EP2094848A2 - Mir-143 regulated genes and pathways as targets for therapeutic intervention - Google Patents

Mir-143 regulated genes and pathways as targets for therapeutic intervention

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Publication number
EP2094848A2
EP2094848A2 EP07842750A EP07842750A EP2094848A2 EP 2094848 A2 EP2094848 A2 EP 2094848A2 EP 07842750 A EP07842750 A EP 07842750A EP 07842750 A EP07842750 A EP 07842750A EP 2094848 A2 EP2094848 A2 EP 2094848A2
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EP
European Patent Office
Prior art keywords
mirna
cell
mir
carcinoma
nucleic acid
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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Application number
EP07842750A
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German (de)
French (fr)
Inventor
Andreas G. Bader
Mike Byrom
Charles D. Johnson
David Brown
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Asuragen Inc
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Asuragen Inc
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Publication date
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Publication of EP2094848A2 publication Critical patent/EP2094848A2/en
Withdrawn legal-status Critical Current

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Definitions

  • the present invention relates to the fields of molecular biology and medicine
  • the invention relates to methods and compositions for the treatment of diseases or conditions that are affected by miR-143 microRNAs, micro RN A expression, and genes and cellular pathways directly and indirectly modulated by such II.
  • miRNAs are distinct miRNAs thus far observed have been approximately 21-22 nucleotides in length, and they arise from longer precursors transcribed from non-protem-encodmg genes See review of Carrington et al (2003) The precursors form structures that fold back on themselves in self-complementary regions, they are then processed by the nuclease Dicer (in animals) or DCLl (in plants) to generate the short double- stranded miRNA
  • One of the miRNA strands is incorporated into a complex of proteins and miRNA called
  • hsa-miR-143 is involved with the regulation of numerous cell activities that represent intervention points for cancer therapy and for therapy of other diseases and disorders (U S Patent Applications serial number 11/141,707 filed May 31, 2005 and se ⁇ al number 11/273,640 filed November 14, 2005)
  • hsa-miR-143 was found to be preferentially expressed in human prostate and colon tissue samples
  • the inventors observed that hsa-miR-143 expression is lower in many human cancer tumor samples including lung, colon, breast, bladder, and thyroid tumors, than in normal cells from the same patients
  • Overexpression of hsa-miR-143 in human leukemia cells (Jurkat) increased proliferation of those cells
  • the inventors also found hsa-miR-143 to be up-regulated in bram tissues of Alzheimer's patients
  • miR-143 is down-regulated in colorectal tumors when compared with matched normal samples (Michael et al 2003, Akao
  • Bioinformatics analyses suggest that any given miRNA may bind to and alter the expression of up to several hundred different genes
  • a single gene may be regulated by several miRNAs
  • each miRNA may regulate a complex interaction among genes, gene pathways, and gene networks Mis-regulation or alteration of these regulatory pathways and networks, involving miRNAs, are likely to contribute to the development of disorders and diseases such as cancer
  • bioinformatics tools are helpful in predicting miRNA binding targets, all have limitations Because of the imperfect complementarity with their target binding sites, it is difficult to accurately predict the mRNA targets of miRNAs with biomformatics tools alone
  • the complicated interactive regulatory networks among miRNAs and target genes make it difficult to accurately predict which genes will actually be mis-regulated in response to a given miRNA
  • compositions of the invention are administered to a subject having, suspected of having, or at ⁇ sk of developing a metabolic, an immunologic, an infectious, a cardiovascular, a digestive, an endoc ⁇ ne, an ocular, a genitourinary, a blood, a musculoskeletal, a nervous system, a congenital, a respiratory, a skin, or a cancerous disease or condition
  • a subject or patient may be selected for treatment based on expression and/or aberrant expression of one or more miRNA or mRNA
  • a subject or patient may be selected for treatment based on aberrations in one
  • an infectious disease or condition includes a bacterial, viral, parasite, or fungal infection
  • Cancerous conditions include, but are not limited to astrocytoma, acute myelogenous leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gast ⁇ c carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, lung carcinoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, urothelial carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck,
  • the present invention provides methods and compositions for identifying genes that are direct targets for miR-143 regulation or that are downstream targets of regulation following the miR-143-mediated modification of upstream gene expression Furthermore, the invention descnbes gene pathways and networks that are influenced by miR-143 expression in biological samples Many of these genes and pathways are associated with various cancers and other diseases The altered expression or function of miR-143 in cells would lead to changes in the expression of these key genes and contribute to the development of disease Introducing miR-143 (for diseases where the miRNA is down-regulated) or a miR-143 inhibitor (for diseases where the miRNA is up-regulated) into disease cells or tissues would result in a therapeutic response.
  • miR-143 for diseases where the miRNA is down-regulated
  • a miR-143 inhibitor for diseases where the miRNA is up-regulated
  • a cell may be an epithelial, stromal, or mucosal cell
  • the cell can be, but is not limited to bram, a neuronal, a blood, an esophage
  • a cell, tissue, or subject may be a cancer cell, a cancerous tissue, harbor cancerous tissue, or be a subject or patient diagnosed or at nsk of developing a disease or condition
  • a cancer cell is a neuronal, glial, lung, liver, bram, breast, bladder, blood, leukemic, colon, endomet ⁇ al, stomach, skin, ovarian, fat, bone, cervical, esophageal, pancreatic, prostate, kidney, or thyroid cell
  • cancer includes, but is not limited to astrocytoma, acute myelogenous leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma,
  • Embodiments of the invention include methods of modulating gene expression, or biologic or physiologic pathways in a cell, a tissue, or a subject composing administering to the cell, tissue, or subject an amount of an isolated nucleic acid or mimetic thereof comp ⁇ sing a miR-143 nucleic acid, mimetic, or inhibitor in an amount sufficient to modulate the expression of a gene positively or negatively modulated by a miR-143 miRNA
  • a "miR-143 nucleic acid sequence” or “miR-143 inhibitor” includes the full length precursor of miR-143, or complement thereof, as well as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more nucleotides of a precursor miRNA or its processed sequence, or complement thereof, including all ranges and integers there between.
  • the miR-143 nucleic acid sequence or miR-143 inhibitor contains the full-length processed miRNA sequence or complement thereof and is referred to as the "miR-143 full-length processed nucleic acid sequence" or "miR-143 full-length processed inhibitor sequence.”
  • the miR-143 nucleic acid composes at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
  • miR-143 includes all members of the miR-143 family that share at least part of a mature miR- 143 sequence (UGAGAUGAAGCACUGUAGCUCA (SEQ ID NO:1)) or a
  • a "miR-143 nucleic acid sequence” includes the full length precursor of miR- 143 and other family members that include lla-mir-143 (MI0002552) GCGCAGCGCCCUGUC UCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGA
  • a nucleic acid or mimetic of the present invention will comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more nucleotides of the precursor miRNA or its processed sequence, including all ranges and integers there between.
  • the miR-143 nucleic acid sequence contains the full-length processed miRNA sequence and is referred to as the "miR-143 full-length processed nucleic acid sequence.”
  • a miR-143 comprises at least one 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 50 nucleotide (including all ranges and integers there between) segment of miR-143 that is at least 75, 80, 85, 90, 95, 98, 99 or 100% identical to SEQ ID NOs provided herein.
  • a miR-143 or miR-143 inhibitor containing nucleic acid is hsa-miR-143 or hsa-miR-143 inhibitor, or a variation thereof
  • a miR-143 nucleic acid or miR-143 inhibitor can be administered with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more miRNAs or miRNA inhibitors miRNA or its complement can be administer concurrently, in sequence or in an ordered progression
  • a miR-143 or miR-143 inhibitor can be administered in combination with one or more of let-7, miR-15a, miR-16, miR-20, miR-21, miR-26a, miR-31, miR-34a, miR-126, miR-145, miR-147, miR-188, miR-200b, miR-200c, miR-215, miR-216, miR-292-3p, and/or miR-331 All or combinations of miRNAs or inhibotrs thereof may be administered in a
  • the miR-143 nucleic acid or miR-143 inhibitor is a synthetic nucleic acid
  • nucleic acids of the invention may be fully or partially synthetic
  • a nucleic acid of the invention or a DNA encoding such can be administered at 0 001, 0 01, 0 1, 1, 10, 20, 30, 40, 50, 100, 200,
  • nucleic acids of the invention can be administered at 0 001, 0 01, 0 1, 1, 10, 20, 30, 40, 50, 100, to 200 ⁇ g or mg per kilogram (kg) of body weight
  • Each of the amounts descnbed herein may be administered over a pe ⁇ od of time, including 0 5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, minutes, hours, days, weeks, months or years, including all values and ranges there between
  • composition(s) can be enteral or parenteral
  • enteral administration is oral
  • parenteral administration is mtralesional, intravascular, intracranial, intrapleural, intratumoral, intraperitoneal, intramuscular, lntralymphatic, mtraglandular, subcutaneous, topical, lntrabronchial, intratracheal, intranasal, inhaled, or instilled
  • Compositions of the invention may be administered regionally or locally and not necessa ⁇ ly directly into a lesion
  • the gene or genes modulated comprises 1, 2, 3, 4, 5, 6, 7, 8,
  • the gene or genes modulated may exclude 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200 or more genes or combinations of genes identified m Tables 1, 3, 4, and/or 5
  • Modulation includes modulating transc ⁇ ption, mRNA levels, mRNA translation, and/or protein levels in a cell, tissue, or organ
  • the expression of a gene or level of a gene product, such as mRNA or encoded protein is down-regulated or up-regulated
  • the gene modulated comprises or is selected from (and may even exclude) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 27, 28, or all of the genes identified in Tables 1, 3, 4, and/or 5, or any combinations thereof
  • a gene modulated or selected comprises or is selected from (and may even exclude) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 27, 28, or all of the genes identified in Tables 1, 3, 4, and
  • a further embodiment of the invention is directed to methods of modulating a cellular pathway comprising administering to the cell an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence or a miR-143 inhibitor
  • a cell, tissue, or subject may be a cancer cell, a cancerous tissue or harbor cancerous tissue, or a cancer patient
  • the database content related to all nucleic acids and genes designated by an accession number or a database submission are incorporated herein by reference as of the filing date of this application
  • a further embodiment of the invention is directed to methods of modulating a cellular pathway comprising administering to the cell an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence m an amount sufficient to modulate the expression, function, status, or state of a cellular pathway, in particular those pathways desc ⁇ bed m Table 2 or the pathways known to include one or more genes from Table 1, 3, 4, and/or 5
  • Modulation of a cellular pathway includes, but is not limited to modulating the expression of one or more gene(s)
  • Modulation of a gene can include inhibiting the function of an endogenous miRNA or providing a functional miRNA to a cell, tissue, or subject Modulation refers to the expression levels or activities of a gene or its related gene product (e g , mRNA) or protein, e g , the mRNA levels may be modulated or the translation of an mRNA may be modulated Modulation may increase or up regulate a gene or gene product or it may decrease or down regulate a gene or gene product (
  • Still a further embodiment includes methods of administering an miRNA or mimic thereof, and/or treating a subject or patient having, suspected of having, or at ⁇ sk of developing a pathological condition comp ⁇ sing one or more of step (a) administering to a patient or subject an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence or a miR-143 inhibitor in an amount sufficient to modulate expression of a cellular pathway, and (b) administering a second therapy, wherein the modulation of the cellular pathway sensitizes the patient or subject, or increases the efficacy of a second therapy
  • An increase in efficacy can include a reduction in toxicity, a reduced dosage or duration of the second therapy, or an additive or synergistic effect
  • a cellular pathway may include, but is not limited to one or more pathway descnbed in Table 2 below or a pathway that is know to include one or more genes of Tables 1, 3, 4, and/or 5
  • the second therapy may be administered before, du ⁇ ng, and/or
  • a second therapy can include administration of a second miRNA or therapeutic nucleic acid such as a siRNA or antisense oligonucleotide, or may include various standard therapies, such as pharmaceuticals, chemotherapy, radiation therapy, drug therapy, immunotherapy, and the like Embodiments of the invention may also include the determination or assessment of gene expression or gene expression profile for the selection of an approp ⁇ ate therapy
  • a second therapy is a chemotherapy
  • a chemotherapy can include, but is not limited to pachtaxel, cisplatm, carboplatm, doxorubicin, oxahplatin, larotaxel, taxol, lapatmib, docetaxel, methotrexate, capecitabine, vinorelbine, cyclophosphamide, gemcitabine, amrubicin, cytarabme, etoposide, camptothecin, dexamethasone, dasatimb, tipifarnib, bevacizumab, siroh
  • RNA is used according to its ordinary and plain meaning and refers to a microRNA molecule found in eukaryotes that is involved in RNA-based gene regulation See, e g , Car ⁇ ngton et al , 2003, which is hereby incorporated by reference
  • the term can be used to refer to the single-stranded RNA molecule processed from a precursor or in certain instances the precursor itself
  • methods include assaying a cell or a sample containing a cell for the presence of one or more marker gene or mRNA or other analyte indicative of the expression level of a gene of interest Consequently, in some embodiments, methods include a step of generating an RNA profile for a sample
  • RNA profile or "gene expression profile” refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample (eg , a plurality of nucleic acid probes that identify one or more markers from Tables 1, 3, 4, and/or 5), it is contemplated that the nucleic acid profile can be obtained using a set of RNAs, using for example nucleic acid amplification or hybridization techniques well know to one of ordinary skill in the art The difference in the expression profile m the sample from
  • miR-143 or a miR-143 inhibitor and let-7 can be administered to patients with acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gast ⁇ c carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, melanoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma
  • Further aspects include administering miR-143 or a miR-143 inhibitor and miR-15 to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endomet ⁇ al carcinoma, glioma, glio
  • miR-143 or a miR-143 inhibitor and miR-16 are administered to patients with astrocytoma, breast carcinoma, bladder carcinoma, colorectal carcinoma, endometrial carcinoma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, non-small cell lung carcinoma, ova ⁇ an carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
  • aspects of the invention include methods where miR-143 or a miR-143 inhibitor and miR-20 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, melanoma, mantle
  • miR-143 or a miR-143 inhibitor and miR-21 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, multiple myeloma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
  • miR-143 or a miR-143 inhibitor and miR-26a are administered to patients with acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, melanoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, or prostate carcinoma
  • miR-143 or a miR-143 inhibitor and miR-34a are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, multiple myeloma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovanan carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma
  • miR-143 or a miR-143 inhibitor and miR-126 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
  • miR-143 or a miR-143 inhibitor and miR-147 are administered to patients with astrocytoma, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometnal carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gast ⁇ c carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, non-Hodgkm lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
  • miR-143 or a miR-143 inhibitor and miR-188 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma,
  • miR-143 or a miR-143 inhibitor and miR-215 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometnal carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovanan carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma
  • miR-143 or a miR-143 inhibitor and miR-216 are administered to patients with astrocytoma,
  • miR-143 or a miR-143 inhibitor and miR-292-3p are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, lipoma, melanoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma
  • miR-143 or a miR-143 inhibitor and miR-331 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorec
  • miR-143 or a miR-143 inhibitor and miR-200b/c are administered to patients with breast carcinoma, cervical carcinoma, colorectal carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, lipoma, multiple myeloma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
  • miRNA-143 or a miR-143 inhibitor when given in combination with one or more other miRNA molecules, the two different miRNAs or inhibitors may be given at the same time or sequentially
  • therapy proceeds with one miRNA or inhibitor and that therapy is followed up with therapy with the other miRNA or inhibitor 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 minutes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, 1, 2, 3, 4, 5, 6, 7 days, 1, 2, 3, 4, 5 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months or any such combination later
  • RNA is used according to its ordinary and plain meaning and refers to a microRNA molecule found in eukaryotes that is involved m RNA-based gene regulation See, e g , Car ⁇ ngton et al , 2003, which is hereby incorporated by reference The term can be used to refer to the smgle-stranded RNA molecule processed from a precursor or in certain instances the precursor itself or a mimetic thereof
  • methods include assaying a cell or a sample containing a cell for the presence of one or more miRNA marker gene or mRNA or other analyte indicative of the expression level of a gene of interest Consequently, in some embodiments, methods include a step of generating an RNA profile for a sample
  • RNA profile or "gene expression profile” refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample (e g , a plurality of nucleic acid probes that identify one or more markers or genes from Tables 1, 3, 4, and/or 5), it is contemplated that the nucleic acid profile can be obtained using a set of RNAs, using for example nucleic acid amplification or hybridization techniques well know to one of ordinary skill in the art The difference in the expression profile
  • Certain embodiments of the invention are directed to compositions and methods for assessing, prognosing, or treating a pathological condition in a patient comprising measuring or determining an expression profile of one or more miRNA or marker(s) in a sample from the patient, wherein a difference in the expression profile in the sample from the patient and an expression profile of a normal sample or reference expression profile is indicative of pathological condition and particularly cancer (e g ,
  • the miRNAs, cellular pathway, gene, or genetic marker is or is representative of one or more pathway or marker described in Table 1, 2, 3, 4, and/or 5, including any combination thereof
  • aspects of the invention include diagnosing, assessing, or treating a pathologic condition or preventing a pathologic condition from manifesting
  • the methods can be used to screen for a pathological condition, assess prognosis of a pathological condition, stage a pathological condition, assess response of a pathological condition to therapy, or to modulate the expression of a gene, genes, or related pathway as a first therapy or to render a
  • hsa-miR-143 targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miR hsa-miR-143 for Ref Seq ID reference - Pruitt et al , 2005
  • hsa-miR-143 whose mRNA expression levels are affected by hsa-miR-143 represent particularly useful candidates for cancer therapy and therapy of other diseases through manipulation of their expression levels
  • Certain embodiments of the invention include determining expression of one or more marker, gene, or nucleic acid segment representative of one or more genes, by using an amplification assay, a hybridization assay, or protein assay, a variety of which are well known to one of ordinary skill in the art
  • an amplification assay can be a quantitative amplification assay, such as quantitative RT- PCR or the like
  • a hybridization assay can include array hybridization assays or solution hybridization assays
  • the nucleic acids from a sample may be labeled from the sample and/or hybridizing the labeled nucleic acid to one or more nucleic acid probes
  • Nucleic acids, mRNA, and/or nucleic acid probes may be coupled to a support Such supports are well known to those of ordinary skill
  • kits for assessment of a pathological condition or the ⁇ sk of developing a pathological condition in a patient by nucleic acid profiling of a sample comprising, in suitable container means, two or more nucleic acid hybridization or amplification reagents
  • the kit can comp ⁇ se reagents for labeling nucleic acids in a sample and/or nucleic acid hybridization reagents
  • the hybridization reagents typically comprise hybridization probes
  • Amplification reagents include, but are not limited to amplification primers, reagents, and enzymes
  • an expression profile is generated by steps that include (a) labeling nucleic acid in the sample, (b) hybridizing the nucleic acid to a number of probes, or amplifying a number of nucleic acids, and (c) determining and/or quantitatmg nucleic acid hybridization to the probes or detecting and quantitatmg amplification products, wherein an expression profile is generated See U S Provisional Patent Application 60/575,743 and the U S Provisional Patent Application 60/649,584, and U S Patent Application Serial No 11/141,707 and U S Patent Application Senal No 11/273,640, all of which are hereby incorporated by reference
  • Methods of the invention involve diagnosing and/or assessing the prognosis of a patient based on a miRNA and/or a marker nucleic acid expression profile
  • the elevation or reduction in the level of expression of a particular gene or genetic pathway or set of nucleic acids in a cell is correlated with a disease state or pathological
  • AC astrocytoma
  • ALCL anaplastic large cell lymphoma, ALL, acute lymphoblastic leukemia, AML, acute myelogenous leukemia, BC, breast carcinoma, BCL, B-cell lymphoma, BIdC, bladder carcinoma, CeC, cervical carcinoma, CLL, chronic lymphoblastic leukemia, CRC, colorectal carcinoma, EC, endometrial carcinoma, G, glioma, GB, glioblastoma, GC, gast ⁇ c carcinoma, HCC, hepatocellular carcinoma, HL, Hodgkin lymphoma, L, leukemia, LC, lung carcinoma, M, melanoma, MB, medulloblastoma, MCL, mantle cell lymphoma, MM, multiple myeloma, My, myeloma, NHL, non-Hodgkin lymphoma, NSCLC, non-small cell lung carcinoma, OC, ovarian carcinoma
  • the methods can further comprise one or more of the steps including (a) obtaining a sample from the patient, (b) isolating nucleic acids from the sample, (c) labeling the nucleic acids isolated from the sample, and (d) hybridizing the labeled nucleic acids to one or more probes
  • Nucleic acids of the invention include one or more nucleic acid comprising at least one segment having a sequence or complementary sequence of to a nucleic acid representative of one or more of genes or markers in Table 1, 3, 4, and/or 5
  • any method or composition descnbed herein can be implemented with respect to any other method or composition descnbed herein and that different embodiments may be combined It is specifically contemplated that any methods and compositions discussed herein with respect to miRNA molecules, miRNA, genes, and nucleic acids representative of genes may be implemented with respect to synthetic nucleic acids In some embodiments the synthetic nucleic acid is exposed to the proper conditions to allow it to become a processed or mature nucleic acid, such as a miRNA under physiological circumstances.
  • any embodiment of the invention involving specific genes (including representative fragments there of), mRNA, or miRNAs by name is contemplated also to cover embodiments involving miRNAs whose sequences are at least 80, 81, 82, 83, 84, 85,
  • a genenc description of a gene or marker thereof, or of an miRNA refers to any of its gene family members (distinguished by a number) or representative fragments thereof, unless otherwise indicated
  • a “gene family” refers to a group of genes having the same coding sequence or miRNA coding sequence
  • miRNA members of a gene family are identified by a number following the initial designation
  • miR-16-1 and miR-16-2 are members of the miR-16 gene family and "mir-7" refers to miR-7-1, miR-7-2 and miR-7-3
  • a shorthand notation refers to related miRNAs (distinguished by a letter) Exceptions to these shorthand notations will be otherwise identified
  • Other embodiments of the invention are discussed throughout this application Any embodiment discussed with respect to one aspect of the invention applies to other aspects of the invention as well and vice versa The embodiments in the Example and Detailed
  • the words “comprising” (and any form of composing, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), "including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps
  • the present invention is directed to compositions and methods relating to the identification and characterization of genes and biological pathways related to these genes as represented by the expression of the identified genes, as well as use of miRNAs related to such, for therapeutic, prognostic, and diagnostic applications, particularly those methods and compositions related to assessing and/or identifying pathological conditions directly or indirectly related to miR-143 expression or the aberrant expression thereof
  • the invention is directed to methods for the assessment, analysis, and/or therapy of a cell or subject where certain genes have a reduced or increased expression (relative to normal) as a result of an increased or decreased expression of any one or a combination of miR-143 family members (including, but not limited to Ua-mir-143 MI0002552, xtr-mir-143 MI0004937, dre-mir-143-2 MI0002008, rno-mir-143 MI0000916, ptr-mir-143 MI0002549, ppy-mir-143 MI0002551 , ggo-mir-143 MI0002550, dre-mir-143-1 MI0002007, hsa-mir-143 MI0000459, ppa-mir-143 MI0002553, mdo-rmr-143 MI0005302, and mmu-mir-143 MI0000257) and/or genes with an increased expression (relative to normal) as a result of decreased expression thereof
  • miR-143 family members including, but not limited to Ua
  • Prognostic assays featuring any one or combination of the miRNAs listed or the markers listed could be used in assessment of a patient to determine what if any treatment regimen is justified
  • the absolute values that define low expression will depend on the platform used to measure the miRNA(s)
  • the same methods desc ⁇ bed for the diagnostic assays could be used for prognostic assays I. THERAPEUTIC METHODS
  • nucleic acids that perform the activities of or inhibit endogenous miRNAs when introduced into cells
  • nucleic acids are synthetic or non-synthetic miRNA Sequence-specific miRNA inhibitors can be used to inhibit sequentially or in combination the activities of one or more endogenous miRNAs in cells, as well those genes and associated pathways modulated by the endogenous miRNA
  • the present invention concerns, in some embodiments, short nucleic acid molecules that function as miRNAs or as inhibitors of miRNA in a cell
  • short refers to a length of a single polynucleotide that is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 50, 100, or 150 nucleotides or fewer, including all integers or ranges de ⁇ vable there between
  • the nucleic acid molecules are typically synthetic
  • synthetic refers to a nucleic acid molecule that is not produced naturally in a cell In certain aspects the chemical structure deviates from a naturally-occurring nucleic acid molecule,
  • miRNA or a synthetic miRNA having a length of between 17 and 130 residues
  • the present invention concerns miRNA or synthetic miRNA molecules that are, are at least, or are at most 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,
  • synthetic miRNA have (a) a "miRNA region” whose sequence or binding region from 5' to 3' is identical or complementary to all or a segment of a mature miRNA sequence, and (b) a "complementary region” whose sequence from 5' to 3' is between 60% and 100% complementary to the miRNA sequence in (a) In certain embodiments, these synthetic miRNA are also isolated, as defined above
  • miRNA region refers to a region on the synthetic miRNA that is at least 75, 80, 85, 90, 95, or 100% identical, including all integers there between, to the entire sequence of a mature, naturally occurring miRNA sequence or a complement thereof
  • the miRNA region is or is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99 1, 99 2, 99 3, 99 4, 99 5, 99 6, 99 7, 99 8, 99 9 or 100% identical to the sequence of a naturally-occurring miRNA or complement thereof
  • complementary region or "complementary region” or "complementary region” or "complement
  • a synthetic miRNA or inhibitor contains one or more design element(s)
  • design elements include, but are not limited to (i) a replacement group for the phosphate or hydroxyl of the nucleotide at the 5' terminus of the complementary region, (ii) one or more sugar modifications m the first or last 1 to 6 residues of the complementary region, or, (m) noncomplementanty between one or more nucleotides in the last 1 to 5 residues at the 3' end of the complementary region and the corresponding nucleotides of the miRNA region
  • design elements include, but are not limited to (i) a replacement group for the phosphate or hydroxyl of the nucleotide at the 5' terminus of the complementary region, (ii) one or more sugar modifications m the first or last 1 to 6 residues of the complementary region, or, (m) noncomplementanty between one or more nucleotides in the last 1 to 5 residues at the 3' end of the complementary region and the corresponding nucleotides of the mi
  • a synthetic miRNA has a nucleotide at its 5' end of the complementary region in which the phosphate and/or hydroxyl group has been replaced with another chemical group (referred to as the "replacement design")
  • the replacement group is biotin, an amine group, a lower alkylamine group, an acetyl group, 2'O-Me (2'oxygen-methyl), DMTO (4,4'-dimethoxyt ⁇ tyl with oxygen), fluorescein, a thiol, or acndme, though other replacement groups are well known to those of skill in the art and can be used as well
  • This design element can also be used with a miRNA inhibitor
  • Additional embodiments concern a synthetic miRNA having one or more sugar modifications in the first or last 1 to 6 residues of the complementary region (referred to as the "sugar replacement design")
  • the sugar modification is a 2'O-Me modification
  • noncomplementa ⁇ ty (referred to as the “noncomplementa ⁇ ty design)
  • the noncomplementa ⁇ ty may be in the last 1, 2, 3, 4, and/or 5 residues of the complementary miRNA
  • synthetic miRNA of the invention have one or more of the replacement, sugar modification, or noncomplementa ⁇ ty designs
  • synthetic RNA molecules have two of them, while in others these molecules have all three designs in place
  • the miRNA region and the complementary region may be on the same or separate polynucleotides
  • the miRNA molecule will be considered a single polynucleotide
  • the synthetic miRNA will be considered to be compnsed of two polynucleotides
  • the RNA molecule is a single polynucleotide
  • the single polynucleotide is capable of forming a hairpin loop structure as a result of bonding between the miRNA region and the complementary region
  • the linker constitutes the hairpin loop It is contemplated that in some embodiments, the linker
  • Methods of the invention include reducing or eliminating activity of one or more miRNAs in a cell comprising introducing into a cell a miRNA inhibitor (which may be desc ⁇ bed generally herein as an miRNA, so that a description of miRNA, where appropriate, also will refer to a miRNA inhibitor), or supplying or enhancing the activity of one or more miRNAs in a cell
  • a miRNA inhibitor which may be desc ⁇ bed generally herein as an miRNA, so that a description of miRNA, where appropriate, also will refer to a miRNA inhibitor
  • the present invention also concerns inducing certain cellular characteristics by providing to a cell a particular nucleic acid, such as a specific synthetic miRNA molecule or a synthetic miRNA inhibitor molecule
  • the miRNA molecule or miRNA inhibitor need not be synthetic They may have a sequence that is identical to
  • the particular nucleic acid molecule provided to the cell is understood to correspond to a particular miRNA in the cell, and thus, the miRNA in the cell is referred to as the "corresponding miRNA "
  • the corresponding miRNA will be understood to be the induced or inhibited miRNA or induced or inhibited miRNA function It is contemplated, however, that the miRNA molecule introduced into a cell is not a mature miRNA but is capable of becoming or functioning as a mature miRNA under the appropriate physiological conditions
  • the particular miRNA will be referred to as the “targeted miRNA " It is contemplated that multiple corresponding miRNAs may be involved
  • more than one miRNA molecule is introduced into a cell
  • more than one miRNA inhibitor is introduced into a cell
  • a combination of miRNA molecule(s) and miRNA inhibitors) may be introduced into a combination of miRNA molecule(s) and miRNA inhibitors) may be introduced into a cell.
