region has a length of 10-19 bp.
  • the length of the double-stranded region can be 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 bp.
  • the double-stranded region of the RNA molecule does not contain any mismatch or bulge, and the two strands are perfectly complementary to each other in the double-stranded region.
  • the double-stranded region of the RNA molecule contains mismatch and/or bulge.
  • the terminal overhang is 1-10 nucleotides. In a further embodiment, the terminal overhang is 1-8 nucleotides. In another embodiment, the terminal overhang is 3 nt.
  • the present invention also provides a method of modulating K-Ras gene expression in a cell or an organism (silencing method).
  • the method comprises the steps of contacting said cell or organism with the duplex RNA molecule under conditions wherein selective K-Ras gene silencing can occur, and mediating a selective K-Ras gene silencing effected by the said duplex RNA molecule towards a target K-Ras nucleic acid having a sequence portion substantially corresponding to the double-stranded RNA.
  • the contacting step comprises the step of introducing said duplex RNA molecule into a target cell in culture or in an organism in which the selective gene silencing can occur.
  • the introducing step comprises transfection, lipofection, infection, electroporation, or other delivery technologies.
  • the silencing method is used for determining the function or utility of a gene in a cell or an organism.
  • the silencing method can be used for modulating the expression of a gene in a cell or an organism.
  • the gene is associated with a disease, e.g., a human disease or an animal disease, a pathological condition, or an undesirable condition.
  • the disease is gastric cancer.
  • the RNA molecules of the present invention can be used for the treatment and or prevention of various diseases or undesirable conditions, including gastric cancer.
  • the present invention can be used as a cancer therapy or to prevent or to delay the progression of cancer.
  • the RNA molecules of the present invention can he used to silence or knock down k-Ras, which is involved with cell proliferation or other cancer phenotypes.
  • the present invention provides a method to treat a disease or undesirable condition.
  • the method comprises using the asymmetrical duplex RNA molecule to effect gene silencing of a gene associated with the disease or undesirable condition.
  • the present invention further provided a pharmaceutical composition.
  • the pharmaceutical comprises (as an active agent) at least one asymmetrical duplex RNA molecule.
  • the pharmaceutical comprises one or more carriers selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a nanoemulsion, a lipid, and a lipoid.
  • the composition is for diagnostic applications.
  • the composition is for therapeutic applications.
  • the pharmaceutical compositions and formulations of the present invention can be the same or similar to the pharmaceutical compositions and formulations developed for siRNA, miRNA, and antisense RNA (see e.g., de Fougerolles et al, 2007, "Interfering with disease: a progress report on siRNA-based therapeutics.” Nat Rev Drug Discov 6, 443453; Kim and Rossi, 2007, “Strategies for silencing human disease using RNA interference.” Nature reviews 8, 173-184), except for the RNA ingredient.
  • the siRNA, miRNA, and antisense RNA in the pharmaceutical compositions and formulations can be replaced by the duplex RNA molecules of the present disclosure.
  • the pharmaceutical compositions and formulations can also be further modified to accommodate the duplex RNA molecules of the present disclosure.
  • a "pharmaceutically acceptable salt” or “salt” of the disclosed duplex RNA molecule is a product of the disclosed duplex RNA molecule that contains an ionic bond, and is typically produced by reacting the disclosed duplex RNA molecule with either an acid or a base, suitable for administering to a subject.
  • Pharmaceutically acceptable salt can include, but is not limited to, acid addition salts including hydrochlorides, hydrobromides, phosphates, sulphates, hydrogen sulphates, alkylsulphonates, arylsulphonates, acetates, benzoates, citrates, maleates, fumarates, succinates, lactates, and tartrates; alkali metal cations such as Na, K, Li, alkali earth metal salts such as Mg or Ca, or organic amine salts.
  • a "pharmaceutical composition” is a formulation containing the disclosed duplex RNA molecules in a form suitable for administration to a subject.
  • the pharmaceutical composition is in bulk or in unit dosage form.
  • the unit dosage form is any of a variety of forms, including, for example, a capsule, an IV bag, a tablet, a single pump on an aerosol inhaler, or a vial.
  • the quantity of active ingredient (e.g., a formulation of the disclosed duplex RNA molecule or salts thereof) in a unit dose of composition is an effective amount and is varied according to the particular treatment involved.
  • active ingredient e.g., a formulation of the disclosed duplex RNA molecule or salts thereof
  • the dosage will also depend on the route of administration.
  • RNA molecules of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants.
  • the active duplex RNA molecule is mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that are required.
  • the present invention provides a method of treatment comprising administering an effective amount of the pharmaceutical composition to a subject in need.
  • the pharmaceutical composition is administered via a route selected from the group consisting of iv, sc, topical, po, and ip.
  • the effective amount is 1 ng to 1 g per day, 100 ng to 1 g per day, or 1 ug to 1 mg per day.
  • the present invention also provides pharmaceutical formulations comprising a duplex RNA molecule of the present invention in combination with at least one pharmaceutically acceptable excipient or carrier.
  • pharmaceutically acceptable excipient or “pharmaceutically acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Suitable carriers are described in "Remington: The Science and Practice of Pharmacy, Twentieth Edition," Lippincott Williams & Wilkins, Philadelphia, PA., which is incorporated herein by reference. Examples of such carriers or diluents include, but are not limited to, water, saline, Ringer's solutions, dextrose solution, and 5% human serum albumin. Liposomes and non-aqueous vehicles such as fixed oils may also be used.
  • a duplex RNA molecule of the present invention is administered in a suitable dosage form prepared by combining a therapeutically effective amount (e.g., an efficacious level sufficient to achieve the desired therapeutic effect through inhibition of tumor growth, killing of tumor cells, treatment or prevention of cell proliferative disorders, etc.) of a duplex RNA molecule of the present invention (as an active ingredient) with standard pharmaceutical carriers or diluents according to conventional procedures (i.e., by producing a pharmaceutical composition of the invention). These procedures may involve mixing, granulating, compressing, or dissolving the ingredients as appropriate to attain the desired preparation.
  • a therapeutically effective amount of a duplex RNA molecule of the present invention is administered in a suitable dosage form without standard pharmaceutical carriers or diluents.
  • Pharmaceutically acceptable carriers include solid carriers such as lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like.
  • Exemplary liquid carriers include syrup, peanut oil, olive oil, water and the like.
  • the carrier or diluent may include time-delay material known in the art, such as glyceryl monostearate or glyceryl distearate, alone or with a wax, ethylcellulose, hydroxypropylmethylcellulose, methylmethacrylate or the like.
  • compositions containing active duplex RNA molecules of the present invention may be manufactured in a manner that is generally known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • Pharmaceutical compositions may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and/or auxiliaries which facilitate processing of the active duplex RNA molecules into preparations that can be used pharmaceutically. Of course, the appropriate formulation is dependent upon the route of administration chosen.
  • a duplex RNA molecule or pharmaceutical composition of the invention can be administered to a subject in many of the well-known methods currently used for chemotherapeutic treatment.
  • a duplex RNA molecule of the invention may be injected directly into tumors, injected into the blood stream or body cavities or taken orally or applied through the skin with patches.
  • systemic administration e.g., oral administration
  • topical administration to affected areas of the skin are preferred routes of administration.
  • the dose chosen should be sufficient to constitute effective treatment but not as high as to cause unacceptable side effects.
  • the state of the disease condition e.g., gastric cancer
  • the health of the patient should be closely monitored during and for a reasonable period after treatment.
  • Figure 1(A) shows an in vitro study in which aiRNA ID NO: 21 ("aiK-Ras
  • FIG. 1(B) shows an in vitro study in which aiRNA ID NO: 142 ("aiK-Ras
  • aiK-Ras #2 was used to target K-Ras Target SEQ ID NO: 142 to determine the IC 50 for aiK-Ras #2.
  • DLD1 cells were transfected with aiK-Ras #2. 48 hours after transfection, cells were collected and RNA was isolated. The IC 50 of aiK-Ras #2 was determined by qPCR. Remaining mRNA was standardized to the GAPDH expression level. The IC 50 of 3.5 pM indicates that aiK-Ras #1 silences K-Ras gene expression with high potency.
  • Figure 2(A) shows detection of siRNA and aiRNA loading to RISC by northern blot analysis.
  • HEK293 Flag-Ago2 stable cells were transfected with aiRNA or siRNA duplexes. Cells were lysed at the indicated time points and immunoprecipitated with Flag antibody (Sigma, Catalog # F1804). Immunoprecipitates were washed, RNA isolated from the complex by TRIZOL (Life Technologies, 15596-018) extraction, and loaded on 15% TBE-Urea PAGE or 15% TBE non-denaturing PAGE gels. Following electrophoreses, RNA was transferred to Hybonad-XL Nylon membrane.
  • HEK293 cells Invivogen, Catalog # 293-null
  • Flag-Ago2 were transfected with siRNA or aiRNA, after which an immunoprecipitation assay was conducted.
  • FLAG-Ago2 HEK 293 cells stably expressing FLAG-Ago2 cells were generated through transient transfection of FLAG-Ago2 neomycin plasmid DNA vectors. After selective neomycin containing medium culture, the monoclonal populations were selected by western blot. Non-denatured gel was used to detect dsRNA.
  • Figure 2(B) shows reduced off-target of aiRNA.
  • HeLa cells were transfected with luciferase reporter genes fused with antisense or sense strand-based aiRNA or siRNA target sequences and aiK-Ras#2 or siK-Ras#2 (5 nM).
  • Figure 2(C) shows that TLR3/RNA complexes were immunoprecipitated with anti-HA antibody (Invivogen, Catalog # ab-hatag). RNA was extracted from the pellet, and northern blot analysis was performed to determine the interaction between aiRNA/siRNA and the TLR3 receptor.
  • Figures 2(A)-(C) show that the asymmetric structure of aiK-Ras #1 and aiK-
  • Figure 3(A) shows colony formation assay in AGS (ATCC) and DLD1 cells transfected with aiK-Ras #1 or aiK-Ras #2.
  • Cells were transfected with 1 nM GFP aiRNA (control; GGTTATGTACAGGAACGCA (SEQ ID NO: 956)) or 1 nM aiK-Ras #1 or aiK- Ras #2 for 24 hours. Cells were then trypsinized and re-plated on 6-well plates at 500-2000 cells/well to determine the colony formation ability of the cells. After 11-14 days, colonies were stained with Giemsa stain and were counted.
  • Figure 3(B) shows western blot analysis of lysate from AGS and DLD1, and the transfection effects of aiK-Ras #1 and aiK-Ras #2 on K-Ras expression, cleaved caspase 3, and cleaved PARP.
  • Figure 3(C) shows colony formation assay results in a large cell panel. All cell lines in the panel were obtained from ATCC. Cells harboring K-Ras mutant are highlighted.
  • FIG. 4 shows western blot analysis of K-Ras and EGFR-RAS pathway molecules. Lysate (10 ⁇ g/lane) was loaded and total and phosphorylated forms of EGFR, cRaf, MEK, and ERK were detected. Activated form of K-Ras (K-Ras GTP) was affinity- purified from cell lysate using GST-Raf-RBD and analyzed by western blotting with K-Ras antibody.
  • RBD pulldown was performed using a Ras Activation Kit (Abeam, Catalog # ab 128504) according to the manufacturer's protocol. Precipitations were blotted for K-Ras (Santa Cruz, Catalog # sc30). Actin (Sigma, Catalog # A5316) was blotted as loading control.
  • Figure 4 shows that aiK-Ras sensitivity correlates with K-Ras amplification, and not with the activation state of the Ras pathway molecules.
  • Figure 5(A) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel. All cell lines in the panel were obtained from ATCC. Copy number of K-Ras was analyzed by qPCR. Statistical difference was determined by two-sided Mann-Whitney's U test. Difference with p ⁇ 0.05 was considered statistically significant.
  • FIG. 5(B) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel.
  • K-Ras protein expression level was measured by western blot. Band of western blot was quantified by Image Lab (Biorad). Statistical difference was determined by two-sided Mann- Whitney's U test. Difference with p ⁇ 0.05 was considered statistically significant.
  • Figures 3(A)-(C) and 5(A)-(B) show that aiK-Ras sensitivity varies in K-Ras mutant cells and it correlates with K-Ras copy number.
  • EXAMPLE 6 Effect of aiK-Ras on CSC-like phenotvpe in sensitive cell lines
  • FIG. 6(A) shows sternness gene expression in CSC culture.
  • AGS cells were cultured in CSC medium [DMEM nutrient mixture F- 12 (DMEM/F- 12, Life technologies, Catalog # 1 1320-033) containing B-27 supplement (Life Technologies, Catalog # 17504- 044), 20 ng/mL EGF (R&D Systems, Catalog # 236-EG), 10 ng/mL FGF (R&D Systems, Catalog # 233-FB), and 1% penicillin/streptomycin] for 2 weeks.
  • Nanog, Oct4, and Sox2 gene expression of CSC spheres was quantified by qPCR.
  • Figure 6(B) shows the results of sphere formation assay in various cell lines.
  • agarose coated plates were prepared to dispense autoclaved 0.5% agar and aspirated immediately. Transfected cells were trypsinized and counted, then diluted to 2000 cells/100 uL of 1 x CSC medium. 1.9 mL of warmed CSC medium including 0.33% agarose (Sigma type VII, Catalog # A-4018) was added to the cells in CSC medium for final agarose concentration of 0.3%. The plate was placed at 4°C for 10 minutes to cool. The plate was placed 10 minutes at room temperature and 1 mL of CSC medium was added to the top layer. The plate was incubated in a 37°C 15% CO 2 incubator for 18-25 days. To count spheres, CSC medium was aspirated and Crystal violet (EMD, Catalog # 192- 12) solution in PBS were added and incubated for 1 hour at room temperature to stain spheres.
  • EMD Crystal violet
  • Figure 6(C) shows depletion of CD44-high population in AGS and DLD1 cells with aiK-Ras #1 and aiK-Ras #2.
  • CD44 expression was detected by flow cytometry, wherein AGS and DLD 1 cells were stained with PE conjugated anti-CD44 (BD Pharmingen, Catalog # 555479) in Stain Buffer (BD Pharmingen, Catalog # 554657) on ice for 45 minutes and washed once with Stain Buffer.
  • CD44 positive population was detected with flow cytometry (Attune Acoustic Focusing Cytometer, Life technologies).
  • Figures 6(A)-(C) show that aiK-Ras according to the present invention modulate CSC-like phenotype in sensitive cell lines.
  • EXAMPLE 7 Effect of K-Ras knockdown on CSC-related gene expression patterns.
  • Figure 7(A) shows heat map of CSC-related genes in cancer cells transfected with aiK-Ras.
  • Cells were transfected with 1 nM control aiRNA or aiK-Ras #1 for 48 hours.
  • Real-time PCR was performed on total RNA using specific validated primers for 84 CSC- related genes with RT2 Profiler PCR array.
  • the fold change in gene expression was calculated as the ratio between aiK-Ras #1 and the control aiRNA samples.
  • Figure 7(B) shows confirmation of down-regulated Notch signaling by western blot. Table 3 below summarizes the genes down-regulated >3 fold with aiK-Ras #1 corresponding to the heat map as shown in Figure 7(A)

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Abstract

The invention provides novel compositions for use in silencing K-Ras gene expression. More particularly, the invention provides novel asymmetrical interfering RNA molecules as inhibitors of K-Ras expression, and to pharmaceutical compositions and uses thereof in the treatment of cancer or a related disorder in a mammal.

Description

ASYMMETRIC INTERFERING RNA COMPOSITIONS THAT SILENCE K- RAS AND METHODS OF USES THEREOF
FIELD OF THE INVENTION
[0001] The invention generally relates to compositions for use in silencing K-Ras gene expression. More particularly, the invention relates to novel asymmetrical interfering RNA molecules as inhibitors of K-Ras expression, and to pharmaceutical compositions and uses thereof in the treatment of cancer or a related disorder in a mammal.
BACKGROUND OF THE INVENTION
[0002] Gene silencing through RNAi (RNA-interference) by use of small or short interfering RNA (siRNA) has emerged as a therapeutic tool. However, other than the prominent delivery issue, the development of RNAi-based drugs faces challenges of limited efficacy of siRNA, non-specific effects of siRNA such as interferon-like responses and sense- strand mediated off-target gene silencing, and the prohibitive or high cost associated with siRNA synthesis. The gene silencing efficacy by siRNA is limited to about 50% or less for majority of genes in mammalian cells. The manufacture of these molecules is expensive (much more expensive than manufacturing anti sense deoxynucleotides), inefficient, and requires chemical modification. Finally, the observation that the extracellular administration of synthetic siRNAs can trigger interferon-like responses has added a significant barrier for RNAi-based research and RNAi-based therapeutic development.