  • methods can involve providing synthetic or nonsynthetic miRNA molecules It is contemplated that in these embodiments, that the methods may or may not be limited to providing only one or more synthetic miRNA molecules or only one or more nonsynthetic miRNA molecules Thus, in certain embodiments, methods may involve providing both synthetic and nonsynthetic miRNA molecules In this situation, a cell or cells are most likely provided a synthetic miRNA molecule corresponding to a particular miRNA and a nonsynthetic miRNA molecule corresponding to a different miRNA Furthermore, any method articulated using a list of miRNAs using Markush group language may be articulated without the Markush group language and a disjunctive article (; e , or) instead, and vice versa
  • an endogenous gene, miRNA or mRNA is modulated m the cell
  • the nucleic acid sequence comp ⁇ ses at least one segment that is at least 70, 75, 80, 85, 90, 95, or 100% identical in nucleic acid sequence to one or more miRNA or gene sequence
  • Modulation of the expression or processing of an endogenous gene, miRNA, or mRNA can be through modulation of the processing of a mRNA, such processing including transcription, transportation and/or translation with in a cell Modulation may also be effected by the inhibition or enhancement of miRNA activity with a cell, tissue, or organ Such processing may affect the expression of an encoded product or the stability of the mRNA
  • a nucleic acid sequence can compose a modified nucleic acid sequence
  • one or more miRNA sequence may include or comprise a modified nucleobase or nucleic acid sequence
  • a cell or other biological matter such as an organism (including patients) can be provided a miRNA or miRNA molecule corresponding to a particular miRNA by administering to the cell or organism a nucleic acid molecule that functions as the corresponding miRNA once mside the cell
  • the form of the molecule provided to the cell may not be the form that acts a miRNA once inside the cell
  • a synthetic miRNA or a nonsynthetic miRNA is provided such that it becomes processed into a mature and active miRNA once it has access to the cell's miRNA processing machinery
  • the miRNA molecule provided is not a mature miRNA molecule but a nucleic acid molecule that can be processed into the mature miRNA once it is accessible to miRNA processing machinery
  • nonsynthetic in the context of miRNA means that the miRNA is not "synthetic," as defined herein Furthermore, it is contemplated that in embodiments
  • methods also include targeting a miRNA to modulate in a cell or organism
  • targeting a miRNA to modulate means a nucleic acid of the invention will be employed so as to modulate the selected miRNA
  • the modulation is achieved with a synthetic or non-synthetic miRNA that corresponds to the targeted miRNA, which effectively provides the targeted miRNA to the cell or organism (positive modulation)
  • the modulation is achieved with a miRNA inhibitor, which effectively inhibits the targeted miRNA in the cell or organism (negative modulation)
  • the miRNA targeted to be modulated is a miRNA that affects a disease, condition, or pathway
  • the miRNA is targeted because a treatment can be provided by negative modulation of the targeted miRNA
  • the miRNA is targeted because a treatment can be provided by positive modulation of the targeted miRNA or its targets
  • the miRNA compositions may be provided as part of a therapy to a patient, m conjunction with traditional therapies or preventative agents
  • any method discussed in the context of therapy may be applied preventatively, particularly in a patient identified to be potentially in need of the therapy or at ⁇ sk of the condition or disease for which a therapy is needed
  • methods of the invention concern employing one or more nucleic acids corresponding to a miRNA and a therapeutic drug
  • the nucleic acid can enhance the effect or efficacy of the drug, reduce any side effects or toxicity, modify its bioavailability, and/or decrease the dosage or frequency needed
  • the therapeutic drug is a cancer therapeutic Consequently, in some embodiments, there is a method of treating cancer in a patient comprising administering to the patient the cancer therapeutic and an effective amount of at least one miRNA molecule that improves the efficacy of the cancer therapeutic or protects non-cancer cells
  • Cancer therapies also include a variety of combination therapies with both chemical and radiation based treatments
  • Combination chemotherapies include but are not limited to, for example, 5-fluorouracil, alemtuzumab, amrubicm, bevacizumab, bleomycin, bortezomib, busulfan, camptothecin, capecitabme, carboplatin, cetuximab, chlorambucil,
  • inhibitors of miRNAs can be given to decrease the activity of an endogenous miRNA
  • inhibitors of miRNA molecules that increase cell proliferation can be provided to cells to decrease cell proliferation
  • the present invention contemplates these embodiments in the context of the different physiological effects observed with the different miRNA molecules and miRNA inhibitors disclosed herein These include, but are not limited to, the following physiological effects increase and decreasing cell proliferation, increasing or decreasing apoptosis, increasing transformation, increasing or decreasing cell viability, activating or inhibiting a kinase (e g , Erk), activating/inducing or inhibiting hTert, inhibit stimulation of growth promoting pathway (e g , Stat 3 signaling), reduce or increase viable cell number, and increase or decrease number of cells at a particular phase of the cell cycle
  • Methods of the invention are generally contemplated to include providing or introducing one or more different nucleic acid molecules corresponding to one or more different miRNA molecules It is contemplated that the following, at least the following, or at most the following number of different nucleic acid
  • Methods of the present invention include the delivery of an effective amount of a miRNA or an expression construct encoding the same
  • An "effective amount" of the pharmaceutical composition generally, is defined as that amount sufficient to detectably and repeatedly to achieve the stated desired result, for example, to ameliorate, reduce, minimize or limit the extent of the disease or its symptoms Other more rigorous definitions may apply, including elimination, eradication or cure of disease A. Administration
  • the routes of administration will vary, naturally, with the location and nature of the lesion or site to be targeted, and include, e g , intradermal, subcutaneous, regional, parenteral, intravenous, intramuscular, intranasal, systemic, and oral administration and formulation
  • Direct injection, mtratumoral injection, or injection into tumor vasculature is specifically contemplated for discrete, solid, accessible tumors, or other accessible target areas
  • Local, regional, or systemic administration also may be approp ⁇ ate
  • the volume to be administered will be about 4-10 ml (preferably 10 ml), while for tumors of ⁇ 4 cm, a volume of about 1-3 ml will be used (preferably 3 ml)
  • compositions of the invention may be administered m multiple injections to a tumor or a targeted site In certain aspects, injections may be spaced at approximately 1 cm intervals
  • the present invention may be used preoperatively, to render an inoperable tumor subject to resection
  • the present invention may be used at the time of surgery, and/or thereafter, to treat residual or metastatic disease
  • a resected tumor bed may be injected or perfused with a formulation comprising a miRNA or combinations thereof Administration may be continued post-resection, for example, by leaving a catheter implanted at the site of the surgery
  • Pe ⁇ odic post-surgical treatment also is envisioned
  • Continuous perfusion of an expression construct or a viral construct also is contemplated
  • Continuous administration also may be applied where approp ⁇ ate, for example, where a tumor or other undesired affected area is excised and the tumor bed or targeted site is treated to eliminate residual, microscopic disease Delivery via syringe or cathe ⁇ zation is contemplated
  • Such continuous perfusion may take place for a pe ⁇ od from about 1-2 hours, to about 2-6 hours, to about 6-12 hours, to about 12-24 hours, to about 1-2 days, to about 1-2 wk or longer following the initiation of treatment
  • the dose of the therapeutic composition via continuous perfusion will be equivalent to that given by a single or multiple injections, adjusted over a pe ⁇ od of time dunng which the perfusion occurs
  • Treatment regimens may vary as well and often depend on tumor type, tumor location, immune condition, target site, disease progression, and health and age of the patient
  • the tumor or affected area being treated may not, at least initially, be resectable Treatments with compositions of the invention may increase the resectability of the tumor due to shrinkage at the margins or by elimination of certain particularly invasive portions Following treatments, resection may be possible Additional treatments subsequent to resection may serve to eliminate microscopic residual disease at the tumor or targeted site
  • Treatments may include va ⁇ ous "unit doses"
  • a unit dose is defined as containing a predetermined quantity of a therapeutic composition(s)
  • the quantity to be administered, and the particular route and formulation, are within the skill of those in the clinical arts
  • a unit dose need not be administered as a single injection but may compose continuous infusion over a set period of time
  • a unit dose may conveniently be desc ⁇ bed in terms of ⁇ g or mg of miRNA or miRNA mimetic
  • the amount specified may be the amount administered as the average daily, average weekly, or average monthly dose miRNA can be administered to the patient in a dose or doses of about or of at least about 0 5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340
  • the method for the delivery of a miRNA or an expression construct encoding such or combinations thereof is via systemic administration
  • the pharmaceutical compositions disclosed herein may also be administered parenterally, subcutaneously, directly, intratracheally, intravenously, lntradermally, intramuscularly, or even mtrapentoneally as descnbed in U S Patents 5,543,158, 5,641,515 and 5,399,363 (each specifically incorporated herein by reference in its entirety)
  • nucleic acids may be delivered by syringe or any other method used for injection of a solution, as long as the nucleic acid and any associated components can pass through the particular gauge of needle required for injection
  • a syringe system has also been descnbed for use in gene therapy that permits multiple injections of predetermined quantities of a solution precisely at any depth (U S Patent 5,846,225)
  • Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose Dispersions may also be prepared in glycerol, liquid polyethylene glycols, mixtures thereof, and in oils Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms
  • a surfactant such as hydroxypropylcellulose Dispersions
  • glycerol liquid polyethylene glycols, mixtures thereof, and in oils
  • oils Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms
  • the pharmaceutical forms suitable for injectable use include ste ⁇ le aqueous solutions or dispersions and ste ⁇ le powders for the extemporaneous preparation of stenle injectable solutions or dispersions (U S Patent 5,466,468, specifically incorporated herein by reference in its entirety)
  • the form must be stenle and must be fluid to the extent that easy s
  • a water-based formulation is employed while m others, it may be hpid-based
  • a composition comp ⁇ sing a tumor suppressor protein or a nucleic acid encoding the same is in a water-based formulation
  • the formulation is lipid based
  • aqueous solutions For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose
  • aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, mtratumoral, intralesional, and intraperitoneal administration
  • ste ⁇ le aqueous media which can be employed will be known to those of skill m the art in light of the present disclosure
  • one dosage may be dissolved m 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences" 15th Edition, pages 1035-1038 and 1570-1580)
  • a “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, earner solutions, suspensions, colloids, and the like.
  • solvents dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, earner solutions, suspensions, colloids, and the like.
  • Supplementary active ingredients can also be incorporated into the compositions
  • nucleic acid(s) are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective
  • the quantity to be administered depends on the subject to be treated, including, e g , the aggressiveness of the disease or cancer, the size of any tumor(s) or lesions, the previous or other courses of treatment
  • Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner Suitable regimes for initial administration and subsequent administration are also variable, but are typified by an initial administration followed by other administrations
  • Such administration may be systemic, as a single dose, continuous over a period of time spanning 10, 20, 30, 40, 50, 60 minutes, and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more hours, and/or 1, 2, 3, 4, 5, 6, 7, days or more
  • administration may be through a time release or sustained release mechanism
  • compositions and methods of the present invention involve a miRNA, or expression construct encoding such These miRNA composition can be used in combination with a second therapy to enhance the effect of the miRNA therapy, or increase the therapeutic effect of another therapy being employed These compositions would be provided in a combined amount effective to achieve the desired effect, such as the killing of a cancer cell and/or the inhibition of cellular hyperprohferation This process may involve contacting the cells with the miRNA or second therapy at the same or different time
  • compositions or pharmacological formulation that includes or more of the agents, or by contacting the cell with two or more distinct compositions or formulations, wherein one composition provides
  • a second composition or method may be administered that includes a chemotherapy, radiotherapy, surgical therapy, immunotherapy or gene therapy
  • a course of treatment will last 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90 days or more It is contemplated that one agent may be given on day 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
  • any compound or therapy of the present invention to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the vector or any protein or other agent Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy It is expected that the treatment cycles would be repeated as necessary It also is contemplated that va ⁇ ous standard therapies, as well as surgical intervention, may be applied in combination with the desc ⁇ bed therapy In specific aspects, it is contemplated that a second therapy, such
  • chemotherapeutic agents A wide va ⁇ ety of chemotherapeutic agents may be used in accordance with the present invention
  • the term "chemotherapy” refers to the use of drugs to treat cancer
  • a "chemotherapeutic agent” is used to connote a compound or composition that is administered in the treatment of cancer
  • agents or drugs are categonzed by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle
  • an agent may be characte ⁇ zed based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis
  • Most chemotherapeutic agents fall into the following categones alkylating agents, antimetabolites, antitumor antibiotics, mitotic inhibitors, and nitrosoureas a Alkylating agents
  • Alkylating agents are drugs that directly interact with genomic DNA to prevent the cancer cell from proliferating This category of chemotherapeutic drugs represents agents
  • Antimetabolites disrupt DNA and RNA synthesis Unlike alkylating agents, they specifically influence the cell cycle du ⁇ ng S phase They have been used to combat chronic leukemias in addition to tumors of breast, ovary and the gastrointestinal tract
  • Antimetabolites include 5-fluorouracil (5-FU), cytarabme (Ara-C), fludarabine, gemcitabine, and methotrexate
  • 5-Fluorouracil has the chemical name of 5-fluoro-2,4(lH,3H)- py ⁇ midinedione Its mechanism of action is thought to be by blocking the methylation reaction of deoxyu ⁇ dylic acid to thymidylic acid Thus, 5-FU interferes with the synthesis of deoxyribonucleic acid (DNA) and to a lesser extent inhibits the formation of ribonucleic acid (RNA) Since DNA and RNA are essential for cell division and proliferation, it is thought that the effect of 5-FU is to create a thymidine deficiency leading to cell death Thus, the effect of 5-FU is found m cells that rapidly divide, a characteristic of metastatic cancers c Antitumor Antibiotics
  • Antitumor antibiotics have both antimicrobial and cytotoxic activity These drugs also interfere with DNA by chemically inhibiting enzymes and mitosis or alte ⁇ ng cellular membranes These agents are not phase specific so they work in all phases of the cell cycle Thus, they are widely used for a va ⁇ ety of cancers
  • antitumor antibiotics include bleomycin, dactmomycm, daunorubicm, doxorubicin (Ad ⁇ amycin), and ldarubicm, some of which are discussed in more detail below
  • these compounds are administered through bolus injections intravenously at doses ranging from 25-75 mg/m 2 at 21 day intervals for ad ⁇ amycm, to 35- 100 mg/m 2 for etoposide intravenously or orally d Mitotic Inhibitors
  • Mitotic inhibitors include plant alkaloids and other natural agents that can inhibit either protein synthesis required for cell division or mitosis They operate du ⁇ ng a specific phase du ⁇ ng the cell cycle Mitotic inhibitors comp ⁇ se docetaxel, etoposide (VPl 6), pachtaxel, taxol, taxotere, vinblastine, vincristine, and vinorelbine e Nitrosureas
  • Nitrosureas like alkylating agents, inhibit DNA repair proteins They are used to treat non-Hodgkin's lymphomas, multiple myeloma, malignant melanoma, in addition to brain tumors Examples include carmustine and lomustme 2. Radiotherapy
  • Radiotherapy also called radiation therapy, is the treatment of cancer and other diseases with ionizing radiation
  • Ionizing radiation deposits energy that injures or destroys cells in the area being treated by damaging their genetic material, making it impossible for these cells to continue to grow
  • Radiotherapy may be used to treat localized solid tumors, such as cancers of the skin, tongue, larynx, brain, breast, or cervix It can also be used to treat leukemia and lymphoma (cancers of the blood-forming cells and lymphatic system, respectively)
  • Radiation therapy used according to the present invention may include, but is not limited to, the use of ⁇ -rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells
  • Other forms of DNA damaging factors are also contemplated such as microwaves, proton beam irradiation (U S Patents 5,760,395 and 4,870,287) and UV-irradiation It is most likely that all of these factors effect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes
  • Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens
  • Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells Radio
  • Stereotactic radio-surgery for brain and other tumors does not use a knife, but very precisely targeted beams of gamma radiotherapy from hundreds of different angles Only one session of radiotherapy, taking about four to five hours, is needed For this treatment a specially made metal frame is attached to the head Then, several scans and x- rays are earned out to find the precise area where the treatment is needed Du ⁇ ng the radiotherapy for bram tumors, the patient lies with their head in a large helmet, which has hundreds of holes in it to allow the radiotherapy beams through Related approaches permit positioning for the treatment of tumors in other areas of the body
  • immunotherapeutics In the context of cancer treatment, immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells Trastuzumab
  • the immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell
  • the antibody alone may serve as an effector of therapy or it may recruit other cells to actually affect cell killing
  • the antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ⁇ cin A chain, cholera toxm, pertussis toxin, etc ) and serve merely as a targeting agent
  • the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target
  • Various effector cells include cytotoxic T cells and NK cells
  • the combination of therapeutic modalities, ; e , direct cytotoxic activity and inhibition or reduction of ErbB2 would provide therapeutic benefit in the treatment of ErbB2 overexpressing cancers
  • the tumor or disease cell must bear some marker that is amenable to targeting, i e , is not present on the majo ⁇ ty of other cells
  • Common tumor markers include carcinoembryomc antigen, prostate specific antigen, urinary tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, estrogen receptor, lamimn receptor, erb B and pi 55
  • An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects
  • Immune stimulating molecules also exist including cytokines such as IL-2, IL-4, IL- 12, GM-CSF, gamma-IFN, chemokmes such as MIP-I, MCP-I, IL-8 and growth factors such as FLT3 ligand Combining immune stimulating molecules, either as proteins or
  • immunotherapies currently under investigation or in use are immune adjuvants e g , Mycobacterium bovis, Plasmodium falciparum, dimtrochlorobenzene and aromatic compounds (U S Patents 5,801,005 and 5,739,169, Hm and Hashimoto, 1998, Ch ⁇ stodoulides et al , 1998), cytokine therapy e g , interferons ⁇ , ⁇ and ⁇ , IL-I, GM-CSF and TNF (Bukowski et al , 1998, Davidson et al , 1998, Hellstrand et al , 1998) gene therapy e g , TNF, IL-I, IL-2, p53 (Qin et al , 1998, Austm-Ward and Villaseca, 1998, U S Patents 5,830,880 and 5,846,945) and monoclonal antibodies e g , anti-ganghoside GM2, anti-HER- 2, anti-pl85, Pie
  • a combination treatment involves gene therapy in which a therapeutic polynucleotide is administered before, after, or at the same time as one or more therapeutic miRNA Delivery of a therapeutic polypeptide or encoding nucleic acid in conjunction with a miRNA may have a combined therapeutic effect on target tissues
  • a therapeutic polypeptide or encoding nucleic acid in conjunction with a miRNA may have a combined therapeutic effect on target tissues
  • genes that may be targeted for gene therapy of some form in combination with the present invention include, but are not limited to inducers of cellular proliferation, inhibitors of cellular proliferation, regulators of programmed cell death, cytokines and other therapeutic nucleic acids or nucleic acid that encode therapeutic proteins
  • the tumor suppressor oncogenes function to inhibit excessive cellular proliferation
  • the inactivation of these genes destroys their inhibitory activity, resulting in unregulated proliferation
  • the tumor suppressors e g , therapeutic polypeptides
  • p53 e g , therapeutic polypeptides
  • FHIT eukaryotic cell cycle
  • pi 6 eukaryotic cell cycle
  • pl6 Another inhibitor of cellular proliferation
  • the major transitions of the eukaryotic cell cycle are triggered by cychn-dependent kinases, or CDK's One CDK, cychn-dependent kinase 4 (CDK4), regulates progression through the Gl
  • CDK4 cychn-dependent kinase 4
  • the activity of this enzyme may be to phosphorylate Rb at late Gl
  • the activity of CDK4 is controlled by an activating subunit, D-type cyclin, and by an inhibitory subumt, the pl6INK4 has been biochemically characte ⁇
  • genes that may be employed according to the present invention include Rb, APC, DCC, NF-I, NF-2, WT-I, MEN-I, MEN-II, zacl, p73, VHL, MMACl / PTEN, DBCCR-I, FCC, rsk-3, p27, p27/pl6 fusions, p21/p27 fusions, anti-thrombotic genes ⁇ e g , COX-I, TFPI), PGS, Dp, E2F, ras, myc, neu, raf, erb, fins, trk, ret, gsp, hst, abl, ElA, p300, genes involved in angiogenesis (e g , VEGF, FGF, thrombospondin, BAI-I, GDAIF, or their receptors) and MCC 5.