[0003] The protein K-Ras is a molecular switch that under normal conditions regulates cell growth and cell division. Mutations in this protein lead to the formation of tumors through continuous cell growth. About 30% of human cancers have a mutated Ras protein that is constitutively bound to GTP due to decreased GTPase activity and insensitivity to GAP action. Ras is also an important factor in many cancers in which it is not mutated but rather functionally activated through inappropriate activity of other signal transduction elements. Mutated K-Ras proteins are found in a large proportion of all tumour cells. K-Ras protein occupies a central position of interest. The identification of oncogenically mutated K- Ras in many human cancers led to major efforts to target this constitutively activated protein as a rational and selective treatment. Despite decades of active agent research, significant challenges still remain to develop therapeutic inhibitors of K-Ras. [0004] Hypermalignant cancer cells that are highly tumorigenic and metastatic have been isolated from cancer patients with a variety of tumor types and found to have high sternness properties, termed cancer stem cells (CSCs). These stemness-high cancer cells are hypothesized to be fundamentally responsible for cancer metastasis and relapse. A number of sternness genes, such as β-catenin, Nanog, Sox2, Oct3/4 have been implicated in cancer cell sternness. However, the role of oncogenes, such as K-Ras, in cancer cell sternness is not clear.
[0005] Accordingly, there exists a need to develop novel compositions and methods for selectively silencing K-Ras gene express or K-Ras activity in a subject diagnosed with cancer, with better efficacy and potency, rapid onset of action, better durability, and fewer adverse side effects.
SUMMARY OF THE INVENTION
[0006] To elucidate the role of K-Ras in the maintenance of cancer cell sternness, the present inventors employed asymmetric silencing RNA technology (aiRNA) which is able to silence target genes with high potency and precision. Moreover, aiRNA technology can be readily applied to CSCs. The present inventors made a surprising discovery that CSCs are not only addicted to activating mutations of K-Ras, or activation of the downstream regulators of the Ras pathway, but also that CSCs with amplified mutant K-Ras become highly sensitive to K-Ras silencing. Furthermore, the present inventors made a surprising discovery that the DNA copy numbers of the mutant K-Ras directly predicts sensitivity of cancer stem cells to K-Ras silencing, which suggests that amplified mutated K-Ras is required to the maintenance of the malignancy and cancer cell sternness, which may have significant implication for understanding the connection between oncogene and cancer cell sternness and for developing cancer stem cell inhibitors.
[0007] The present invention provides compositions and methods that use a class of small duplex RNA that can induce potent gene silencing in mammalian cells, which is termed herein asymmetrical interfering RNAs (aiRNA). aiRNA is described, for example, in PCT Publication No. WO 2009/029688, the contents of which are hereby incorporated by reference in their entirety. This class of RNAi-inducers is identified by the length asymmetry of the two RNA strands. This structural design is not only functionally potent in effecting gene silencing, but offers several advantages over the current state-of-art siRNAs. Among the advantages, aiRNA can have RNA duplex structure of much shorter length than the other siRNA, which should reduce the cost of synthesis and abrogate/reduce the length-dependent triggering of nonspecific interferon-like responses. In addition, the asymmetry of the aiRNA structure abrogates and/or otherwise reduces the sense-strand mediated off-target effects. Furthermore, aiRNA is more efficacious, potent, rapid-onset, and durable than siRNA in inducing gene silencing. AiRNA can be used in all areas that other siRNA or shRNA are being applied or contemplated to be used, including biology research, R&D research in biotechnology and pharmaceutical industry, and RNAi-based therapies.
[0008] The duplex RNA molecule comprises a first strand with a length from 18-23 nucleotides and a second strand with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing in a eukaryotic cell. In some embodiments, the first strand comprises a sequence being substantially complementary to a target K-Ras mRNA sequence. In a further embodiment, the first strand comprises a sequence being at least 70 percent complementary to a target K-Ras mRNA sequence. In another embodiment, the eukaryotic cell is a mammalian cell or an avian cell.
[0009] In some embodiments, the target K-Ras mRNA sequence is a human K-Ras target sequence. In some embodiments, the target K-Ras mRNA sequence is a human K-Ras target sequence selected from at least a portion of the sequence shown in GenBank Accession No. NM_004985 shown below as SEQ ID NO: 1 :
1 tcctaggcgg cggccgcggc ggcggaggca gcagcggcgg cggcagtggc ggcggcgaag 61 gtggcggcgg ctcggccagt actcccggcc cccgccattt cggactggga gcgagcgcgg 121 cgcaggcact gaaggcggcg gcggggccag aggctcagcg gctcccaggt gcgggagaga 181 ggcctgctga aaatgactga atataaactt gtggtagttg gagctggtgg cgtaggcaag 241 agtgccttga cgatacagct aattcagaat cattttgtgg acgaatatga tccaacaata 301 gaggattcct acaggaagca agtagtaatt gatggagaaa cctgtctctt ggatattctc 361 gacacagcag gtcaagagga gtacagtgca atgagggacc agtacatgag gactggggag 421 ggctttcttt gtgtatttgc cataaataat actaaatcat ttgaagatat tcaccattat 481 agagaacaaa ttaaaagagt taaggactct gaagatgtac ctatggtcct agtaggaaat 541 aaatgtgatt tgccttctag aacagtagac acaaaacagg ctcaggactt agcaagaagt 601 tatggaattc cttttattga aacatcagca aagacaagac agggtgttga tgatgccttc 661 tatacattag ttcgagaaat tcgaaaacat aaagaaaaga tgagcaaaga tggtaaaaag 721 aagaaaaaga agtcaaagac aaagtgtgta attatgtaaa tacaatttgt acttttttct 781 taaggcatac tagtacaagt ggtaattttt gtacattaca ctaaattatt agcatttgtt 841 ttagcattac ctaatttttt tcctgctcca tgcagactgt tagcttttac cttaaatgct 901 tattttaaaa tgacagtgga agtttttttt tcctctaagt gccagtattc ccagagtttt 961 ggtttttgaa ctagcaatgc ctgtgaaaaa gaaactgaat acctaagatt tctgtcttgg
1021 ggtttttggt gcatgcagtt gattacttct tatttttctt accaattgtg aatgttggtg
1081 tgaaacaaat taatgaagct tttgaatcat ccctattctg tgttttatct agtcacataa
1141 atggattaat tactaatttc agttgagacc ttctaattgg tttttactga aacattgagg
1201 gaacacaaat ttatgggctt cctgatgatg attcttctag gcatcatgtc ctatagtttg
1261 tcatccctga tgaatgtaaa gttacactgt tcacaaaggt tttgtctcct ttccactgct
1321 attagtcatg gtcactctcc ccaaaatatt atattttttc tataaaaaga aaaaaatgga
1381 aaaaaattac aaggcaatgg aaactattat aaggccattt ccttttcaca ttagataaat
1441 tactataaag actcctaata gcttttcctg ttaaggcaga cccagtatga aatggggatt
1501 attatagcaa ccattttggg gctatattta catgctacta aatttttata ataattgaaa
1561 agattttaac aagtataaaa aattctcata ggaattaaat gtagtctccc tgtgtcagac
1621 tgctctttca tagtataact ttaaatcttt tcttcaactt gagtctttga agatagtttt
1681 aattctgctt gtgacattaa aagattattt gggccagtta tagcttatta ggtgttgaag
1741 agaccaaggt tgcaaggcca ggccctgtgt gaacctttga gctttcatag agagtttcac
1801 agcatggact gtgtccccac ggtcatccag tgttgtcatg cattggttag tcaaaatggg
1861 gagggactag ggcagtttgg atagctcaac aagatacaat ctcactctgt ggtggtcctg
1921 ctgacaaatc aagagcattg cttttgtttc ttaagaaaac aaactctttt ttaaaaatta
1981 cttttaaata ttaactcaaa agttgagatt ttggggtggt ggtgtgccaa gacattaatt
2041 ttttttttaa acaatgaagt gaaaaagttt tacaatctct aggtttggct agttctctta
2101 acactggtta aattaacatt gcataaacac ttttcaagtc tgatccatat ttaataatgc
2161 tttaaaataa aaataaaaac aatccttttg ataaatttaa aatgttactt attttaaaat
2221 aaatgaagtg agatggcatg gtgaggtgaa agtatcactg gactaggaag aaggtgactt
2281 aggttctaga taggtgtctt ttaggactct gattttgagg acatcactta ctatccattt
2341 cttcatgtta aaagaagtca tctcaaactc ttagtttttt ttttttacaa ctatgtaatt
2401 tatattccat ttacataagg atacacttat ttgtcaagct cagcacaatc tgtaaatttt
2461 taacctatgt tacaccatct tcagtgccag tcttgggcaa aattgtgcaa gaggtgaagt
2521 ttatatttga atatccattc tcgttttagg actcttcttc catattagtg tcatcttgcc
2581 tccctacctt ccacatgccc catgacttga tgcagtttta atacttgtaa ttcccctaac
2641 cataagattt actgctgctg tggatatctc catgaagttt tcccactgag tcacatcaga
2701 aatgccctac atcttatttc ctcagggctc aagagaatct gacagatacc ataaagggat
2761 ttgacctaat cactaatttt caggtggtgg ctgatgcttt gaacatctct ttgctgccca
2821 atccattagc gacagtagga tttttcaaac ctggtatgaa tagacagaac cctatccagt
2881 ggaaggagaa tttaataaag atagtgctga aagaattcct taggtaatct ataactagga
2941 ctactcctgg taacagtaat acattccatt gttttagtaa ccagaaatct tcatgcaatg
3001 aaaaatactt taattcatga agcttacttt ttttttttgg tgtcagagtc tcgctcttgt
3061 cacccaggct ggaatgcagt ggcgccatct cagctcactg caacctccat ctcccaggtt
3121 caagcgattc tcgtgcctcg gcctcctgag tagctgggat tacaggcgtg tgccactaca
3181 ctcaactaat ttttgtattt ttaggagaga cggggtttca ccctgttggc caggctggtc
3241 tcgaactcct gacctcaagt gattcaccca ccttggcctc ataaacctgt tttgcagaac
3301 tcatttattc agcaaatatt tattgagtgc ctaccagatg ccagtcaccg cacaaggcac
3361 tgggtatatg gtatccccaa acaagagaca taatcccggt ccttaggtag tgctagtgtg 3421 gtctgtaata tcttactaag gcctttggta tacgacccag agataacacg atgcgtattt
3481 tagttttgca aagaaggggt ttggtctctg tgccagctct ataattgttt tgctacgatt
3541 ccactgaaac tcttcgatca agctacttta tgtaaatcac ttcattgttt taaaggaata
3601 aacttgatta tattgttttt ttatttggca taactgtgat tcttttagga caattactgt
3661 acacattaag gtgtatgtca gatattcata ttgacccaaa tgtgtaatat tccagttttc
3721 tctgcataag taattaaaat atacttaaaa attaatagtt ttatctgggt acaaataaac
3781 aggtgcctga actagttcac agacaaggaa acttctatgt aaaaatcact atgatttctg
3841 aattgctatg tgaaactaca gatctttgga acactgttta ggtagggtgt taagacttac
3901 acagtacctc gtttctacac agagaaagaa atggccatac ttcaggaact gcagtgctta
3961 tgaggggata tttaggcctc ttgaattttt gatgtagatg ggcatttttt taaggtagtg
4021 gttaattacc tttatgtgaa ctttgaatgg tttaacaaaa gatttgtttt tgtagagatt
4081 ttaaaggggg agaattctag aaataaatgt tacctaatta ttacagcctt aaagacaaaa
4141 atccttgttg aagttttttt aaaaaaagct aaattacata gacttaggca ttaacatgtt
4201 tgtggaagaa tatagcagac gtatattgta tcatttgagt gaatgttccc aagtaggcat
4261 tctaggctct atttaactga gtcacactgc ataggaattt agaacctaac ttttataggt
4321 tatcaaaact gttgtcacca ttgcacaatt ttgtcctaat atatacatag aaactttgtg
4381 gggcatgtta agttacagtt tgcacaagtt catctcattt gtattccatt gatttttttt
4441 ttcttctaaa cattttttct tcaaacagta tataactttt tttaggggat ttttttttag
4501 acagcaaaaa ctatctgaag atttccattt gtcaaaaagt aatgatttct tgataattgt
4561 gtagtaatgt tttttagaac ccagcagtta ccttaaagct gaatttatat ttagtaactt
4621 ctgtgttaat actggatagc atgaattctg cattgagaaa ctgaatagct gtcataaaat
4681 gaaactttct ttctaaagaa agatactcac atgagttctt gaagaatagt cataactaga
4741 ttaagatctg tgttttagtt taatagtttg aagtgcctgt ttgggataat gataggtaat
4801 ttagatgaat ttaggggaaa aaaaagttat ctgcagatat gttgagggcc catctctccc
4861 cccacacccc cacagagcta actgggttac agtgttttat ccgaaagttt ccaattccac
4921 tgtcttgtgt tttcatgttg aaaatacttt tgcatttttc ctttgagtgc caatttctta
4981 ctagtactat ttcttaatgt aacatgttta cctggaatgt attttaacta tttttgtata
5041 gtgtaaactg aaacatgcac attttgtaca ttgtgctttc ttttgtggga catatgcagt
5101 gtgatccagt tgttttccat catttggttg cgctgaccta ggaatgttgg tcatatcaaa
5161 cattaaaaat gaccactctt ttaattgaaa ttaactttta aatgtttata ggagtatgtg
5221 ctgtgaagtg atctaaaatt tgtaatattt ttgtcatgaa ctgtactact cctaattatt
5281 gtaatgtaat aaaaatagtt acagtgacta tgagtgtgta tttattcatg aaatttgaac
5341 tgtttgcccc gaaatggata tggaatactt tataagccat agacactata gtataccagt
5401 gaatctttta tgcagcttgt tagaagtatc ctttatttct aaaaggtgct gtggatatta
5461 tgtaaaggcg tgtttgctta aacttaaaac catatttaga agtagatgca aaacaaatct
5521 gcctttatga caaaaaaata ggataacatt atttatttat ttccttttat caaagaaggt
5581 aattgataca caacaggtga cttggtttta ggcccaaagg tagcagcagc aacattaata
5641 atggaaataa ttgaatagtt agttatgtat gttaatgcca gtcaccagca ggctatttca
5701 aggtcagaag taatgactcc atacatatta tttatttcta taactacatt taaatcatta
5761 ccagg (SEQ ID NO: 1) [0010] In some embodiments, the target K-Ras mRNA sequence is a target sequence shown in Table 1 below.
Table 1. Target K-Ras Sequences
Figure imgf000008_0001
Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
43 304 GAAGCAAGTAGTAATTGAT 42
44 1206 GCTTCCTGATGATGATTCT 43
45 3237 CCTGACCTCAAGTGATTCA 44
46 2567 GCCTCCCTACCTTCCACAT W45
47 1403 GCCATTTCCTTTTCACATT W46
48 4207 GACGTATATTGTATCATTT W47
49 1402 GGCCATTTCCTTTTCACAT W48
50 4075 GGGGGAGAATTCTAGAAAT W49
51 4234 GTTCCCAAGTAGGCATTCT 50
52 268 GGACGAATATGATCCAACA 51
53 304 GAAGCAAGTAGTAATTGAT 52
54 1206 GCTTCCTGATGATGATTCT 53
55 5247 GAACTGTACTACTCCTAAT 54
56 3237 CCTGACCTCAAGTGATTCA 55
57 3386 GTCCTTAGGTAGTGCTAGT 56
58 1601 GTGTCAGACTGCTCTTTCA 57
59 1607 GACTGCTCTTTCATAGTAT 58
60 1255 CCTGATGAATGTAAAGTTA 59
61 2124 CAAGTCTGATCCATATTTA 60
62 688 GATGAGCAAAGATGGTAAA 61
63 2497 CAAGAGGTGAAGTTTATAT 62
64 3870 GGTAGGGTGTTAAGACTTA 63
65 1226 CTAGGCATCATGTCCTATA 64
66 4226 GAGTGAATGTTCCCAAGTA 65
67 517 CCTAGTAGGAAATAAATGT 66
68 3774 GCCTGAACTAGTTCACAGA 67
69 2970 CCAGAAATCTTCATGCAAT 68
70 2646 GCTGTGGATATCTCCATGA 69
71 303 GGAAGCAAGTAGTAATTGA 70
72 4203 CAGACGTATATTGTATCAT 71
73 233 GCCTTGACGATACAGCTAA 72
74 2259 GAAGGTGACTTAGGTTCTA 73
75 2076 GGCTAGTTCTCTTAACACT 74
76 3660 GTGTATGTCAGATATTCAT 75
77 1760 GAACCTTTGAGCTTTCATA 76
78 3789 CAGACAAGGAAACTTCTAT 77
79 3541 CTTCGATCAAGCTACTTTA 78
80 4954 GAGTGCCAATTTCTTACTA 79
81 1909 GCTGACAAATCAAGAGCAT 80
82 2346 GTCATCTCAAACTCTTAGT 81
83 638 GATGATGCCTTCTATACAT 82
84 2840 CTGGTATGAATAGACAGAA 83
85 2673 CACTGAGTCACATCAGAAA 84
86 4320 GTTGTCACCATTGCACAAT 85
87 2422 GTCAAGCTCAGCACAATCT 86
88 1484 GGGATTATTATAGCAACCA 87 Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
89 2252 CTAGGAAGAAGGTGACTTA 88
90 493 GGACTCTGAAGATGTACCT 89
91 3135 CTGAGTAGCTGGGATTACA 90
92 4921 CATGAGTTCTTGAAGAATA 91
93 266 GTGGACGAATATGATCCAA 92
94 2647 CTGTGGATATCTCCATGAA 93
95 3791 GACAAGGAAACTTCTATGT 94
96 4197 GAATATAGCAGACGTATAT 95
97 3544 CGATCAAGCTACTTTATGT 96
98 2839 CCTGGTATGAATAGACAGA 97
99 2943 CAGTAATACATTCCATTGT 98
100 1758 GTGAACCTTTGAGCTTTCA 99
101 175 GCTGAAAATGACTGAATAT 101
102 176 CTGAAAATGACTGAATATA 102
103 178 GAAAATGACTGAATATAAA 103
104 240 CGATACAGCTAATTCAGAA 104
105 245 CAGCTAATTCAGAATCATT 105
106 247 GCTAATTCAGAATCATTTT 106
107 256 GAATCATTTTGTGGACGAA 107
108 271 CGAATATGATCCAACAATA 108
109 278 GATCCAACAATAGAGGATT 109
110 282 CAACAATAGAGGATTCCTA 110
111 292 GGATTCCTACAGGAAGCAA 111
112 297 CCTACAGGAAGCAAGTAGT 112
113 298 CTACAGGAAGCAAGTAGTA 113
114 301 CAGGAAGCAAGTAGTAATT 114
115 307 GCAAGTAGTAATTGATGGA 115
116 311 GTAGTAATTGATGGAGAAA 116
117 320 GATGGAGAAACCTGTCTCT 117
118 324 GAGAAACCTGTCTCTTGGA 118
119 326 GAAACCTGTCTCTTGGATA 119
120 333 GTCTCTTGGATATTCTCGA 120
121 335 CTCTTGGATATTCTCGACA 121
122 337 CTTGGATATTCTCGACACA 122
123 340 GGATATTCTCGACACAGCA 123
124 347 CTCGACACAGCAGGTCAAG 124
125 356 GCAGGTCAAGAGGAGTACA 125
126 362 CAAGAGGAGTACAGTGCAA 126
127 365 GAGGAGTACAGTGCAATGA 127
128 377 CAATGAGGGACCAGTACA 128
129 385 GGACCAGTACATGAGGACT 129
130 405 GGGAGGGCTTTCTTTGTGT 130
131 407 GAGGGCTTTCTTTGTGTAT 131
132 409 GGGCTTTCTTTGTGTATTT 132
133 416 CTTTGTGTATTTGCCATAA 133
134 422 GTATTTGCCATAAATAAT 134 Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
135 441 CTAAATCATTTGAAGATAT 135
136 452 GAAGATATTCACCATTATA 136
137 463 CCATTATAGAGAACAAATT 137
138 464 CATTATAGAGAACAAATTA 138
139 471 GAGAACAAATTAAAAGAGT 139
140 473 GAACAAATTAAAAGAGTTA 140
141 486 GAGTTAAGGACTCTGAAGA 141
142 488 GTTAAGGACTCTGAAGATG 142
143 493 GGACTCTGAAGATGTACCT 143
144 494 GACTCTGAAGATGTACCTA 144
145 498 CTGAAGATGTACCTATGGT 145
146 509 CCTATGGTCCTAGTAGGAA 146
147 510 CTATGGTCCTAGTAGGAAA 147
148 515 GTCCTAGTAGGAAATAAAT 148
149 521 GTAGGAAATAAATGTGATT 149
150 542 CCTTCTAGAACAGTAGACA 150
151 546 CTAGAACAGTAGACACAAA 151
152 549 GAACAGTAGACACAAAACA 152
153 561 CAAAACAGGCTCAGGACTT 153
154 566 CAGGCTCAGGACTTAGCAA 154
155 568 GGCTCAGGACTTAGCAAGA 155
156 572 CAGGACTTAGCAAGAAGTT 156
157 577 CTTAGCAAGAAGTTATGGA 157
158 581 GCAAGAAGTTATGGAATTC 158
159 585 GAAGTTATGGAATTCCTTT 159
160 588 GTTATGGAATTCCTTTTAT 160
161 593 GGAATTCCTTTTATTGAAA 161
162 608 GAAACATCAGCAAAGACAA 162
163 612 CATCAGCAAAGACAAGACA 163
164 618 GCAAAGACAAGACAGGGTG 164
165 619 CAAAGACAAGACAGGGTGT 165
166 622 GACAAGACAGGGTGTTGAT 166
167 624 CAAGACAGGGTGTTGATGA 167
168 629 CAGGGTGTTGATGATGCCT 168
169 632 GGTGTTGATGATGCCTTCT 169
170 633 GTGTTGATGATGCCTTCTA 170
171 635 GTTGATGATGCCTTCTATA 171
172 639 ATGATGCCTTCTATACATT 172
173 641 GATGCCTTCTATACATTAG 173
174 644 GCCTTCTATACATTAGTTC 174
175 646 CTTCTATACATTAGTTCGA 175
176 649 CTATACATTAGTTCGAGAA 176
177 662 CGAGAAATTCGAAAACATA 177
178 663 GAGAAATTCGAAAACATAA 178
179 671 CGAAAACATAAAGAAAAGA 179
180 672 GAAAACATAAAGAAAAGAT 180 Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
181 677 CATAAAGAAAAGATGAGCA 181
182 693 GCAAAGATGGTAAAAAGAA 182
183 694 CAAAGATGGTAAAAAGAAG 183
184 698 GATGGTAAAAAGAAGAAAA 184
185 701 GGTAAAAAGAAGAAAAAGA 185
186 702 GTAAAAAGAAGAAAAAGAA 186
187 709 GAAGAAAAAGAAGTCAAAG 187
188 712 GAAAAAGAAGTCAAAGACA 188
189 718 GAAGTCAAAGACAAAGTGT 189
190 721 GTCAAAGACAAAGTGTGTA 190
191 723 CAAAGACAAAGTGTGTAAT 191
192 727 GACAAAGTGTGTAATTATG 192
193 729 CAAAGTGTGTAATTATGTA 193
194 752 CAATTTGTACTTTTTTCTT 194
195 758 GTACTTTTTTCTTAAGGCA 195
196 761 CTTTTTTCTTAAGGCATAC 196
197 768 CTTAAGGCATACTAGTACA 197
198 775 CATACTAGTACAAGTGGTA 198
199 779 CTAGTACAAGTGGTAATTT 199
200 782 GTACAAGTGGTAATTTTTG 200
201 788 GTGGTAATTTTTGTACATT 201
202 791 GTAATTTTTGTACATTACA 202
203 800 GUACAUUACACUAAAUUAU 203
204 808 CATTACACTAAATTATTAG 204
205 810 CTAAATTATTAGCATTTGT 205
206 821 GCATTTGTTTTAGCATTAC 206
207 827 GTTTTAGCATTACCTAATT 207
208 851 CCTGCTCCATGCAGACTGT 208
209 852 CTGCTCCATGCAGACTGTT 209
210 854 GCTCCATGCAGACTGTTAG 210
211 857 CCATGCAGACTGTTAGCTT 211
212 862 GACTGTTAGCTTTTACCTTA 212
213 868 GUUAGCUUUUACCUUAAAU 213
214 872 GCUUUUACCUUAAAUGCUU 214
215 873 CUUUUACCUUAAAUGCUUA 215
216 911 GUUUUUUUUUCCUCUAAGU 216
217 931 CCAGUAUUCCCAGAGUUUU 217
218 941 CAGAGUUUUGGUUUUUGAA 218
219 943 GAGUUUUGGUUUUUGAACU 219
220 960 CUAGCAAUGCCUGUGAAAA 220
221 970 CUGUGAAAAAGAAACUGAA 221
222 972 GUGAAAAAGAAACUGAAUA 222
223 984 CUGAAUACCUAAGAUUUCU 223
224 986 GAAUACCUAAGAUUUCUGU 224
225 1025 CAGUUGAUUACUUCUUAUU 225
226 1027 GUUGAUUACUUCUUAUUUU 226 Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
227 1030 GAUUACUUCUUAUUUUUCU 227
228 1038 CUUAUUUUUCUUACCAAUU 228
229 1047 CUUACCAAUUGUGAAUGUU 229
230 1059 GAAUGUUGGUGUGAAACAA 230
231 1067 GUGUGAAACAAAUUAAUGA 231
232 1101 CCUAUUCUGUGUUUUAUCU 232
233 1102 CUAUUCUGUGUUUUAUCUA 233
234 1125 CAUAAAUGGAUUAAUUACU 234
235 1159 CUUCUAAUUGGUUUUUACU 235
236 1162 CUAAUUGGUUUUUACUGAA 236
237 1169 GUUUUUACUGAAACAUUGA 237
238 1230 GCAUCAUGUCCUAUAGUUU 238
239 1278 GUUCACAAAGGUUUUGUCU 239
240 1403 GCCAUUUCCUUUUCACAUU 240
241 1404 CCAUUUCCUUUUCACAUUA 241
242 855 CTCCATGCAGACTGTTAGC 242
243 858 CATGCAGACTGTTAGCTTT 243
244 861 GCAGACTGTTAGCTTTTAC 244
245 866 CTGTTAGCTTTTACCTTAA 245
246 879 CCTTAAATGCTTATTTTAA 246
247 901 GACAGTGGAAGTTTTTTTT 247
248 902 ACAGTGGAAGTTTTTTTTT 248
249 921 CCTCTAAGTGCCAGTATTC 249
250 924 CTAAGTGCCAGTATTCCCA 250
251 928 GTGCCAGTATTCCCAGAGT 251
252 930 GCCAGTATTCCCAGAGTTT 252
253 931 CCAGTATTCCCAGAGTTTT 253
254 932 CAGTATTCCCAGAGTTTTG 254
255 934 GTATTCCCAGAGTTTTGGT 255
256 939 CCCAGAGTTTTGGTTTTTG 256
257 940 CCAGAGTTTTGGTTTTTGA 257
258 942 AGAGTTTTGGTTTTTGAAC 258
259 945 GTTTTGGTTTTTGAACTAG 259
260 950 GGTTTTTGAACTAGCAATG 260
261 957 GAACTAGCAATGCCTGTGA 261
262 963 GCAATGCCTGTGAAAAAGA 262
263 964 CAATGCCTGTGAAAAAGAA 263
264 968 GCCTGTGAAAAAGAAACTG 264
265 969 CCTGTGAAAAAGAAACTGA 265
266 973 TGAAAAAGAAACTGAATAC 266
267 980 GAAACTGAATACCTAAGAT 267
268 1001 CTGTCTTGGGGTTTTTGGT 268
269 1003 GTCTTGGGGTTTTTGGTGC 269
270 1005 CTTGGGGTTTTTGGTGCAT 270
271 1010 GCATGCAGTGTTTTTGGTG 271
272 1011 GTTTTTGGTGCATGCAGTT 272 Target Position in
K-Ras Target Targeted by aiRNA ID SEQ ID NM_004985
Sequence NO:
NO: Sequence
273 1410 CCTTTTCACATTAGATAAA 273
274 1411 CTTTTCACATTAGATAAAT 274
275 1474 GTATGAAATGGGGATTATT 275
276 1450 CCATTTTGGGGCTATATTT 276
277 1451 CATTTTGGGGCTATATTTA 277
278 1546 GAAAAGATTTTAACAAGTA 278
279 1559 CAAGTATAAAAAATTCTCA 279
280 1576 CATAGGAATTAAATGTAGT 280
281 1611 GCTCTTTCATAGTATAACT 281
282 1612 CTCTTTCATAGTATAACTT 282
283 1614 CTTTCATAGTATAACTTTA 283
284 1628 CTTTAAATCTTTTCTTCAA 284
285 1641 CTTCAACTTGAGTCTTTGA 285
286 1644 CAACTTGAGTCTTTGAAGA 286
287 1650 GAGTCTTTGAAGATAGTTT 287
288 1652 GTCTTTGAAGATAGTTTTA 288
289 1654 CTTTGAAGATAGTTTTAAT 289
290 1704 CAGTTATAGCTTATTAGGT 290
291 1712 GCTTATTAGGTGTTGAAGA 291
292 1770 GCTTTCATAGAGAGTTTCA 292
293 1826 CATGCATTGGTTAGTCAAA 293
294 1925 CATTGCTTTTGTTTCTTAA 294
295 1929 GCTTTTGTTTCTTAAGAAA 295
296 1930 CTTTTGTTTCTTAAGAAAA 296
297 1939 CTTAAGAAAACAAACTCTT 297
298 1944 GAAAACAAACTCTTTTTTA 298
299 2041 CAATGAAGTGAAAAAGTTT 299
300 2045 GAAGTGAAAAAGTTTTACA 300
301 2084 CTCTTAACACTGGTTAAAT 301
302 2086 CTTAACACTGGTTAAATTA 302
303 2096 GTTAAATTAACATTGCATA 303
304 2110 GCATAAACACTTTTCAAGT 304
305 2169 CAATCCTTTTGATAAATTT 305
306 2263 GTGACTTAGGTTCTAGATA 306
307 2287 CTTTTAGGACTCTGATTTT 307
308 2311 CATCACTTACTATCCATTT 308
309 2314 CACTTACTATCCATTTCTT 309
310 2316 CTTACTATCCATTTCTTCA 310
311 2320 CTATCCATTTCTTCATGTT 311
312 2324 CCATTTCTTCATGTTAAAA 312
313 2343 GAAGTCATCTCAAACTCTT 313
314 2348 CATCTCAAACTCTTAGTTT 314
315 2351 CTCAAACTCTTAGTTTTTT 315
316 2380 CTATGTAATTTATATTCCA 316
317 2403 CATAAGGATACACTTATTT 317
318 2432 GCACAATCTGTAAATTTTT 318 Target Position in
K-Ras Target Targeted by aiRNA ID
SEQ ID NM_004985
Sequence NO:
NO: Sequence
319 2454 CTATGTTACACCATCTTCA 319
[0011] In some embodiments, the RNA duplex molecule, also referred to herein as an asymmetrical interfering RNA molecule or aiRNA molecule, comprises a sense strand sequence, an antisense strand sequence or a combination of a sense strand sequence and antisense strand sequence selected from those shown in Table 2 below.
Table 2.