  • angiogenesis e g , VEGF, FGF, thrombos
  • Curative surgery is a cancer treatment that may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies
  • Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed Tumor resection refers to physical removal of at least part of a tumor
  • treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs' surgery) It is further contemplated that the present invention may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue
  • Treatment may be accomplished by perfusion, direct injection or local application of the area with an additional anti-cancer therapy Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months These treatments may be of varying dosages as well
  • agents may be used in combination with the present invention to improve the therapeutic efficacy of treatment
  • additional agents include immunomodulatory agents, agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperprohferative cells to apoptotic inducers, or other biological agents
  • Immunomodulatory agents include tumor necrosis factor, interferon alpha, beta, and gamma, IL-2 and other cytokines, F42K and other cytokine analogs, or MIP-I, MIP-lbeta, MCP-I, RANTES, and other chemokmes
  • the upregulation of cell surface receptors or their hgands such as Fas / Fas hgand, DR4 or DR5 / TRAIL (Apo-2 hgand) would potentiate the apoptotic inducing abilities of the present invention by establishment of an autocn
  • Apo2 hgand (Apo2L, also called TRAIL) is a member of the tumor necrosis factor (TNF) cytokine family TRAIL activates rapid apoptosis in many types of cancer cells, yet is not toxic to normal cells TRAIL mRNA occurs m a wide va ⁇ ety of tissues Most normal cells appear to be resistant to TRAIL'S cytotoxic action, suggesting the existence of mechanisms that can protect against apoptosis induction by TRAIL
  • the first receptor desc ⁇ bed for TRAIL, called death receptor 4 (DR4) contains a cytoplasmic "death domain", DR4 transmits the apoptosis signal carried by TRAIL Additional receptors have been identified that bind to TRAIL One receptor, called DR5, contains a cytoplasmic death domain and signals apoptosis much like DR4
  • DR4 and DR5 mRNAs are expressed in many normal tissues and tumor cell lines Recently, decoy receptors such as DcRl
  • hyperthermia is a procedure in which a patient's tissue is exposed to high temperatures (up to 106 0 F)
  • External or internal heating devices may be involved in the application of local, regional, or whole-body hyperthermia
  • Local hyperthermia involves the application of heat to a small area, such as a tumor Heat may be generated externally with high-frequency waves targeting a tumor from a device outside the body Internal heat may involve a sterile probe , including thin, heated wires or hollow tubes filled with warm water, implanted microwave antennae, or radiofrequency electrodes
  • a patient's organ or a limb is heated for regional therapy, which is accomplished using devices that produce high energy, such as magnets
  • some of the patient's blood may be removed and heated before being perfused into an area that will be internally heated
  • Whole-body heating may also be implemented in cases where cancer has spread throughout the body Warm-water blankets, hot wax, inductive coils, and thermal chambers may be used for this purpose
  • Hormonal therapy may also be used in conjunction with the present invention or in combination with any other cancer therapy previously described
  • the use of hormones may be employed in the treatment of certain cancers such as breast, prostate, ovarian, or cervical cancer to lower the level or block the effects of certain hormones such as testosterone or estrogen This treatment is often used in combination with at least one other cancer therapy as a treatment option or to reduce the risk of metastases
  • miRNAs are generally 21 to 22 nucleotides in length, though lengths of 19 and up to 23 nucleotides have been reported
  • the miRNAs are each processed from a longer precursor RNA molecule (“precursor miRNA”)
  • Precursor miRNAs are transc ⁇ bed from non-protein-encoding genes
  • the precursor miRNAs have two regions of complementarity that enables them to form a stem-loop- or fold-back-like structure, which is cleaved m animals by a ⁇ bonuclease Ill-hke nuclease enzyme called Dicer
  • the processed miRNA is typically a portion of the stem
  • the processed miRNA (also referred to as "mature miRNA”) becomes part of a large complex to down-regulate a particular target gene or its gene product
  • miRNAs include those that imperfectly basepair with the target, which halts translation
  • siRNA molecules also are processed by Dicer, but from a long, double-stranded RNA molecule siRNAs are not naturally found in animal cells, but they can direct the sequence-specific cleavage of an mRNA target through a RNA- induced silencing complex (RISC) (Denh et al , 2003)
  • RISC RNA- induced silencing complex
  • Certain embodiments of the present invention concerns the preparation and use of mRNA or nucleic acid arrays, miRNA or nucleic acid arrays, and/or miRNA or nucleic acid probe arrays, which are macroarrays or microarrays of nucleic acid molecules (probes) that are fully or nearly complementary (over the length of the prove) or identical (over the length of the prove) to a plurality of nucleic acid, mRNA or miRNA molecules, precursor miRNA molecules, or nucleic acids de ⁇ ved from the various genes and gene pathways modulated by miR-143 miRNAs and that are positioned on a support or support material in a spatially separated organization
  • Macroarrays are typically sheets of nitrocellulose or nylon upon which probes have been spotted
  • Microarrays position the nucleic acid probes more densely such that up to 10,000 nucleic acid molecules can be fit into a region typically 1 to 4 square centimeters
  • Microarrays can be fab ⁇ cated by spotting nucleic acid molecules, e
  • array devices in which a plurality of distinct nucleic acid probes are stably associated with the surface of a solid support are known to those of skill in the art
  • Useful substrates for arrays include nylon, glass, metal, plastic, latex, and silicon
  • Such arrays may vary in a number of different ways, including average probe length, sequence or types of probes, nature of bond between the probe and the array surface, e g covalent or non- covalent, and the like
  • the labeling and screening methods of the present invention and the arrays are not limited m its utility with respect to any parameter except that the probes detect miRNA, or genes or nucleic acid representative of genes, consequently, methods and compositions may be used with a variety of different types of nucleic acid arrays
  • the arrays can be high density arrays, such that they contain 2, 20, 25, 50, 80, 100 or more different probes It is contemplated that they may contain 1000, 16,000, 65,000, 250,000 or 1,000,000 or more different probes
  • the probes can be directed to mRNA and/or miRNA targets in one or more different organisms or cell types
  • the oligonucleotide probes range from 5 to 50, 5 to 45, 10 to 40, 9 to 34, or 15 to 40 nucleotides m length in some embodiments In certain embodiments, the oligonucleotide probes are 5, 10, 15, 20 to 20, 25, 30, 35, 40 nucleotides in length including all integers and ranges there between
  • each different probe sequence in the array is generally known Moreover, the large number of different probes can occupy a relatively small area providing a high density array having a probe density of generally greater than about 60, 100, 600, 1000, 5,000, 10,000, 40,000, 100,000, or 400,000 different oligonucleotide probes per cm 2
  • the surface area of the array can be about or less than about 1, 1 6, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cm 2
  • RNA and/or miRNA of a wide variety of samples can be analyzed using the arrays, index of probes, or array technology of the invention While endogenous miRNA is contemplated for use with compositions and methods of the invention, recombinant miRNA - including nucleic acids that are complementary or identical to endogenous miRNA or precursor miRNA - can also be handled and analyzed as descnbed herein Samples may be biological samples, in which case, they can be from biopsy, fine needle aspirates, exfoliates, blood, tissue, organs, semen, saliva, tears, other bodily fluid, hair follicles, skm, or any sample containing or constituting biological cells, particularly cancer or hyperproliferative cells
  • samples may be, but are not limited to, biopsy, or cells purified or enriched to some extent from a biopsy or other bodily fluids or tissues Alternatively, the sample may not be a biological sample, but be a chemical mixture, such as a cell-
  • the population of target nucleic acids is contacted with the array or probes under hybridization conditions, where such conditions can be adjusted, as desired, to provide for an optimum level of specificity in view of the particular assay being performed Suitable hybridization conditions are well known to those of skill in the art and reviewed in Sambrook et al (2001) and WO 95/21944 Of particular interest in many embodiments is the use of st ⁇ ngent conditions during hybridization Stringent conditions are known to those of skill in the art It is specifically contemplated that a single array or set of probes may be contacted with multiple samples The samples may be labeled with different labels to distinguish the samples For example, a single array can be contacted with a tumor tissue sample labeled with Cy3, and normal tissue sample labeled with Cy5 Differences between the samples for particular miRNAs corresponding to probes on the array can be readily ascertained and quantified
  • hybridization may be earned out in extremely small fluid volumes (e g , about 250 ⁇ l or less, including volumes of about or less than about 5, 10, 25, 50, 60, 70, 80, 90, 100 ⁇ l, or any range de ⁇ vable therein) In small volumes, hybridization may proceed very rapidly
  • Arrays of the invention can be used to detect differences between two samples Specifically contemplated applications include identifying and/or quantifying differences between miRNA or gene expression from a sample that is normal and from a sample that is not normal, between a disease or condition and a cell not exhibiting such a disease or condition, or between two differently treated samples Also, miRNA or gene expression may be compared between a sample believed to be susceptible to a particular disease or condition and one believed to be not susceptible or resistant to that disease or condition A sample that is not normal is one exhibiting phenotypic or genotypic trait(s) of a disease or condition, or one believed to be not normal with respect to that disease or condition It may be compared to a cell that is normal with respect to that disease or condition Phenotypic traits include symptoms of, or susceptibility to, a disease or condition of which a component is or may or may not be genetic, or caused by a hyperproliferative or neoplastic cell or cells An array composes a solid support with nucleic acid probes attached to the support
  • arrays typically comp ⁇ se a plurality of different nucleic acid probes that are coupled to a surface of a substrate in different, known locations
  • These arrays also desc ⁇ bed as “microarrays” or colloquially “chips” have been generally desc ⁇ bed in the art, for example, U S Patents 5,143,854, 5,445,934, 5,744,305, 5,677,195, 6,040,193, 5,424,186 and Fodor et al , (1991), each of which is incorporated by reference in its entirety for all purposes
  • Techniques for the synthesis of these arrays using mechanical synthesis methods are desc ⁇ bed in, e g , U S Patent 5,384,261, incorporated herein by reference in its entirety for all purposes
  • a planar array surface is used in certain aspects, the array may be fab ⁇ cated on a surface of virtually any shape or even a multiplicity of surfaces
  • Arrays may be nucleic acids on beads, gels, polyme ⁇ c surfaces, fibers such as fiber optic
  • arrays can be used to evaluate samples with respect to pathological condition such as cancer and related conditions It is specifically contemplated that the invention can be used to evaluate differences between stages or sub-classifications of disease, such as between benign, cancerous, and metastatic tissues or tumors
  • Phenotypic traits to be assessed include characte ⁇ stics such as longevity, morbidity, expected survival, susceptibility or receptivity to particular drugs or therapeutic treatments (drug efficacy), and nsk of drug toxicity Samples that differ m these phenotypic traits may also be evaluated using the compositions and methods desc ⁇ bed
  • miRNA and/or expression profiles may be generated to evaluate and correlate those profiles with pharmacokinetics or therapies For example, these profiles may be created and evaluated for patient tumor and blood samples p ⁇ or to the patient's being treated or during treatment to determine if there are miRNA or genes whose expression correlates with the outcome of the patient's treatment Identification of differential miRNAs or genes can lead to a diagnostic assay for evaluation of tumor and/or blood samples to determine what drug regimen the patient should be provided In addition, it can be used to identify or select patients suitable for a particular clinical t ⁇ al If an expression profile is determined to be correlated with drug efficacy or drug toxicity that profile is relevant to whether that patient is an expression profile is
  • samples from patients with a va ⁇ ety of diseases can be evaluated to determine if different diseases can be identified based on miRNA and/or related gene expression levels
  • a diagnostic assay can be created based on the profiles that doctors can use to identify individuals with a disease or who are at nsk to develop a disease
  • treatments can be designed based on miRNA profiling Examples of such methods and compositions are desc ⁇ bed in the U S Provisional Patent Application entitled "Methods and Compositions Involving miRNA and miRNA Inhibitor Molecules" filed on May 23, 2005, which is hereby incorporated by reference in its entirety
  • assays include, but are not limited to, nucleic acid amplification, polymerase chain reaction, quantitative PCR, RT-PCR, in situ hybridization, Northern hybridization, hybridization protection assay (HPA)(GenProbe), branched DNA (bDNA) assay (Chiron), rolling circle amplification (RCA), single molecule hybridization detection (US Genomics), Invader assay (ThirdWave Technologies), and/or B ⁇ dge Litigation Assay (Genaco)
  • the present invention concerns nucleic acids, modified or mimetic nucleic acids, miRNAs, mRNAs, genes, and representative fragments thereof that can be labeled, used in array analysis, or employed in diagnostic, therapeutic, or prognostic applications, particularly those related to pathological conditions such as cancer
  • the molecules may have been endogenously produced by a cell, or been synthesized or produced chemically or recombmantly They may be isolated and/or purified
  • the name of a miRNA is often abbreviated and referred to without a "hsa-" prefix and will be understood as such, depending on the context Unless otherwise indicated, miRNAs referred to in the application are human sequences identified as miR-X or let-X, where X is a number and/or letter
  • a miRNA probe designated by a suffix "5P” or “3P” can be used "5P” indicates that the mature miRNA de ⁇ ves from the 5' end of the precursor and a 5 corresponding "3P” indicates that it de ⁇ ves from the 3' end of the precursor, as descnbed on the world wide web at Sanger ac uk Moreover, in some embodiments, a miRNA probe is used that does not correspond to a known human miRNA It is contemplated that these non- human miRNA probes may be used in embodiments of the invention or that there may exist a human miRNA that is homologous to the non-human miRNA In other embodiments, any 10 mammalian cell, biological sample, or preparation thereof may be employed
  • methods and compositions involving miRNA may concern rniRNA, markers (mRNAs), and/or other nucleic acids
  • Nucleic acids may be, be at least, or be at most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
  • miRNA are 19-24 nucleotides in length, while miRNA probes are 19-35 nucleotides in length, depending on the length of the processed miRNA and any flanking regions added miRNA precursors are generally between 62 and 110 nucleotides in humans
  • Nucleic acids of the invention may have regions of identity or complementarity to another nucleic acid It is contemplated that the region of complementarity or identity can be at least 5 contiguous residues, though it is specifically contemplated that the region is, is at least, or is at most 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 5 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,
  • complementarity is or is at least 90%, 95% or 100%
  • lengths may be applied to any nucleic acid comp ⁇ sing a nucleic acid sequence identified m any of SEQ ID NO 1-13, accession number, or any other sequence disclosed herein
  • the commonly used name of the miRNA is given (with its identifying source in the prefix, for example, "hsa" for human sequences)
  • miRNA probe refers to a nucleic acid probe that can identify a particular miRNA or structurally related miRNAs
  • nucleic acids are de ⁇ ved from genomic sequences or a gene
  • the term "gene” is used for simplicity to refer to the genomic sequence encoding the precursor nucleic acid or miRNA for a given miRNA or gene
  • embodiments of the invention may involve genomic sequences of a miRNA that are involved m its expression, such as a promoter or other regulatory sequences
  • nucleic acid is well known in the art
  • a “nucleic acid” as used herein will generally refer to a molecule (one or more strands) of DNA, RNA or a denvative or analog thereof, comp ⁇ sing a nucleobase
  • a nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e g , an adenine "A,” a guanine "G,” a thymine “T” or a cytosine "C”) or RNA (e g , an A, a G, an uracil "U” or a C)
  • nucleic acid encompasses the terms “oligonucleotide” and “polynucleotide,” each as a subgenus of the term "
  • miRNA generally refers to a single-stranded molecule, but in specific embodiments, molecules implemented in the invention will also encompass a region or an additional strand that is partially (between 10 and 50% complementary across length of strand), substantially (greater than 50% but less than 100% complementary across length of strand) or fully complementary to another region of the same smgle-stranded molecule or to another nucleic acid
  • miRNA may encompass a molecule that composes one or more complementary or self-complementary strand(s) or "complement(s)" of a particular sequence
  • precursor miRNA may have a self complementary region, which is up to 100% complementary miRNA probes or nucleic acids of the invention can include, can be or can be at least 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or 100% complementary to their target
  • a “synthetic nucleic acid” of the invention means that the nucleic acid does not have all or part of a chemical structure or sequence of a naturally occurring nucleic acid Consequently, it will be understood that the term “synthetic miRNA” refers to a
  • synthetic nucleic acid that functions in a cell or under physiological conditions as a naturally occurring miRNA
  • nucleic acid molecule(s) need not be "synthetic"
  • a non-synthetic nucleic acid or miRNA employed m methods and compositions of the invention may have the entire sequence and structure of a naturally occurring mRNA or miRNA precursor or the mature mRNA or miRNA
  • non-synthetic miRNAs used m methods and compositions of the invention may not have one or more modified nucleotides or nucleotide analogs
  • the non-synthetic miRNA may or may not be recombinantly produced
  • the nucleic acid in methods and/or compositions of the invention is specifically a synthetic miRNA and not a non-synthetic miRNA (that is, not an miRNA that qualifies as "synthetic”), though in other embodiments, the invention specifically involves a non- synthetic miRNA and not a synthetic miRNA
  • a synthetic miRNA molecule does not have the sequence of a naturally occurring miRNA molecule
  • a synthetic miRNA molecule may have the sequence of a naturally occurring miRNA molecule, but the chemical structure of the molecule, particularly in the part unrelated specifically to the precise sequence (non-sequence chemical structure) differs from chemical structure of the naturally occurring miRNA molecule with that sequence
  • the synthetic miRNA has both a sequence and non-sequence chemical structure that are not found in a naturally-occurnng miRNA
  • the sequence of the synthetic molecules will identify which miRNA is effectively being provided or inhibited, the endogenous miRNA will be referred to as the "corresponding miRNA "
  • Corresponding miRNA sequences that can be used in the context of the invention include, but are not limited to, all or a portion of those sequence
  • hybridization As used herein, “hybridization”, “hybridizes” or “capable of hybridizing” is understood to mean the forming of a double or t ⁇ ple stranded molecule or a molecule with partial double or t ⁇ ple stranded nature
  • the term “anneal” as used herein is synonymous with “hybridize”
  • the term “hybridization”, “hybndize(s)” or “capable of hybridizing” encompasses the terms “stringent condition(s)” or “high stringency” and the terms “low stringency” or “low stringency condition(s) " As used herein "stringent condition(s)” or “high stringency” are those conditions that allow hybridization between or within one or more nucleic acid strand(s) containing complementary sequence(s), but preclude hybridization of random sequences Stringent conditions tolerate little, if any, mismatch between a nucleic acid and a target strand Such conditions are well known to those of ordinary skill m the art,
  • Stringent conditions may compose low salt and/or high temperature conditions, such as provided by about 0 02 M to about 0 5 M NaCl at temperatures of about 42°C to about 70 0 C It is understood that the temperature and iomc strength of a desired stringency are determined in part by the length of the particular nucleic acid(s), the length and nucleobase content of the target sequence(s), the charge composition of the nucleic acid(s), and to the presence or concentration of formamide, tetramethylammonium chloride or other solvent(s) in a hybridization mixture
  • nucleobase refers to a heterocyclic base, such as for example a naturally occurring nucleobase ( ⁇ e , an A, T, G, C or U) found in at least one naturally occurring nucleic acid ( ⁇ e , DNA and RNA), and naturally or non-naturally occurring de ⁇ vative(s) and analogs of such a nucleobase
  • a nucleobase generally can form one or more hydrogen bonds ("anneal” or “hybridize") with at least one naturally occurring nucleobase m a manner that may substitute for naturally occurring nucleobase pai ⁇ ng ⁇ e g , the hydrogen bonding between A and T, G and C, and A and U)
  • "Purine” and/or "pynmidme” nucleobase(s) encompass naturally occurring pu ⁇ ne and/or pynmidme nucleobases and also de ⁇ vative(s) and analog(s) thereof, including but not limited to, those a pu ⁇ ne or py
  • nucleotide refers to a nucleoside further compnsmg a "backbone moiety"
  • a backbone moiety generally covalently attaches a nucleotide to another molecule compnsmg a nucleotide, or to another nucleotide to form a nucleic acid
  • the "backbone moiety” in naturally occurring nucleotides typically compnses a phosphorus moiety, which is covalently attached to a 5-carbon sugar The attachment of the backbone moiety typically occurs at either the 3'- or 5'-position of the 5-carbon sugar
  • other types of attachments are known in the art, particularly when a nucleotide compnses denvatives or analogs of a naturally occurring 5-carbon sugar or phosphorus moiety
  • a nucleic acid may compnse, or be composed entirely of, a denvative or analog of a nucleobase, a nucleobase linker moiety and/or backbone moiety that may be present in a naturally occurring nucleic acid RNA with nucleic acid analogs may also be labeled according to methods of the invention
  • a "derivative” refers to a chemically modified or altered form of a naturally occurring molecule
  • the terms “mimic” or “analog” refer to a molecule that may or may not structurally resemble a naturally occurring molecule or moiety, but possesses similar functions
  • a "moiety” generally refers to a smaller chemical or molecular component of a larger chemical or molecular structure
  • Nucleobase, nucleoside and nucleotide analogs or derivatives are well known in the art, and have been desc ⁇ bed (see for example, Scheit, 1980, incorporated herein by reference) Additional non-hmitmg examples of nucleo
  • nucleotides that are both modified for attachment of a label and can be incorporated into a miRNA molecule
  • nucleotides include those that can be labeled with a dye, including a fluorescent dye, or with a molecule such as biotin Labeled nucleotides are readily available, they can be acquired commercially or they can be synthesized by reactions known to those of skill in the art
  • Modified nucleotides for use in the invention are not naturally occurring nucleotides, but instead, refer to prepared nucleotides that have a reactive moiety on them
  • Specific reactive functionalities of interest include ammo, sulfhydryl, sulfoxyl, aminosulfhydryl, azido, epoxide, isothiocyanate, isocyanate, anhydride, monochlorotnazine, dichlorot ⁇ azine, mono-or dihalogen substituted pyridine, mono- or disubstituted diazme, maleimide, epoxide, azmdme, sulfonyl hahde, acid halide, alkyl halide, aryl hahde, alkylsulfonate, N- hydroxysuccimmide ester, imido ester, hydrazine, azidomtrophenyl, azide, 3-(2-py ⁇ dyl dithio)-pro
  • a nucleic acid may be made by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production, or biological production It is specifically contemplated that miRNA probes of the invention are chemically synthesized
  • miRNAs are recovered or isolated from a biological sample
  • the miRNA may be recombinant or it may be natural or endogenous to the cell (produced from the cell's genome) It is contemplated that a biological sample may be treated m a way so as to enhance the recovery of small RNA molecules such as miRNA U S Patent Application Senal No 10/667,126 desc ⁇ bes such methods and it is specifically incorporated by reference herein
  • methods involve lysmg cells with a solution having guamdinium and a detergent
  • nucleic acid synthesis is performed according to standard methods
  • Non-limiting examples of a synthetic nucleic acid include a nucleic acid made by in vitro chemically synthesis using phosphotnester, phosphite, or phosphoramidite chemistry and solid phase techniques such as described in EP 266,032, incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as desc ⁇ bed by Froehler et al , 1986 and U S Patent 5,705,629, each incorporated herein by reference Vanous different mechanisms of oligonucleotide synthesis have been disclosed in for example, U S Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146,
  • a non-limiting example of an enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCRTM (see for example, U S Patents 4,683,202 and 4,682,195, each incorporated herein by reference), or the synthesis of an oligonucleotide desc ⁇ bed in U S Patent 5,645,897, incorporated herein by reference See also Sambrook et al , 2001, incorporated herein by reference)
  • Oligonucleotide synthesis is well known to those of skill in the art Vanous different mechanisms of oligonucleotide synthesis have been disclosed in for example, U S Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference
  • Recombinant methods for producing nucleic acids in a cell are well known to those of skill in the art These include the use of vectors (viral and non-viral), plasmids, cosmids, and other vehicles for delivering a nucleic acid to a cell, which may be the target cell (e g , a cancer cell) or simply a host cell (to produce large quantities of the desired RNA molecule) Alternatively, such vehicles can be used in the context of a cell free system so long as the reagents for generating the RNA molecule are present Such methods include those desc ⁇ bed in Sam
  • Nucleic acids may be isolated using techniques well known to those of skill m the art, though m particular embodiments, methods for isolating small nucleic acid molecules, and/or isolating RNA molecules can be employed Chromatography is a process often used to separate or isolate nucleic acids from protein or from other nucleic acids Such methods can involve electrophoresis with a gel matrix, filter columns, alcohol precipitation, and/or other chromatography If miRNA from cells is to be used or evaluated, methods generally involve lysmg the cells with a chaotropic (e g , guamdimum isothiocyanate) and/or detergent (e g , N- lauroyl sarcosme) p ⁇ or to implementing processes for isolating particular populations of RNA
  • a chaotropic e g , guamdimum isothiocyanate
  • detergent e g , N- lauroyl sarcosme
  • a gel matrix is prepared using polyacrylamide, though agarose can also be used
  • the gels may be graded by concentration or they may be uniform Plates or tubmg can be used to hold the gel mat ⁇ x for electrophoresis
  • one-dimensional electrophoresis is employed for the separation of nucleic acids Plates are used to prepare a slab gel, while the tubmg (glass or rubber, typically) can be used to prepare a tube gel
  • tube electrophoresis refers to the use of a tube or tubmg, instead of plates, to form the gel Matenals for implementing tube electrophoresis can be readily prepared by a person of skill in the art or purchased, such as from C B S Scientific Co , Inc or Scie-Plas
  • Methods may involve the use of organic solvents and/or alcohol to isolate nucleic acids, particularly miRNA used in methods and compositions of the invention
  • nucleic acids particularly miRNA used in methods and compositions of the invention
  • this disclosure provides methods for efficiently isolating small RNA molecules from cells comprising adding an alcohol solution to a cell lysate and applying the alcohol/lysate mixture to a solid support before elutmg the RNA molecules from the solid support
  • the amount of alcohol added to a cell lysate achieves an alcohol concentration of about 55% to 60% While different alcohols can be employed, ethanol works well
  • a solid support may be any structure, and it includes beads, filters, and columns, which may include a mineral or polymer support with electronegative groups A glass fiber filter or column has worked particularly well for such isolation procedures
  • miRNA isolation processes include a) lysmg cells m the sample with a lysing solution comprising guamdimum, wherein a lysate with a concentration of at least about 1 M guamdimum is produced, b) extracting miRNA molecules from the lysate with an extraction solution composing phenol, c) adding to the lysate an alcohol solution for forming a lysate/alcohol mixture, wherein the concentration of alcohol in the mixture is between about 35% to about 70%, d) applying the lysate/alcohol mixture to a solid support, e) eluting the miRNA molecules from the solid support with an ionic solution, and, f) captu ⁇ ng the miRNA molecules Typically the sample is dried and resuspended m a liquid and volume appropnate for subsequent manipulation V.
  • LABELS AND LABELING TECHNIQUES LABELS AND LABELING TECHNIQUES
  • the present invention concerns miRNA that are labeled It is contemplated that miRNA may first be isolated and/or purified poor to labeling This may achieve a reaction that more efficiently labels the miRNA, as opposed to other RNA in a sample in which the miRNA is not isolated or punfied p ⁇ or to labeling In many embodiments of the invention, the label is non-radioactive Generally, nucleic acids may be labeled by adding labeled nucleotides (one-step process) or adding nucleotides and labeling the added nucleotides (two-step process)
  • nucleic acids are labeled by catalytically adding to the nucleic acid an already labeled nucleotide or nucleotides
  • One or more labeled nucleotides can be added to miRNA molecules See U S Patent 6,723,509, which is hereby incorporated by reference
  • an unlabeled nucleotide or nucleotides is catalytically added to a miRNA, and the unlabeled nucleotide is modified with a chemical moiety that enables it to be subsequently labeled
  • the chemical moiety is a reactive amine such that the nucleotide is an amine-modified nucleotide
  • amine- modified nucleotides are well known to those of skill in the art, many being commercially available such as from Ambion, Sigma, Jena Bioscience, and T ⁇ Link
  • the issue for labeling miRNA is how to label the already existing molecule
  • the present invention concerns the use of an enzyme capable of using a di- or tn-phosphate ribonucleotide or deoxyribonucleotide as a substrate for its addition to a miRNA Moreover, in specific embodiments, it involves using a modified di- or t ⁇ -phosphate ribonucleotide, which is added to the 3' end of a miRNA Enzymes capable of adding such nucleotides include, but are not limited to, poly(A) polymerase, terminal transferase, and polynucleotide phosphorylase
  • a ligase is contemplated as not being the enzyme used to add the label, and instead, a non-hgase enzyme is employed Terminal transferase catalyzes the addition of nucleotides to the 3' terminus of a nucleic acid Polynucleotide
  • Labels on miRNA or miRNA probes may be colo ⁇ metnc (includes visible and UV spectrum, including fluorescent), luminescent, enzymatic, or positron emitting (including radioactive) The label may be detected directly or indirectly Radioactive labels include 125 1, 32 P, 33 P, and 35 S Examples of enzymatic labels include alkaline phosphatase, luciferase, horseradish peroxidase, and ⁇ -galactosidase Labels can also be proteins with luminescent properties, e g , green fluorescent protein and phicoerythnn
  • the colo ⁇ met ⁇ c and fluorescent labels contemplated for use as conjugates include, but are not limited to, Alexa Fluor dyes, BODIPY dyes, such as BODIPY FL, Cascade Blue, Cascade Yellow, couma ⁇ n and its de ⁇ vatives, such as 7-amino-4-methylcoumarm, ammocouma ⁇ n and hydroxycouma ⁇ n, cyanine dyes, such as Cy3 and Cy5, eosms and erythrosins, fluorescein and its de ⁇ vatives, such as fluorescein isothiocyanate, macrocyclic chelates of lanthamde ions, such as Quantum DyeTM, Manna Blue, Oregon Green, rhodamine dyes, such as rhodamine red, tetramethylrhodamme and rhodamme 6G, Texas Red, , fluorescent energy transfer dyes, such as thiazole orange-ethidium heterodimer, and, TOTAB
  • Molecular Probes include, Alexa Fluor 488-5-UTP, Fluorescein- 12-UTP, BODIPY FL-14-UTP, BODIPY TMR-14-UTP, Tetramethylrhodamine-6-UTP, Alexa Fluor 546-14- UTP, Texas Red-5-UTP, and BODIPY TR-14-UTP
  • fluorescent ribonucleotides are available from Amersham Biosciences, such as Cy3-UTP and Cy5-UTP
  • Examples of fluorescently labeled deoxy ⁇ bonucleotides include Dmitrophenyl
  • (DNP)-11-dUTP Cascade Blue-7-dUTP, Alexa Fluor 488-5-dUTP, Fluorescein-12-dUTP, Oregon Green 488-5-dUTP, BODIPY FL-14-dUTP, Rhodamine Green-5-dUTP, Alexa Fluor 532-5-dUTP, BODIPY TMR-14-dUTP, Tetramethylrhodamine-6-dUTP, Alexa Fluor 546- 14-dUTP, Alexa Fluor 568-5-dUTP, Texas Red-12-dUTP, Texas Red-5-dUTP, BODIPY TR- 14-dUTP, Alexa Fluor 594-5-dUTP, BODIPY 630/650-14-dUTP, BODIPY 650/665-14- dUTP, Alexa Fluor 488-7-OBEA-dCTP, Alexa Fluor 546-16-OBEA-dCTP, Alexa Fluor 594- 7-OBEA-dCTP,
  • FRET fluorescence resonance energy transfer
  • the label may not be detectable per se, but indirectly detectable or allowing for the isolation or separation of the targeted nucleic acid
  • the label could be biotm, digoxigemn, polyvalent cations, chelator groups and the other hgands, include hgands for an antibody C.
  • a number of techniques for visualizing or detecting labeled nucleic acids are readily available such techniques include, microscopy, arrays, Fluorometry, Light cyclers or other real time PCR machines, FACS analysis, scintillation counters, Phosphoimagers, Geiger counters, MRI, CAT, antibody-based detection methods (Westerns, immunofluorescence, lmmunohistochermstry), histochemical techniques, HPLC (Griffey et al , 1997), spectroscopy, capillary gel electrophoresis (Cummins et al , 1996), spectroscopy, mass spectroscopy, radiological techniques, and mass balance techniques
  • FRET fluorescent resonance energy transfer
  • compositions desc ⁇ bed herein may be comprised in a kit
  • reagents for isolating miRNA, labeling miRNA, and/or evaluating a miRNA population using an array, nucleic acid amplification, and/or hybridization can be included in a kit, as well reagents for preparation of samples from blood samples
  • the kit may further include reagents for creating or synthesizing miRNA probes
  • the kits will thus comp ⁇ se, in suitable container means, an enzyme for labeling the miRNA by incorporating labeled nucleotide or unlabeled nucleotides that are subsequently labeled
  • the kit can include amplification reagents
  • the kit may include various supports, such as glass, nylon, polymeric beads, and the like, and/or reagents for coupling any probes and/or target nucleic acids It may also include one or more buffers, such as reaction buffer, labeling buffer, washing buffer, or a hybridization buffer
  • kits of the invention include an array containing miRNA probes, as descnbed in the application
  • An array may have probes corresponding to all known miRNAs of an organism or a particular tissue or organ in particular conditions, or to a subset of such probes
  • the subset of probes on arrays of the invention may be or include those identified as relevant to a particular diagnostic, therapeutic, or prognostic application
  • the array may contain one or more probes that is indicative or suggestive of (1) a disease or condition (acute myeloid leukemia), (2) susceptibility or resistance to a particular drug or treatment, (3) susceptibility to toxicity from a drug or substance, (4) the stage of development or seventy of a disease or condition (prognosis), and (5) genetic predisposition to a disease or condition
  • kits including an array
  • nucleic acid molecules that contain or can be used to amplify a sequence that is a variant of, identical to or complementary to all or part of any of SEQ IDs descnbed herein
  • a kit or array of the invention can contain one or more probes for the miRNAs identified by the SEQ IDs described herein Any nucleic acid discussed above may be implemented as part of a kit
  • kits may be packaged either in aqueous media or in lyophihzed form
  • the container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably ahquoted Where there is more than one component in the kit
  • kits of the present invention also will typically include a means for containing the nucleic acids, and any other reagent containers in close confinement for commercial sale Such containers may include injection or blow molded plastic containers into which the desired vials are retained
  • the liquid solution is an aqueous solution, with a ste ⁇ le aqueous solution being particularly preferred
  • the components of the kit may be provided as d ⁇ ed powder(s)
  • the powder can be reconstituted by the addition of a suitable solvent
  • the solvent may also be provided m another container means
  • labeling dyes are provided as a dried power It is contemplated that 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 120, 130, 140, 150, 160, 170, 180, 190, 200, 300, 400, 500, 600, 700, 800, 900, 1000 ⁇ g or at least or at most those amounts of dried dye are provided in kits of the invention
  • the dye may then be resuspended in any suitable solvent, such as DMSO
  • kits generally will comprise, m suitable means, distinct containers for each individual reagent or solution
  • kits will also include instructions for employing the kit components as well the use of any other reagent not included in the kit Instructions may include variations that can be implemented
  • Kits of the invention may also include one or more of the following Control RNA, nuclease-free water, RNase-free containers, such as 1 5 ml rubes, RNase-free elution tubes, PEG or dextran, ethanol, acetic acid, sodium acetate, ammonium acetate, guanidimum, detergent, nucleic acid size marker, RNase-free tube tips, and RNase or DNase inhibitors It is contemplated that such reagents are embodiments of kits of the invention Such kits, however, are not limited to the particular items identified above and may include any reagent used for the manipulation or characterization of miRNA
  • HSA-MIR-143 miRNAs are believed to regulate gene expression by binding to target mRNA transcripts and (1) initiating transcript degradation or (2) alte ⁇ ng protein translation from the transcript Translational regulation leading to an up or down change in protein expression may lead to changes in activity and expression of downstream gene products and genes that are in turn regulated by those proteins These numerous regulatory effects may be revealed as changes in the global mRNA expression profile Microarray gene expression analyses were performed to identify genes that are mis-regulated by hsa-miR-143 expression
  • Manipulation of the expression levels of the genes listed in Table 1 represents a potentially useful therapy for cancer and other diseases in which increased or reduced expression of hsa-miR-143 has a role in the disease
  • EXAMPLE 2 CELLULAR PATHWAYS AFFECTED BY HSA-miR-143
  • Table 1 The mis-regulation of gene expression by hsa-miR-143 (Table 1) affects many cellular pathways that represent potential therapeutic targets for the control of cancer and other diseases and disorders
  • the inventors determined the identity and nature of the cellular genetic pathways affected by the regulatory cascade induced by hsa-miR-143 expression
  • Cellular pathway analyses were performed using Ingenuity Pathways Analysis (Version 40, Ingenuity ® Systems, Redwood City, CA) Alteration of a given pathway was determined by Fisher's Exact test (Fisher, 1922) The most significantly affected pathways following over- expression of hsa-miR-143 in A549 cells are shown in Table 2
  • Table 2 These data demonstrate that hsa-miR-143 directly or indirectly affects the expression of several, cellular proliferation-, development-, and cell growth-related genes and thus primarily affects functional pathways related to cellular growth,
  • the predicted gene targets of hsa-miR-143 whose mRNA expression levels are affected by hsa-miR-143 represent particularly useful candidates for cancer therapy and therapy of other diseases through manipulation of their expression levels
  • Hsa- miR-143 directly or indirectly regulates the transc ⁇ pts of proteins that are critical in the regulation of these pathways. Many of these targets have inherent oncogenic or tumor suppressor activity Hsa- miR-143 targets that have prognostic and/or therapeutic value for the treatment of va ⁇ ous malignancies are shown in Table 5
  • Hsa-miR-143 targeted cancer genes are regulators of the cell cycle, transc ⁇ ption, intracellular signaling, apoptosis and the thioredoxm redox pathway Hsa-miR-143 regulates cell cycle progression by alte ⁇ ng the expression of Weel, the retinoblastoma-like 1 protein
  • RBLl cyclins Dl and Gl
  • RBLl also known as plO7
  • plO7 is a member of the retinoblastoma tumor suppressor protein family that includes the pocket proteins plO7, pl30 and pRb
  • RBLl interacts with the E2F family of transcription factors and blocks cell cycle progression and DNA replication (Sherr and McCormick, 2002)
  • a subset of cancers show deregulated expression of RBLl (Takimoto et al , 1998, Claudio et al , 2002, Wu et al , 2002, Ito et al , 2003)
  • Transient transfection of hsa-miR-143 leads to a decrease in RBLl mRNA levels which may suggest a proliferative function for hsa-miR-143
  • negative regulation of cyclm Dl and positive regulation of cyclm Gl are indicators of a growth-inhibitory role for hsa-miR-143 Cych
  • Pdcd-4 (programmed cell death 4) is a tumor suppressor that is induced in response to apoptosis in normal cells
  • the growth inhibitory properties of Pdcd-4 are due to Pdcd-4 mediated inhibition of the c-Jun proto- oncoprotein, inhibition of cap-dependent mRNA translation and activation of the p21Wafl/Cipl CDK inhibitor (Yang et al , 2003, Bitomsky et al , 2004, Goke et al , 2004)
  • Pdcd-4 frequently shows reduced or lost expression in va ⁇ ous human malignancies, such as gliomas, hepatocellular carcinomas, lung and renal cell carcinomas (Jansen et al , 2004, Zhang et al , 2006, Gao et al , 2007) Expression of Pdcd-4 interferes
  • TGF- ⁇ transforming growth factor beta receptor 2
  • AKAP 12 A-kinase anchor protein 12
  • TGFBR-2 forms a functional complex with TGFBR-I and is the primary receptor for TGF- ⁇ (Massague et al , 2000)
  • Central role of TGF- ⁇ is inhibition of cellular growth of numerous cell types, such as epithelial, endothelial, hematopoietic neural and mesenchymal cells Many mammary and colorectal carcinomas with microsatellite instability harbor inactivating mutations of TGFBR-2, and therefore escape the growth-inhibitory function of TGF- ⁇
  • hsa-miR-143 appears to have tumor suppressor potential This view is supported by our observation that most cancers show reduced expression of miR-143
  • hsa- miR-143 also regulates gene expression in a manner that suggests a role for hsa-miR-143 in the development or progression of disease
  • hsa-miR-143 stimulates the expression of thioredoxin (TXN), a 12-kDa thiol reductase targeting various proteins and multiple pathways Thioredoxin modulates the activity of transcnption factors, induces the expression of angiogenic Hif-l ⁇ (hypoxia induced factor l ⁇ ) as well as VEGF (vascular endothelial growth factor) and can act as a proliferative and anti-apoptotic agent (Marks, 2006) In accord, carcinomas of the lung, pancreas, cervix
  • hsa- miR-143 governs the activity of proteins that are critical regulators of cell proliferation and survival These targets are frequently deregulated m human cancer Based on this review of the genes and related pathways that are regulated by miR-143, introduction of hsa-miR-143 or an anti-hsa-miR-143 into a variety of cancer cell types would likely result in a therapeutic response

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Abstract

The present invention concerns methods and compositions for identifying genes or genetic pathways modulated by miR-143, using miR-143 to modulate a gene or gene pathway, using this profile in assessing the condition of a patient and/or treating the patient with an appropriate miRNA.