Figure imgf000015_0001
Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
W34 AAAAGAAACUGAAUA 353 AAGUAUUCAGUUUCUUUUUCA 671
35 AGCACAAUCUGUAAA 354 AAAUUUACAGAUUGUGCUGAG 672
36 CUUUCAUAGUAUAAC 355 AAAGUUAUACUAUGAAAGAGC 673
37 CUAGUGUGGUCUGUA 356 AAUUACAGACCACACUAGCAC 674
38 GUGUGGUCUGUAAUA 357 AAAUAUUACAGACCACACUAG 675
39 GACGUAUAUUGUAUC 358 AAUGAUACAAUAUACGUCUGC 676
40 CCCAAGUAGGCAUUC 359 AAAGAAUGCCUACUUGGGAAC 677
41 CGAAUAUGAUCCAAC 360 AAUGUUGGAUCAUAUUCGUCC 678
42 GCAAGUAGUAAUUGA 361 AAAUCAAUUACUACUUGCUUC 679
43 UCCUGAUGAUGAUUC 362 AAAGAAUCAUCAUCAGGAAGC 680
44 GACCUCAAGUGAUUC 363 AAUGAAUCACUUGAGGUCAGG 681
W45 UCCCUACCUUCCACA 364 AAAUGUGGAAGGUAGGGAGGC 682
W46 AUUUCCUUUUCACAU 365 AAAAUGUGAAAAGGAAAUGGC 683
W47 GUAUAUUGUAUCAUU 366 AAAAAUGAUACAAUAUACGUC 684
W48 CAUUUCCUUUUCACA 367 AAAUGUGAAAAGGAAAUGGCC 685
W49 GGAGAAUUCUAGAAA 368 AAAUUUCUAGAAUUCUCCCCC 686
50 CCCAAGUAGGCAUUC 369 AAAGAAUGCCUACUUGGGAAC 687
51 CGAAUAUGAUCCAAC 370 AAUGUUGGAUCAUAUUCGUCC 688
52 GCAAGUAGUAAUUGA 371 AAAUCAAUUACUACUUGCUUC 689
53 UCCUGAUGAUGAUUC 372 AAAGAAUCAUCAUCAGGAAGC 690
54 CUGUACUACUCCUAA 373 AAAUUAGGAGUAGUACAGUUC 691
55 GACCUCAAGUGAUUC 374 AAUGAAUCACUUGAGGUCAGG 692
56 CUUAGGUAGUGCUAG 375 AAACUAGCACUACCUAAGGAC 693
57 UCAGACUGCUCUUUC 376 AAUGAAAGAGCAGUCUGACAC 694
58 UGCUCUUUCAUAGUA 377 AAAUACUAUGAAAGAGCAGUC 695
59 GAUGAAUGUAAAGUU 378 AAUAACUUUACAUUCAUCAGG 696
60 GUCUGAUCCAUAUUU 379 AAUAAAUAUGGAUCAGACUUG 697
61 GAGCAAAGAUGGUAA 380 AAUUUACCAUCUUUGCUCAUC 698
62 GAGGUGAAGUUUAUA 381 AAAUAUAAACUUCACCUCUUG 699
63 AGGGUGUUAAGACUU 382 AAUAAGUCUUAACACCCUACC 700
64 GGCAUCAUGUCCUAU 383 AAUAUAGGACAUGAUGCCUAG 701
65 UGAAUGUUCCCAAGU 384 AAUACUUGGGAACAUUCACUC 702
66 AGUAGGAAAUAAAUG 385 AAACAUUUAUUUCCUACUAGG 703
67 UGAACUAGUUCACAG 386 AAUCUGUGAACUAGUUCAGGC 704
68 GAAAUCUUCAUGCAA 387 AAAUUGCAUGAAGAUUUCUGG 705
69 GUGGAUAUCUCCAUG 388 AAUCAUGGAGAUAUCCACAGC 706
70 AGCAAGUAGUAAUUG 389 AAUCAAUUACUACUUGCUUCC 707
71 ACGUAUAUUGUAUCA 390 AAAUGAUACAAUAUACGUCUG 708
72 UUGACGAUACAGCUA 391 AAUUAGCUGUAUCGUCAAGGC 709
73 GGUGACUUAGGUUCU 392 AAUAGAACCUAAGUCACCUUC 710
74 UAGUUCUCUUAACAC 393 AAAGUGUUAAGAGAACUAGCC 711
75 UAUGUCAGAUAUUCA 394 AAAUGAAUAUCUGACAUACAC 712
76 CCUUUGAGCUUUCAU 395 AAUAUGAAAGCUCAAAGGUUC 713
77 ACAAGGAAACUUCUA 396 AAAUAGAAGUUUCCUUGUCUG 714
78 CGAUCAAGCUACUUU 397 AAUAAAGUAGCUUGAUCGAAG 715
79 UGCCAAUUUCUUACU 398 AAUAGUAAGAAAUUGGCACUC 716 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
80 GACAAAUCAAGAGCA 399 AAAUGCUCUUGAUUUGUCAGC 717
81 AUCUCAAACUCUUAG 400 AAACUAAGAGUUUGAGAUGAC 718
82 GAUGCCUUCUAUACA 401 AAAUGUAUAGAAGGCAUCAUC 719
83 GUAUGAAUAGACAGA 402 AAUUCUGUCUAUUCAUACCAG 720
84 UGAGUCACAUCAGAA 403 AAUUUCUGAUGUGACUCAGUG 721
85 GUCACCAUUGCACAA 404 AAAUUGUGCAAUGGUGACAAC 722
86 AAGCUCAGCACAAUC 405 AAAGAUUGUGCUGAGCUUGAC 723
87 AUUAUUAUAGCAACC 406 AAUGGUUGCUAUAAUAAUCCC 724
88 GGAAGAAGGUGACUU 407 AAUAAGUCACCUUCUUCCUAG 725
89 CUCUGAAGAUGUACC 408 AAAGGUACAUCUUCAGAGUCC 726
90 AGUAGCUGGGAUUAC 409 AAUGUAAUCCCAGCUACUCAG 727
91 GAGUUCUUGAAGAAU 410 AAUAUUCUUCAAGAACUCAUG 728
92 GACGAAUAUGAUCCA 411 AAUUGGAUCAUAUUCGUCCAC 729
93 UGGAUAUCUCCAUGA 412 AAUUCAUGGAGAUAUCCACAG 730
94 AAGGAAACUUCUAUG 413 AAACAUAGAAGUUUCCUUGUC 731
95 UAUAGCAGACGUAUA 414 AAAUAUACGUCUGCUAUAUUC 732
96 UCAAGCUACUUUAUG 415 AAACAUAAAGUAGCUUGAUCG 733
97 GGUAUGAAUAGACAG 416 AAUCUGUCUAUUCAUACCAGG 734
98 UAAUACAUUCCAUUG 417 AAACAAUGGAAUGUAUUACUG 735
99 AACCUUUGAGCUUUC 418 AAUGAAAGCUCAAAGGUUCAC 736
101 GAAAAUGACUGAAUA 419 AAAUAUUCAGUCAUUUUCAGC 737
102 AAAAUGACUGAAUAU 420 AAUAUAUUCAGUCAUUUUCAG 738
103 AAUGACUGAAUAUAA 421 AAUUUAUAUUCAGUCAUUUUC 739
104 UACAGCUAAUUCAGA 422 AAUUCUGAAUUAGCUGUAUCG 740
105 CUAAUUCAGAAUCAU 423 AAAAUGAUUCUGAAUUAGCUG 741
106 AAUUCAGAAUCAUUU 424 AAAAAAUGAUUCUGAAUUAGC 742
107 UCAUUUUGUGGACGA 425 AAUUCGUCCACAAAAUGAUUC 743
108 AUAUGAUCCAACAAU 426 AAUAUUGUUGGAUCAUAUUCG 744
109 CCAACAAUAGAGGAU 427 AAAAUCCUCUAUUGUUGGAUC 745
110 CAAUAGAGGAUUCCU 428 AAUAGGAAUCCUCUAUUGUUG 746
111 UUCCUACAGGAAGCA 429 AAUUGCUUCCUGUAGGAAUCC 747
112 ACAGGAAGCAAGUAG 430 AAACUACUUGCUUCCUGUAGG 748
113 CAGGAAGCAAGUAGU 431 AAUACUACUUGCUUCCUGUAG 749
114 GAAGCAAGUAGUAAU 432 AAAAUUACUACUUGCUUCCUG 750
115 AGUAGUAAUUGAUGG 433 AAUCCAUCAAUUACUACUUGC 751
116 GUAAUUGAUGGAGAA 434 AAUUUCUCCAUCAAUUACUAC 752
117 GGAGAAACCUGUCUC 435 AAAGAGACAGGUUUCUCCAUC 753
118 AAACCUGUCUCUUGG 436 AAUCCAAGAGACAGGUUUCUC 754
119 ACCUGUCUCUUGGAU 437 AAUAUCCAAGAGACAGGUUUC 755
120 UCUUGGAUAUUCUCG 438 AAUCGAGAAUAUCCAAGAGAC 756
121 UUGGAUAUUCUCGAC 439 AAUGUCGAGAAUAUCCAAGAG 757
122 GGAUAUUCUCGACAC 440 AAUGUGUCGAGAAUAUCCAAG 758
123 UAUUCUCGACACAGC 441 AAUGCUGUGUCGAGAAUAUCC 759
124 GACACAGCAGGUCAA 442 AACUUGACCUGCUGUGUCGAG 760
125 GGUCAAGAGGAGUAC 443 AAUGUACUCCUCUUGACCUGC 761
126 GAGGAGUACAGUGCA 444 AAUUGCACUGUACUCCUCUUG 762 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
127 GAGUACAGUGCAAUG 445 AAUCAUUGCACUGUACUCCUC 763
128 UGAGGGACCAGUAC 446 AAUGUACUGGUCCCUCAUUG 764
129 CCAGUACAUGAGGAC 447 AAAGUCCUCAUGUACUGGUCC 765
130 AGGGCUUUCUUUGUG 448 AAACACAAAGAAAGCCCUCCC 766
131 GGCUUUCUUUGUGUA 449 AAAUACACAAAGAAAGCCCUC 767
132 CUUUCUUUGUGUAUU 450 AAAAAUACACAAAGAAAGCCC 768
133 UGUGUAUUUGCCAUA 451 AAUUAUGGCAAAUACACAAAG 769
134 UUUGCCAUAAAUAA 452 AAAUUAUUUAUGGCAAAUAC 770
135 AAUCAUUUGAAGAUA 453 AAAUAUCUUCAAAUGAUUUAG 771
136 GAUAUUCACCAUUAU 454 AAUAUAAUGGUGAAUAUCUUC 772
137 UUAUAGAGAACAAAU 455 AAAAUUUGUUCUCUAUAAUGG 773
138 UAUAGAGAACAAAUU 456 AAUAAUUUGUUCUCUAUAAUG 774
139 AACAAAUUAAAAGAG 457 AAACUCUUUUAAUUUGUUCUC 775
140 CAAAUUAAAAGAGUU 458 AAUAACUCUUUUAAUUUGUUC 776
141 UUAAGGACUCUGAAG 459 AAUCUUCAGAGUCCUUAACUC 777
142 AAGGACUCUGAAGAU 460 AACAUCUUCAGAGUCCUUAAC 778
143 CUCUGAAGAUGUACC 461 AAAGGUACAUCUUCAGAGUCC 779
144 UCUGAAGAUGUACCU 462 AAUAGGUACAUCUUCAGAGUC 780
145 AAGAUGUACCUAUGG 463 AAACCAUAGGUACAUCUUCAG 781
146 AUGGUCCUAGUAGGA 464 AAUUCCUACUAGGACCAUAGG 782
147 UGGUCCUAGUAGGAA 465 AAUUUCCUACUAGGACCAUAG 783
148 CUAGUAGGAAAUAAA 466 AAAUUUAUUUCCUACUAGGAC 784
149 GGAAAUAAAUGUGAU 467 AAAAUCACAUUUAUUUCCUAC 785
150 UCUAGAACAGUAGAC 468 AAUGUCUACUGUUCUAGAAGG 786
151 GAACAGUAGACACAA 469 AAUUUGUGUCUACUGUUCUAG 787
152 CAGUAGACACAAAAC 470 AAUGUUUUGUGUCUACUGUUC 788
153 AACAGGCUCAGGACU 471 AAAAGUCCUGAGCCUGUUUUG 789
154 GCUCAGGACUUAGCA 472 AAUUGCUAAGUCCUGAGCCUG 790
155 UCAGGACUUAGCAAG 473 AAUCUUGCUAAGUCCUGAGCC 791
156 GACUUAGCAAGAAGU 474 AAAACUUCUUGCUAAGUCCUG 792
157 AGCAAGAAGUUAUGG 475 AAUCCAUAACUUCUUGCUAAG 793
158 AGAAGUUAUGGAAUU 476 AAGAAUUCCAUAACUUCUUGC 794
159 GUUAUGGAAUUCCUU 477 AAAAAGGAAUUCCAUAACUUC 795
160 AUGGAAUUCCUUUUA 478 AAAUAAAAGGAAUUCCAUAAC 796
161 AUUCCUUUUAUUGAA 479 AAUUUCAAUAAAAGGAAUUCC 797
162 ACAUCAGCAAAGACA 480 AAUUGUCUUUGCUGAUGUUUC 798
163 CAGCAAAGACAAGAC 481 AAUGUCUUGUCUUUGCUGAUG 799
164 AAGACAAGACAGGGU 482 AACACCCUGUCUUGUCUUUGC 800
165 AGACAAGACAGGGUG 483 AAACACCCUGUCUUGUCUUUG 801
166 AAGACAGGGUGUUGA 484 AAAUCAACACCCUGUCUUGUC 802
167 GACAGGGUGUUGAUG 485 AAUCAUCAACACCCUGUCUUG 803
168 GGUGUUGAUGAUGCC 486 AAAGGCAUCAUCAACACCCUG 804
169 GUUGAUGAUGCCUUC 487 AAAGAAGGCAUCAUCAACACC 805
170 UUGAUGAUGCCUUCU 488 AAUAGAAGGCAUCAUCAACAC 806
171 GAUGAUGCCUUCUAU 489 AAUAUAGAAGGCAUCAUCAAC 807
172 AUGCCUUCUAUACAU 490 AAAAUGUAUAGAAGGCAUCAU 808 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
173 GCCUUCUAUACAUUA 491 AACUAAUGUAUAGAAGGCAUC 809
174 UUCUAUACAUUAGUU 492 AAGAACUAAUGUAUAGAAGGC 810
175 CUAUACAUUAGUUCG 493 AAUCGAACUAAUGUAUAGAAG 811
176 UACAUUAGUUCGAGA 494 AAUUCUCGAACUAAUGUAUAG 812
177 GAAAUUCGAAAACAU 495 AAUAUGUUUUCGAAUUUCUCG 813
178 AAAUUCGAAAACAUA 496 AAUUAUGUUUUCGAAUUUCUC 814
179 AAACAUAAAGAAAAG 497 AAUCUUUUCUUUAUGUUUUCG 815
180 AACAUAAAGAAAAGA 498 AAAUCUUUUCUUUAUGUUUUC 816
181 AAAGAAAAGAUGAGC 499 AAUGCUCAUCUUUUCUUUAUG 817
182 AAGAUGGUAAAAAGA 500 AAUUCUUUUUACCAUCUUUGC 818
183 AGAUGGUAAAAAGAA 501 AACUUCUUUUUACCAUCUUUG 819
184 GGUAAAAAGAAGAAA 502 AAUUUUCUUCUUUUUACCAUC 820
185 AAAAAGAAGAAAAAG 503 AAUCUUUUUCUUCUUUUUACC 821
186 AAAAGAAGAAAAAGA 504 AAUUCUUUUUCUUCUUUUUAC 822
187 GAAAAAGAAGUCAAA 505 AACUUUGACUUCUUUUUCUUC 823
188 AAAGAAGUCAAAGAC 506 AAUGUCUUUGACUUCUUUUUC 824
189 GUCAAAGACAAAGUG 507 AAACACUUUGUCUUUGACUUC 825
190 AAAGACAAAGUGUGU 508 AAUACACACUUUGUCUUUGAC 826
191 AGACAAAGUGUGUAA 509 AAAUUACACACUUUGUCUUUG 827
192 AAAGUGUGUAAUUAU 510 AACAUAAUUACACACUUUGUC 828
193 AGUGUGUAAUUAUGU 511 AAUACAUAAUUACACACUUUG 829
194 UUUGUACUUUUUUCU 512 AAAAGAAAAAAGUACAAAUUG 830
195 CUUUUUUCUUAAGGC 513 AAUGCCUUAAGAAAAAAGUAC 831
196 UUUUCUUAAGGCAUA 514 AAGUAUGCCUUAAGAAAAAAG 832
197 AAGGCAUACUAGUAC 515 AAUGUACUAGUAUGCCUUAAG 833
198 ACUAGUACAAGUGGU 516 AAUACCACUUGUACUAGUAUG 834
199 GUACAAGUGGUAAUU 517 AAAAAUUACCACUUGUACUAG 835
200 CAAGUGGUAAUUUUU 518 AACAAAAAUUACCACUUGUAC 836
201 GUAAUUUUUGUACAU 519 AAAAUGUACAAAAAUUACCAC 837
202 AUUUUUGUACAUUAC 520 AAUGUAAUGUACAAAAAUUAC 838
203 CAUUACACUAAAUUA 521 AAAUAAUUUAGUGUAAUGUAC 839
204 UACACUAAAUUAUUA 522 AACUAAUAAUUUAGUGUAAUG 840
205 AAUUAUUAGCAUUUG 523 AAACAAAUGCUAAUAAUUUAG 841
206 UUUGUUUUAGCAUUA 524 AAGUAAUGCUAAAACAAAUGC 842
207 UUAGCAUUACCUAAU 525 AAAAUUAGGUAAUGCUAAAAC 843
208 GCUCCAUGCAGACUG 526 AAACAGUCUGCAUGGAGCAGG 844
209 CUCCAUGCAGACUGU 527 AAAACAGUCUGCAUGGAGCAG 845
210 CCAUGCAGACUGUUA 528 AACUAACAGUCUGCAUGGAGC 846
211 UGCAGACUGUUAGCU 529 AAAAGCUAACAGUCUGCAUGG 847
212 UGUUAGCUUUUACCUU 530 AAUAAGGUAAAAGCUAACAGUC 848
213 AGCUUUUACCUUAAA 531 AAAUUUAAGGUAAAAGCUAAC 849
214 UUUACCUUAAAUGCU 532 AAAAGCAUUUAAGGUAAAAGC 850
215 UUACCUUAAAUGCUU 533 AAUAAGCAUUUAAGGUAAAAG 851
216 UUUUUUUCCUCUAAG 534 AAACUUAGAGGAAAAAAAAAC 852
217 GUAUUCCCAGAGUUU 535 AAAAAACUCUGGGAAUACUGG 853
218 AGUUUUGGUUUUUGA 536 AAUUCAAAAACCAAAACUCUG 854 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
219 UUUUGGUUUUUGAAC 537 AAAGUUCAAAAACCAAAACUC 855
220 GCAAUGCCUGUGAAA 538 AAUUUUCACAGGCAUUGCUAG 856
221 UGAAAAAGAAACUGA 539 AAUUCAGUUUCUUUUUCACAG 857
222 AAAAAGAAACUGAAU 540 AAUAUUCAGUUUCUUUUUCAC 858
223 AAUACCUAAGAUUUC 541 AAAGAAAUCUUAGGUAUUCAG 859
224 UACCUAAGAUUUCUG 542 AAACAGAAAUCUUAGGUAUUC 860
225 UUGAUUACUUCUUAU 543 AAAAUAAGAAGUAAUCAACUG 861
226 GAUUACUUCUUAUUU 544 AAAAAAUAAGAAGUAAUCAAC 862
227 UACUUCUUAUUUUUC 545 AAAGAAAAAUAAGAAGUAAUC 863
228 AUUUUUCUUACCAAU 546 AAAAUUGGUAAGAAAAAUAAG 864
229 ACCAAUUGUGAAUGU 547 AAAACAUUCACAAUUGGUAAG 865
230 UGUUGGUGUGAAACA 548 AAUUGUUUCACACCAACAUUC 866
231 UGAAACAAAUUAAUG 549 AAUCAUUAAUUUGUUUCACAC 867
232 AUUCUGUGUUUUAUC 550 AAAGAUAAAACACAGAAUAGG 868
233 UUCUGUGUUUUAUCU 551 AAUAGAUAAAACACAGAAUAG 869
234 AAAUGGAUUAAUUAC 552 AAAGUAAUUAAUCCAUUUAUG 870
235 CUAAUUGGUUUUUAC 553 AAAGUAAAAACCAAUUAGAAG 871
236 AUUGGUUUUUACUGA 554 AAUUCAGUAAAAACCAAUUAG 872
237 UUUACUGAAACAUUG 555 AAUCAAUGUUUCAGUAAAAAC 873
238 UCAUGUCCUAUAGUU 556 AAAAACUAUAGGACAUGAUGC 874
239 CACAAAGGUUUUGUC 557 AAAGACAAAACCUUUGUGAAC 875
240 AUUUCCUUUUCACAU 558 AAAAUGUGAAAAGGAAAUGGC 876
241 UUUCCUUUUCACAUU 559 AAUAAUGUGAAAAGGAAAUGG 877
242 CAUGCAGACUGUUAG 560 AAGCUAACAGUCUGCAUGGAG 878
243 GCAGACUGUUAGCUU 561 AAAAAGCUAACAGUCUGCAUG 879
244 GACUGUUAGCUUUUA 562 AAGUAAAAGCUAACAGUCUGC 880
245 UUAGCUUUUACCUUA 563 AAUUAAGGUAAAAGCUAACAG 881
246 UAAAUGCUUAUUUUA 564 AAUUAAAAUAAGCAUUUAAGG 882
247 AGUGGAAGUUUUUUU 565 AAAAAAAAAACUUCCACUGUC 883
248 GUGGAAGUUUUUUUU 566 AAAAAAAAAAACUUCCACUGU 884
249 CUAAGUGCCAGUAUU 567 AAGAAUACUGGCACUUAGAGG 885
250 AGUGCCAGUAUUCCC 568 AAUGGGAAUACUGGCACUUAG 886
251 CCAGUAUUCCCAGAG 569 AAACUCUGGGAAUACUGGCAC 887
252 AGUAUUCCCAGAGUU 570 AAAAACUCUGGGAAUACUGGC 888
253 GUAUUCCCAGAGUUU 571 AAAAAACUCUGGGAAUACUGG 889
254 UAUUCCCAGAGUUUU 572 AACAAAACUCUGGGAAUACUG 890
255 UUCCCAGAGUUUUGG 573 AAACCAAAACUCUGGGAAUAC 891
256 AGAGUUUUGGUUUUU 574 AACAAAAACCAAAACUCUGGG 892
257 GAGUUUUGGUUUUUG 575 AAUCAAAAACCAAAACUCUGG 893
258 GUUUUGGUUUUUGAA 576 AAGUUCAAAAACCAAAACUCU 894
259 UUGGUUUUUGAACUA 577 AACUAGUUCAAAAACCAAAAC 895
260 UUUUGAACUAGCAAU 578 AACAUUGCUAGUUCAAAAACC 896
261 CUAGCAAUGCCUGUG 579 AAUCACAGGCAUUGCUAGUUC 897
262 AUGCCUGUGAAAAAG 580 AAUCUUUUUCACAGGCAUUGC 898
263 UGCCUGUGAAAAAGA 581 AAUUCUUUUUCACAGGCAUUG 899
264 UGUGAAAAAGAAACU 582 AACAGUUUCUUUUUCACAGGC 900 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
265 GUGAAAAAGAAACUG 583 AAUCAGUUUCUUUUUCACAGG 901
266 AAAAGAAACUGAAUA 584 AAGUAUUCAGUUUCUUUUUCA 902
267 ACUGAAUACCUAAGA 585 AAAUCUUAGGUAUUCAGUUUC 903
268 UCUUGGGGUUUUUGG 586 AAACCAAAAACCCCAAGACAG 904
269 UUGGGGUUUUUGGUG 587 AAGCACCAAAAACCCCAAGAC 905
270 GGGGUUUUUGGUGCA 588 AAAUGCACCAAAAACCCCAAG 906
271 UGCAGUGUUUUUGGU 589 AACACCAAAAACACUGCAUGC 907
272 UUUGGUGCAUGCAGU 590 AAAACUGCAUGCACCAAAAAC 908
273 UUUCACAUUAGAUAA 591 AAUUUAUCUAAUGUGAAAAGG 909
274 UUCACAUUAGAUAAA 592 AAAUUUAUCUAAUGUGAAAAG 910
275 UGAAAUGGGGAUUAU 593 AAAAUAAUCCCCAUUUCAUAC 911
276 UUUUGGGGCUAUAUU 594 AAAAAUAUAGCCCCAAAAUGG 912
277 UUUGGGGCUAUAUUU 595 AAUAAAUAUAGCCCCAAAAUG 913
278 AAGAUUUUAACAAGU 596 AAUACUUGUUAAAAUCUUUUC 914
279 GUAUAAAAAAUUCUC 597 AAUGAGAAUUUUUUAUACUUG 915
280 AGGAAUUAAAUGUAG 598 AAACUACAUUUAAUUCCUAUG 916
281 CUUUCAUAGUAUAAC 599 AAAGUUAUACUAUGAAAGAGC 917
282 UUUCAUAGUAUAACU 600 AAAAGUUAUACUAUGAAAGAG 918
283 UCAUAGUAUAACUUU 601 AAUAAAGUUAUACUAUGAAAG 919
284 UAAAUCUUUUCUUCA 602 AAUUGAAGAAAAGAUUUAAAG 920
285 CAACUUGAGUCUUUG 603 AAUCAAAGACUCAAGUUGAAG 921
286 CUUGAGUCUUUGAAG 604 AAUCUUCAAAGACUCAAGUUG 922
287 UCUUUGAAGAUAGUU 605 AAAAACUAUCUUCAAAGACUC 923
288 UUUGAAGAUAGUUUU 606 AAUAAAACUAUCUUCAAAGAC 924
289 UGAAGAUAGUUUUAA 607 AAAUUAAAACUAUCUUCAAAG 925
290 UUAUAGCUUAUUAGG 608 AAACCUAAUAAGCUAUAACUG 926
291 UAUUAGGUGUUGAAG 609 AAUCUUCAACACCUAAUAAGC 927
292 UUCAUAGAGAGUUUC 610 AAUGAAACUCUCUAUGAAAGC 928
293 GCAUUGGUUAGUCAA 611 AAUUUGACUAACCAAUGCAUG 929
294 UGCUUUUGUUUCUUA 612 AAUUAAGAAACAAAAGCAAUG 930
295 UUUGUUUCUUAAGAA 613 AAUUUCUUAAGAAACAAAAGC 931
296 UUGUUUCUUAAGAAA 614 AAUUUUCUUAAGAAACAAAAG 932
297 AAGAAAACAAACUCU 615 AAAAGAGUUUGUUUUCUUAAG 933
298 AACAAACUCUUUUUU 616 AAUAAAAAAGAGUUUGUUUUC 934
299 UGAAGUGAAAAAGUU 617 AAAAACUUUUUCACUUCAUUG 935
300 GUGAAAAAGUUUUAC 618 AAUGUAAAACUUUUUCACUUC 936
301 UUAACACUGGUUAAA 619 AAAUUUAACCAGUGUUAAGAG 937
302 AACACUGGUUAAAUU 620 AAUAAUUUAACCAGUGUUAAG 938
303 AAAUUAACAUUGCAU 621 AAUAUGCAAUGUUAAUUUAAC 939
304 UAAACACUUUUCAAG 622 AAACUUGAAAAGUGUUUAUGC 940
305 UCCUUUUGAUAAAUU 623 AAAAAUUUAUCAAAAGGAUUG 941
306 ACUUAGGUUCUAGAU 624 AAUAUCUAGAACCUAAGUCAC 942
307 UUAGGACUCUGAUUU 625 AAAAAAUCAGAGUCCUAAAAG 943
308 CACUUACUAUCCAUU 626 AAAAAUGGAUAGUAAGUGAUG 944
309 UUACUAUCCAUUUCU 627 AAAAGAAAUGGAUAGUAAGUG 945
310 ACUAUCCAUUUCUUC 628 AAUGAAGAAAUGGAUAGUAAG 946 Antisense aiRNA Sense Strand Sense Strand Antisense Strand
Strand SEQ ID NO: Sequence SEQ ID NO: Sequence
ID NO:
311 UCCAUUUCUUCAUGU 629 AAAACAUGAAGAAAUGGAUAG 947
312 UUUCUUCAUGUUAAA 630 AAUUUUAACAUGAAGAAAUGG 948
313 GUCAUCUCAAACUCU 631 AAAAGAGUUUGAGAUGACUUC 949
314 CUCAAACUCUUAGUU 632 AAAAACUAAGAGUUUGAGAUG 950
315 AAACUCUUAGUUUUU 633 AAAAAAAACUAAGAGUUUGAG 951
316 UGUAAUUUAUAUUCC 634 AAUGGAAUAUAAAUUACAUAG 952
317 AAGGAUACACUUAUU 635 AAAAAUAAGUGUAUCCUUAUG 953
318 CAAUCUGUAAAUUUU 636 AAAAAAAUUUACAGAUUGUGC 954
319 UGUUACACCAUCUUC 637 AAUGAAGAUGGUGUAACAUAG 955
[0012] In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
[0013] In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955.
[0014] In some embodiments, at least one nucleotide of the sequence of 5' overhang is selected from the group consisting of A, U, and dT.
[0015] In some embodiments, the GC content of the double stranded region is
20%-70%.
[0016] In some embodiments, the first strand has a length from 19-22 nucleotides. [0017] In some embodiments, the first strand has a length of 21 nucleotides. In a further embodiment, the second strand has a length of 14-16 nucleotides.
[0018] In some embodiments, the first strand has a length of 21 nucleotides, and the second strand has a length of 15 nucleotides. In a further embodiment, the first strand has a 3'-overhang of 2-4 nucleotides. In an even further embodiment, the first strand has a 3'- overhang of 3 nucleotides.
[0019] In some embodiments, the duplex RNA molecule contains at least one modified nucleotide or its analogue. In a further embodiment, the at least one modified nucleotide or its analogue is sugar-, backbone-, and/or base- modified ribonucleotide. In an even further embodiment, the backbone-modified ribonucleotide has a modification in a phosphodiester linkage with another ribonucleotide. In some embodiments, the phosphodiester linkage is modified to include at least one of a nitrogen or a sulphur heteroatom. In another embodiment, the nucleotide analogue is a backbone-modified ribonucleotide containing a phosphothioate group.
[0020] In some embodiments, the at least one modified nucleotide or its analogue is an unusual base or a modified base. In another embodiment, the at least one modified nucleotide or its analogue comprises inosine, or a tritylated base.
[0021] In a further embodiment, the nucleotide analogue is a sugar-modified ribonucleotide, wherein the 2'-OH group is replaced by a group selected from H, OR, R, halo, SH, SR, NH2, NHR, NR2, or CN, wherein each R is independently C1-C6 alkyl, alkenyl or alkynyl, and halo is F, CI, Br or I.
[0022] In some embodiments, the first strand comprises at least one deoxynucleotide. In a further embodiment, the at least one deoxynucleotides are in one or more regions selected from the group consisting of 3 '-overhang, 5 '-overhang, and double- stranded region. In another embodiment, the second strand comprises at least one deoxynucleotide.
[0023] The present invention also provides a method of modulating K-Ras expression, e.g., silencing K-Ras expression or otherwise reducing K-Ras expression, in a cell or an organism comprising the steps of contacting said cell or organism with an asymmetrical duplex RNA molecule of the disclosure under conditions wherein selective K-Ras gene silencing can occur, and mediating a selective K-Ras gene silencing effected by the duplex RNA molecule towards K-Ras or nucleic acid having a sequence portion substantially corresponding to the double-stranded RNA. In a further embodiment, said contacting step comprises the step of introducing said duplex RNA molecule into a target cell in culture or in an organism in which the selective K-Ras silencing can occur. In an even further embodiment, the introducing step is selected from the group consisting of transfection, lipofection, electroporation, infection, injection, oral administration, inhalation, topical and regional administration. In another embodiment, the introducing step comprises using a pharmaceutically acceptable excipient, carrier, or diluent selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a nanoemulsion, a lipid, and a lipoid.
[0024] In some embodiments, the modulating method is used for determining the function or utility of a gene in a cell or an organism.
[0025] In some embodiments, the modulating method is used for treating or preventing a disease or an undesirable condition. In some embodiments, the disease or undesirable condition is a cancer, for example, gastric cancer.
[0026] The disclosure provides compositions and methods for targeting K-Ras in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer. In some embodiments, the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure. In some embodiments, the subject is human. In some embodiments, the subject is suffering from gastric cancer. In some embodiments, the subject is diagnosed with gastric cancer. In some embodiments, the subject is predisposed to gastric cancer.
[0027] The disclosure also provides compositions and methods for targeting K-Ras to inhibit the survival and/or proliferation of cancer stem cells. In some embodiments, the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure. In some embodiments, the subject is human. In some embodiments, the subject is suffering from gastric cancer. In some embodiments, the subject is diagnosed with gastric cancer. In some embodiments, the subject is predisposed to gastric cancer.
[0028] The disclosure also provides compositions and methods for targeting K-Ras in the inhibition of to inhibit the survival and/or proliferation of CSCs in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer. In some embodiments, the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure. In some embodiments, the subject is human. In some embodiments, the subject is suffering from gastric cancer. In some embodiments, the subject is diagnosed with gastric cancer. In some embodiments, the subject is predisposed to gastric cancer. [0029] The disclosure also provides a method for treating cancer in a selected patient population, the method comprising the steps of: (a) measuring a level of mutant K-Ras gene amplification in a biological sample obtained from a patient candidate diagnosed of a cancer; (b) confirming that the patient candidate's mutant K-Ras gene amplification level is above a benchmark level; and (c) administering to the patient candidate a duplex RNA molecule comprising a first strand comprising a nucleotide sequence with a length from 18- 23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a 5 '-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
[0030] In some embodiments, the steps (a), (b), and (c) may be performed by one actor or several actors.