Description

DESCRIPTION
MIR-143 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
BACKGROUND OF THE INVENTION This application claims the benefit of priority to U S Provisional Patent
Application Seπal No 60/939,573 filed May 22, 2007 and U S Provisional Patent Application Seπal No 60/826,173 filed September 19, 2006, which are hereby incorporated by reference in their entirety
I. FIELD OF THE INVENTION The present invention relates to the fields of molecular biology and medicine
More specifically, the invention relates to methods and compositions for the treatment of diseases or conditions that are affected by miR-143 microRNAs, micro RN A expression, and genes and cellular pathways directly and indirectly modulated by such II. BACKGROUND
In 2001, several groups used a cloning method to isolate and identify a large group of "microRNAs" (miRNAs) from C elegans, Drosophila, and humans (Lagos- Qumtana et al , 2001, Lau et al , 2001, Lee and Ambros, 2001) Several hundred miRNAs have been identified in plants and animals — including humans — that do not appear to have endogenous siRNAs Thus, while similar to siRNAs, miRNAs are distinct miRNAs thus far observed have been approximately 21-22 nucleotides in length, and they arise from longer precursors transcribed from non-protem-encodmg genes See review of Carrington et al (2003) The precursors form structures that fold back on themselves in self-complementary regions, they are then processed by the nuclease Dicer (in animals) or DCLl (in plants) to generate the short double- stranded miRNA One of the miRNA strands is incorporated into a complex of proteins and miRNA called the RNA-mduced silencing complex (RISC) The miRNA guides the RISC complex to a target mRNA, which is then cleaved or translationally silenced, depending on the degree of sequence complementarity of the miRNA to its target mRNA Currently, it is believed that perfect or nearly perfect complementaπty leads to mRNA degradation, as is most commonly observed in plants In contrast, imperfect base pairing, as is primarily found in animals, leads to translational silencing However, recent data suggest additional complexity (Bagga et al , 2005, Lim et al , 2005), and mechanisms of gene silencing by miRNAs remain under intense study
Recent studies have shown that expression levels of numerous miRNAs are associated with vaπous cancers (reviewed in Esquela-Kerscher and Slack, 2006, Calm and Croce, 2006) miRNAs have also been implicated in regulating cell growth and cell and tissue differentiation - cellular processes that are associated with the development of cancer
The inventors previously demonstrated that hsa-miR-143 is involved with the regulation of numerous cell activities that represent intervention points for cancer therapy and for therapy of other diseases and disorders (U S Patent Applications serial number 11/141,707 filed May 31, 2005 and seπal number 11/273,640 filed November 14, 2005) Upon evaluation of 24 different human tissues, hsa-miR-143 was found to be preferentially expressed in human prostate and colon tissue samples The inventors observed that hsa-miR-143 expression is lower in many human cancer tumor samples including lung, colon, breast, bladder, and thyroid tumors, than in normal cells from the same patients Overexpression of hsa-miR-143 in human leukemia cells (Jurkat) increased proliferation of those cells The inventors also found hsa-miR-143 to be up-regulated in bram tissues of Alzheimer's patients Other investigators have also observed that miR-143 is down-regulated in colorectal tumors when compared with matched normal samples (Michael et al 2003, Akao et al 2006) and that miR-143 may be involved in the differentiation of human adipocytes (fat storage cells) (Esau et al 2004)
Bioinformatics analyses suggest that any given miRNA may bind to and alter the expression of up to several hundred different genes In addition, a single gene may be regulated by several miRNAs Thus, each miRNA may regulate a complex interaction among genes, gene pathways, and gene networks Mis-regulation or alteration of these regulatory pathways and networks, involving miRNAs, are likely to contribute to the development of disorders and diseases such as cancer Although bioinformatics tools are helpful in predicting miRNA binding targets, all have limitations Because of the imperfect complementarity with their target binding sites, it is difficult to accurately predict the mRNA targets of miRNAs with biomformatics tools alone Furthermore, the complicated interactive regulatory networks among miRNAs and target genes make it difficult to accurately predict which genes will actually be mis-regulated in response to a given miRNA
Correcting gene expression errors by manipulating miRNA expression or by repamng miRNA mis-regulation represent promising methods to repair genetic disorders and cure diseases like cancer A current, disabling limitation of this approach is that, as mentioned above, the details of the regulatory pathways and networks that are affected by any given miRNA, including miR-143, remain largely unknown This represents a significant limitation for treatment of cancers in which miR-143 may play a role A need exists to identify the genes, genetic pathways, and genetic networks that are regulated by or that may regulate hsa-miR-143 expression
SUMMARY OF THE INVENTION The present invention provides additional compositions and methods by identifying genes that are direct targets for miR-143 regulation or that are indirect or downstream targets of regulation following the miR-143-mediated modification of another gene(s) expression Furthermore, the invention describes gene, disease, and/or physiologic pathways and networks that are influenced by miR-143 and its family members In certain aspects, compositions of the invention are administered to a subject having, suspected of having, or at πsk of developing a metabolic, an immunologic, an infectious, a cardiovascular, a digestive, an endocπne, an ocular, a genitourinary, a blood, a musculoskeletal, a nervous system, a congenital, a respiratory, a skin, or a cancerous disease or condition In particular aspects, a subject or patient may be selected for treatment based on expression and/or aberrant expression of one or more miRNA or mRNA In a further aspect, a subject or patient may be selected for treatment based on aberrations in one or more biologic or physiologic pathway(s), including aberrant expression of one or more gene associated with a pathway, or the aberrant expression of one or more protein encoded by one or more gene associated with a pathway In still a further aspect, a subject or patient may be selected based on aberrations in miRNA expression, or biologic and/or physiologic pathway(s) A subject may be assessed for sensitivity, resistance, and/or efficacy of a therapy or treatment regime based on the evaluation and/or analysis of miRNA or mRNA expression or lack thereof A subject may be evaluated for amenability to certain therapy pπor to, during, or after administration of one or therapy to a subject or patient Typically, evaluation or assessment may be done by analysis of miRNA and/or mRNA, as well as combination of other assessment methods that include but are not limited to histology, lmmunohistochemistry, blood work, etc
In some embodiments, an infectious disease or condition includes a bacterial, viral, parasite, or fungal infection Many of these genes and pathways are associated with various cancers and other diseases Cancerous conditions include, but are not limited to astrocytoma, acute myelogenous leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastπc carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, lung carcinoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, urothelial carcinoma wherein the modulation of one or more gene is sufficient for a therapeutic response Typically a cancerous condition is an aberrant hyperprohferative condition associated with the uncontrolled growth or inability to undergo cell death, including apoptosis
The present invention provides methods and compositions for identifying genes that are direct targets for miR-143 regulation or that are downstream targets of regulation following the miR-143-mediated modification of upstream gene expression Furthermore, the invention descnbes gene pathways and networks that are influenced by miR-143 expression in biological samples Many of these genes and pathways are associated with various cancers and other diseases The altered expression or function of miR-143 in cells would lead to changes in the expression of these key genes and contribute to the development of disease Introducing miR-143 (for diseases where the miRNA is down-regulated) or a miR-143 inhibitor (for diseases where the miRNA is up-regulated) into disease cells or tissues would result in a therapeutic response The identities of key genes that are regulated directly or indirectly by miR-143 and the disease with which they are associated are provided herein In certain aspects a cell may be an epithelial, stromal, or mucosal cell The cell can be, but is not limited to bram, a neuronal, a blood, an esophageal, a lung, a cardiovascular, a liver, a breast, a bone, a thyroid, a glandular, an adrenal, a pancreatic, a stomach, a intestinal, a kidney, a bladder, a prostate, a uterus, an ovarian, a testicular, a splenic, a skin, a smooth muscle, a cardiac muscle, or a stπated muscle cell In certain aspects, the cell, tissue, or target may not be defective in miRNA expression yet may still respond therapeutically to expression or over expression of a miRNA miR- 143 could be used as a therapeutic target for any of these diseases In certain embodiments miR-143 can be used to modulate the activity of miR-143 m a subject, organ, tissue, or cell
A cell, tissue, or subject may be a cancer cell, a cancerous tissue, harbor cancerous tissue, or be a subject or patient diagnosed or at nsk of developing a disease or condition In certain aspects a cancer cell is a neuronal, glial, lung, liver, bram, breast, bladder, blood, leukemic, colon, endometπal, stomach, skin, ovarian, fat, bone, cervical, esophageal, pancreatic, prostate, kidney, or thyroid cell In still a further aspect cancer includes, but is not limited to astrocytoma, acute myelogenous leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, lung carcinoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, urothelial carcinoma
Embodiments of the invention include methods of modulating gene expression, or biologic or physiologic pathways in a cell, a tissue, or a subject composing administering to the cell, tissue, or subject an amount of an isolated nucleic acid or mimetic thereof compπsing a miR-143 nucleic acid, mimetic, or inhibitor in an amount sufficient to modulate the expression of a gene positively or negatively modulated by a miR-143 miRNA A "miR-143 nucleic acid sequence" or "miR-143 inhibitor" includes the full length precursor of miR-143, or complement thereof, as well as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more nucleotides of a precursor miRNA or its processed sequence, or complement thereof, including all ranges and integers there between. In 5 certain embodiments, the miR-143 nucleic acid sequence or miR-143 inhibitor contains the full-length processed miRNA sequence or complement thereof and is referred to as the "miR-143 full-length processed nucleic acid sequence" or "miR-143 full-length processed inhibitor sequence." In still further aspects, the miR-143 nucleic acid composes at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
10 232, 24, 25, 50 nucleotide (including all ranges and integers there between) segment or complementary segment of miR-143 that is at least 75, 80, 85, 90, 95, 98, 99 or 100% identical to SEQ ID NO-I to SEQ ID NO:13 The general term miR-143 includes all members of the miR-143 family that share at least part of a mature miR- 143 sequence (UGAGAUGAAGCACUGUAGCUCA (SEQ ID NO:1)) or a
15 complement thereof.
A "miR-143 nucleic acid sequence" includes the full length precursor of miR- 143 and other family members that include lla-mir-143 (MI0002552) GCGCAGCGCCCUGUC UCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGA
20 GAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUCUGCAGC (SEQ ID NO:2); xtr-mir-143 (MI0004937)
UGUCUCCCAGCCCAAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGA GUCUGAGAUGAAGCACUGUAGCUCGGGAAGGGGGAAU (SEQ ID NO.3); dre-mir-143-2 (MI0002008)
25 GAUCUACAGUCGUCUGGCCCGCGGUGCAGUGCUGCAUCUCUG
GUCAACUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGAGGACAACAC UGUCAGCUC (SEQ ID NO:4); rno-mir-143 (MI0000916) GCGGAGCGCCUG UCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCU GAGAUGAAGCACUGUAGCUCAGGAAGGGAGAAGAUGUUCUGCAGC (SEQ
30 ID NO.5), ptr-mir-143 (MI0002549)
GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUG CAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAA GAGAGAAGUUUUUCUGCAGC (SEQ ID NO:6); ppy-mir-143 (MI0002551) GCGCAGC
GCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGG AGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUCUGCA GC (SEQ ID NO:7); ggo-mir-143 (MI0002550) GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCU
GCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA AGAGAGAAGUUGUUCUGCAGC (SEQ ID NO:8); dre-mir-143-1 (MI0002007) GAUCUACAGUCGUCUGGCCCGCGGUGCAGUGCUGCAUCUCUGGUCAACU GGGAGUCUGAGAUGAAGCACUGUAGCUCGGGAGGACAACACUGUCAGC UC (SEQ ID NO:9); hsa-mir-143 (MI0000459)
GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUG
CUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAG GAAGAGAGAAGUUGUUCUGCAGC (SEQ ID NO: 10); ppa-mir-143 (MI0002553) GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUC AGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUU UUCUGCAGC (SEQ ID NO:11); mdo-mir-143 (MI0005302) CCCGAGGUGCAGUGCUGCAUCUCUGGUC AGUUGUGAGUCUGAGAUGAAGCACUGUAGCUCGGG (SEQ ID NO: 12); mmu-mir-143 (MI0000257)
CCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGA GAUGAAGCACUGUAGCUCAGG (SEQ ID NO: 13). In certain aspects, a nucleic acid or mimetic of the present invention will comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more nucleotides of the precursor miRNA or its processed sequence, including all ranges and integers there between. In certain embodiments, the miR-143 nucleic acid sequence contains the full-length processed miRNA sequence and is referred to as the "miR-143 full-length processed nucleic acid sequence." In still further aspects, a miR-143 comprises at least one 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 50 nucleotide (including all ranges and integers there between) segment of miR-143 that is at least 75, 80, 85, 90, 95, 98, 99 or 100% identical to SEQ ID NOs provided herein. In specific embodiments, a miR-143 or miR-143 inhibitor containing nucleic acid is hsa-miR-143 or hsa-miR-143 inhibitor, or a variation thereof In a further aspect, a miR-143 nucleic acid or miR-143 inhibitor can be administered with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more miRNAs or miRNA inhibitors miRNA or its complement can be administer concurrently, in sequence or in an ordered progression In certain aspects, a miR-143 or miR-143 inhibitor can be administered in combination with one or more of let-7, miR-15a, miR-16, miR-20, miR-21, miR-26a, miR-31, miR-34a, miR-126, miR-145, miR-147, miR-188, miR-200b, miR-200c, miR-215, miR-216, miR-292-3p, and/or miR-331 All or combinations of miRNAs or inhibotrs thereof may be administered in a single formulation Administration may be before, duπng or after a second therapy miR-143 nucleic acids or complement thereof may also include vaπous heterologous nucleic acid sequence, ; e those sequences not typically found operatively coupled with miR-143 in nature, such as promoters, enhancers, and the like The miR-143 nucleic acid is a recombinant nucleic acid, and can be a ribonucleic acid or a deoxyribonucleic acid The recombinant nucleic acid may comprise a miR-143 or miR-143 inhibitor expression cassette, i e , a nucleic acid segment that expresses a nucleic acid when introduce mto an environment containing components for nucleic acid synthesis In a further aspect, the expression cassette is composed in a viral, or plasmid DNA vector or other therapeutic nucleic acid vector or delivery vehicle, including liposomes and the like In certain aspects, viral vectors can be administered at IxIO2, IxIO3, IxIO4 IxIO5, IxIO6, IxIO7, IxIO8, IxIO9, IxIO10, IxIO11, IxIO12, IxIO13, lxlθ'4 pfu or viral particle (vp)
In a particular aspect, the miR-143 nucleic acid or miR-143 inhibitor is a synthetic nucleic acid Moreover, nucleic acids of the invention may be fully or partially synthetic In still further aspects, a nucleic acid of the invention or a DNA encoding such can be administered at 0 001, 0 01, 0 1, 1, 10, 20, 30, 40, 50, 100, 200,
400, 600, 800, 1000, 2000, to 4000 μg or mg, including all values and ranges there between In yet a further aspect, nucleic acids of the invention, including synthetic nucleic acid, can be administered at 0 001, 0 01, 0 1, 1, 10, 20, 30, 40, 50, 100, to 200 μg or mg per kilogram (kg) of body weight Each of the amounts descnbed herein may be administered over a peπod of time, including 0 5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, minutes, hours, days, weeks, months or years, including all values and ranges there between
In certain embodiments, administration of the composition(s) can be enteral or parenteral In certain aspects, enteral administration is oral In further aspects, parenteral administration is mtralesional, intravascular, intracranial, intrapleural, intratumoral, intraperitoneal, intramuscular, lntralymphatic, mtraglandular, subcutaneous, topical, lntrabronchial, intratracheal, intranasal, inhaled, or instilled Compositions of the invention may be administered regionally or locally and not necessaπly directly into a lesion In certain aspects, the gene or genes modulated comprises 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200 or more genes or combinations of genes identified m Tables 1, 3, 4, and/or 5 In still further aspects, the gene or genes modulated may exclude 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 175 or more genes or combinations of genes identified m Tables 1, 3, 4, and/or 5 Modulation includes modulating transcπption, mRNA levels, mRNA translation, and/or protein levels in a cell, tissue, or organ In certain aspects the expression of a gene or level of a gene product, such as mRNA or encoded protein, is down-regulated or up-regulated In a particular aspect the gene modulated comprises or is selected from (and may even exclude) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 27, 28, or all of the genes identified in Tables 1, 3, 4, and/or 5, or any combinations thereof In certain embodiments a gene modulated or selected to be modulated is from Table 1 In further embodiments a gene modulated or selected to be modulated is from Table 3 In still further embodiments a gene modulated or selected to be modulated is from Table 4 In yet further embodiments a gene modulated or selected to be modulated is from Table 5 Embodiments of the invention may also include obtaining or assessing a gene expression profile or miRNA profile of a target cell pπor to selecting the mode of treatment, e g , administration of a miR-143 nucleic acid, inhibitor of miR-143, or mimetics thereof The database content related to nucleic acids and genes designated by an accession number or a database submission are incorporated herein by reference as of the filing date of this application In certain aspects of the invention one or more miRNA or miRNA inhibitor may modulate a single gene In a further aspect, one or more genes in one or more genetic, cellular, or physiologic pathways can be modulated by one or more miRNAs or complements thereof, including miR-143 nucleic acids and miR-143 inhibitors m combination with other miRNAs miR-143 nucleic acids may also include vanous heterologous nucleic acid sequence, i e , those sequences not typically found operatively coupled with miR-143 in nature, such as promoters, enhancers, and the like The miR-143 nucleic acid is a recombinant nucleic acid, and can be a ribonucleic acid or a deoxyribonucleic acid The recombinant nucleic acid may compose a miR-143 expression cassette In a further aspect, the expression cassette is comprised in a viral, or plasmid DNA vector or other therapeutic nucleic acid vector or delivery vehicle, including liposomes and the like In a particular aspect, the miR-143 nucleic acid is a synthetic nucleic acid Moreover, nucleic acids of the invention may be fully or partially synthetic
Table 1. Genes with increased (positive values) or decreased (negative values) expression following transfection of human cancer cells with pre-miR hsa-miR-143
A further embodiment of the invention is directed to methods of modulating a cellular pathway comprising administering to the cell an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence or a miR-143 inhibitor A cell, tissue, or subject may be a cancer cell, a cancerous tissue or harbor cancerous tissue, or a cancer patient The database content related to all nucleic acids and genes designated by an accession number or a database submission are incorporated herein by reference as of the filing date of this application
A further embodiment of the invention is directed to methods of modulating a cellular pathway comprising administering to the cell an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence m an amount sufficient to modulate the expression, function, status, or state of a cellular pathway, in particular those pathways descπbed m Table 2 or the pathways known to include one or more genes from Table 1, 3, 4, and/or 5 Modulation of a cellular pathway includes, but is not limited to modulating the expression of one or more gene(s) Modulation of a gene can include inhibiting the function of an endogenous miRNA or providing a functional miRNA to a cell, tissue, or subject Modulation refers to the expression levels or activities of a gene or its related gene product (e g , mRNA) or protein, e g , the mRNA levels may be modulated or the translation of an mRNA may be modulated Modulation may increase or up regulate a gene or gene product or it may decrease or down regulate a gene or gene product (e g , protein levels or activity)
Still a further embodiment includes methods of administering an miRNA or mimic thereof, and/or treating a subject or patient having, suspected of having, or at πsk of developing a pathological condition compπsing one or more of step (a) administering to a patient or subject an amount of an isolated nucleic acid comprising a miR-143 nucleic acid sequence or a miR-143 inhibitor in an amount sufficient to modulate expression of a cellular pathway, and (b) administering a second therapy, wherein the modulation of the cellular pathway sensitizes the patient or subject, or increases the efficacy of a second therapy An increase in efficacy can include a reduction in toxicity, a reduced dosage or duration of the second therapy, or an additive or synergistic effect A cellular pathway may include, but is not limited to one or more pathway descnbed in Table 2 below or a pathway that is know to include one or more genes of Tables 1, 3, 4, and/or 5 The second therapy may be administered before, duπng, and/or after the isolated nucleic acid or miRNA or inhibitor is administered
A second therapy can include administration of a second miRNA or therapeutic nucleic acid such as a siRNA or antisense oligonucleotide, or may include various standard therapies, such as pharmaceuticals, chemotherapy, radiation therapy, drug therapy, immunotherapy, and the like Embodiments of the invention may also include the determination or assessment of gene expression or gene expression profile for the selection of an appropπate therapy In a particular aspect, a second therapy is a chemotherapy A chemotherapy can include, but is not limited to pachtaxel, cisplatm, carboplatm, doxorubicin, oxahplatin, larotaxel, taxol, lapatmib, docetaxel, methotrexate, capecitabine, vinorelbine, cyclophosphamide, gemcitabine, amrubicin, cytarabme, etoposide, camptothecin, dexamethasone, dasatimb, tipifarnib, bevacizumab, sirohmus, temsirolimus, everohmus, lonafarnib, cetuximab, erlotimb, gefϊtmib, imatmib mesylate, πtuximab, trastuzumab, nocodazole, sorafemb, sumtimb, bortezomib, alemtuzumab, gemtuzumab, tositumomab or ibritumomab Embodiments of the invention include methods of treating a subject with a disease or condition comprising one or more of the steps of (a) determining an expression profile of one or more genes selected from Table 1, 3, 4, and/or 5, (b) assessing the sensitivity of the subject to therapy based on the expression profile, (c) selecting a therapy based on the assessed sensitivity, and (d) treating the subject using a selected therapy Typically, the disease or condition will have as a component, indicator, or resulting mis-regulation of one or more gene of Table 1, 3, 4, and/or 5 In certain aspects, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more miRNA may be used in sequence or m combination For instance, any combination of miR-143 or a miR-143 inhibitor with another miRNA Further embodiments include the identification and assessment of an expression profile indicative of miR-143 status m a cell or tissue compπsing expression assessment of one or more gene from Table 1, 3, 4, and/or 5, or any combination thereof
The term "miRNA" is used according to its ordinary and plain meaning and refers to a microRNA molecule found in eukaryotes that is involved in RNA-based gene regulation See, e g , Carπngton et al , 2003, which is hereby incorporated by reference The term can be used to refer to the single-stranded RNA molecule processed from a precursor or in certain instances the precursor itself
In some embodiments, it may be useful to know whether a cell expresses a particular miRNA endogenously or whether such expression is affected under particular conditions or when it is in a particular disease state Thus, in some embodiments of the invention, methods include assaying a cell or a sample containing a cell for the presence of one or more marker gene or mRNA or other analyte indicative of the expression level of a gene of interest Consequently, in some embodiments, methods include a step of generating an RNA profile for a sample The term "RNA profile" or "gene expression profile" refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample (eg , a plurality of nucleic acid probes that identify one or more markers from Tables 1, 3, 4, and/or 5), it is contemplated that the nucleic acid profile can be obtained using a set of RNAs, using for example nucleic acid amplification or hybridization techniques well know to one of ordinary skill in the art The difference in the expression profile m the sample from the patient and a reference expression profile, such as an expression profile from a normal or non-pathologic sample, is indicative of a pathologic, disease, or cancerous condition A nucleic acid or probe set compπsing or inhibitor can be selected based on observing two given miRNAs share a set of target genes or pathways listed in Tables 1 , 2, 4 and/or 5 that are altered in a particular disease or condition These two miRNAs may result in an improved therapy {e g , reduced toxicity, greater efficacy, prolong remission, or other improvements in a subjects condition), result in an increased efficacy, an additive efficacy, or a synergistic efficacy providing an additional or an improved therapeutic response Without being bound by any particular theorty, synergy of two miRNA can be a consequence of regulating the same genes or related genes (related by a common pathway or biologic end result) more effectively (e g , due to distinct binding sites on the same target or related target(s)) and/or a consequence of regulating different genes, but all of which have been implicated m a disease or condition
In certain aspects, miR-143 or a miR-143 inhibitor and let-7 can be administered to patients with acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastπc carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, melanoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma Further aspects include administering miR-143 or a miR-143 inhibitor and miR-15 to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometπal carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
In still further aspects, miR-143 or a miR-143 inhibitor and miR-16 are administered to patients with astrocytoma, breast carcinoma, bladder carcinoma, colorectal carcinoma, endometrial carcinoma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, non-small cell lung carcinoma, ovaπan carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma Aspects of the invention include methods where miR-143 or a miR-143 inhibitor and miR-20 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, melanoma, mantle cell lymphoma, neuroblastoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, or squamous cell carcinoma of the head and neck
In a further aspect, miR-143 or a miR-143 inhibitor and miR-21 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, multiple myeloma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
In still further aspects, miR-143 or a miR-143 inhibitor and miR-26a are administered to patients with acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, melanoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, or prostate carcinoma
In yet further aspects, miR-143 or a miR-143 inhibitor and miR-34a are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, multiple myeloma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovanan carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma
In certain aspects, miR-143 or a miR-143 inhibitor and miR-126 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, melanoma, mantle cell lymphoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
In still a further aspect, miR-143 or a miR-143 inhibitor and miR-147 are administered to patients with astrocytoma, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometnal carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastπc carcinoma, hepatocellular carcinoma, Hodgkm lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, non-Hodgkm lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma In yet another aspect, miR-143 or a miR-143 inhibitor and miR-188 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometnal carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, leukemia, melanoma, multiple myeloma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovanan carcinoma, esophageal carcinoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
In other aspects, miR-143 or a miR-143 inhibitor and miR-215 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometnal carcinoma, esophageal squamous cell carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, lipoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovanan carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma In certain aspects, miR-143 or a miR-143 inhibitor and miR-216 are administered to patients with astrocytoma, breast carcinoma, cervical carcinoma, colorectal carcinoma, endometπal carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, non-Hodgkm lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, prostate carcinoma, or squamous cell carcinoma of the head and neck
In a further aspect, miR-143 or a miR-143 inhibitor and miR-292-3p are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, lipoma, melanoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, thyroid carcinoma, or urothelial carcinoma In still a further aspect, miR-143 or a miR-143 inhibitor and miR-331 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carcinoma, cervical carcinoma, colorectal carcinoma, endometπal carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, leukemia, melanoma, myxofibrosarcoma, multiple myeloma, neuroblastoma, non-Hodgkin lymphoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
In yet a further aspect, miR-143 or a miR-143 inhibitor and miR-200b/c are administered to patients with breast carcinoma, cervical carcinoma, colorectal carcinoma, glioma, glioblastoma, gastnc carcinoma, hepatocellular carcinoma, leukemia, lipoma, multiple myeloma, non-small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, squamous cell carcinoma of the head and neck, or thyroid carcinoma
It is contemplated that when miR-143 or a miR-143 inhibitor is given in combination with one or more other miRNA molecules, the two different miRNAs or inhibitors may be given at the same time or sequentially In some embodiments, therapy proceeds with one miRNA or inhibitor and that therapy is followed up with therapy with the other miRNA or inhibitor 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 minutes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, 1, 2, 3, 4, 5, 6, 7 days, 1, 2, 3, 4, 5 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months or any such combination later
Further embodiments include the identification and assessment of an expression profile indicative of miR-143 status in a cell or tissue compπsing expression assessment of one or more gene from Table 1, 3, 4, and/or 5, or any combination thereof The term "miRNA" is used according to its ordinary and plain meaning and refers to a microRNA molecule found in eukaryotes that is involved m RNA-based gene regulation See, e g , Carπngton et al , 2003, which is hereby incorporated by reference The term can be used to refer to the smgle-stranded RNA molecule processed from a precursor or in certain instances the precursor itself or a mimetic thereof