[0031] In some embodiments, a patient candidate's mutant K-Ras gene amplification level is considered to be above a benchmark level if it is at least, e.g., 2-fold greater relative to that of a control patient who would not respond favorably to the claimed treatment method according to the present invention. Likewise, a skilled physician may determine that the optimal benchmark level of the DNA copy number is, e.g., about 3-fold or 4-fold greater relative to that of a non-responsive patient, based on the data presented in the present disclosure.
[0032] The disclosure also provides a method for treating cancer in a selected patient population, the method comprising the steps of: (a) measuring an expression level of mutant K-Ras protein in a biological sample obtained from a patient candidate diagnosed of a cancer; (b) confirming that the patient candidate's mutant K-Ras protein expression level is above a benchmark level; and (c) administering to the patient candidate a duplex RNA molecule comprising a first strand comprising a nucleotide sequence with a length from 18- 23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a 5 '-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
[0033] In some embodiments, the steps (a), (b), and (c) may be performed by one actor or several actors.
[0034] In some embodiments, a patient candidate's mutant K-Ras protein expression level is considered to be above a benchmark level if it is at least, e.g., 2-fold greater relative to that of a control patient who would not respond favorably to the claimed treatment method according to the present invention. Likewise, a skilled physician may determine that the optimal benchmark level of the mutant K-Ras protein expression is, e.g., about 3-fold or 4- fold greater relative to that of a non-responsive patient, based on the data presented in the present disclosure.
[0035] The present invention further provides a kit. The kit comprises a first RNA strand with a length from 18-23 nucleotides and a second RNA strand with a length from 12- 17 nucleotides, wherein the second strand is substantially complementary to the first strand, and capable of forming a duplex RNA molecule with the first strand, wherein the duplex RNA molecule has a 3 '-overhang from 1-9 nucleotides, and a 5 '-overhang from 0-8 nucleotides, wherein said duplex RNA molecule is capable of effecting K-Ras specific gene silencing.
[0036] The present invention also provides a method of preparing the duplex RNA molecule. The method comprises the steps of synthesizing the first strand and the second strand, and combining the synthesized strands under conditions, wherein the duplex RNA molecule is formed, which is capable of effecting sequence-specific gene silencing. In some embodiments, the method further comprises a step of introducing at least one modified nucleotide or its analogue into the duplex RNA molecule during the synthesizing step, after the synthesizing and before the combining step, or after the combining step. In another embodiment, the RNA strands are chemically synthesized, or biologically synthesized.
[0037] The present invention provides an expression vector. The vector comprises a nucleic acid or nucleic acids encoding the duplex RNA molecule operably linked to at least one expression-control sequence. In some embodiments, the vector comprises a first nucleic acid encoding the first strand operably linked to a first expression-control sequence, and a second nucleic acid encoding the second strand operably linked to a second expression-control sequence. In another embodiment, the vector is a viral, eukaryotic, or bacterial expression vector. [0038] The present invention also provides a cell. In some embodiments, the cell comprises the vector. In another embodiment, the cell comprises the duplex RNA molecule. In a further embodiment, the cell is a mammalian, avian, or bacterial cell.
[0039] The modulating method can also be used for studying drug target in vitro or in vivo. The present invention provides a reagent comprising the duplex RNA molecule.
[0040] The present invention also provides a method of preparing a duplex RNA molecule of the disclosure comprising the steps of synthesizing the first strand and the second strand, and combining the synthesized strands under conditions, wherein the duplex RNA molecule is formed, which is capable of effecting K-Ras sequence-specific gene silencing. In some embodiments, the RNA strands are chemically synthesized, or biologically synthesized. In another embodiment, the first strand and the second strand are synthesized separately or simultaneously.
[0041] In some embodiments, the method further comprises a step of introducing at least one modified nucleotide or its analogue into the duplex RNA molecule during the synthesizing step, after the synthesizing and before the combining step, or after the combining step.
[0042] The present invention further provides a pharmaceutical composition. The pharmaceutical composition comprises as an active agent at least one duplex RNA molecule and one or more carriers selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a cholesterol, a lipid, and a lipoid.
[0043] Other features and advantages of the present invention are apparent from the additional descriptions provided herein including the different examples. The provided examples illustrate different components and methodology useful in practicing the present invention. The examples do not limit the claimed invention. Based on the present disclosure the skilled artisan can identify and employ other components and methodology useful for practicing the present invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0044] Figure 1(A) shows an in vitro study in which aiRNA ID NO: 21 ("aiK-Ras
#1") was used to target K-Ras Target SEQ ID NO: 22 to determine the IC50 for aiK-Ras #1.
[0045] Figure 1(B) shows an in vitro study in which aiRNA ID NO: 142 ("aiK-Ras
#2") was used to target K-Ras Target SEQ ID NO: 142 to determine the IC50 for aiK-Ras #2. [0046] Figure 2(A) shows detection of siRNA and aiR A loading to RISC by northern blot analysis.
[0047] Figure 2(B) shows detection of TLR3/aiRNA or siRNA binding.
[0048] Figure 2(C) shows that TLR3/RNA complexes were immunoprecipitated with anti-HA antibody.
[0049] Figure 3(A) shows colony formation assay in AGS and DLD1 transfected with aiK-Ras #1 or aiK-Ras #2.
[0050] Figure 3(B) shows western blot analysis of lysate from AGS and DLD1.
[0051] Figure 3(C) shows colony formation assay results in large cell panel.
[0052] Figure 4 shows western blot analysis of K-Ras and EGFR-RAS pathway molecules.
[0053] Figure 5(A) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel.
[0054] Figure 5(B) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel.
[0055] Figure 6(A) shows sternness gene expression in CSC culture.
[0056] Figure 6(B) shows the results of sphere formation assay in various cell lines.
[0057] Figure 6(C) shows depletion of CD44-high population in AGS and DLD1 cells with aiK-Ras #1 and aiK-Ras #2.
[0058] Figure 7(A) shows heat map of CSC-related genes in cancer cells transfected with aiK-Ras.
[0059] Figure 7(B) shows confirmation of down-regulated Notch signaling by western blot.
DETAILED DESCRIPTION OF THE INVENTION
[0060] The present invention relates to asymmetric duplex RNA molecules that are capable of effecting selective K-Ras gene silencing in a eukaryotic cell. In some embodiments, the duplex RNA molecule comprises a first strand and a second strand. The first strand is longer than the second strand. The second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand.
[0061] The protein K-Ras is a molecular switch that under normal conditions regulates cell growth and cell division. Mutations in this protein lead to the formation of tumors through continuous cell growth. About 30% of human cancers have a mutated Ras protein that is constitutively bound to GTP due to decreased GTPase activity and insensitivity to GAP action. Ras is also an important factor in many cancers in which it is not mutated but rather functionally activated through inappropriate activity of other signal transduction elements. Mutated K-Ras proteins are found in a large proportion of all tumor cells. K-Ras protein occupies a central position of interest. The identification of oncogenically mutated K- Ras in many human cancers led to major efforts to target this constitutively activated protein as a rational and selective treatment. Despite decades of active agent research, significant challenges still remain to develop therapeutic inhibitors of K-Ras.
[0062] The compositions and methods provided herein are useful in elucidating the function of K-Ras in the cancer development and maintenance. The compositions and methods use asymmetric interfering RNAs (aiRNAs) that are able to silence target genes with high potency leading to long-lasting knockdown, and reducing off-target effects, and investigated the dependency of K-Ras on cell survival in several types of human cancer cell lines. Much to our surprise, we found K-Ras plays a more significant role for gastric cancer maintenance compared to other types of cancer. aiRNA-induced silencing of K-Ras was found to inhibit the cell proliferation of gastric cancer cells and the ability of gastric cancer cells to form colonies compared to other cancer types. Accumulating evidence has revealed that cancer stem cells (CSCs) are highly associated with prognosis, metastasis, and recurrence. To investigate the effect of K-Ras on CSCs, we tested the K-Ras gene silencing effects on an in vitro CSC culturing system. As a result, K-Ras inhibition decreased the colonies derived from gastric CSCs and altered the gene expression patterns of several genes involved in "sternness" compared to other cancer types. The results of these studies suggest that gastric cancer and gastric CSCs are affected by the K-Ras oncogene and that Kras aiRNAs are promising therapeutic candidates for the treatment of gastric cancer. Accordingly, the disclosure provides compositions and methods for targeting K-Ras in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer. The disclosure also provides compositions and methods for targeting K-Ras to inhibit the survival and/or proliferation of CSCs, as well as compositions and methods for targeting K-Ras in the inhibition of to inhibit the survival and/or proliferation of CSCs in the treatment, prevention, delaying the progression of, or otherwise ameliorating a symptom of gastric cancer. In some embodiments, the method comprises administering to subject in need thereof a therapeutically effective amount of a duplex RNA molecule of the disclosure. In some embodiments, the subject is human. In some embodiments, the subject is suffering from gastric cancer. In some embodiments, the subject is diagnosed with gastric cancer. In some embodiments, the subject is predisposed to gastric cancer. [0063] In some embodiments, the duplex RNA molecule used in the compositions and methods of the disclosure has a 3'-overhang from 1-8 nucleotides and a 5'-overhang from 1 -8 nucleotides, a 3 '-overhang from 1-10 nucleotides and a blunt end, or a 5'- overhang from 1- 10 nucleotides and a blunt end. In another embodiment, the duplex RNA molecule has two 5'-overhangs from 1-8 nucleotides or two 3'-overhangs from 1- 10 nucleotides. In a further embodiment, the first strand has a 3 '-overhang from 1-8 nucleotides and a 5'-overhang from 1 -8 nucleotides. In an even further embodiment, the duplex RNA molecule is an isolated duplex RNA molecule.
[0064] In some embodiments, the first strand has a 3'-overhang from 1-10 nucleotides, and a 5'-overhang from 1-10 nucleotides or a 5'-blunt end. In another embodiment, the first strand has a 3 ^overhang from 1-10 nucleotides, and a 5 ^overhang from 1-10 nucleotides. In an alternative embodiment, the first strand has a 3 '-overhang from 1-10 nucleotides, and a 5 '-blunt end.
[0065] In some embodiments, the first strand has a length from 5-100 nucleotides, from 12-30 nucleotides, from 15-28 nucleotides, from 18-27 nucleotides, from 19-23 nucleotides, from 20-22 nucleotides, or 21 nucleotides.
[0066] In another embodiment, the second strand has a length from 3-30 nucleotides, from 12-26 nucleotides, from 13-20 nucleotides, from 14-23 nucleotides, 14 or 15 nucleotides.
[0067] In some embodiments, the first strand has a length from 5-100 nucleotides, and the second strand has a length from 3-30 nucleotides; or the first strand has a length from 10-30 nucleotides, and the second strand has a length from 3-29 nucleotides; or the first strand has a length from 12-30 nucleotides and the second strand has a length from 10-26 nucleotides; or the first strand has a length from 15-28 nucleotides and the second strand has a length from 12-26 nucleotides; or the first strand has a length from 19-27 nucleotides and the second strand has a length from 14-23 nucleotides; or the first strand has a length from 20-22 nucleotides and the second strand has a length from 14-15 nucleotides. In a further embodiment, the first strand has a length of 21 nucleotides and the second strand has a length of 13-20 nucleotides, 14-19 nucleotides, 14-17 nucleotides, 14 or 15 nucleotides.
[0068] In some embodiments, the first strand is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides longer than the second strand.
[0069] In some embodiments, the duplex RNA molecule further comprises 1 -10 unmatched or mismatched nucleotides. In a further embodiment, the unmatched or mismatched nucleotides are at or near the 3' recessed end. In an alternative embodiment, the unmatched or mismatched nucleotides are at or near the 5' recessed end. In an alternative embodiment, the unmatched or mismatched nucleotides are at the double- stranded region. In another embodiment, the unmatched or mismatched nucleotide sequence has a length from 1-5 nucleotides. In an even further embodiment, the unmatched or mismatched nucleotides form a loop structure.
[0070] In some embodiments, the first strand or the second strand contains at least one nick, or formed by two nucleotide fragments.
[0071] In some embodiments, the gene silencing is achieved through one or two, or all of RNA interference, modulation of translation, and DNA epigenetic modulations.
[0072] In some embodiments, the target K-Ras mRNA sequence to be silenced is a target sequence shown in Table 1.
[0073] In some embodiments, the RNA duplex molecule, also referred to herein as an asymmetrical interfering RNA molecule or aiRNA molecule, comprises a sense strand sequence, an antisense strand sequence or a combination of a sense strand sequence and antisense strand sequence selected from those shown in Table 2.
[0074] In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
[0075] In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence that is at least, e.g, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637. In some embodiments, the RNA duplex molecule (aiRNA) comprises an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955. In some embodiments, the RNA duplex molecule (aiRNA) comprises a sense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 320-637 and an antisense strand sequence that is at least, e.g., 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 638-955. [0076] As used in the specification and claims, the singular form "a", "an", and "the" include plural references unless the context clearly dictate otherwise. For example, the term "a cell" includes a plurality of cells including mixtures thereof.
[0077] As used herein, a "double stranded RNA," a "duplex RNA" or a "RNA duplex" refers to an RNA of two strands and with at least one double-stranded region, and includes RNA molecules that have at least one gap, nick, bulge, and/or bubble either within a double-stranded region or between two neighboring double-stranded regions. If one strand has a gap or a single-stranded region of unmatched nucleotides between two double-stranded regions, that strand is considered as having multiple fragments. A double- stranded RNA as used here can have terminal overhangs on either end or both ends.. In some embodiments, the two strands of the duplex RNA can be linked through certain chemical linker.
[0078] As used herein, an "antisense strand" refers to an RNA strand that has substantial sequence complementarity against a target messenger RNA.
[0079] The term "isolated" or "purified" as used herein refers to a material that is substantially or essentially free from components that normally accompany it in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography.
[0080] As used herein, "modulating" and its grammatical equivalents refer to either increasing or decreasing (e.g., silencing), in other words, either up-regulating or down- regulating. As used herein, "gene silencing" refers to reduction of gene expression, and may refer to a reduction of gene expression about, e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the targeted gene.
[0081] As used herein, the term "subject" refers to any animal (e.g., a mammal), including, but not limited to humans, non-human primates, rodents, and the like, which is to be the recipient of a particular treatment. Under some circumstances, the terms "subject" and "patient" are used interchangeably herein in reference to a human subject.
[0082] Terms such as "treating" or "treatment" or "to treat" or "alleviating" or "to alleviate" as used herein refer to both (1) therapeutic measures that cure, slow down, lessen symptoms of, and/or halt progression of a diagnosed pathologic condition or disorder and (2) prophylactic or preventative measures that prevent or slow the development of a targeted pathologic condition or disorder. Thus those in need of treatment include those already with the disorder; those prone to have the disorder; and those in whom the disorder is to be prevented. A subject is successfully "treated" according to the methods of the present invention if the patient shows one or more of the following: a reduction in the number of or complete absence of cancer cells; a reduction in the tumor size; inhibition of or an absence of cancer cell infiltration into peripheral organs including the spread of cancer into soft tissue and bone; inhibition of or an absence of tumor metastasis; inhibition or an absence of tumor growth; relief of one or more symptoms associated with the specific cancer; reduced morbidity and mortality; and improvement in quality of life.
[0083] As used herein, the terms "inhibiting", "to inhibit" and their grammatical equivalents, when used in the context of a bioactivity, refer to a down-regulation of the bioactivity, which may reduce or eliminate the targeted function, such as the production of a protein or the phosphorylation of a molecule. When used in the context of an organism (including a cell), the terms refer to a down-regulation of a bioactivity of the organism, which may reduce or eliminate a targeted function, such as the production of a protein or the phosphorylation of a molecule. In particular embodiments, inhibition may refer to a reduction of about, e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the targeted activity. When used in the context of a disorder or disease, the terms refer to success at preventing the onset of symptoms, alleviating symptoms, or eliminating the disease, condition or disorder.