In some embodiments, it may be useful to know whether a cell expresses a particular miRNA endogenously or whether such expression is affected under particular conditions or when it is in a particular disease state Thus, in some embodiments of the invention, methods include assaying a cell or a sample containing a cell for the presence of one or more miRNA marker gene or mRNA or other analyte indicative of the expression level of a gene of interest Consequently, in some embodiments, methods include a step of generating an RNA profile for a sample The term "RNA profile" or "gene expression profile" refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample (e g , a plurality of nucleic acid probes that identify one or more markers or genes from Tables 1, 3, 4, and/or 5), it is contemplated that the nucleic acid profile can be obtained using a set of RNAs, using for example nucleic acid amplification or hybridization techniques well know to one of ordinary skill in the art The difference in the expression profile in the sample from a patient and a reference expression profile, such as an expression profile from a normal or non-pathologic sample, or a digitized reference, is indicative of a pathologic, disease, or cancerous condition In certain aspects the expression profile is an indicator of a propensity to or probability of (i e , risk factor for a disease or condition) developing such a condition(s) Such a risk or propensity may indicate a treatment, increased monitoring, prophylactic measures, and the like A nucleic acid or probe set may comprise or identify a segment of a corresponding mRNA and may include all or part of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 ,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 100, 200, 500, or more segments, including any integer or range deπvable there between, of a gene or genetic marker, or a nucleic acid, mRNA or a probe representative thereof that is listed in Tables 1, 3, 4, and/or 5 or identified by the methods descπbed herein
Certain embodiments of the invention are directed to compositions and methods for assessing, prognosing, or treating a pathological condition in a patient comprising measuring or determining an expression profile of one or more miRNA or marker(s) in a sample from the patient, wherein a difference in the expression profile in the sample from the patient and an expression profile of a normal sample or reference expression profile is indicative of pathological condition and particularly cancer (e g , In certain aspects of the invention, the miRNAs, cellular pathway, gene, or genetic marker is or is representative of one or more pathway or marker described in Table 1, 2, 3, 4, and/or 5, including any combination thereof Aspects of the invention include diagnosing, assessing, or treating a pathologic condition or preventing a pathologic condition from manifesting For example, the methods can be used to screen for a pathological condition, assess prognosis of a pathological condition, stage a pathological condition, assess response of a pathological condition to therapy, or to modulate the expression of a gene, genes, or related pathway as a first therapy or to render a subject sensitive or more responsive to a second therapy In particular aspects, assessing the pathological condition of the patient can be assessing prognosis of the patient Prognosis may include, but is not limited to an estimation of the time or expected time of survival, assessment of response to a therapy, and the like In certain aspects, the altered expression of one or more gene or marker is prognostic for a patient having a pathologic condition, wherein the marker is one or more of Table 1, 3, 4, and/or 5, including any combination thereof Table 2. Significantly affected functional cellular pathways following hsa-miR-143 over-expression in human cancer cells
Table 3. Predicted target genes of hsa-miR-143 for Ref Seq ID reference - Pruitt et α/, 2005
Table 4. hsa-miR-143 targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miR hsa-miR-143 for Ref Seq ID reference - Pruitt et al , 2005
The predicted gene targets of hsa-miR-143 whose mRNA expression levels are affected by hsa-miR-143 represent particularly useful candidates for cancer therapy and therapy of other diseases through manipulation of their expression levels Certain embodiments of the invention include determining expression of one or more marker, gene, or nucleic acid segment representative of one or more genes, by using an amplification assay, a hybridization assay, or protein assay, a variety of which are well known to one of ordinary skill in the art In certain aspects, an amplification assay can be a quantitative amplification assay, such as quantitative RT- PCR or the like In still further aspects, a hybridization assay can include array hybridization assays or solution hybridization assays The nucleic acids from a sample may be labeled from the sample and/or hybridizing the labeled nucleic acid to one or more nucleic acid probes Nucleic acids, mRNA, and/or nucleic acid probes may be coupled to a support Such supports are well known to those of ordinary skill m the art and include, but are not limited to glass, plastic, metal, or latex In particular aspects of the invention, the support can be planar or in the form of a bead or other geometric shapes or configurations known in the art Proteins are typically assayed by lmmunoblottmg, chromatography, or mass spectrometry or other methods known to those of ordinary skill in the art The present invention also concerns kits containing compositions of the invention or compositions to implement methods of the invention In some embodiments, kits can be used to evaluate one or more marker molecules, and/or express one or more miRNA or miRNA inhibitor In certain embodiments, a kit contains, contains at least or contains at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 100, 150, 200 or more probes, recombinant nucleic acid, or synthetic nucleic acid molecules related to the markers to be assessed or an miRNA or miRNA inhibitor to be expressed or modulated, and may include any range or combination deπvable therein Kits may compose components, which may be individually packaged or placed in a container, such as a tube, bottle, vial, syringe, or other suitable container means Individual components may also be provided m a kit in concentrated amounts, in some embodiments, a component is provided individually in the same concentration as it would be in a solution with other components Concentrations of components may be provided as Ix, 2x, 5x, 1Ox, or 2Ox or more Kits for using probes, synthetic nucleic acids, recombinant nucleic acids, or non-synthetic nucleic acids of the invention for therapeutic, prognostic, or diagnostic applications are included as part of the invention Specifically contemplated are any such molecules corresponding to any miRNA reported to influence biological activity or expression of one or more marker gene or gene pathway descπbed herein In certain aspects, negative and/or positive controls are included in some kit embodiments The control molecules can be used to verify transfection efficiency and/or control for transfection- induced changes m cells
Certain embodiments are directed to a kit for assessment of a pathological condition or the πsk of developing a pathological condition in a patient by nucleic acid profiling of a sample comprising, in suitable container means, two or more nucleic acid hybridization or amplification reagents The kit can compπse reagents for labeling nucleic acids in a sample and/or nucleic acid hybridization reagents The hybridization reagents typically comprise hybridization probes Amplification reagents include, but are not limited to amplification primers, reagents, and enzymes
In some embodiments of the invention, an expression profile is generated by steps that include (a) labeling nucleic acid in the sample, (b) hybridizing the nucleic acid to a number of probes, or amplifying a number of nucleic acids, and (c) determining and/or quantitatmg nucleic acid hybridization to the probes or detecting and quantitatmg amplification products, wherein an expression profile is generated See U S Provisional Patent Application 60/575,743 and the U S Provisional Patent Application 60/649,584, and U S Patent Application Serial No 11/141,707 and U S Patent Application Senal No 11/273,640, all of which are hereby incorporated by reference Methods of the invention involve diagnosing and/or assessing the prognosis of a patient based on a miRNA and/or a marker nucleic acid expression profile In certain embodiments, the elevation or reduction in the level of expression of a particular gene or genetic pathway or set of nucleic acids in a cell is correlated with a disease state or pathological condition compared to the expression level of the same in a normal or non-pathologic cell or tissue sample This correlation allows for diagnostic and/or prognostic methods to be earned out when the expression level of one or more nucleic acid is measured in a biological sample being assessed and then compared to the expression level of a normal or non-pathologic cell or tissue sample It is specifically contemplated that expression profiles for patients, particularly those suspected of having or having a propensity for a particular disease or condition such as cancer, can be generated by evaluating any of or sets of the miRNAs and/or nucleic acids discussed in this application The expression profile that is generated from the patient will be one that provides information regarding the particular disease or condition In many embodiments, the profile is generated using nucleic acid hybridization or amplification, (e g , array hybridization or RT-PCR) In certain aspects, an expression profile can be used m conjunction with other diagnostic and/or prognostic tests, such as histology, protein profiles in the serum and/or cytogenetic assessment
Table 5. Tumor associated mRNAs altered by hsa-miR-143 having prognostic or therapeutic value for the treatment of various mali nancies
Abbreviations AC, astrocytoma, ALCL, anaplastic large cell lymphoma, ALL, acute lymphoblastic leukemia, AML, acute myelogenous leukemia, BC, breast carcinoma, BCL, B-cell lymphoma, BIdC, bladder carcinoma, CeC, cervical carcinoma, CLL, chronic lymphoblastic leukemia, CRC, colorectal carcinoma, EC, endometrial carcinoma, G, glioma, GB, glioblastoma, GC, gastπc carcinoma, HCC, hepatocellular carcinoma, HL, Hodgkin lymphoma, L, leukemia, LC, lung carcinoma, M, melanoma, MB, medulloblastoma, MCL, mantle cell lymphoma, MM, multiple myeloma, My, myeloma, NHL, non-Hodgkin lymphoma, NSCLC, non-small cell lung carcinoma, OC, ovarian carcinoma, ODG, oligodendroglioma, OepC, oesophageal carcinoma, OS, osteosarcoma, PaC, pancreatic carcinoma, PC, prostate carcinoma, RCC, renal cell carcinoma, SCCHN, squamous cell carcinoma of the head and neck, SCLC, small cell lung carcinoma, TC, thyroid carcinoma, TT, testicular tumor
The methods can further comprise one or more of the steps including (a) obtaining a sample from the patient, (b) isolating nucleic acids from the sample, (c) labeling the nucleic acids isolated from the sample, and (d) hybridizing the labeled nucleic acids to one or more probes Nucleic acids of the invention include one or more nucleic acid comprising at least one segment having a sequence or complementary sequence of to a nucleic acid representative of one or more of genes or markers in Table 1, 3, 4, and/or 5
It is contemplated that any method or composition descnbed herein can be implemented with respect to any other method or composition descnbed herein and that different embodiments may be combined It is specifically contemplated that any methods and compositions discussed herein with respect to miRNA molecules, miRNA, genes, and nucleic acids representative of genes may be implemented with respect to synthetic nucleic acids In some embodiments the synthetic nucleic acid is exposed to the proper conditions to allow it to become a processed or mature nucleic acid, such as a miRNA under physiological circumstances The claims originally filed are contemplated to cover claims that are multiply dependent on any filed claim or combination of filed claims
Also, any embodiment of the invention involving specific genes (including representative fragments there of), mRNA, or miRNAs by name is contemplated also to cover embodiments involving miRNAs whose sequences are at least 80, 81, 82, 83, 84, 85,
86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% identical to the mature sequence of the specified miRNA
It will be further understood that shorthand notations are employed such that a genenc description of a gene or marker thereof, or of an miRNA refers to any of its gene family members (distinguished by a number) or representative fragments thereof, unless otherwise indicated It is understood by those of skill in the art that a "gene family" refers to a group of genes having the same coding sequence or miRNA coding sequence Typically, miRNA members of a gene family are identified by a number following the initial designation For example, miR-16-1 and miR-16-2 are members of the miR-16 gene family and "mir-7" refers to miR-7-1, miR-7-2 and miR-7-3 Moreover, unless otherwise indicated, a shorthand notation refers to related miRNAs (distinguished by a letter) Exceptions to these shorthand notations will be otherwise identified Other embodiments of the invention are discussed throughout this application Any embodiment discussed with respect to one aspect of the invention applies to other aspects of the invention as well and vice versa The embodiments in the Example and Detailed
Descπption section are understood to be embodiments of the invention that are applicable to all aspects of the invention
The terms "inhibiting," "reducing," or "prevention," or any vaπation of these terms, when used in the claims and/or the specification includes any measurable decrease or complete inhibition to achieve a desired result
The use of the word "a" or "an" when used in conjunction with the term "comprising" m the claims and/or the specification may mean "one," but it is also consistent with the meaning of "one or more," "at least one," and "one or more than one "
Throughout this application, the term "about" is used to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value The use of the term "or" in the claims is used to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and "and/or "
As used in this specification and claim(s), the words "comprising" (and any form of composing, such as "comprise" and "comprises"), "having" (and any form of having, such as "have" and "has"), "including" (and any form of including, such as "includes" and "include") or "containing" (and any form of containing, such as "contains" and "contain") are inclusive or open-ended and do not exclude additional, unrecited elements or method steps
Other objects, features and advantages of the present invention will become apparent from the following detailed descπption It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spiπt and scope of the invention will become apparent to those skilled in the art from this detailed descnption DETAILED DESCRIPTION OF THE INVENTION
The present invention is directed to compositions and methods relating to the identification and characterization of genes and biological pathways related to these genes as represented by the expression of the identified genes, as well as use of miRNAs related to such, for therapeutic, prognostic, and diagnostic applications, particularly those methods and compositions related to assessing and/or identifying pathological conditions directly or indirectly related to miR-143 expression or the aberrant expression thereof
In certain aspects, the invention is directed to methods for the assessment, analysis, and/or therapy of a cell or subject where certain genes have a reduced or increased expression (relative to normal) as a result of an increased or decreased expression of any one or a combination of miR-143 family members (including, but not limited to Ua-mir-143 MI0002552, xtr-mir-143 MI0004937, dre-mir-143-2 MI0002008, rno-mir-143 MI0000916, ptr-mir-143 MI0002549, ppy-mir-143 MI0002551 , ggo-mir-143 MI0002550, dre-mir-143-1 MI0002007, hsa-mir-143 MI0000459, ppa-mir-143 MI0002553, mdo-rmr-143 MI0005302, and mmu-mir-143 MI0000257) and/or genes with an increased expression (relative to normal) as a result of decreased expression thereof The expression profile and/or response to miR-143 expression or lack of expression may be indicative of an individual with a pathological condition, e g , cancer
Prognostic assays featuring any one or combination of the miRNAs listed or the markers listed (including nucleic acids representative thereof) could be used in assessment of a patient to determine what if any treatment regimen is justified As with the diagnostic assays mentioned above, the absolute values that define low expression will depend on the platform used to measure the miRNA(s) The same methods descπbed for the diagnostic assays could be used for prognostic assays I. THERAPEUTIC METHODS
Embodiments of the invention concern nucleic acids that perform the activities of or inhibit endogenous miRNAs when introduced into cells In certain aspects, nucleic acids are synthetic or non-synthetic miRNA Sequence-specific miRNA inhibitors can be used to inhibit sequentially or in combination the activities of one or more endogenous miRNAs in cells, as well those genes and associated pathways modulated by the endogenous miRNA The present invention concerns, in some embodiments, short nucleic acid molecules that function as miRNAs or as inhibitors of miRNA in a cell The term "short" refers to a length of a single polynucleotide that is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 50, 100, or 150 nucleotides or fewer, including all integers or ranges deπvable there between The nucleic acid molecules are typically synthetic The term "synthetic" refers to a nucleic acid molecule that is not produced naturally in a cell In certain aspects the chemical structure deviates from a naturally-occurring nucleic acid molecule, such as an endogenous precursor miRNA or miRNA molecule or complement thereof While in some embodiments, nucleic acids of the invention do not have an entire sequence that is identical or complementary to a sequence of a naturally-occurring nucleic acid, such molecules may encompass all or part of a naturally-occurring sequence or a complement thereof It is contemplated, however, that a synthetic nucleic acid administered to a cell may subsequently be modified or altered in the cell such that its structure or sequence is the same as non-synthetic or naturally occurring nucleic acid, such as a mature miRNA sequence For example, a synthetic nucleic acid may have a sequence that differs from the sequence of a precursor miRNA, but that sequence may be altered once m a cell to be the same as an endogenous, processed miRNA or an inhibitor thereof The term "isolated" means that the nucleic acid molecules of the invention are initially separated from different (m terms of sequence or structure) and unwanted nucleic acid molecules such that a population of isolated nucleic acids is at least about 90% homogenous, and may be at least about 95, 96, 97, 98, 99, or 100% homogenous with respect to other polynucleotide molecules In many embodiments of the invention, a nucleic acid is isolated by virtue of it having been synthesized in vitro separate from endogenous nucleic acids in a cell It will be understood, however, that isolated nucleic acids may be subsequently mixed or pooled together In certain aspects, synthetic miRNA of the invention are RNA or RNA analogs miRNA inhibitors may be DNA or RNA, or analogs thereof miRNA and miRNA inhibitors of the invention are collectively referred to as "synthetic nucleic acids "
In some embodiments, there is a miRNA or a synthetic miRNA having a length of between 17 and 130 residues The present invention concerns miRNA or synthetic miRNA molecules that are, are at least, or are at most 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 140, 145, 150, 160, 170, 180, 190, 200 or more residues in length, including any integer or any range there between
In certain embodiments, synthetic miRNA have (a) a "miRNA region" whose sequence or binding region from 5' to 3' is identical or complementary to all or a segment of a mature miRNA sequence, and (b) a "complementary region" whose sequence from 5' to 3' is between 60% and 100% complementary to the miRNA sequence in (a) In certain embodiments, these synthetic miRNA are also isolated, as defined above The term "miRNA region" refers to a region on the synthetic miRNA that is at least 75, 80, 85, 90, 95, or 100% identical, including all integers there between, to the entire sequence of a mature, naturally occurring miRNA sequence or a complement thereof In certain embodiments, the miRNA region is or is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99 1, 99 2, 99 3, 99 4, 99 5, 99 6, 99 7, 99 8, 99 9 or 100% identical to the sequence of a naturally-occurring miRNA or complement thereof The term "complementary region" or "complement" refers to a region of a nucleic acid or mimetic that is or is at least 60% complementary to the mature, naturally occurring miRNA sequence The complementary region is or is at least 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99 1, 99 2, 99 3, 994, 99 5, 99 6, 99 7, 99 8, 99 9 or 100% complementary, or any range deπvable therein With single polynucleotide sequences, there may be a hairpm loop structure as a result of chemical bonding between the miRNA region and the complementary region In other embodiments, the complementary region is on a different nucleic acid molecule than the miRNA region, in which case the complementary region is on the complementary strand and the miRNA region is on the active strand In other embodiments of the invention, there are synthetic nucleic acids that are miRNA inhibitors A miRNA inhibitor is between about 17 to 25 nucleotides in length and compπses a 5' to 3' sequence that is at least 90% complementary to the 5' to 3' sequence of a mature miRNA In certain embodiments, a miRNA inhibitor molecule is 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, or any range deπvable therein Moreover, an miRNA inhibitor may have a sequence (from 5' to 3') that is or is at least 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99 1, 99 2, 99 3, 99 4, 99 5, 99 6, 99 7, 99 8, 99 9 or 100% complementary, or any range denvable therein, to the 5' to 3' sequence of a mature miRNA, particularly a mature, naturally occurring miRNA One of skill m the art could use a portion of the miRNA sequence that is complementary to the sequence of a mature miRNA as the sequence for a miRNA inhibitor Moreover, that portion of the nucleic acid sequence can be altered so that it is still compπses the appropriate percentage of complementaπty to the sequence of a mature miRN A
In some embodiments, of the invention, a synthetic miRNA or inhibitor contains one or more design element(s) These design elements include, but are not limited to (i) a replacement group for the phosphate or hydroxyl of the nucleotide at the 5' terminus of the complementary region, (ii) one or more sugar modifications m the first or last 1 to 6 residues of the complementary region, or, (m) noncomplementanty between one or more nucleotides in the last 1 to 5 residues at the 3' end of the complementary region and the corresponding nucleotides of the miRNA region A vanety of design modifications are known in the art, see below
In certain embodiments, a synthetic miRNA has a nucleotide at its 5' end of the complementary region in which the phosphate and/or hydroxyl group has been replaced with another chemical group (referred to as the "replacement design") In some cases, the phosphate group is replaced, while m others, the hydroxyl group has been replaced In particular embodiments, the replacement group is biotin, an amine group, a lower alkylamine group, an acetyl group, 2'O-Me (2'oxygen-methyl), DMTO (4,4'-dimethoxytπtyl with oxygen), fluorescein, a thiol, or acndme, though other replacement groups are well known to those of skill in the art and can be used as well This design element can also be used with a miRNA inhibitor
Additional embodiments concern a synthetic miRNA having one or more sugar modifications in the first or last 1 to 6 residues of the complementary region (referred to as the "sugar replacement design") In certain cases, there is one or more sugar modifications in the first 1, 2, 3, 4, 5, 6 or more residues of the complementary region, or any range denvable therein In additional cases, there is one or more sugar modifications in the last 1 , 2, 3, 4, 5, 6 or more residues of the complementary region, or any range denvable therein, have a sugar modification It will be understood that the terms "first" and "last" are with respect to the order of residues from the 5' end to the 3' end of the region In particular embodiments, the sugar modification is a 2'O-Me modification In further embodiments, there is one or more sugar modifications in the first or last 2 to 4 residues of the complementary region or the first or last 4 to 6 residues of the complementary region This design element can also be used with an miRNA inhibitor Thus, an miRNA inhibitor can have this design element and/or a replacement group on the nucleotide at the 5' terminus, as discussed above
In other embodiments of the invention, there is a synthetic miRNA or inhibitor in which one or more nucleotides in the last 1 to 5 residues at the 3' end of the complementary region are not complementary to the corresponding nucleotides of the miRNA region
("noncomplementaπty") (referred to as the "noncomplementaπty design") The noncomplementaπty may be in the last 1, 2, 3, 4, and/or 5 residues of the complementary miRNA In certain embodiments, there is noncomplementaπty with at least 2 nucleotides in the complementary region
It is contemplated that synthetic miRNA of the invention have one or more of the replacement, sugar modification, or noncomplementaπty designs In certain cases, synthetic RNA molecules have two of them, while in others these molecules have all three designs in place The miRNA region and the complementary region may be on the same or separate polynucleotides In cases in which they are contained on or in the same polynucleotide, the miRNA molecule will be considered a single polynucleotide In embodiments in which the different regions are on separate polynucleotides, the synthetic miRNA will be considered to be compnsed of two polynucleotides When the RNA molecule is a single polynucleotide, there can be a linker region between the miRNA region and the complementary region In some embodiments, the single polynucleotide is capable of forming a hairpin loop structure as a result of bonding between the miRNA region and the complementary region The linker constitutes the hairpin loop It is contemplated that in some embodiments, the linker region is, is at least, or is at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 residues in length, or any range denvable therein In certain embodiments, the linker is between 3 and 30 residues (inclusive) in length
In addition to having a miRNA or inhibitor region and a complementary region, there may be flanking sequences as well at either the 5' or 3' end of the region In some embodiments, there is or is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 nucleotides or more, or any range denvable therein, flanking one or both sides of these regions Methods of the invention include reducing or eliminating activity of one or more miRNAs in a cell comprising introducing into a cell a miRNA inhibitor (which may be descπbed generally herein as an miRNA, so that a description of miRNA, where appropriate, also will refer to a miRNA inhibitor), or supplying or enhancing the activity of one or more miRNAs in a cell The present invention also concerns inducing certain cellular characteristics by providing to a cell a particular nucleic acid, such as a specific synthetic miRNA molecule or a synthetic miRNA inhibitor molecule However, m methods of the invention, the miRNA molecule or miRNA inhibitor need not be synthetic They may have a sequence that is identical to a naturally occurring miRNA or they may not have any design modifications In certain embodiments, the miRNA molecule and/or the miRNA inhibitor are synthetic, as discussed above
The particular nucleic acid molecule provided to the cell is understood to correspond to a particular miRNA in the cell, and thus, the miRNA in the cell is referred to as the "corresponding miRNA " In situations in which a named miRNA molecule is introduced into a cell, the corresponding miRNA will be understood to be the induced or inhibited miRNA or induced or inhibited miRNA function It is contemplated, however, that the miRNA molecule introduced into a cell is not a mature miRNA but is capable of becoming or functioning as a mature miRNA under the appropriate physiological conditions In cases in which a particular corresponding miRNA is being inhibited by a miRNA inhibitor, the particular miRNA will be referred to as the "targeted miRNA " It is contemplated that multiple corresponding miRNAs may be involved In particular embodiments, more than one miRNA molecule is introduced into a cell Moreover, in other embodiments, more than one miRNA inhibitor is introduced into a cell Furthermore, a combination of miRNA molecule(s) and miRNA inhibitors) may be introduced into a cell The inventors contemplate that a combination of miRNA may act at one or more points in cellular pathways of cells with aberrant phenotypes and that such combination may have increased efficacy on the target cell while not adversely effecting normal cells Thus, a combination of miRNA may have a minimal adverse effect on a subject or patient while supplying a sufficient therapeutic effect, such as amelioration of a condition, growth inhibition of a cell, death of a targeted cell, alteration of cell phenotype or physiology, slowing of cellular growth, sensitization to a second therapy, sensitization to a particular therapy, and the like Methods include identifying a cell or patient in need of inducing those cellular characteristics Also, it will be understood that an amount of a synthetic nucleic acid that is provided to a cell or organism is an "effective amount," which refers to an amount needed (or a sufficient amount) to achieve a desired goal, such as inducing a particular cellular characteristics) Certain embodiments of the methods include providing or introducing to a cell a nucleic acid molecule corresponding to a mature miRNA in the cell in an amount effective to achieve a desired physiological result
Moreover, methods can involve providing synthetic or nonsynthetic miRNA molecules It is contemplated that in these embodiments, that the methods may or may not be limited to providing only one or more synthetic miRNA molecules or only one or more nonsynthetic miRNA molecules Thus, in certain embodiments, methods may involve providing both synthetic and nonsynthetic miRNA molecules In this situation, a cell or cells are most likely provided a synthetic miRNA molecule corresponding to a particular miRNA and a nonsynthetic miRNA molecule corresponding to a different miRNA Furthermore, any method articulated using a list of miRNAs using Markush group language may be articulated without the Markush group language and a disjunctive article (; e , or) instead, and vice versa
Typically, an endogenous gene, miRNA or mRNA is modulated m the cell In particular embodiments, the nucleic acid sequence compπses at least one segment that is at least 70, 75, 80, 85, 90, 95, or 100% identical in nucleic acid sequence to one or more miRNA or gene sequence Modulation of the expression or processing of an endogenous gene, miRNA, or mRNA can be through modulation of the processing of a mRNA, such processing including transcription, transportation and/or translation with in a cell Modulation may also be effected by the inhibition or enhancement of miRNA activity with a cell, tissue, or organ Such processing may affect the expression of an encoded product or the stability of the mRNA In still other embodiments, a nucleic acid sequence can compose a modified nucleic acid sequence In certain aspects, one or more miRNA sequence may include or comprise a modified nucleobase or nucleic acid sequence
It will be understood in methods of the invention that a cell or other biological matter such as an organism (including patients) can be provided a miRNA or miRNA molecule corresponding to a particular miRNA by administering to the cell or organism a nucleic acid molecule that functions as the corresponding miRNA once mside the cell The form of the molecule provided to the cell may not be the form that acts a miRNA once inside the cell Thus, it is contemplated that m some embodiments, a synthetic miRNA or a nonsynthetic miRNA is provided such that it becomes processed into a mature and active miRNA once it has access to the cell's miRNA processing machinery In certain embodiments, it is specifically contemplated that the miRNA molecule provided is not a mature miRNA molecule but a nucleic acid molecule that can be processed into the mature miRNA once it is accessible to miRNA processing machinery The term "nonsynthetic" in the context of miRNA means that the miRNA is not "synthetic," as defined herein Furthermore, it is contemplated that in embodiments of the invention that concern the use of synthetic miRNAs, the use of corresponding nonsynthetic miRNAs is also considered an aspect of the invention, and vice versa It will be understand that the term "providing" an agent is used to include "administering" the agent to a patient
In certain embodiments, methods also include targeting a miRNA to modulate in a cell or organism The term "targeting a miRNA to modulate" means a nucleic acid of the invention will be employed so as to modulate the selected miRNA In some embodiments the modulation is achieved with a synthetic or non-synthetic miRNA that corresponds to the targeted miRNA, which effectively provides the targeted miRNA to the cell or organism (positive modulation) In other embodiments, the modulation is achieved with a miRNA inhibitor, which effectively inhibits the targeted miRNA in the cell or organism (negative modulation) In some embodiments, the miRNA targeted to be modulated is a miRNA that affects a disease, condition, or pathway In certain embodiments, the miRNA is targeted because a treatment can be provided by negative modulation of the targeted miRNA In other embodiments, the miRNA is targeted because a treatment can be provided by positive modulation of the targeted miRNA or its targets In certain methods of the invention, there is a further step of administering the selected miRNA modulator to a cell, tissue, organ, or organism (collectively "biological matter") in need of treatment related to modulation of the targeted miRNA or in need of the physiological or biological results discussed herein (such as with respect to a particular cellular pathway or result like decrease m cell viability) Consequently, in some methods of the invention there is a step of identifying a patient in need of treatment that can be provided by the miRNA modulator(s) It is contemplated that an effective amount of a miRNA modulator can be administered in some embodiments In particular embodiments, there is a therapeutic benefit conferred on the biological matter, where a "therapeutic benefit" refers to an improvement in the one or more conditions or symptoms associated with a disease or condition or an improvement m the prognosis, duration, or status with respect to the disease It is contemplated that a therapeutic benefit includes, but is not limited to, a decrease in pain, a decrease in morbidity, a decrease in a symptom For example, with respect to cancer, it is contemplated that a therapeutic benefit can be inhibition of tumor growth, prevention of metastasis, reduction in number of metastases, inhibition of cancer cell proliferation, induction of cell death in cancer cells, inhibition of angiogenesis near cancer cells, induction of apoptosis of cancer cells, reduction m pain, reduction in πsk of recurrence, induction of chemo- or radiosensitivity in cancer cells, prolongation of life, and/or delay of death directly or indirectly related to cancer
Furthermore, it is contemplated that the miRNA compositions may be provided as part of a therapy to a patient, m conjunction with traditional therapies or preventative agents
Moreover, it is contemplated that any method discussed in the context of therapy may be applied preventatively, particularly in a patient identified to be potentially in need of the therapy or at πsk of the condition or disease for which a therapy is needed
In addition, methods of the invention concern employing one or more nucleic acids corresponding to a miRNA and a therapeutic drug The nucleic acid can enhance the effect or efficacy of the drug, reduce any side effects or toxicity, modify its bioavailability, and/or decrease the dosage or frequency needed In certain embodiments, the therapeutic drug is a cancer therapeutic Consequently, in some embodiments, there is a method of treating cancer in a patient comprising administering to the patient the cancer therapeutic and an effective amount of at least one miRNA molecule that improves the efficacy of the cancer therapeutic or protects non-cancer cells Cancer therapies also include a variety of combination therapies with both chemical and radiation based treatments Combination chemotherapies include but are not limited to, for example, 5-fluorouracil, alemtuzumab, amrubicm, bevacizumab, bleomycin, bortezomib, busulfan, camptothecin, capecitabme, carboplatin, cetuximab, chlorambucil, cisplatm (CDDP), COX-2 inhibitors (e g , celecoxib), cyclophosphamide, cytarabme, dactinomycm, dasatinib, daunorubicin, dexamethasone, docetaxel, doxorubicin (adπamycin), EGFR inhibitors (gefitimb and cetuximab), erlotimb, estrogen receptor binding agents, etoposide (VP16), everohmus, farnesyl-protem transferase inhibitors, gefitimb, gemcitabme, gemtuzumab, lbntumomab, lfosfamide, imatimb mesylate, larotaxel, lapatimb, lonafarmb, mechlorethamme, melphalan, methotrexate, mitomycin, navelbine, mtrosurea, nocodazole, oxahplatin, paclitaxel, plicomycin, procarbazine, raloxifene, πtuximab, sirohmus, sorafemb, sumtimb, tamoxifen, taxol, taxotere, temsirohmus, tipifarmb, tositumomab, transplatmum, trastuzumab, vmblastin, vincπstm, or vinorelbme or any analog or deπvative vaπant of the foregoing
Generally, inhibitors of miRNAs can be given to decrease the activity of an endogenous miRNA For example, inhibitors of miRNA molecules that increase cell proliferation can be provided to cells to decrease cell proliferation The present invention contemplates these embodiments in the context of the different physiological effects observed with the different miRNA molecules and miRNA inhibitors disclosed herein These include, but are not limited to, the following physiological effects increase and decreasing cell proliferation, increasing or decreasing apoptosis, increasing transformation, increasing or decreasing cell viability, activating or inhibiting a kinase (e g , Erk), activating/inducing or inhibiting hTert, inhibit stimulation of growth promoting pathway (e g , Stat 3 signaling), reduce or increase viable cell number, and increase or decrease number of cells at a particular phase of the cell cycle Methods of the invention are generally contemplated to include providing or introducing one or more different nucleic acid molecules corresponding to one or more different miRNA molecules It is contemplated that the following, at least the following, or at most the following number of different nucleic acid or miRNA molecules may be provided or introduced 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or any range deπvable therein This also applies to the number of different miRNA molecules that can be provided or introduced into a cell
II. PHARMACEUTICAL FORMULATIONS AND DELIVERY
Methods of the present invention include the delivery of an effective amount of a miRNA or an expression construct encoding the same An "effective amount" of the pharmaceutical composition, generally, is defined as that amount sufficient to detectably and repeatedly to achieve the stated desired result, for example, to ameliorate, reduce, minimize or limit the extent of the disease or its symptoms Other more rigorous definitions may apply, including elimination, eradication or cure of disease A. Administration
In certain embodiments, it is desired to kill cells, inhibit cell growth, inhibit metastasis, decrease tumor or tissue size, and/or reverse or reduce the malignant or disease phenotype of cells The routes of administration will vary, naturally, with the location and nature of the lesion or site to be targeted, and include, e g , intradermal, subcutaneous, regional, parenteral, intravenous, intramuscular, intranasal, systemic, and oral administration and formulation Direct injection, mtratumoral injection, or injection into tumor vasculature is specifically contemplated for discrete, solid, accessible tumors, or other accessible target areas Local, regional, or systemic administration also may be appropπate For tumors of >4 cm, the volume to be administered will be about 4-10 ml (preferably 10 ml), while for tumors of <4 cm, a volume of about 1-3 ml will be used (preferably 3 ml)
Multiple injections delivered as a single dose compπse about 0 1 to about 0 5 ml volumes Compositions of the invention may be administered m multiple injections to a tumor or a targeted site In certain aspects, injections may be spaced at approximately 1 cm intervals
In the case of surgical intervention, the present invention may be used preoperatively, to render an inoperable tumor subject to resection Alternatively, the present invention may be used at the time of surgery, and/or thereafter, to treat residual or metastatic disease For example, a resected tumor bed may be injected or perfused with a formulation comprising a miRNA or combinations thereof Administration may be continued post-resection, for example, by leaving a catheter implanted at the site of the surgery Peπodic post-surgical treatment also is envisioned Continuous perfusion of an expression construct or a viral construct also is contemplated
Continuous administration also may be applied where appropπate, for example, where a tumor or other undesired affected area is excised and the tumor bed or targeted site is treated to eliminate residual, microscopic disease Delivery via syringe or catheπzation is contemplated Such continuous perfusion may take place for a peπod from about 1-2 hours, to about 2-6 hours, to about 6-12 hours, to about 12-24 hours, to about 1-2 days, to about 1-2 wk or longer following the initiation of treatment Generally, the dose of the therapeutic composition via continuous perfusion will be equivalent to that given by a single or multiple injections, adjusted over a peπod of time dunng which the perfusion occurs Treatment regimens may vary as well and often depend on tumor type, tumor location, immune condition, target site, disease progression, and health and age of the patient
Certain tumor types will require more aggressive treatment The clinician will he best suited to make such decisions based on the known efficacy and toxicity (if any) of the therapeutic formulations
In certain embodiments, the tumor or affected area being treated may not, at least initially, be resectable Treatments with compositions of the invention may increase the resectability of the tumor due to shrinkage at the margins or by elimination of certain particularly invasive portions Following treatments, resection may be possible Additional treatments subsequent to resection may serve to eliminate microscopic residual disease at the tumor or targeted site
Treatments may include vaπous "unit doses " A unit dose is defined as containing a predetermined quantity of a therapeutic composition(s) The quantity to be administered, and the particular route and formulation, are within the skill of those in the clinical arts A unit dose need not be administered as a single injection but may compose continuous infusion over a set period of time With respect to a viral component of the present invention, a unit dose may conveniently be descπbed in terms of μg or mg of miRNA or miRNA mimetic Alternatively, the amount specified may be the amount administered as the average daily, average weekly, or average monthly dose miRNA can be administered to the patient in a dose or doses of about or of at least about 0 5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000 μg or mg, or more, or any range derivable therein Alternatively, the amount specified may be the amount administered as the average daily, average weekly, or average monthly dose, or it may be expressed in terms of mg/kg, where kg refers to the weight of the patient and the mg is specified above In other embodiments, the amount specified is any number discussed above but expressed as mg/m2 (with respect to tumor size or patient surface area) B. Injectable Compositions and Formulations
In some embodiments, the method for the delivery of a miRNA or an expression construct encoding such or combinations thereof is via systemic administration However, the pharmaceutical compositions disclosed herein may also be administered parenterally, subcutaneously, directly, intratracheally, intravenously, lntradermally, intramuscularly, or even mtrapentoneally as descnbed in U S Patents 5,543,158, 5,641,515 and 5,399,363 (each specifically incorporated herein by reference in its entirety)
Injection of nucleic acids may be delivered by syringe or any other method used for injection of a solution, as long as the nucleic acid and any associated components can pass through the particular gauge of needle required for injection A syringe system has also been descnbed for use in gene therapy that permits multiple injections of predetermined quantities of a solution precisely at any depth (U S Patent 5,846,225)
Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose Dispersions may also be prepared in glycerol, liquid polyethylene glycols, mixtures thereof, and in oils Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms The pharmaceutical forms suitable for injectable use include steπle aqueous solutions or dispersions and steπle powders for the extemporaneous preparation of stenle injectable solutions or dispersions (U S Patent 5,466,468, specifically incorporated herein by reference in its entirety) In all cases the form must be stenle and must be fluid to the extent that easy syringabihty exists It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bactena and fungi The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e g , glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants The prevention of the action of microorganisms can be brought about by vanous antibacteπal and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chlonde Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin
In certain formulations, a water-based formulation is employed while m others, it may be hpid-based In particular embodiments of the invention, a composition compπsing a tumor suppressor protein or a nucleic acid encoding the same is in a water-based formulation In other embodiments, the formulation is lipid based
For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, mtratumoral, intralesional, and intraperitoneal administration In this connection, steπle aqueous media which can be employed will be known to those of skill m the art in light of the present disclosure For example, one dosage may be dissolved m 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences" 15th Edition, pages 1035-1038 and 1570-1580) Some vaπation in dosage will necessanly occur depending on the condition of the subject being treated The person responsible for administration will, in any event, determine the appropriate dose for the individual subject Moreover, for human administration, preparations should meet sterility, pyrogemcity, general safety and purity standards as required by FDA Office of Biologies standards
As used herein, a "carrier" includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, earner solutions, suspensions, colloids, and the like The use of such media and agents for pharmaceutical active substances is well known in the art Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated Supplementary active ingredients can also be incorporated into the compositions
The phrase "pharmaceutically acceptable" refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human The nucleic acid(s) are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective The quantity to be administered depends on the subject to be treated, including, e g , the aggressiveness of the disease or cancer, the size of any tumor(s) or lesions, the previous or other courses of treatment Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner Suitable regimes for initial administration and subsequent administration are also variable, but are typified by an initial administration followed by other administrations Such administration may be systemic, as a single dose, continuous over a period of time spanning 10, 20, 30, 40, 50, 60 minutes, and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more hours, and/or 1, 2, 3, 4, 5, 6, 7, days or more Moreover, administration may be through a time release or sustained release mechanism, implemented by formulation and/or mode of administration
C. Combination Treatments
In certain embodiments, the compositions and methods of the present invention involve a miRNA, or expression construct encoding such These miRNA composition can be used in combination with a second therapy to enhance the effect of the miRNA therapy, or increase the therapeutic effect of another therapy being employed These compositions would be provided in a combined amount effective to achieve the desired effect, such as the killing of a cancer cell and/or the inhibition of cellular hyperprohferation This process may involve contacting the cells with the miRNA or second therapy at the same or different time
This may be achieved by contacting the cell with one or more compositions or pharmacological formulation that includes or more of the agents, or by contacting the cell with two or more distinct compositions or formulations, wherein one composition provides
(1) miRNA, and/or (2) a second therapy A second composition or method may be administered that includes a chemotherapy, radiotherapy, surgical therapy, immunotherapy or gene therapy
It is contemplated that one may provide a patient with the miRNA therapy and the second therapy withm about 12-24 h of each other and, more preferably, within about 6-12 h of each other In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6,
7 or 8) lapse between the respective administrations In certain embodiments, a course of treatment will last 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90 days or more It is contemplated that one agent may be given on day 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, and/or 90, any combination thereof, and another agent is given on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, and/or 90, or any combination thereof Within a single day (24-hour period), the patient may be given one or multiple administrations of the agent(s) Moreover, after a course of treatment, it is contemplated that there is a peπod of time at which no treatment is administered This time period may last 1 , 2, 3, 4, 5, 6, 7 days, and/or 1, 2, 3, 4, 5 weeks, and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months or more, depending on the condition of the patient, such as their prognosis, strength, health, etc Vaπous combinations may be employed, for example miRNA therapy is "A" and a second therapy is "B"
A/B/A B/A/B B/B/A A/A/B A/B/B B/A/A A/B/B/B B/A/B/B B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/A B/A/B/A B/A/A/B A/A/A/B B/A/A/A A/B/A/A A/A/B/A Administration of any compound or therapy of the present invention to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the vector or any protein or other agent Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy It is expected that the treatment cycles would be repeated as necessary It also is contemplated that vaπous standard therapies, as well as surgical intervention, may be applied in combination with the descπbed therapy In specific aspects, it is contemplated that a second therapy, such as chemotherapy, radiotherapy, immunotherapy, surgical therapy or other gene therapy, is employed in combination with the miRNA therapy, as descπbed herein
1. Chemotherapy A wide vaπety of chemotherapeutic agents may be used in accordance with the present invention The term "chemotherapy" refers to the use of drugs to treat cancer A "chemotherapeutic agent" is used to connote a compound or composition that is administered in the treatment of cancer These agents or drugs are categonzed by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle Alternatively, an agent may be characteπzed based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis Most chemotherapeutic agents fall into the following categones alkylating agents, antimetabolites, antitumor antibiotics, mitotic inhibitors, and nitrosoureas a Alkylating agents Alkylating agents are drugs that directly interact with genomic DNA to prevent the cancer cell from proliferating This category of chemotherapeutic drugs represents agents that affect all phases of the cell cycle, that is, they are not phase-specific Alkylating agents can be implemented to treat chronic leukemia, non-Hodgkin's lymphoma, Hodgkin's disease, multiple myeloma, and particular cancers of the breast, lung, and ovary They include busulfan, chlorambucil, cisplatin, cyclophosphamide (Cytoxan), dacarbazine, lfosfamide, mechlorethamine (mustargen), and melphalan Troghtazaone can be used to treat cancer in combination with any one or more of these alkylating agents b Antimetabolites
Antimetabolites disrupt DNA and RNA synthesis Unlike alkylating agents, they specifically influence the cell cycle duπng S phase They have been used to combat chronic leukemias in addition to tumors of breast, ovary and the gastrointestinal tract
Antimetabolites include 5-fluorouracil (5-FU), cytarabme (Ara-C), fludarabine, gemcitabine, and methotrexate
5-Fluorouracil (5-FU) has the chemical name of 5-fluoro-2,4(lH,3H)- pyπmidinedione Its mechanism of action is thought to be by blocking the methylation reaction of deoxyuπdylic acid to thymidylic acid Thus, 5-FU interferes with the synthesis of deoxyribonucleic acid (DNA) and to a lesser extent inhibits the formation of ribonucleic acid (RNA) Since DNA and RNA are essential for cell division and proliferation, it is thought that the effect of 5-FU is to create a thymidine deficiency leading to cell death Thus, the effect of 5-FU is found m cells that rapidly divide, a characteristic of metastatic cancers c Antitumor Antibiotics
Antitumor antibiotics have both antimicrobial and cytotoxic activity These drugs also interfere with DNA by chemically inhibiting enzymes and mitosis or alteπng cellular membranes These agents are not phase specific so they work in all phases of the cell cycle Thus, they are widely used for a vaπety of cancers Examples of antitumor antibiotics include bleomycin, dactmomycm, daunorubicm, doxorubicin (Adπamycin), and ldarubicm, some of which are discussed in more detail below Widely used in clinical setting for the treatment of neoplasms, these compounds are administered through bolus injections intravenously at doses ranging from 25-75 mg/m2 at 21 day intervals for adπamycm, to 35- 100 mg/m2 for etoposide intravenously or orally d Mitotic Inhibitors
Mitotic inhibitors include plant alkaloids and other natural agents that can inhibit either protein synthesis required for cell division or mitosis They operate duπng a specific phase duπng the cell cycle Mitotic inhibitors compπse docetaxel, etoposide (VPl 6), pachtaxel, taxol, taxotere, vinblastine, vincristine, and vinorelbine e Nitrosureas
Nitrosureas, like alkylating agents, inhibit DNA repair proteins They are used to treat non-Hodgkin's lymphomas, multiple myeloma, malignant melanoma, in addition to brain tumors Examples include carmustine and lomustme 2. Radiotherapy
Radiotherapy, also called radiation therapy, is the treatment of cancer and other diseases with ionizing radiation Ionizing radiation deposits energy that injures or destroys cells in the area being treated by damaging their genetic material, making it impossible for these cells to continue to grow Although radiation damages both cancer cells and normal cells, the latter are able to repair themselves and function properly Radiotherapy may be used to treat localized solid tumors, such as cancers of the skin, tongue, larynx, brain, breast, or cervix It can also be used to treat leukemia and lymphoma (cancers of the blood-forming cells and lymphatic system, respectively)
Radiation therapy used according to the present invention may include, but is not limited to, the use of γ-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells Other forms of DNA damaging factors are also contemplated such as microwaves, proton beam irradiation (U S Patents 5,760,395 and 4,870,287) and UV-irradiation It is most likely that all of these factors effect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells Radiotherapy may compπse the use of radiolabeled antibodies to deliver doses of radiation directly to the cancer site (radioimmunotherapy) Once injected into the body, the antibodies actively seek out the cancer cells, which are destroyed by the cell-killing (cytotoxic) action of the radiation This approach can minimize the πsk of radiation damage to healthy cells
Stereotactic radio-surgery (gamma knife) for brain and other tumors does not use a knife, but very precisely targeted beams of gamma radiotherapy from hundreds of different angles Only one session of radiotherapy, taking about four to five hours, is needed For this treatment a specially made metal frame is attached to the head Then, several scans and x- rays are earned out to find the precise area where the treatment is needed Duπng the radiotherapy for bram tumors, the patient lies with their head in a large helmet, which has hundreds of holes in it to allow the radiotherapy beams through Related approaches permit positioning for the treatment of tumors in other areas of the body
3. Immunotherapy
In the context of cancer treatment, immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells Trastuzumab
(Herceptin™) is such an example The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell The antibody alone may serve as an effector of therapy or it may recruit other cells to actually affect cell killing The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, πcin A chain, cholera toxm, pertussis toxin, etc ) and serve merely as a targeting agent Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target Various effector cells include cytotoxic T cells and NK cells The combination of therapeutic modalities, ; e , direct cytotoxic activity and inhibition or reduction of ErbB2 would provide therapeutic benefit in the treatment of ErbB2 overexpressing cancers
In one aspect of immunotherapy, the tumor or disease cell must bear some marker that is amenable to targeting, i e , is not present on the majoπty of other cells Many tumor markers exist and any of these may be suitable for targeting in the context of the present invention Common tumor markers include carcinoembryomc antigen, prostate specific antigen, urinary tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, estrogen receptor, lamimn receptor, erb B and pi 55 An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects Immune stimulating molecules also exist including cytokines such as IL-2, IL-4, IL- 12, GM-CSF, gamma-IFN, chemokmes such as MIP-I, MCP-I, IL-8 and growth factors such as FLT3 ligand Combining immune stimulating molecules, either as proteins or using gene delivery in combination with a tumor suppressor such as MDA-7 has been shown to enhance anti-tumor effects (Ju et al , 2000) Moreover, antibodies against any of these compounds can be used to target the anti-cancer agents discussed herein
Examples of immunotherapies currently under investigation or in use are immune adjuvants e g , Mycobacterium bovis, Plasmodium falciparum, dimtrochlorobenzene and aromatic compounds (U S Patents 5,801,005 and 5,739,169, Hm and Hashimoto, 1998, Chπstodoulides et al , 1998), cytokine therapy e g , interferons α, β and γ, IL-I, GM-CSF and TNF (Bukowski et al , 1998, Davidson et al , 1998, Hellstrand et al , 1998) gene therapy e g , TNF, IL-I, IL-2, p53 (Qin et al , 1998, Austm-Ward and Villaseca, 1998, U S Patents 5,830,880 and 5,846,945) and monoclonal antibodies e g , anti-ganghoside GM2, anti-HER- 2, anti-pl85, Pietras et al , 1998, Hambuchi et al , 1998, U S Patent 5,824,311) Herceptin (trastuzumab) is a chimeπc (mouse-human) monoclonal antibody that blocks the HER2-neu receptor It possesses anti-tumor activity and has been approved for use in the treatment of malignant tumors (Dillman, 1999) Table 6 is a non-hmitmg list of several known anti- cancer immunotherapeutic agents and their targets It is contemplated that one or more of these therapies may be employed with the miRNA therapies descπbed herein
A number of different approaches for passive immunotherapy of cancer exist They may be broadly categoπzed into the following injection of antibodies alone, injection of antibodies coupled to toxms or chemo therapeutic agents, injection of antibodies coupled to radioactive isotopes, injection of anti-idiotype antibodies, and finally, purging of tumor cells in bone marrow
4. Gene Therapy
In yet another embodiment, a combination treatment involves gene therapy in which a therapeutic polynucleotide is administered before, after, or at the same time as one or more therapeutic miRNA Delivery of a therapeutic polypeptide or encoding nucleic acid in conjunction with a miRNA may have a combined therapeutic effect on target tissues A variety of proteins are encompassed within the invention, some of which are descπbed below
Various genes that may be targeted for gene therapy of some form in combination with the present invention include, but are not limited to inducers of cellular proliferation, inhibitors of cellular proliferation, regulators of programmed cell death, cytokines and other therapeutic nucleic acids or nucleic acid that encode therapeutic proteins
The tumor suppressor oncogenes function to inhibit excessive cellular proliferation The inactivation of these genes destroys their inhibitory activity, resulting in unregulated proliferation The tumor suppressors (e g , therapeutic polypeptides) p53, FHIT, pi 6 and C- CAM can be employed In addition to p53, another inhibitor of cellular proliferation is pl6 The major transitions of the eukaryotic cell cycle are triggered by cychn-dependent kinases, or CDK's One CDK, cychn-dependent kinase 4 (CDK4), regulates progression through the Gl The activity of this enzyme may be to phosphorylate Rb at late Gl The activity of CDK4 is controlled by an activating subunit, D-type cyclin, and by an inhibitory subumt, the pl6INK4 has been biochemically characteπzed as a protein that specifically binds to and inhibits CDK4, and thus may regulate Rb phosphorylation (Serrano et al , 1993, Serrano et al , 1995) Since the pl6INK4 protein is a CDK4 inhibitor (Serrano, 1993), deletion of this gene may increase the activity of CDK4, resulting in hyperphosphorylation of the Rb protein pi 6 also is known to regulate the function of CDK6 pl6INK4 belongs to a newly descπbed class of CDK-inhibitory proteins that also includes pl6B, pl9, p21WAFl, and p27KIPl The pl6INK4 gene maps to 9p21, a chromosome region frequently deleted in many tumor types Homozygous deletions and mutations of the pl6INK4 gene are frequent in human tumor cell lines This evidence suggests that the pl6ENK4 gene is a tumor suppressor gene This interpretation has been challenged, however, by the observation that the frequency of the pl6INK4 gene alterations is much lower in primary uncultured tumors than in cultured cell lines (Caldas et al , 1994, Cheng et al , 1994, Hussussian et al , 1994, Kamb et al , 1994, Moπ et al , 1994, Okamoto et al , 1994, Nobon et al , 1995, Orlow et al , 1994, Arap et al , 1995) Restoration of wild-type pl6INK4 function by transfection with a plasmid expression vector reduced colony formation by some human cancer cell lines (Okamoto, 1994, Arap, 1995)
Other genes that may be employed according to the present invention include Rb, APC, DCC, NF-I, NF-2, WT-I, MEN-I, MEN-II, zacl, p73, VHL, MMACl / PTEN, DBCCR-I, FCC, rsk-3, p27, p27/pl6 fusions, p21/p27 fusions, anti-thrombotic genes {e g , COX-I, TFPI), PGS, Dp, E2F, ras, myc, neu, raf, erb, fins, trk, ret, gsp, hst, abl, ElA, p300, genes involved in angiogenesis (e g , VEGF, FGF, thrombospondin, BAI-I, GDAIF, or their receptors) and MCC 5. Surgery
Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative and palliative surgery Curative surgery is a cancer treatment that may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies
Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed Tumor resection refers to physical removal of at least part of a tumor In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs' surgery) It is further contemplated that the present invention may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue
Upon excision of part of all of cancerous cells, tissue, or tumor, a cavity may be formed in the body Treatment may be accomplished by perfusion, direct injection or local application of the area with an additional anti-cancer therapy Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months These treatments may be of varying dosages as well
6. Other Agents
It is contemplated that other agents may be used in combination with the present invention to improve the therapeutic efficacy of treatment These additional agents include immunomodulatory agents, agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperprohferative cells to apoptotic inducers, or other biological agents Immunomodulatory agents include tumor necrosis factor, interferon alpha, beta, and gamma, IL-2 and other cytokines, F42K and other cytokine analogs, or MIP-I, MIP-lbeta, MCP-I, RANTES, and other chemokmes It is further contemplated that the upregulation of cell surface receptors or their hgands such as Fas / Fas hgand, DR4 or DR5 / TRAIL (Apo-2 hgand) would potentiate the apoptotic inducing abilities of the present invention by establishment of an autocnne or paracrine effect on hyperprohferative cells Increases intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperprohferative effects on the neighboring hyperprohferative cell population In other embodiments, cytostatic or differentiation agents can be used in combination with the present invention to improve the anti-hyperproliferative efficacy of the treatments Inhibitors of cell adhesion are contemplated to improve the efficacy of the present invention Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin It is further contemplated that other agents that increase the sensitivity of a hyperprohferative cell to apoptosis, such as the antibody c225, could be used in combination with the present invention to improve the treatment efficacy