[0084] As used herein, the term "substantially complementary" refers to complementarity in a base-paired, double-stranded region between two nucleic acids and not any single-stranded region such as a terminal overhang or a gap region between two double- stranded regions. The complementarity does not need to be perfect; there may be any number of base pair mismatches, for example, between the two nucleic acids. However, if the number of mismatches is so great that no hybridization can occur under even the least stringent hybridization conditions, the sequence is not a substantially complementary sequence. When two sequences are referred to as "substantially complementary" herein, it means that the sequences are sufficiently complementary to each other to hybridize under the selected reaction conditions. The relationship of nucleic acid complementarity and stringency of hybridization sufficient to achieve specificity is well known in the art. Two substantially complementary strands can be, for example, perfectly complementary or can contain from 1 to many mismatches so long as the hybridization conditions are sufficient to allow, for example discrimination between a pairing sequence and a non-pairing sequence. Accordingly, substantially complementary sequences can refer to sequences with base- pair complementarity of, e.g., 100%, 95%, 90%, 80%, 75%, 70%, 60%, 50% or less, or any number in between, in a double-stranded region. [0085] RNA interference (abbreviated as RNAi) is a cellular process for the targeted destruction of single-stranded RNA (ssRNA) induced by double-stranded RNA (dsRNA). The ssRNA is gene transcript such as a messenger RNA (mRNA). RNAi is a form of post-transcriptional gene silencing in which the dsRNA can specifically interfere with the expression of genes with sequences that are complementary to the dsRNA. The antisense RNA strand of the dsRNA targets a complementary gene transcript such as a messenger RNA (mRNA) for cleavage by a ribonuclease.
[0086] In RNAi process, long dsRNA is processed by a ribonuclease protein Dicer to short forms called small interfering RNA (siRNA). The siRNA is separated into guide (or antisense) strand and passenger (or sense) strand. The guide strand is integrated into RNA- induced-silencing-complex (RISC), which is a ribonuclease-containing multi-protein complex. The complex then specifically targets complementary gene transcripts for destruction.
[0087] RNAi has been shown to be a common cellular process in many eukaryotes.
RISC, as well as Dicer, is conserved across the eukaryotic domain. RNAi is believed to play a role in the immune response to virus and other foreign genetic material.
[0088] Small interfering RNAs (siRNAs) are a class of short double-stranded RNA
(dsRNA) molecules that play a variety of roles in biology. Most notably, it is involved in the RNA interference (RNAi) pathway where the siRNA interferes with the expression of a specific gene. In addition, siRNAs also play roles in the processes such as an antiviral mechanism or shaping the chromatin structure of a genome. In some embodiments, siRNA has a short (19-21 nt) double- strand RNA (dsRNA) region with 2-3 nucleotide 3' overhangs with 5 '-phosphate and 3'-hydroxyl termini.
[0089] Dicer is a member of RNase III ribonuclease family. Dicer cleaves long, double-stranded RNA (dsRNA), pre-microRNA (miRNA), and short hairpin RNA (shRNA) into short double-stranded RNA fragments called small interfering RNA (siRNA) about 20- 25 nucleotides long, usually with a two-base overhang on the 3' end. Dicer catalyzes the first step in the RNA interference pathway and initiates formation of the RNA-induced silencing complex (RISC), whose catalytic component argonaute is an endonuclease capable of degrading messenger RNA (mRNA) whose sequence is complementary to that of the siRNA guide strand.
[0090] As used herein, an effective siRNA sequence is a siRNA that is effective in triggering RNAi to degrade the transcripts of a target gene. Not every siRNA complementary to the target gene is effective in triggering RNAi to degrade the transcripts of the gene. Indeed, time-consuming screening is usually necessary to identify an effective siRNA sequence. In some embodiments, the effective siRNA sequence is capable of reducing the expression of the target gene by more than 90%, more than 80%, more than 70%, more than 60%, more than 50%, more than 40%, or more than 30%.
[0091] The present invention uses a structural scaffold called asymmetric interfering
RNA (aiRNA) that can be used to effect siRNA-like results, and also to modulate miRNA pathway activities, initially described in detail PCT Publications WO 2009/029688 and WO 2009/029690, the contents of which are hereby incorporated by reference in their entirety.
[0092] The structural design of aiRNA is not only functionally potent in effecting gene regulation, but also offers several advantages over the current state-of-art, RNAi regulators (mainly antisense, siRNA). Among the advantages, aiRNA can have RNA duplex structure of much shorter length than the current siRNA constructs, which should reduce the cost of synthesis and abrogate or reduce length-dependent triggering of nonspecific interferon-like immune responses from host cells. The shorter length of the passenger strand in aiRNA should also eliminate or reduce the passenger strand's unintended incorporation in RISC, and in turn, reduce off-target effects observed in miRNA-mediated gene silencing. AiRNA can be used in all areas that current miRNA-based technologies are being applied or contemplated to be applied, including biology research, R&D in biotechnology and pharmaceutical industries, and miRNA-based diagnostics and therapies.
[0093] In some embodiments, the first strand comprises a sequence being substantially complimentary to a target K-Ras mRNA sequence. In another embodiment, the second strand comprises a sequence being substantially complimentary to a target K-Ras mRNA sequence.
[0094] The present invention is pertinent to asymmetrical double stranded RNA molecules that are capable of effecting K-Ras gene silencing. In some embodiments, an RNA molecule of the present invention comprises a first strand and a second strand, wherein the second strand is substantially complementary, or partially complementary to the first strand, and the first strand and the second strand form at least one double-stranded region, wherein the first strand is longer than the second strand (length asymmetry). The RNA molecule of the present invention has at least one double-stranded region, and two ends independently selected from the group consisting of a 5 '-overhang, a 3'-overhang, and a blunt.
[0095] Any single-stranded region of the RNA molecule of the invention, including any terminal overhangs and gaps in between two double-stranded regions, can be stabilized against degradation, either through chemical modification or secondary structure. The RNA strands can have unmatched or imperfectly matched nucleotides. Each strand may have one or more nicks (a cut in the nucleic acid backbone), gaps (a fragmented strand with one or more missing nucleotides), and modified nucleotides or nucleotide analogues. Not only can any or all of the nucleotides in the RNA molecule chemically modified, each strand may be conjugated with one or more moieties to enhance its functionality, for example, with moieties such as one or more peptides, antibodies, antibody fragments, aptamers, polymers and so on.
[0096] In some embodiments, the first strand is at least 1 nt longer than the second strand. In a further embodiment, the first strand is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, or 20 nt longer than the second strand. In another embodiment, the first strand is 20-100 nt longer than the second strand. In a further embodiment, the first strand is 2-12 nt longer than the second strand. In an even further embodiment, the first strand is 3-10 nt longer than the second strand.
[0097] In some embodiments, the first strand, or the long strand, has a length of 5-100 nt, or preferably 10-30 or 12-30 nt, or more preferably 15-28 nt. In one embodiment, the first strand is 21 nucleotides in length. In some embodiments, the second strand, or the short strand, has a length of 3-30 nt, or preferably 3-29 nt or 10-26 nt, or more preferably 12-26 nt. In some embodiments, the second strand has a length of 15 nucleotides.
[0098] In some embodiments, the double-stranded region has a length of 3-98 basepairs (bp). In a further embodiment, the double-stranded region has a length of 5-28 bp. In an even further embodiment, the double-stranded region has a length of 10-19 bp. The length of the double-stranded region can be 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 bp.
[0099] In some embodiments, the double-stranded region of the RNA molecule does not contain any mismatch or bulge, and the two strands are perfectly complementary to each other in the double-stranded region. In another embodiment, the double-stranded region of the RNA molecule contains mismatch and/or bulge.
[00100] In some embodiments, the terminal overhang is 1-10 nucleotides. In a further embodiment, the terminal overhang is 1-8 nucleotides. In another embodiment, the terminal overhang is 3 nt.
[00101] The present invention also provides a method of modulating K-Ras gene expression in a cell or an organism (silencing method). The method comprises the steps of contacting said cell or organism with the duplex RNA molecule under conditions wherein selective K-Ras gene silencing can occur, and mediating a selective K-Ras gene silencing effected by the said duplex RNA molecule towards a target K-Ras nucleic acid having a sequence portion substantially corresponding to the double-stranded RNA.
[00102] In some embodiments, the contacting step comprises the step of introducing said duplex RNA molecule into a target cell in culture or in an organism in which the selective gene silencing can occur. In a further embodiment, the introducing step comprises transfection, lipofection, infection, electroporation, or other delivery technologies.
[00103] In some embodiments, the silencing method is used for determining the function or utility of a gene in a cell or an organism.
[00104] The silencing method can be used for modulating the expression of a gene in a cell or an organism. In some embodiments, the gene is associated with a disease, e.g., a human disease or an animal disease, a pathological condition, or an undesirable condition. In some embodiments, the disease is gastric cancer.
[00105] The RNA molecules of the present invention can be used for the treatment and or prevention of various diseases or undesirable conditions, including gastric cancer. In some embodiments, the present invention can be used as a cancer therapy or to prevent or to delay the progression of cancer. The RNA molecules of the present invention can he used to silence or knock down k-Ras, which is involved with cell proliferation or other cancer phenotypes.
[00106] The present invention provides a method to treat a disease or undesirable condition. The method comprises using the asymmetrical duplex RNA molecule to effect gene silencing of a gene associated with the disease or undesirable condition.
[00107] The present invention further provided a pharmaceutical composition. The pharmaceutical comprises (as an active agent) at least one asymmetrical duplex RNA molecule. In some embodiments, the pharmaceutical comprises one or more carriers selected from the group consisting of a pharmaceutical carrier, a positive-charge carrier, a liposome, a protein carrier, a polymer, a nanoparticle, a nanoemulsion, a lipid, and a lipoid. In some embodiments, the composition is for diagnostic applications. In some embodiments, the composition is for therapeutic applications.
[00108] The pharmaceutical compositions and formulations of the present invention can be the same or similar to the pharmaceutical compositions and formulations developed for siRNA, miRNA, and antisense RNA (see e.g., de Fougerolles et al, 2007, "Interfering with disease: a progress report on siRNA-based therapeutics." Nat Rev Drug Discov 6, 443453; Kim and Rossi, 2007, "Strategies for silencing human disease using RNA interference." Nature reviews 8, 173-184), except for the RNA ingredient. The siRNA, miRNA, and antisense RNA in the pharmaceutical compositions and formulations can be replaced by the duplex RNA molecules of the present disclosure. The pharmaceutical compositions and formulations can also be further modified to accommodate the duplex RNA molecules of the present disclosure.
[00109] A "pharmaceutically acceptable salt" or "salt" of the disclosed duplex RNA molecule is a product of the disclosed duplex RNA molecule that contains an ionic bond, and is typically produced by reacting the disclosed duplex RNA molecule with either an acid or a base, suitable for administering to a subject. Pharmaceutically acceptable salt can include, but is not limited to, acid addition salts including hydrochlorides, hydrobromides, phosphates, sulphates, hydrogen sulphates, alkylsulphonates, arylsulphonates, acetates, benzoates, citrates, maleates, fumarates, succinates, lactates, and tartrates; alkali metal cations such as Na, K, Li, alkali earth metal salts such as Mg or Ca, or organic amine salts.
[00110] A "pharmaceutical composition" is a formulation containing the disclosed duplex RNA molecules in a form suitable for administration to a subject. In one embodiment, the pharmaceutical composition is in bulk or in unit dosage form. The unit dosage form is any of a variety of forms, including, for example, a capsule, an IV bag, a tablet, a single pump on an aerosol inhaler, or a vial. The quantity of active ingredient (e.g., a formulation of the disclosed duplex RNA molecule or salts thereof) in a unit dose of composition is an effective amount and is varied according to the particular treatment involved. One skilled in the art will appreciate that it is sometimes necessary to make routine variations to the dosage depending on the age and condition of the patient. The dosage will also depend on the route of administration. A variety of routes are contemplated, including oral, pulmonary, rectal, parenteral, transdermal, subcutaneous, intravenous, intramuscular, intraperitoneal, intranasal, and the like. Dosage forms for the topical or transdermal administration of a duplex RNA molecule of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. In one embodiment, the active duplex RNA molecule is mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that are required.
[00111] The present invention provides a method of treatment comprising administering an effective amount of the pharmaceutical composition to a subject in need. In some embodiments, the pharmaceutical composition is administered via a route selected from the group consisting of iv, sc, topical, po, and ip. In another embodiment, the effective amount is 1 ng to 1 g per day, 100 ng to 1 g per day, or 1 ug to 1 mg per day. [00112] The present invention also provides pharmaceutical formulations comprising a duplex RNA molecule of the present invention in combination with at least one pharmaceutically acceptable excipient or carrier. As used herein, "pharmaceutically acceptable excipient" or "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Suitable carriers are described in "Remington: The Science and Practice of Pharmacy, Twentieth Edition," Lippincott Williams & Wilkins, Philadelphia, PA., which is incorporated herein by reference. Examples of such carriers or diluents include, but are not limited to, water, saline, Ringer's solutions, dextrose solution, and 5% human serum albumin. Liposomes and non-aqueous vehicles such as fixed oils may also be used. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active duplex RNA molecule, use thereof in the compositions is contemplated. Supplementary active duplex RNA molecules can also be incorporated into the compositions.
[00113] A duplex RNA molecule of the present invention is administered in a suitable dosage form prepared by combining a therapeutically effective amount (e.g., an efficacious level sufficient to achieve the desired therapeutic effect through inhibition of tumor growth, killing of tumor cells, treatment or prevention of cell proliferative disorders, etc.) of a duplex RNA molecule of the present invention (as an active ingredient) with standard pharmaceutical carriers or diluents according to conventional procedures (i.e., by producing a pharmaceutical composition of the invention). These procedures may involve mixing, granulating, compressing, or dissolving the ingredients as appropriate to attain the desired preparation. In another embodiment, a therapeutically effective amount of a duplex RNA molecule of the present invention is administered in a suitable dosage form without standard pharmaceutical carriers or diluents.
[00114] Pharmaceutically acceptable carriers include solid carriers such as lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like. Exemplary liquid carriers include syrup, peanut oil, olive oil, water and the like. Similarly, the carrier or diluent may include time-delay material known in the art, such as glyceryl monostearate or glyceryl distearate, alone or with a wax, ethylcellulose, hydroxypropylmethylcellulose, methylmethacrylate or the like. Other fillers, excipients, flavorants, and other additives such as are known in the art may also be included in a pharmaceutical composition according to this invention. [00115] The pharmaceutical compositions containing active duplex RNA molecules of the present invention may be manufactured in a manner that is generally known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. Pharmaceutical compositions may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and/or auxiliaries which facilitate processing of the active duplex RNA molecules into preparations that can be used pharmaceutically. Of course, the appropriate formulation is dependent upon the route of administration chosen.
[00116] A duplex RNA molecule or pharmaceutical composition of the invention can be administered to a subject in many of the well-known methods currently used for chemotherapeutic treatment. For example, for treatment of cancers, a duplex RNA molecule of the invention may be injected directly into tumors, injected into the blood stream or body cavities or taken orally or applied through the skin with patches. For treatment of psoriatic conditions, systemic administration (e.g., oral administration), or topical administration to affected areas of the skin, are preferred routes of administration. The dose chosen should be sufficient to constitute effective treatment but not as high as to cause unacceptable side effects. The state of the disease condition (e.g., gastric cancer) and the health of the patient should be closely monitored during and for a reasonable period after treatment.
EXAMPLES
[00117] Examples are provided below to further illustrate different features of the present invention. The examples also illustrate useful methodology for practicing the invention. These examples do not limit the claimed invention.
EXAMPLE 1 : In vitro potency of aiK-Ras
[00118] Figure 1(A) shows an in vitro study in which aiRNA ID NO: 21 ("aiK-Ras
#1") was used to target K-Ras Target SEQ ID NO: 22 to determine the IC5o for aiK-Ras #1. DLD1 cells (ATCC) were transfected with aiK-Ras #1. 48 hours after transfection, cells were collected and RNA was isolated. The IC50 of aiK-Ras #1 was determined by qPCR. Remaining mRNA was standardized to the GAPDH expression level. The IC50 of 3.1 pM indicates that aiK-Ras #1 silences K-Ras gene expression with high potency. [00119] Figure 1(B) shows an in vitro study in which aiRNA ID NO: 142 ("aiK-Ras
#2") was used to target K-Ras Target SEQ ID NO: 142 to determine the IC50 for aiK-Ras #2. DLD1 cells were transfected with aiK-Ras #2. 48 hours after transfection, cells were collected and RNA was isolated. The IC50 of aiK-Ras #2 was determined by qPCR. Remaining mRNA was standardized to the GAPDH expression level. The IC50 of 3.5 pM indicates that aiK-Ras #1 silences K-Ras gene expression with high potency.