Apo2 hgand (Apo2L, also called TRAIL) is a member of the tumor necrosis factor (TNF) cytokine family TRAIL activates rapid apoptosis in many types of cancer cells, yet is not toxic to normal cells TRAIL mRNA occurs m a wide vaπety of tissues Most normal cells appear to be resistant to TRAIL'S cytotoxic action, suggesting the existence of mechanisms that can protect against apoptosis induction by TRAIL The first receptor descπbed for TRAIL, called death receptor 4 (DR4), contains a cytoplasmic "death domain", DR4 transmits the apoptosis signal carried by TRAIL Additional receptors have been identified that bind to TRAIL One receptor, called DR5, contains a cytoplasmic death domain and signals apoptosis much like DR4 The DR4 and DR5 mRNAs are expressed in many normal tissues and tumor cell lines Recently, decoy receptors such as DcRl and DcR2 have been identified that prevent TRAIL from inducing apoptosis through DR4 and DR5 These decoy receptors thus represent a novel mechanism for regulating sensitivity to a pro- apoptotic cytokine directly at the cell's surface The preferential expression of these inhibitory receptors m normal tissues suggests that TRAIL may be useful as an anticancer agent that induces apoptosis in cancer cells while sparing normal cells (Marsters et al , 1999) There have been many advances m the therapy of cancer following the introduction of cytotoxic chemotherapeutic drugs However, one of the consequences of chemotherapy is the development/acquisition of drug-resistant phenotypes and the development of multiple drug resistance The development of drug resistance remains a major obstacle in the treatment of such tumors and therefore, there is an obvious need for alternative approaches such as gene therapy
Another form of therapy for use in conjunction with chemotherapy, radiation therapy or biological therapy includes hyperthermia, which is a procedure in which a patient's tissue is exposed to high temperatures (up to 1060F) External or internal heating devices may be involved in the application of local, regional, or whole-body hyperthermia Local hyperthermia involves the application of heat to a small area, such as a tumor Heat may be generated externally with high-frequency waves targeting a tumor from a device outside the body Internal heat may involve a sterile probe , including thin, heated wires or hollow tubes filled with warm water, implanted microwave antennae, or radiofrequency electrodes A patient's organ or a limb is heated for regional therapy, which is accomplished using devices that produce high energy, such as magnets Alternatively, some of the patient's blood may be removed and heated before being perfused into an area that will be internally heated Whole-body heating may also be implemented in cases where cancer has spread throughout the body Warm-water blankets, hot wax, inductive coils, and thermal chambers may be used for this purpose
Hormonal therapy may also be used in conjunction with the present invention or in combination with any other cancer therapy previously described The use of hormones may be employed in the treatment of certain cancers such as breast, prostate, ovarian, or cervical cancer to lower the level or block the effects of certain hormones such as testosterone or estrogen This treatment is often used in combination with at least one other cancer therapy as a treatment option or to reduce the risk of metastases
This application incorporates U S Application Seπal No 11/349,727 filed on February 8, 2006 claiming priority to U S Provisional Application Serial No 60/650,807 filed February 8, 2005 herein by references in its entirety III. MIRNA MOLECULES
MicroRNA molecules ("miRNAs") are generally 21 to 22 nucleotides in length, though lengths of 19 and up to 23 nucleotides have been reported The miRNAs are each processed from a longer precursor RNA molecule ("precursor miRNA") Precursor miRNAs are transcπbed from non-protein-encoding genes The precursor miRNAs have two regions of complementarity that enables them to form a stem-loop- or fold-back-like structure, which is cleaved m animals by a πbonuclease Ill-hke nuclease enzyme called Dicer The processed miRNA is typically a portion of the stem
The processed miRNA (also referred to as "mature miRNA") becomes part of a large complex to down-regulate a particular target gene or its gene product Examples of animal miRNAs include those that imperfectly basepair with the target, which halts translation
(Olsen et al , 1999, Seggerson et al , 2002) siRNA molecules also are processed by Dicer, but from a long, double-stranded RNA molecule siRNAs are not naturally found in animal cells, but they can direct the sequence-specific cleavage of an mRNA target through a RNA- induced silencing complex (RISC) (Denh et al , 2003)
A. Array Preparation
Certain embodiments of the present invention concerns the preparation and use of mRNA or nucleic acid arrays, miRNA or nucleic acid arrays, and/or miRNA or nucleic acid probe arrays, which are macroarrays or microarrays of nucleic acid molecules (probes) that are fully or nearly complementary (over the length of the prove) or identical (over the length of the prove) to a plurality of nucleic acid, mRNA or miRNA molecules, precursor miRNA molecules, or nucleic acids deπved from the various genes and gene pathways modulated by miR-143 miRNAs and that are positioned on a support or support material in a spatially separated organization Macroarrays are typically sheets of nitrocellulose or nylon upon which probes have been spotted Microarrays position the nucleic acid probes more densely such that up to 10,000 nucleic acid molecules can be fit into a region typically 1 to 4 square centimeters Microarrays can be fabπcated by spotting nucleic acid molecules, e g , genes, oligonucleotides, etc , onto substrates or fabricating oligonucleotide sequences in situ on a substrate Spotted or fabπcated nucleic acid molecules can be applied in a high density matnx pattern of up to about 30 non-identical nucleic acid molecules per square centimeter or higher, e g up to about 100 or even 1000 per square centimeter Microarrays typically use coated glass as the solid support, in contrast to the nitrocellulose-based material of filter arrays By having an ordered array of marker RNA and/or miRNA-complementing nucleic acid samples, the position of each sample can be tracked and linked to the original sample
A variety of different array devices in which a plurality of distinct nucleic acid probes are stably associated with the surface of a solid support are known to those of skill in the art Useful substrates for arrays include nylon, glass, metal, plastic, latex, and silicon Such arrays may vary in a number of different ways, including average probe length, sequence or types of probes, nature of bond between the probe and the array surface, e g covalent or non- covalent, and the like The labeling and screening methods of the present invention and the arrays are not limited m its utility with respect to any parameter except that the probes detect miRNA, or genes or nucleic acid representative of genes, consequently, methods and compositions may be used with a variety of different types of nucleic acid arrays
Representative methods and apparatus for prepaπng a microarray have been described, for example, m U S Patents 5,143,854, 5,202,231, 5,242,974, 5,288,644, 5,324,633, 5,384,261, 5,405,783, 5,412,087, 5,424,186, 5,429,807, 5,432,049, 5,436,327, 5,445,934, 5,468,613, 5,470,710, 5,472,672, 5,492,806, 5,525,464, 5,503,980, 5,510,270, 5,525,464, 5,527,681, 5,529,756, 5,532,128, 5,545,531, 5,547,839, 5,554,501, 5,556,752, 5,561,071, 5,571,639, 5,580,726, 5,580,732, 5,593,839, 5,599,695, 5,599,672, 5,610,287, 5,624,711 , 5,631,134, 5,639,603, 5,654,413, 5,658,734, 5,661,028, 5,665,547, 5,667,972, 5,695,940, 5,700,637, 5,744,305, 5,800,992, 5,807,522, 5,830,645, 5,837,196, 5,871,928, 5,847,219, 5,876,932, 5,919,626, 6,004,755, 6,087,102, 6,368,799, 6,383,749, 6,617,112, 6,638,717, 6,720,138, as well as WO 93/17126, WO 95/11995, WO 95/21265, WO 95/21944, WO 95/35505, WO 96/31622, WO 97/10365, WO 97/27317, WO 99/35505, WO 09923256, WO 09936760, WO0138580, WO 0168255, WO 03020898, WO 03040410, WO 03053586, WO 03087297, WO 03091426, WO03100012, WO 04020085, WO 04027093, EP 373 203, EP 785 280, EP 799 897 and UK 8 803 000, the disclosures of which are all herein incorporated by reference
It is contemplated that the arrays can be high density arrays, such that they contain 2, 20, 25, 50, 80, 100 or more different probes It is contemplated that they may contain 1000, 16,000, 65,000, 250,000 or 1,000,000 or more different probes The probes can be directed to mRNA and/or miRNA targets in one or more different organisms or cell types The oligonucleotide probes range from 5 to 50, 5 to 45, 10 to 40, 9 to 34, or 15 to 40 nucleotides m length in some embodiments In certain embodiments, the oligonucleotide probes are 5, 10, 15, 20 to 20, 25, 30, 35, 40 nucleotides in length including all integers and ranges there between
The location and sequence of each different probe sequence in the array are generally known Moreover, the large number of different probes can occupy a relatively small area providing a high density array having a probe density of generally greater than about 60, 100, 600, 1000, 5,000, 10,000, 40,000, 100,000, or 400,000 different oligonucleotide probes per cm2 The surface area of the array can be about or less than about 1, 1 6, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cm2
Moreover, a person of ordinary skill in the art could readily analyze data generated using an array Such protocols are disclosed above, and include information found in WO
9743450, WO 03023058, WO 03022421, WO 03029485, WO 03067217, WO 03066906,
WO 03076928, WO 03093810, WO 03100448 Al, all of which are specifically incorporated by reference
B. Sample Preparation It is contemplated that the RNA and/or miRNA of a wide variety of samples can be analyzed using the arrays, index of probes, or array technology of the invention While endogenous miRNA is contemplated for use with compositions and methods of the invention, recombinant miRNA - including nucleic acids that are complementary or identical to endogenous miRNA or precursor miRNA - can also be handled and analyzed as descnbed herein Samples may be biological samples, in which case, they can be from biopsy, fine needle aspirates, exfoliates, blood, tissue, organs, semen, saliva, tears, other bodily fluid, hair follicles, skm, or any sample containing or constituting biological cells, particularly cancer or hyperproliferative cells In certain embodiments, samples may be, but are not limited to, biopsy, or cells purified or enriched to some extent from a biopsy or other bodily fluids or tissues Alternatively, the sample may not be a biological sample, but be a chemical mixture, such as a cell-free reaction mixture (which may contain one or more biological enzymes)
C. Hybridization
After an array or a set of probes is prepared and/or the nucleic acid in the sample or probe is labeled, the population of target nucleic acids is contacted with the array or probes under hybridization conditions, where such conditions can be adjusted, as desired, to provide for an optimum level of specificity in view of the particular assay being performed Suitable hybridization conditions are well known to those of skill in the art and reviewed in Sambrook et al (2001) and WO 95/21944 Of particular interest in many embodiments is the use of stπngent conditions during hybridization Stringent conditions are known to those of skill in the art It is specifically contemplated that a single array or set of probes may be contacted with multiple samples The samples may be labeled with different labels to distinguish the samples For example, a single array can be contacted with a tumor tissue sample labeled with Cy3, and normal tissue sample labeled with Cy5 Differences between the samples for particular miRNAs corresponding to probes on the array can be readily ascertained and quantified
The small surface area of the array permits uniform hybridization conditions, such as temperature regulation and salt content Moreover, because of the small area occupied by the high density arrays, hybridization may be earned out in extremely small fluid volumes (e g , about 250 μl or less, including volumes of about or less than about 5, 10, 25, 50, 60, 70, 80, 90, 100 μl, or any range deπvable therein) In small volumes, hybridization may proceed very rapidly
D. Differential Expression Analyses
Arrays of the invention can be used to detect differences between two samples Specifically contemplated applications include identifying and/or quantifying differences between miRNA or gene expression from a sample that is normal and from a sample that is not normal, between a disease or condition and a cell not exhibiting such a disease or condition, or between two differently treated samples Also, miRNA or gene expression may be compared between a sample believed to be susceptible to a particular disease or condition and one believed to be not susceptible or resistant to that disease or condition A sample that is not normal is one exhibiting phenotypic or genotypic trait(s) of a disease or condition, or one believed to be not normal with respect to that disease or condition It may be compared to a cell that is normal with respect to that disease or condition Phenotypic traits include symptoms of, or susceptibility to, a disease or condition of which a component is or may or may not be genetic, or caused by a hyperproliferative or neoplastic cell or cells An array composes a solid support with nucleic acid probes attached to the support
Arrays typically compπse a plurality of different nucleic acid probes that are coupled to a surface of a substrate in different, known locations These arrays, also descπbed as "microarrays" or colloquially "chips" have been generally descπbed in the art, for example, U S Patents 5,143,854, 5,445,934, 5,744,305, 5,677,195, 6,040,193, 5,424,186 and Fodor et al , (1991), each of which is incorporated by reference in its entirety for all purposes Techniques for the synthesis of these arrays using mechanical synthesis methods are descπbed in, e g , U S Patent 5,384,261, incorporated herein by reference in its entirety for all purposes Although a planar array surface is used in certain aspects, the array may be fabπcated on a surface of virtually any shape or even a multiplicity of surfaces Arrays may be nucleic acids on beads, gels, polymeπc surfaces, fibers such as fiber optics, glass or any other appropπate substrate, see U S Patents 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, which are hereby incorporated in their entirety for all purposes Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all inclusive device, see for example, U S Patents 5,856,174 and 5,922,591 incorporated in their entirety by reference for all purposes See also U S patent application Ser No 09/545,207, filed Apπl 7, 2000 for additional information concerning arrays, their manufacture, and their characteristics, which is incorporated by reference in its entirety for all purposes
Particularly, arrays can be used to evaluate samples with respect to pathological condition such as cancer and related conditions It is specifically contemplated that the invention can be used to evaluate differences between stages or sub-classifications of disease, such as between benign, cancerous, and metastatic tissues or tumors
Phenotypic traits to be assessed include characteπstics such as longevity, morbidity, expected survival, susceptibility or receptivity to particular drugs or therapeutic treatments (drug efficacy), and nsk of drug toxicity Samples that differ m these phenotypic traits may also be evaluated using the compositions and methods descπbed In certain embodiments, miRNA and/or expression profiles may be generated to evaluate and correlate those profiles with pharmacokinetics or therapies For example, these profiles may be created and evaluated for patient tumor and blood samples pπor to the patient's being treated or during treatment to determine if there are miRNA or genes whose expression correlates with the outcome of the patient's treatment Identification of differential miRNAs or genes can lead to a diagnostic assay for evaluation of tumor and/or blood samples to determine what drug regimen the patient should be provided In addition, it can be used to identify or select patients suitable for a particular clinical tπal If an expression profile is determined to be correlated with drug efficacy or drug toxicity that profile is relevant to whether that patient is an appropπate patient for receiving a drug, for receiving a combination of drugs, or for a particular dosage of the drug
In addition to the above prognostic assay, samples from patients with a vaπety of diseases can be evaluated to determine if different diseases can be identified based on miRNA and/or related gene expression levels A diagnostic assay can be created based on the profiles that doctors can use to identify individuals with a disease or who are at nsk to develop a disease Alternatively, treatments can be designed based on miRNA profiling Examples of such methods and compositions are descπbed in the U S Provisional Patent Application entitled "Methods and Compositions Involving miRNA and miRNA Inhibitor Molecules" filed on May 23, 2005, which is hereby incorporated by reference in its entirety
E. Other Assays
In addition to the use of arrays and microarrays, it is contemplated that a number of different assays could be employed to analyze miRNAs or related genes, their activities, and their effects Such assays include, but are not limited to, nucleic acid amplification, polymerase chain reaction, quantitative PCR, RT-PCR, in situ hybridization, Northern hybridization, hybridization protection assay (HPA)(GenProbe), branched DNA (bDNA) assay (Chiron), rolling circle amplification (RCA), single molecule hybridization detection (US Genomics), Invader assay (ThirdWave Technologies), and/or Bπdge Litigation Assay (Genaco)
IV. NUCLEIC ACIDS
The present invention concerns nucleic acids, modified or mimetic nucleic acids, miRNAs, mRNAs, genes, and representative fragments thereof that can be labeled, used in array analysis, or employed in diagnostic, therapeutic, or prognostic applications, particularly those related to pathological conditions such as cancer The molecules may have been endogenously produced by a cell, or been synthesized or produced chemically or recombmantly They may be isolated and/or purified Each of the miRNAs descπbed herein and include the corresponding SEQ ID NO and accession numbers for these miRNA sequences The name of a miRNA is often abbreviated and referred to without a "hsa-" prefix and will be understood as such, depending on the context Unless otherwise indicated, miRNAs referred to in the application are human sequences identified as miR-X or let-X, where X is a number and/or letter
In certain aspects, a miRNA probe designated by a suffix "5P" or "3P" can be used "5P" indicates that the mature miRNA deπves from the 5' end of the precursor and a 5 corresponding "3P" indicates that it deπves from the 3' end of the precursor, as descnbed on the world wide web at Sanger ac uk Moreover, in some embodiments, a miRNA probe is used that does not correspond to a known human miRNA It is contemplated that these non- human miRNA probes may be used in embodiments of the invention or that there may exist a human miRNA that is homologous to the non-human miRNA In other embodiments, any 10 mammalian cell, biological sample, or preparation thereof may be employed
In some embodiments of the invention, methods and compositions involving miRNA may concern rniRNA, markers (mRNAs), and/or other nucleic acids Nucleic acids may be, be at least, or be at most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
15 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, -260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530,
20 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 nucleotides, or any range deπvable therein, in length Such lengths cover the lengths of processed miRNA, miRNA probes, precursor miRNA, miRNA containing vectors, mRNA, mRNA probes, control nucleic acids,
25 and other probes and primers
In many embodiments, miRNA are 19-24 nucleotides in length, while miRNA probes are 19-35 nucleotides in length, depending on the length of the processed miRNA and any flanking regions added miRNA precursors are generally between 62 and 110 nucleotides in humans
30 Nucleic acids of the invention may have regions of identity or complementarity to another nucleic acid It is contemplated that the region of complementarity or identity can be at least 5 contiguous residues, though it is specifically contemplated that the region is, is at least, or is at most 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 5 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810,
10 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 contiguous nucleotides It is further understood that the length of complementarity within a precursor miRNA or other nucleic acid or between a miRNA probe and a miRNA or a miRNA gene are such lengths Moreover, the complementarity may be expressed as a percentage, meaning that the complementarity between a probe and its target is 90% or
15 greater over the length of the probe In some embodiments, complementarity is or is at least 90%, 95% or 100% In particular, such lengths may be applied to any nucleic acid compπsing a nucleic acid sequence identified m any of SEQ ID NO 1-13, accession number, or any other sequence disclosed herein Typically, the commonly used name of the miRNA is given (with its identifying source in the prefix, for example, "hsa" for human sequences)
20 and the processed miRNA sequence Unless otherwise indicated, a miRNA without a prefix will be understood to refer to a human miRNA Moreover, a lowercase letter in a miRNA name may or may not be lowercase, for example, hsa-mir-130b can also be referred to as miR-130B The term "miRNA probe" refers to a nucleic acid probe that can identify a particular miRNA or structurally related miRNAs
25 It is understood that some nucleic acids are deπved from genomic sequences or a gene In this respect, the term "gene" is used for simplicity to refer to the genomic sequence encoding the precursor nucleic acid or miRNA for a given miRNA or gene However, embodiments of the invention may involve genomic sequences of a miRNA that are involved m its expression, such as a promoter or other regulatory sequences
30 The term "recombinant" may be used and this generally refers to a molecule that has been manipulated in vitro or that is a replicated or expressed product of such a molecule The term "nucleic acid" is well known in the art A "nucleic acid" as used herein will generally refer to a molecule (one or more strands) of DNA, RNA or a denvative or analog thereof, compπsing a nucleobase A nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e g , an adenine "A," a guanine "G," a thymine "T" or a cytosine "C") or RNA (e g , an A, a G, an uracil "U" or a C) The term "nucleic acid" encompasses the terms "oligonucleotide" and "polynucleotide," each as a subgenus of the term "nucleic acid "
The term "miRNA" generally refers to a single-stranded molecule, but in specific embodiments, molecules implemented in the invention will also encompass a region or an additional strand that is partially (between 10 and 50% complementary across length of strand), substantially (greater than 50% but less than 100% complementary across length of strand) or fully complementary to another region of the same smgle-stranded molecule or to another nucleic acid Thus, miRNA may encompass a molecule that composes one or more complementary or self-complementary strand(s) or "complement(s)" of a particular sequence For example, precursor miRNA may have a self complementary region, which is up to 100% complementary miRNA probes or nucleic acids of the invention can include, can be or can be at least 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or 100% complementary to their target
It is understood that a "synthetic nucleic acid" of the invention means that the nucleic acid does not have all or part of a chemical structure or sequence of a naturally occurring nucleic acid Consequently, it will be understood that the term "synthetic miRNA" refers to a
"synthetic nucleic acid" that functions in a cell or under physiological conditions as a naturally occurring miRNA
While embodiments of the invention may involve synthetic miRNAs or synthetic nucleic acids, in some embodiments of the invention, the nucleic acid molecule(s) need not be "synthetic " In certain embodiments, a non-synthetic nucleic acid or miRNA employed m methods and compositions of the invention may have the entire sequence and structure of a naturally occurring mRNA or miRNA precursor or the mature mRNA or miRNA For example, non-synthetic miRNAs used m methods and compositions of the invention may not have one or more modified nucleotides or nucleotide analogs In these embodiments, the non-synthetic miRNA may or may not be recombinantly produced In particular embodiments, the nucleic acid in methods and/or compositions of the invention is specifically a synthetic miRNA and not a non-synthetic miRNA (that is, not an miRNA that qualifies as "synthetic"), though in other embodiments, the invention specifically involves a non- synthetic miRNA and not a synthetic miRNA Any embodiments discussed with respect to the use of synthetic miRNAs can be applied with respect to non-synthetic miRNAs, and vice versa
It will be understood that the term "naturally occurring" refers to something found in an organism without any intervention by a person, it could refer to a naturally-occurnng wildtype or mutant molecule In some embodiments a synthetic miRNA molecule does not have the sequence of a naturally occurring miRNA molecule In other embodiments, a synthetic miRNA molecule may have the sequence of a naturally occurring miRNA molecule, but the chemical structure of the molecule, particularly in the part unrelated specifically to the precise sequence (non-sequence chemical structure) differs from chemical structure of the naturally occurring miRNA molecule with that sequence In some cases, the synthetic miRNA has both a sequence and non-sequence chemical structure that are not found in a naturally-occurnng miRNA Moreover, the sequence of the synthetic molecules will identify which miRNA is effectively being provided or inhibited, the endogenous miRNA will be referred to as the "corresponding miRNA " Corresponding miRNA sequences that can be used in the context of the invention include, but are not limited to, all or a portion of those sequences in the SEQ IDs provided herein, as well as any other miRNA sequence, miRNA precursor sequence, or any sequence complementary thereof In some embodiments, the sequence is or is deπved from or contains all or part of a sequence identified herein to target a particular miRNA (or set of miRNAs) that can be used with that sequence
As used herein, "hybridization", "hybridizes" or "capable of hybridizing" is understood to mean the forming of a double or tπple stranded molecule or a molecule with partial double or tπple stranded nature The term "anneal" as used herein is synonymous with "hybridize " The term "hybridization", "hybndize(s)" or "capable of hybridizing" encompasses the terms "stringent condition(s)" or "high stringency" and the terms "low stringency" or "low stringency condition(s) " As used herein "stringent condition(s)" or "high stringency" are those conditions that allow hybridization between or within one or more nucleic acid strand(s) containing complementary sequence(s), but preclude hybridization of random sequences Stringent conditions tolerate little, if any, mismatch between a nucleic acid and a target strand Such conditions are well known to those of ordinary skill m the art, and are preferred for applications requiring high selectivity Non-hmitmg applications include isolating a nucleic acid, such as a gene or a nucleic acid segment thereof, or detecting at least one specific mRNA transcript or a nucleic acid segment thereof, and the like
Stringent conditions may compose low salt and/or high temperature conditions, such as provided by about 0 02 M to about 0 5 M NaCl at temperatures of about 42°C to about 700C It is understood that the temperature and iomc strength of a desired stringency are determined in part by the length of the particular nucleic acid(s), the length and nucleobase content of the target sequence(s), the charge composition of the nucleic acid(s), and to the presence or concentration of formamide, tetramethylammonium chloride or other solvent(s) in a hybridization mixture
It is also understood that these ranges, compositions and conditions for hybridization are mentioned by way of non-limiting examples only, and that the desired stringency for a particular hybridization reaction is often determined empirically by compaπson to one or more positive or negative controls Depending on the application envisioned it is preferred to employ varying conditions of hybridization to achieve varying degrees of selectivity of a nucleic acid towards a target sequence In a non-hmitmg example, identification of a related target nucleic acid that does not hybridize to a nucleic acid under stπngent conditions may be achieved by hybridization at low temperature and/or high ionic strength Such conditions are termed "low stringency" or "low stringency conditions," and non-limiting examples of low stringency include hybridization performed at about 0 15 M to about 0 9 M NaCl at a temperature range of about 200C to about 500C Of course, it is withm the skill of one in the art to further modify the low or high stringency conditions to suite a particular application A. Nucleobase, Nucleoside, Nucleotide, and Modified Nucleotides
As used herein a "nucleobase" refers to a heterocyclic base, such as for example a naturally occurring nucleobase (ι e , an A, T, G, C or U) found in at least one naturally occurring nucleic acid (ι e , DNA and RNA), and naturally or non-naturally occurring deπvative(s) and analogs of such a nucleobase A nucleobase generally can form one or more hydrogen bonds ("anneal" or "hybridize") with at least one naturally occurring nucleobase m a manner that may substitute for naturally occurring nucleobase paiπng {e g , the hydrogen bonding between A and T, G and C, and A and U) "Purine" and/or "pynmidme" nucleobase(s) encompass naturally occurring puπne and/or pynmidme nucleobases and also deπvative(s) and analog(s) thereof, including but not limited to, those a puπne or pynmidme substituted by one or more of an alkyl, caboxyalkyl, amino, hydroxyl, halogen (ι e , fluoro, chloro, bromo, or iodo), thiol or alkylthiol moiety Preferred alkyl (e g , alkyl, caboxyalkyl, etc ) moieties compπse of from about 1, about 2, about 3, about 4, about 5, to about 6 carbon atoms Other non-limiting examples of a puπne or pynmidme include a deazapuπne, a 2,6-diaminopuπne, a 5-fluorouracil, a xanthine, a hypoxanthine, a 8-bromoguamne, a 8-chloroguamne, a bromothymine, a 8-aminoguamne, a 8-hydroxyguanine, a 8-methylguamne, a 8-thioguamne, an azaguanme, a 2-ammopuπne, a 5- ethylcytosine, a 5-methylcyosine, a 5-bromouracil, a 5-ethyluracil, a 5-iodouracil, a 5- chlorouracil, a 5-propyluracil, a thiouracil, a 2-methyladenme, a methylthioademne, a N1N- diemethyladenme, an azaademnes, a 8-bromoadenme, a 8-hydroxyadenme, a 6- hydroxyammopuπne, a 6-thiopuπne, a 4-(6-ammohexyl/cytosme), and the like Other examples are well known to those of skill in the art As used herein, a "nucleoside" refers to an individual chemical unit comprising a nucleobase covalently attached to a nucleobase linker moiety A non-hmitmg example of a "nucleobase linker moiety" is a sugar compnsing 5-carbon atoms (i β , a "5-carbon sugar"), including but not limited to a deoxyπbose, a πbose, an arabinose, or a deπvative or an analog of a 5-carbon sugar Non-hmitmg examples of a denvative or an analog of a 5-carbon sugar include a 2'-fluoro-2'-deoxyπbose or a carbocychc sugar where a carbon is substituted for an oxygen atom in the sugar nng Different types of covalent attachment(s) of a nucleobase to a nucleobase linker moiety are known in the art (Romberg and Baker, 1992)
As used herein, a "nucleotide" refers to a nucleoside further compnsmg a "backbone moiety" A backbone moiety generally covalently attaches a nucleotide to another molecule compnsmg a nucleotide, or to another nucleotide to form a nucleic acid The "backbone moiety" in naturally occurring nucleotides typically compnses a phosphorus moiety, which is covalently attached to a 5-carbon sugar The attachment of the backbone moiety typically occurs at either the 3'- or 5'-position of the 5-carbon sugar However, other types of attachments are known in the art, particularly when a nucleotide compnses denvatives or analogs of a naturally occurring 5-carbon sugar or phosphorus moiety
A nucleic acid may compnse, or be composed entirely of, a denvative or analog of a nucleobase, a nucleobase linker moiety and/or backbone moiety that may be present in a naturally occurring nucleic acid RNA with nucleic acid analogs may also be labeled according to methods of the invention As used herein a "derivative" refers to a chemically modified or altered form of a naturally occurring molecule, while the terms "mimic" or "analog" refer to a molecule that may or may not structurally resemble a naturally occurring molecule or moiety, but possesses similar functions As used herein, a "moiety" generally refers to a smaller chemical or molecular component of a larger chemical or molecular structure Nucleobase, nucleoside and nucleotide analogs or derivatives are well known in the art, and have been descπbed (see for example, Scheit, 1980, incorporated herein by reference) Additional non-hmitmg examples of nucleosides, nucleotides or nucleic acids include those in U S Patents 5,681,947, 5,652,099 and 5,763,167, 5,614,617, 5,670,663, 5,872,232, 5,859,221, 5,446,137, 5,886,165, 5,714,606, 5,672,697, 5,466,786, 5,792,847, 5,223,618, 5,470,967, 5,378,825, 5,777,092, 5,623,070, 5,610,289, 5,602,240, 5,858,988, 5,214,136, 5,700,922, 5,708,154, 5,728,525, 5,637,683, 6,251,666, 5,480,980, and 5,728,525, each of which is incorporated herein by reference m its entirety