EXAMPLE 2: Reduced off-target effect of aiK-Ras
[00120] Figure 2(A) shows detection of siRNA and aiRNA loading to RISC by northern blot analysis. To analyze small RNA RISC loading, HEK293 Flag-Ago2 stable cells were transfected with aiRNA or siRNA duplexes. Cells were lysed at the indicated time points and immunoprecipitated with Flag antibody (Sigma, Catalog # F1804). Immunoprecipitates were washed, RNA isolated from the complex by TRIZOL (Life Technologies, 15596-018) extraction, and loaded on 15% TBE-Urea PAGE or 15% TBE non-denaturing PAGE gels. Following electrophoreses, RNA was transferred to Hybonad-XL Nylon membrane. Then hybridizing the r-P32 labeled detect sense strand or anti-sense strand probe to RNA on the membrane. HEK293 cells (Invivogen, Catalog # 293-null) expressing Flag-Ago2 were transfected with siRNA or aiRNA, after which an immunoprecipitation assay was conducted. FLAG-Ago2 HEK 293 cells stably expressing FLAG-Ago2 cells were generated through transient transfection of FLAG-Ago2 neomycin plasmid DNA vectors. After selective neomycin containing medium culture, the monoclonal populations were selected by western blot. Non-denatured gel was used to detect dsRNA.
[00121] Figure 2(B) shows reduced off-target of aiRNA. HeLa cells were transfected with luciferase reporter genes fused with antisense or sense strand-based aiRNA or siRNA target sequences and aiK-Ras#2 or siK-Ras#2 (5 nM). Figure 2(C) shows that TLR3/RNA complexes were immunoprecipitated with anti-HA antibody (Invivogen, Catalog # ab-hatag). RNA was extracted from the pellet, and northern blot analysis was performed to determine the interaction between aiRNA/siRNA and the TLR3 receptor.
[00122] Figures 2(A)-(C) show that the asymmetric structure of aiK-Ras #1 and aiK-
Ras #2 reduced sense strand mediated off-target effect and LTR3 binding.
EXAMPLE 3: aiK-Ras sensitivity in K-Ras mutant cells
[00123] Figure 3(A) shows colony formation assay in AGS (ATCC) and DLD1 cells transfected with aiK-Ras #1 or aiK-Ras #2. Cells were transfected with 1 nM GFP aiRNA (control; GGTTATGTACAGGAACGCA (SEQ ID NO: 956)) or 1 nM aiK-Ras #1 or aiK- Ras #2 for 24 hours. Cells were then trypsinized and re-plated on 6-well plates at 500-2000 cells/well to determine the colony formation ability of the cells. After 11-14 days, colonies were stained with Giemsa stain and were counted. For the western blot analysis, cells were washed with ice-cold PBS and lysed in lysis buffer [50 mM Hepes (pH 7.5), 1% Nonidet P- 40, 150 mM NaCl, 1 mM EDTA, and 1 * Halt Protease Inhibitor Cocktail (Thermo Scientefic, Catalog # 87786)]. Soluble protein (10 μg) was separated by SDS/PAGE and transferred to PVDF membrane. Primary antibodies against were used in this study. The antigen-antibody complexes were visualized by enhanced chemiluminescence (BioRad, Catalog # 170-5060).
[00124] Figure 3(B) shows western blot analysis of lysate from AGS and DLD1, and the transfection effects of aiK-Ras #1 and aiK-Ras #2 on K-Ras expression, cleaved caspase 3, and cleaved PARP.
[00125] Figure 3(C) shows colony formation assay results in a large cell panel. All cell lines in the panel were obtained from ATCC. Cells harboring K-Ras mutant are highlighted.
EXAMPLE 4: Correlation between aiK-Ras sensitivity and K-Ras amplification
[00126] Figure 4 shows western blot analysis of K-Ras and EGFR-RAS pathway molecules. Lysate (10 μg/lane) was loaded and total and phosphorylated forms of EGFR, cRaf, MEK, and ERK were detected. Activated form of K-Ras (K-Ras GTP) was affinity- purified from cell lysate using GST-Raf-RBD and analyzed by western blotting with K-Ras antibody. The following antibodies were used for western blot: Actin (Sigma, Catalog # A5316) K-RAS (Santa Cruz, sc30 and Cell signaling, Catalog # 8955), Cleaved PARP (Cell Signaling, Catalog # 5625), Cleaved Caspase-3 (Cell Signaling, Catalog # 9664), Phospho- EGF Receptor (Cell Signaling, Catalog # 3777), EGF Receptor (Cell Signaling, Catalog # 4267), Phospho-c-Raf (Cell signaling, Catalog # 9427), c-Raf (Cell Signaling, Catalog # 9422), Phospho-MEKl/2 (Cell Signaling, Catalog # 9154), MEK1/2 (Cell Signaling, Catalog # 8727), Phospho-p44/42 MAPK (Erkl/2) (Cell Signaling, Catalog # 4370), p44/42 MAPK (Erkl/2) (Cell Signaling, Catalog # 4695), Jaggedl (Cell Signaling, Catalog # 2620), Notchl (Cell Signaling, Catalog # 3608), c-Myc (Cell Signaling, Catalog # 5605). RBD pulldown was performed using a Ras Activation Kit (Abeam, Catalog # ab 128504) according to the manufacturer's protocol. Precipitations were blotted for K-Ras (Santa Cruz, Catalog # sc30). Actin (Sigma, Catalog # A5316) was blotted as loading control. Figure 4 shows that aiK-Ras sensitivity correlates with K-Ras amplification, and not with the activation state of the Ras pathway molecules.
[00127] Figure 5(A) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel. All cell lines in the panel were obtained from ATCC. Copy number of K-Ras was analyzed by qPCR. Statistical difference was determined by two-sided Mann-Whitney's U test. Difference with p<0.05 was considered statistically significant.
[00128] Figure 5(B) shows that aiK-Ras sensitivity was correlated with K-Ras amplification in K-Ras mutant large cell panel. K-Ras protein expression level was measured by western blot. Band of western blot was quantified by Image Lab (Biorad). Statistical difference was determined by two-sided Mann- Whitney's U test. Difference with p<0.05 was considered statistically significant.
[00129] Figures 3(A)-(C) and 5(A)-(B) show that aiK-Ras sensitivity varies in K-Ras mutant cells and it correlates with K-Ras copy number.
EXAMPLE 6: Effect of aiK-Ras on CSC-like phenotvpe in sensitive cell lines
[00130] Figure 6(A) shows sternness gene expression in CSC culture. AGS cells were cultured in CSC medium [DMEM nutrient mixture F- 12 (DMEM/F- 12, Life technologies, Catalog # 1 1320-033) containing B-27 supplement (Life Technologies, Catalog # 17504- 044), 20 ng/mL EGF (R&D Systems, Catalog # 236-EG), 10 ng/mL FGF (R&D Systems, Catalog # 233-FB), and 1% penicillin/streptomycin] for 2 weeks. Nanog, Oct4, and Sox2 gene expression of CSC spheres was quantified by qPCR.
[00131] Figure 6(B) shows the results of sphere formation assay in various cell lines.
For the sphere formation assay, agarose coated plates were prepared to dispense autoclaved 0.5% agar and aspirated immediately. Transfected cells were trypsinized and counted, then diluted to 2000 cells/100 uL of 1 x CSC medium. 1.9 mL of warmed CSC medium including 0.33% agarose (Sigma type VII, Catalog # A-4018) was added to the cells in CSC medium for final agarose concentration of 0.3%. The plate was placed at 4°C for 10 minutes to cool. The plate was placed 10 minutes at room temperature and 1 mL of CSC medium was added to the top layer. The plate was incubated in a 37°C 15% CO2 incubator for 18-25 days. To count spheres, CSC medium was aspirated and Crystal violet (EMD, Catalog # 192- 12) solution in PBS were added and incubated for 1 hour at room temperature to stain spheres.
[00132] Cells were trypsinized and re-plated in CSC medium/3% soft agar onto agar coated 6-well plates at 2000 cells/well to determine the sphere formation ability of the cells. After 18-25 days, spheres were stained with crystal violet, and the number of spheres was counted.
[00133] Figure 6(C) shows depletion of CD44-high population in AGS and DLD1 cells with aiK-Ras #1 and aiK-Ras #2. CD44 expression was detected by flow cytometry, wherein AGS and DLD 1 cells were stained with PE conjugated anti-CD44 (BD Pharmingen, Catalog # 555479) in Stain Buffer (BD Pharmingen, Catalog # 554657) on ice for 45 minutes and washed once with Stain Buffer. CD44 positive population was detected with flow cytometry (Attune Acoustic Focusing Cytometer, Life technologies).
[00134] Figures 6(A)-(C) show that aiK-Ras according to the present invention modulate CSC-like phenotype in sensitive cell lines.
EXAMPLE 7: Effect of K-Ras knockdown on CSC-related gene expression patterns.
[00135] Figure 7(A) shows heat map of CSC-related genes in cancer cells transfected with aiK-Ras. Cells were transfected with 1 nM control aiRNA or aiK-Ras #1 for 48 hours. Real-time PCR was performed on total RNA using specific validated primers for 84 CSC- related genes with RT2 Profiler PCR array. The fold change in gene expression was calculated as the ratio between aiK-Ras #1 and the control aiRNA samples. Figure 7(B) shows confirmation of down-regulated Notch signaling by western blot. Table 3 below summarizes the genes down-regulated >3 fold with aiK-Ras #1 corresponding to the heat map as shown in Figure 7(A)
Table 3.
Figure imgf000044_0001
[00136] The embodiments illustrated and discussed in this specification are intended only to teach those skilled in the art the best way known to the inventors to make and use the invention. Nothing in this specification should be considered as limiting the scope of the present invention. All examples presented are representative and non-limiting. The above- described embodiments of the invention may be modified or varied, without departing from the invention, as appreciated by those skilled in the art in light of the above teachings. It is therefore to be understood that, within the scope of the claims and their equivalents, the invention may be practiced otherwise than as specifically described.

Claims

What is claimed is:
1. A method of treating cancer in a subject in need thereof, the method comprising administering to a subject in need thereof a duplex RNA molecule comprising (i) a first strand comprising a nucleotide sequence with a length from 18-23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and (ii) a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3'-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
2. A method of treating cancer in a selected patient population, the method comprising the steps of:
(a) measuring a level of mutant K-Ras gene amplification in a biological sample obtained from a patient candidate diagnosed of a cancer;
(b) confirming that the patient candidate's mutant K-Ras gene amplification level is above a benchmark level; and
(c) administering to the patient candidate a duplex RNA molecule comprising (i) a first strand comprising a nucleotide sequence with a length from 18-23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and (ii) a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3'-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
3. A method of treating cancer in a selected patient population, the method comprising the steps of:
(a) measuring an expression level of mutant K-Ras protein in a biological sample obtained from a patient candidate diagnosed of a cancer; (b) confirming that the patient candidate's mutant K-Ras protein expression level is above a benchmark level; and
(c) administering to the patient candidate a duplex RNA molecule comprising (i) a first strand comprising a nucleotide sequence with a length from 18-23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and (ii) a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3'-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
4. The method of any one of the preceding claims, wherein the cancer is gastric cancer, or the subject is suffering from or predisposed to gastric cancer.
5. The method of any one of the preceding claims, wherein the nucleotide sequence of the first strand comprises a sequence that is at least 70% complementary to the target K-Ras mRNA sequence.
6. The method of any one of the preceding claims, wherein the first strand has a length from 19-23 nucleotides.
7. The method of any one of the preceding claims, wherein the first strand has a length of 21 nucleotides.
8. The method of claim 7, wherein the second strand has a length of 14-16 nucleotides.
9. The method of claim 8, wherein the second strand has a length of 15 nucleotides.
10. The method of claim 9, wherein the first strand has a 3'-overhang of 2-4 nucleotides.
11. The method of claim 10, wherein the first strand has a 3 '-overhang of 3 nucleotides.
12. The method of any one of the preceding claims, wherein the duplex RNA molecule contains at least one modified nucleotide or its analogue.
13. The method of claim 12, wherein the at least one modified nucleotide or its analogue is sugar-, backbone-, and/or base- modified ribonucleotide.
14. The method of claim 13, wherein the backbone-modified ribonucleotide has a modification in a phosphodiester linkage with another ribonucleotide.
15. The method of any one of the preceding claims, wherein the first strand comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
16. The method of any one of claims 1-14, wherein the second strand comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637.
17. The method of any one of claims 1-14, wherein the first strand comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955 and the second strand comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637.
18. The method of any one of the preceding claims, wherein the subject is human.
19. A duplex RNA molecule comprising (i) a first strand comprising a nucleotide sequence with a length from 18-23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and (ii) a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3 '-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
20. The duplex RNA molecule of claim 19, wherein the nucleotide sequence of the first strand comprises a sequence that is at least 70% complementary to the target K-Ras mRNA sequence.
21. The duplex RNA molecule of claim 19 or claim 20, wherein the first strand has a length from 19-23 nucleotides.
22. The duplex RNA molecule of any one of claims 19-21, wherein the first strand has a length of 21 nucleotides.
23. The duplex RNA molecule of claim 22, wherein the second strand has a length of 14- 16 nucleotides.
24. The duplex RNA molecule of claim 23, wherein the second strand has a length of 15 nucleotides.
25. The duplex RNA molecule of claim 24, wherein the first strand has a 3'-overhang of 2-4 nucleotides.
26. The duplex RNA molecule of claim 25, wherein the first strand has a 3 '-overhang of 3 nucleotides.
27. The duplex RNA molecule of any one of claims 19-26, wherein the duplex RNA molecule contains at least one modified nucleotide or its analogue.
28. The duplex RNA molecule of claim 27, wherein the at least one modified nucleotide or its analogue is sugar-, backbone-, and/or base- modified ribonucleotide.
29. The duplex RNA molecule of claim 28, wherein the backbone-modified ribonucleotide has a modification in a phosphodiester linkage with another ribonucleotide.
30. The duplex RNA molecule of any one of claims 19-29, wherein the first strand comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955.
31. The duplex RNA molecule of any one of claims 19-29, wherein the second strand comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320- 637.
32. The duplex RNA molecule of any one of claims 19-29, wherein the first strand comprises an antisense strand sequence selected from the group consisting of SEQ ID NOs: 638-955 and the second strand comprises a sense strand sequence selected from the group consisting of SEQ ID NOs: 320-637.
33. A method of treating cancer in a subject in need thereof, comprising inhibiting K-Ras gene expression or K-Ras activity in said subject.
34. A method of inhibiting the survival and/or proliferation of cancer stem cells (CSCs) in a subject in need thereof, comprising inhibiting K-Ras gene expression or K-Ras activity in said subject.
35. The method of claim 34, wherein inhibiting K-Ras gene expression or K-Ras activity comprises administering to a subject in need thereof a duplex RNA molecule comprising (i) a first strand comprising a nucleotide sequence with a length from 18-23 nucleotides, wherein the nucleotide sequence of the first strand is substantially complementary to a target K-Ras mRNA sequence, and (ii) a second strand comprising a nucleotide sequence with a length from 12-17 nucleotides, wherein the second strand is substantially complementary to the first strand, and forms a double-stranded region with the first strand, wherein the first strand has a 3'-overhang from 1-9 nucleotides, and a 5'-overhang from 0-8 nucleotides, and wherein said duplex RNA molecule is capable of effecting selective K-Ras gene silencing.
PCT/US2015/020776 2014-03-14 2015-03-16 Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof WO2015139044A1 (en)

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CN201580012331.XA CN107428794A (en) 2014-03-14 2015-03-16 Silence K RAS asymmetric aiRNA composition and its application method
JP2016549041A JP2017511302A (en) 2014-03-14 2015-03-16 Asymmetric interfering RNA compositions for silencing K-Ras and methods of use thereof
US15/125,655 US20170016001A1 (en) 2014-03-14 2015-03-16 Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof
KR1020167020509A KR20160130986A (en) 2014-03-14 2015-03-16 Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof
RU2016131028A RU2016131028A (en) 2014-03-14 2015-03-16 COMPOSITIONS CONTAINING ASYMMETRIC INTERFERING RNA WHICH ARE K-RAS SILENCED AND WAYS OF APPLICATION
EP15761005.6A EP3116890A4 (en) 2014-03-14 2015-03-16 Asymmetric interfering rna compositions that silence k-ras and methods of uses thereof
AU2015229033A AU2015229033A1 (en) 2014-03-14 2015-03-16 Asymmetric interfering RNA compositions that silence K-Ras and methods of uses thereof
BR112016017680A BR112016017680A2 (en) 2014-03-14 2015-03-16 asymmetric interference mRNA compositions that silence k-ras and methods of using them
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