Labeling methods and kits of the invention specifically contemplate the use of nucleotides that are both modified for attachment of a label and can be incorporated into a miRNA molecule Such nucleotides include those that can be labeled with a dye, including a fluorescent dye, or with a molecule such as biotin Labeled nucleotides are readily available, they can be acquired commercially or they can be synthesized by reactions known to those of skill in the art
Modified nucleotides for use in the invention are not naturally occurring nucleotides, but instead, refer to prepared nucleotides that have a reactive moiety on them Specific reactive functionalities of interest include ammo, sulfhydryl, sulfoxyl, aminosulfhydryl, azido, epoxide, isothiocyanate, isocyanate, anhydride, monochlorotnazine, dichlorotπazine, mono-or dihalogen substituted pyridine, mono- or disubstituted diazme, maleimide, epoxide, azmdme, sulfonyl hahde, acid halide, alkyl halide, aryl hahde, alkylsulfonate, N- hydroxysuccimmide ester, imido ester, hydrazine, azidomtrophenyl, azide, 3-(2-pyπdyl dithio)-propionamide, glyoxal, aldehyde, lodoacetyl, cyanomethyl ester, p-nitrophenyl ester, o-nitrophenyl ester, hydroxypyπdme ester, carbonyl imidazole, and the other such chemical groups In some embodiments, the reactive functionality may be bonded directly to a nucleotide, or it may be bonded to the nucleotide through a linking group The functional moiety and any linker cannot substantially impair the ability of the nucleotide to be added to the miRNA or to be labeled Representative linking groups include carbon containing linking groups, typically ranging from about 2 to 18, usually from about 2 to 8 carbon atoms, where the carbon containing linking groups may or may not include one or more heteroatoms, e g S, O, N etc , and may or may not include one or more sites of unsaturation Of particular interest in many embodiments are alkyl linking groups, typically lower alkyl linking groups of 1 to 16, usually 1 to 4 carbon atoms, where the linking groups may include one or more sites of unsaturation The functionahzed nucleotides (or primers) used in the above methods of functionahzed target generation may be fabπcated using known protocols or purchased from commercial vendors, e g , Sigma, Roche, Ambion, Biosearch Technologies and NEN Functional groups may be prepared according to ways known to those of skill in the art, including the representative information found in U S Patents 4,404,289, 4,405,711, 4,337,063 and 5,268,486, and U K Patent 1,529,202, which are all incorporated by reference Amine-modified nucleotides are used in several embodiments of the invention The amine-modifled nucleotide is a nucleotide that has a reactive amine group for attachment of the label It is contemplated that any ribonucleotide (G, A, U, or C) or deoxyπbonucleotide (G, A, T, or C) can be modified for labeling Examples include, but are not limited to, the following modified πbo- and deoxynbo-nucleotides 5-(3-ammoallyl)-UTP, 8-[(4- amino)butyl]-amino-ATP and 8-[(6-ammo)butyl]-amino-ATP, N6-(4-amino)butyl-ATP, N6- (6-ammo)butyl-ATP, N4-[2,2-oxy-bis-(ethylamine)]-CTP, N6-(6-Amino)hexyl-ATP, 8-[(6- Ammo)hexyl]-amino-ATP, 5-propargylammo-CTP, 5-propargylamino-UTP, 5-(3- ammoallyl)-dUTP, 8-[(4-amino)butyl]-amino-dATP and 8-[(6-ammo)butyl]-amino-dATP, N6-(4-amino)butyl-dATP, N6-(6-amino)butyl-dATP, N4-[2,2-oxy-bis-(ethylamme)]-dCTP, N6-(6-Amino)hexyl-dATP, 8-[(6-Amino)hexyl]-amino-dATP, 5-propargylammo-dCTP, and 5-propargylamino-dUTP Such nucleotides can be prepared according to methods known to those of skill in the art Moreover, a person of ordinary skill in the art could prepare other nucleotide entities with the same amme-modification, such as a 5-(3-ammoallyl)-CTP, GTP, ATP, dCTP, dGTP, dTTP, or dUTP in place of a 5-(3-ammoallyl)-UTP B. Preparation of Nucleic Acids
A nucleic acid may be made by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production, or biological production It is specifically contemplated that miRNA probes of the invention are chemically synthesized
In some embodiments of the invention, miRNAs are recovered or isolated from a biological sample The miRNA may be recombinant or it may be natural or endogenous to the cell (produced from the cell's genome) It is contemplated that a biological sample may be treated m a way so as to enhance the recovery of small RNA molecules such as miRNA U S Patent Application Senal No 10/667,126 descπbes such methods and it is specifically incorporated by reference herein Generally, methods involve lysmg cells with a solution having guamdinium and a detergent Alternatively, nucleic acid synthesis is performed according to standard methods
See, for example, Itakura and Riggs (1980) and U S Patents 4,704,362, 5,221,619, and 5,583,013, each of which is incorporated herein by reference Non-limiting examples of a synthetic nucleic acid (e g , a synthetic oligonucleotide), include a nucleic acid made by in vitro chemically synthesis using phosphotnester, phosphite, or phosphoramidite chemistry and solid phase techniques such as described in EP 266,032, incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as descπbed by Froehler et al , 1986 and U S Patent 5,705,629, each incorporated herein by reference Vanous different mechanisms of oligonucleotide synthesis have been disclosed in for example, U S Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference
A non-limiting example of an enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCR™ (see for example, U S Patents 4,683,202 and 4,682,195, each incorporated herein by reference), or the synthesis of an oligonucleotide descπbed in U S Patent 5,645,897, incorporated herein by reference See also Sambrook et al , 2001, incorporated herein by reference)
Oligonucleotide synthesis is well known to those of skill in the art Vanous different mechanisms of oligonucleotide synthesis have been disclosed in for example, U S Patents 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference Recombinant methods for producing nucleic acids in a cell are well known to those of skill in the art These include the use of vectors (viral and non-viral), plasmids, cosmids, and other vehicles for delivering a nucleic acid to a cell, which may be the target cell (e g , a cancer cell) or simply a host cell (to produce large quantities of the desired RNA molecule) Alternatively, such vehicles can be used in the context of a cell free system so long as the reagents for generating the RNA molecule are present Such methods include those descπbed in Sambrook, 2003, Sambrook, 2001 and Sambrook, 1989, which are hereby incorporated by reference
C. Isolation of Nucleic Acids
Nucleic acids may be isolated using techniques well known to those of skill m the art, though m particular embodiments, methods for isolating small nucleic acid molecules, and/or isolating RNA molecules can be employed Chromatography is a process often used to separate or isolate nucleic acids from protein or from other nucleic acids Such methods can involve electrophoresis with a gel matrix, filter columns, alcohol precipitation, and/or other chromatography If miRNA from cells is to be used or evaluated, methods generally involve lysmg the cells with a chaotropic (e g , guamdimum isothiocyanate) and/or detergent (e g , N- lauroyl sarcosme) pπor to implementing processes for isolating particular populations of RNA
In particular methods for separating miRNA from other nucleic acids, a gel matrix is prepared using polyacrylamide, though agarose can also be used The gels may be graded by concentration or they may be uniform Plates or tubmg can be used to hold the gel matπx for electrophoresis Usually one-dimensional electrophoresis is employed for the separation of nucleic acids Plates are used to prepare a slab gel, while the tubmg (glass or rubber, typically) can be used to prepare a tube gel The phrase "tube electrophoresis" refers to the use of a tube or tubmg, instead of plates, to form the gel Matenals for implementing tube electrophoresis can be readily prepared by a person of skill in the art or purchased, such as from C B S Scientific Co , Inc or Scie-Plas
Methods may involve the use of organic solvents and/or alcohol to isolate nucleic acids, particularly miRNA used in methods and compositions of the invention Some embodiments are descnbed in U S Patent Application Serial No 10/667,126, which is hereby incorporated by reference Generally, this disclosure provides methods for efficiently isolating small RNA molecules from cells comprising adding an alcohol solution to a cell lysate and applying the alcohol/lysate mixture to a solid support before elutmg the RNA molecules from the solid support In some embodiments, the amount of alcohol added to a cell lysate achieves an alcohol concentration of about 55% to 60% While different alcohols can be employed, ethanol works well A solid support may be any structure, and it includes beads, filters, and columns, which may include a mineral or polymer support with electronegative groups A glass fiber filter or column has worked particularly well for such isolation procedures
In specific embodiments, miRNA isolation processes include a) lysmg cells m the sample with a lysing solution comprising guamdimum, wherein a lysate with a concentration of at least about 1 M guamdimum is produced, b) extracting miRNA molecules from the lysate with an extraction solution composing phenol, c) adding to the lysate an alcohol solution for forming a lysate/alcohol mixture, wherein the concentration of alcohol in the mixture is between about 35% to about 70%, d) applying the lysate/alcohol mixture to a solid support, e) eluting the miRNA molecules from the solid support with an ionic solution, and, f) captuπng the miRNA molecules Typically the sample is dried and resuspended m a liquid and volume appropnate for subsequent manipulation V. LABELS AND LABELING TECHNIQUES
In some embodiments, the present invention concerns miRNA that are labeled It is contemplated that miRNA may first be isolated and/or purified poor to labeling This may achieve a reaction that more efficiently labels the miRNA, as opposed to other RNA in a sample in which the miRNA is not isolated or punfied pπor to labeling In many embodiments of the invention, the label is non-radioactive Generally, nucleic acids may be labeled by adding labeled nucleotides (one-step process) or adding nucleotides and labeling the added nucleotides (two-step process)
A. Labeling Techniques
In some embodiments, nucleic acids are labeled by catalytically adding to the nucleic acid an already labeled nucleotide or nucleotides One or more labeled nucleotides can be added to miRNA molecules See U S Patent 6,723,509, which is hereby incorporated by reference
In other embodiments, an unlabeled nucleotide or nucleotides is catalytically added to a miRNA, and the unlabeled nucleotide is modified with a chemical moiety that enables it to be subsequently labeled In embodiments of the invention, the chemical moiety is a reactive amine such that the nucleotide is an amine-modified nucleotide Examples of amine- modified nucleotides are well known to those of skill in the art, many being commercially available such as from Ambion, Sigma, Jena Bioscience, and TπLink
In contrast to labeling of cDNA during its synthesis, the issue for labeling miRNA is how to label the already existing molecule The present invention concerns the use of an enzyme capable of using a di- or tn-phosphate ribonucleotide or deoxyribonucleotide as a substrate for its addition to a miRNA Moreover, in specific embodiments, it involves using a modified di- or tπ-phosphate ribonucleotide, which is added to the 3' end of a miRNA Enzymes capable of adding such nucleotides include, but are not limited to, poly(A) polymerase, terminal transferase, and polynucleotide phosphorylase In specific embodiments of the invention, a ligase is contemplated as not being the enzyme used to add the label, and instead, a non-hgase enzyme is employed Terminal transferase catalyzes the addition of nucleotides to the 3' terminus of a nucleic acid Polynucleotide phosphorylase can polymerize nucleotide diphosphates without the need for a pnmer
B. Labels Labels on miRNA or miRNA probes may be coloπmetnc (includes visible and UV spectrum, including fluorescent), luminescent, enzymatic, or positron emitting (including radioactive) The label may be detected directly or indirectly Radioactive labels include 1251, 32P, 33P, and 35S Examples of enzymatic labels include alkaline phosphatase, luciferase, horseradish peroxidase, and β-galactosidase Labels can also be proteins with luminescent properties, e g , green fluorescent protein and phicoerythnn
The coloπmetπc and fluorescent labels contemplated for use as conjugates include, but are not limited to, Alexa Fluor dyes, BODIPY dyes, such as BODIPY FL, Cascade Blue, Cascade Yellow, coumaπn and its deπvatives, such as 7-amino-4-methylcoumarm, ammocoumaπn and hydroxycoumaπn, cyanine dyes, such as Cy3 and Cy5, eosms and erythrosins, fluorescein and its deπvatives, such as fluorescein isothiocyanate, macrocyclic chelates of lanthamde ions, such as Quantum Dye™, Manna Blue, Oregon Green, rhodamine dyes, such as rhodamine red, tetramethylrhodamme and rhodamme 6G, Texas Red, , fluorescent energy transfer dyes, such as thiazole orange-ethidium heterodimer, and, TOTAB Specific examples of dyes include, but are not limited to, those identified above and the following Alexa Fluor 350, Alexa Fluor 405, Alexa Fluor 430, Alexa Fluor 488, Alexa Fluor 500 Alexa Fluor 514, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 610, Alexa Fluor 633, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700, and, Alexa Fluor 750, amme-reactive BODIPY dyes, such as BODIPY 493/503, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/655, BODIPY FL, BODIPY R6G, BODIPY TMR, and, BODIPY-TR, Cy3, Cy5, 6-FAM, Fluorescein Isothiocyanate, HEX, 6-JOE, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG, Rhodamine Green, Rhodamine Red, Renographin, ROX, SYPRO, TAMRA, 2',4',5',7r- Tetrabromosulfonefluorescem, and TET. Specific examples of fluorescently labeled ribonucleotides are available from
Molecular Probes, and these include, Alexa Fluor 488-5-UTP, Fluorescein- 12-UTP, BODIPY FL-14-UTP, BODIPY TMR-14-UTP, Tetramethylrhodamine-6-UTP, Alexa Fluor 546-14- UTP, Texas Red-5-UTP, and BODIPY TR-14-UTP Other fluorescent ribonucleotides are available from Amersham Biosciences, such as Cy3-UTP and Cy5-UTP Examples of fluorescently labeled deoxyπbonucleotides include Dmitrophenyl
(DNP)-11-dUTP, Cascade Blue-7-dUTP, Alexa Fluor 488-5-dUTP, Fluorescein-12-dUTP, Oregon Green 488-5-dUTP, BODIPY FL-14-dUTP, Rhodamine Green-5-dUTP, Alexa Fluor 532-5-dUTP, BODIPY TMR-14-dUTP, Tetramethylrhodamine-6-dUTP, Alexa Fluor 546- 14-dUTP, Alexa Fluor 568-5-dUTP, Texas Red-12-dUTP, Texas Red-5-dUTP, BODIPY TR- 14-dUTP, Alexa Fluor 594-5-dUTP, BODIPY 630/650-14-dUTP, BODIPY 650/665-14- dUTP, Alexa Fluor 488-7-OBEA-dCTP, Alexa Fluor 546-16-OBEA-dCTP, Alexa Fluor 594- 7-OBEA-dCTP, Alexa Fluor 647-12-OBEA-dCTP
It is contemplated that nucleic acids may be labeled with two different labels. Furthermore, fluorescence resonance energy transfer (FRET) may be employed in methods of the invention (e g , Klostermeier et al , 2002, Emptage, 2001 , Didenko, 2001, each incorporated by reference)
Alternatively, the label may not be detectable per se, but indirectly detectable or allowing for the isolation or separation of the targeted nucleic acid For example, the label could be biotm, digoxigemn, polyvalent cations, chelator groups and the other hgands, include hgands for an antibody C. Visualization Techniques
A number of techniques for visualizing or detecting labeled nucleic acids are readily available Such techniques include, microscopy, arrays, Fluorometry, Light cyclers or other real time PCR machines, FACS analysis, scintillation counters, Phosphoimagers, Geiger counters, MRI, CAT, antibody-based detection methods (Westerns, immunofluorescence, lmmunohistochermstry), histochemical techniques, HPLC (Griffey et al , 1997), spectroscopy, capillary gel electrophoresis (Cummins et al , 1996), spectroscopy, mass spectroscopy, radiological techniques, and mass balance techniques
When two or more differentially colored labels are employed, fluorescent resonance energy transfer (FRET) techniques may be employed to characterize association of one or more nucleic acid Furthermore, a person of ordinary skill in the art is well aware of ways of visualizing, identifying, and characterizing labeled nucleic acids, and accordingly, such protocols may be used as part of the invention Examples of tools that may be used also include fluorescent microscopy, a BioAnalyzer, a plate reader, Storm (Molecular Dynamics), Array Scanner, FACS (fluorescent activated cell sorter), or any instrument that has the ability to excite and detect a fluorescent molecule
VI. KITS
Any of the compositions descπbed herein may be comprised in a kit In a non- hmitmg example, reagents for isolating miRNA, labeling miRNA, and/or evaluating a miRNA population using an array, nucleic acid amplification, and/or hybridization can be included in a kit, as well reagents for preparation of samples from blood samples The kit may further include reagents for creating or synthesizing miRNA probes The kits will thus compπse, in suitable container means, an enzyme for labeling the miRNA by incorporating labeled nucleotide or unlabeled nucleotides that are subsequently labeled In certain aspects, the kit can include amplification reagents In other aspects, the kit may include various supports, such as glass, nylon, polymeric beads, and the like, and/or reagents for coupling any probes and/or target nucleic acids It may also include one or more buffers, such as reaction buffer, labeling buffer, washing buffer, or a hybridization buffer, compounds for preparing the miRNA probes, and components for isolating miRNA Other kits of the invention may include components for making a nucleic acid array comprising miRNA, and thus, may include, for example, a solid support Kits for implementing methods of the invention descnbed herein are specifically contemplated In some embodiments, there are kits for preparing miRNA for multi-labelmg and kits for preparing miRNA probes and/or miRNA arrays In these embodiments, kit comprise, in suitable container means, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more of the following (1) poly(A) polymerase, (2) unmodified nucleotides (G, A, T, C, and/or U), (3) a modified nucleotide (labeled or unlabeled), (4) poly(A) polymerase buffer, and, (5) at least one microfilter, (6) label that can be attached to a nucleotide, (7) at least one miRNA probe, (8) reaction buffer, (9) a miRNA array or components for making such an array, (10) acetic acid, (11) alcohol, (12) solutions for prepaπng, isolating, enriching, and purifying miRNAs or miRNA probes or arrays Other reagents include those generally used for manipulating RNA, such as formarmde, loading dye, πbonuclease inhibitors, and DNase
In specific embodiments, kits of the invention include an array containing miRNA probes, as descnbed in the application An array may have probes corresponding to all known miRNAs of an organism or a particular tissue or organ in particular conditions, or to a subset of such probes The subset of probes on arrays of the invention may be or include those identified as relevant to a particular diagnostic, therapeutic, or prognostic application For example, the array may contain one or more probes that is indicative or suggestive of (1) a disease or condition (acute myeloid leukemia), (2) susceptibility or resistance to a particular drug or treatment, (3) susceptibility to toxicity from a drug or substance, (4) the stage of development or seventy of a disease or condition (prognosis), and (5) genetic predisposition to a disease or condition
For any kit embodiment, including an array, there can be nucleic acid molecules that contain or can be used to amplify a sequence that is a variant of, identical to or complementary to all or part of any of SEQ IDs descnbed herein In certain embodiments, a kit or array of the invention can contain one or more probes for the miRNAs identified by the SEQ IDs described herein Any nucleic acid discussed above may be implemented as part of a kit
The components of the kits may be packaged either in aqueous media or in lyophihzed form The container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably ahquoted Where there is more than one component in the kit
(labeling reagent and label may be packaged together), the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed However, various combinations of components may be compπsed in a vial The kits of the present invention also will typically include a means for containing the nucleic acids, and any other reagent containers in close confinement for commercial sale Such containers may include injection or blow molded plastic containers into which the desired vials are retained
When the components of the kit are provided m one and/or more liquid solutions, the liquid solution is an aqueous solution, with a steπle aqueous solution being particularly preferred However, the components of the kit may be provided as dπed powder(s) When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent It is envisioned that the solvent may also be provided m another container means In some embodiments, labeling dyes are provided as a dried power It is contemplated that 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 120, 130, 140, 150, 160, 170, 180, 190, 200, 300, 400, 500, 600, 700, 800, 900, 1000 μg or at least or at most those amounts of dried dye are provided in kits of the invention The dye may then be resuspended in any suitable solvent, such as DMSO
Such kits may also include components that facilitate isolation of the labeled miRNA
It may also include components that preserve or maintain the miRNA or that protect against its degradation Such components may be RNAse-free or protect against RNAses Such kits generally will comprise, m suitable means, distinct containers for each individual reagent or solution
A kit will also include instructions for employing the kit components as well the use of any other reagent not included in the kit Instructions may include variations that can be implemented
Kits of the invention may also include one or more of the following Control RNA, nuclease-free water, RNase-free containers, such as 1 5 ml rubes, RNase-free elution tubes, PEG or dextran, ethanol, acetic acid, sodium acetate, ammonium acetate, guanidimum, detergent, nucleic acid size marker, RNase-free tube tips, and RNase or DNase inhibitors It is contemplated that such reagents are embodiments of kits of the invention Such kits, however, are not limited to the particular items identified above and may include any reagent used for the manipulation or characterization of miRNA
VII. EXAMPLES The following examples are included to demonstrate preferred embodiments of the invention It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spint and scope of the invention
EXAMPLE 1: GENE EXPRESSION ANALYSIS FOLLOWING TRANSFECTION
WITH HSA-MIR-143 miRNAs are believed to regulate gene expression by binding to target mRNA transcripts and (1) initiating transcript degradation or (2) alteπng protein translation from the transcript Translational regulation leading to an up or down change in protein expression may lead to changes in activity and expression of downstream gene products and genes that are in turn regulated by those proteins These numerous regulatory effects may be revealed as changes in the global mRNA expression profile Microarray gene expression analyses were performed to identify genes that are mis-regulated by hsa-miR-143 expression
Synthetic Pre-miR-143 (Ambion) or two negative control miRNAs (pre-miR-NCl, Ambion cat no AM17110 and pre-miR-NC2, Ambion, cat no AM17111) were reverse transfected into quadruplicate samples of A549 cells for each of three time points Cells were transfected using siPORT NeoFX (Ambion) according to the manufacturer's recommendations using the following parameters 200,000 cells per well in a 6 well plate, 5 0 μl of NeoFX, 30 nM final concentration of miRNA in 2 5 ml Cells were harvested at 4 h, 24 h, and 72 h post transfection Total RNA was extracted using RNAqueous-4PCR (Ambion) according to the manufacturer's recommended protocol mRNA array analyses were performed by Asuragen Services (Austin, TX), according to the company's standard operating procedures Using the MessageAmp™ 11-96 aRNA Amplification Kit (Ambion, cat #1819) 2 μg of total RNA were used for target preparation and labeling with biotin cRNA yields were quantified using an Agilent Bioanalyzer 2100 capillary electrophoresis protocol Labeled target was hybndized to Affymetπx mRNA arrays (Human HG-Ul 33A 2 0 arrays) using the manufacturer's recommendations and the following parameters Hybridizations were carried out at 450C for 16 hr m an Affymetnx Model 640 hybridization oven Arrays were washed and stained on an Affymetπx FS450 Fluidics station, running the wash scπpt Midi_euk2v3_450 The arrays were scanned on a Affymetπx GeneChip Scanner 3000 Summaries of the image signal data, group mean values, p- values with significance flags, log ratios and gene annotations for every gene on the array were generated using the Affymetnx Statistical Algorithm MAS 5 0 (GCOS vl 3) Data were reported in a file (cabinet) containing the Affymetnx data and result files and m files ( eel) containing the pnmary image and processed cell intensities of the arrays Data were normalized for the effect observed by the average of two negative control microRNA sequences and then were averaged together for presentation A list of genes whose expression levels varied by at least 0 7 Iog2 from the average negative control was assembled Results of the microarray gene expression analysis are shown in Table 1 above
Manipulation of the expression levels of the genes listed in Table 1 represents a potentially useful therapy for cancer and other diseases in which increased or reduced expression of hsa-miR-143 has a role in the disease
EXAMPLE 2: CELLULAR PATHWAYS AFFECTED BY HSA-miR-143 The mis-regulation of gene expression by hsa-miR-143 (Table 1) affects many cellular pathways that represent potential therapeutic targets for the control of cancer and other diseases and disorders The inventors determined the identity and nature of the cellular genetic pathways affected by the regulatory cascade induced by hsa-miR-143 expression Cellular pathway analyses were performed using Ingenuity Pathways Analysis (Version 40, Ingenuity® Systems, Redwood City, CA) Alteration of a given pathway was determined by Fisher's Exact test (Fisher, 1922) The most significantly affected pathways following over- expression of hsa-miR-143 in A549 cells are shown in Table 2 These data demonstrate that hsa-miR-143 directly or indirectly affects the expression of several, cellular proliferation-, development-, and cell growth-related genes and thus primarily affects functional pathways related to cellular growth, cellular development, and cell proliferation Those cellular processes have integral roles in the development and progression of vaπous cancers Manipulation of the expression levels of genes in the cellular pathways shown in Table 2 represents a potentially useful therapy for cancer and other diseases in which increased or reduced expression of hsa-miR-143 has a role in the disease
EXAMPLE 3: PREDICTED GENE TARGETS OF HSA-MIR-143
Gene targets for binding of and regulation by hsa-miR-143 were predicted using the propnetary algorithm miRNATarget™ (Asuragen), which is an implementation of the method proposed by Krek et al (2005) Predicted target genes are shown in Table 3
The predicted gene targets that exhibited altered mRNA expression levels in human cancer cells, following transfection with pre-miR hsa-miR-143, are shown in Table 4
The predicted gene targets of hsa-miR-143 whose mRNA expression levels are affected by hsa-miR-143 represent particularly useful candidates for cancer therapy and therapy of other diseases through manipulation of their expression levels
EXAMPLE 4:
CANCER RELATED GENE EXPRESSION ALTERED BY HSA-MIR-143
Cell proliferation, survival, and growth pathways are commonly altered in tumors (Hanahan and Weinberg, 2000) The inventors have shown that hsa-miR-143 directly or indirectly regulates the transcπpts of proteins that are critical in the regulation of these pathways Many of these targets have inherent oncogenic or tumor suppressor activity Hsa- miR-143 targets that have prognostic and/or therapeutic value for the treatment of vaπous malignancies are shown in Table 5
Hsa-miR-143 targeted cancer genes are regulators of the cell cycle, transcπption, intracellular signaling, apoptosis and the thioredoxm redox pathway Hsa-miR-143 regulates cell cycle progression by alteπng the expression of Weel, the retinoblastoma-like 1 protein
(RBLl) as well as the cyclins Dl and Gl RBLl, also known as plO7, is a member of the retinoblastoma tumor suppressor protein family that includes the pocket proteins plO7, pl30 and pRb Similar to the pRb prototype, RBLl interacts with the E2F family of transcription factors and blocks cell cycle progression and DNA replication (Sherr and McCormick, 2002) A subset of cancers show deregulated expression of RBLl (Takimoto et al , 1998, Claudio et al , 2002, Wu et al , 2002, Ito et al , 2003) Transient transfection of hsa-miR-143 leads to a decrease in RBLl mRNA levels which may suggest a proliferative function for hsa-miR-143 In contrast, negative regulation of cyclm Dl and positive regulation of cyclm Gl are indicators of a growth-inhibitory role for hsa-miR-143 Cychns are co-factors of cyclm- dependent kinases (CDKs) and function in the progression of the cell cycle Cyclm Dl is required for the transition from Gl into S phase and is overexpressed in numerous cancer types (Donnellan and Chetty, 1998) (Donnellan and Chetty, 1998) Hsa-miR-143 negatively regulates cyclm Dl expression and therefore might interfere with abnormal cell growth that depends on high levels of cyclin Dl In accordance, cyclm Gl has growth inhibitory activity and is upregulated by hsa-miR-143 (Zhao et al , 2003) Weel is a tyrosine kinase that functions as a mitotic inhibitor by phosphorylating the CDKl(cdc2)/cychnBl complex (Parker and Piwmca- Worms, 1992, McGowan and Russell, 1993) Lack of Weel expression in lung cancer is correlated with a higher proliferation index, a higher relapse rate and poor prognosis (Yoshida et al , 2004) Another hsa-miR-143 target is LMO-4 (LIM domain only 4), a zinc finger protein regulating transcπption LMO-4 is inherently oncogenic and inactivates the BRCA-I tumor suppressor protein (breast cancer 1) (Sum et al , 2002, Sum et al , 2005) LMO-4 is frequently overexpressed m multiple cancer types and predicts poor outcome in breast cancer (Visvader et al , 2001 , Mizunuma et al , 2003, Sum et al , 2005, Tamwaki et al , 2006) Accordingly, RNAi directed against LMO-4 leads to reduced breast cancer cell growth and migration (Sum et al , 2005) Our data indicate that hsa-miR-143 diminishes LMO-4 transcripts and therefore may intercept with the oncogenic properties of LMO-4
Hsa-miR-143 also governs the expression of PDCD4, BCL2L1 and MCLl, all of which are functionally linked to the apoptotic pathway Pdcd-4 (programmed cell death 4) is a tumor suppressor that is induced in response to apoptosis in normal cells The growth inhibitory properties of Pdcd-4 are due to Pdcd-4 mediated inhibition of the c-Jun proto- oncoprotein, inhibition of cap-dependent mRNA translation and activation of the p21Wafl/Cipl CDK inhibitor (Yang et al , 2003, Bitomsky et al , 2004, Goke et al , 2004) Pdcd-4 frequently shows reduced or lost expression in vaπous human malignancies, such as gliomas, hepatocellular carcinomas, lung and renal cell carcinomas (Jansen et al , 2004, Zhang et al , 2006, Gao et al , 2007) Expression of Pdcd-4 interferes with skin carcinogenesis in a mouse model and suppresses growth of human colon carcinoma cells (Jansen et al , 2005, Yang et al , 2006) Loss of Pdcd-4 also correlates with lung tumor progression (Chen et al , 2003) Since hsa-miR-143 positively regulates Pdcd-4 expression, a hsa-miR-143 based therapy may reconstitute Pdcd-4 function BCL2L1 and MCLl are members of the anti-apoptotic BCL-2 (B cell lymphoma 2) gene family that give πse to two alternatively spliced gene products with opposing functions (Boise et al , 1993, Bae et al , 2000) The predominantly expressed protein encoded by BCL2L1 is BcI-XL which - next to BCL-2 - is a major mhibtor of programmed cell death Overexpression of BcI-XL is detected in numerous cancer types and correlates with tumor progression as well as poor survival (Mamon and Hockenbery, 2003) Increased levels of BcI-XL are also associated with resistance to chemo- and radiotherapy (Fesik, 2005) Transient transfection of hsa-miR-143 leads to a reduction of BcI-XL transcripts and therefore might provide a therapeutic benefit to oncogenic cells with increased expression of BcI-XL McI-I (myeloid leukemia 1) is overexpressed in hepatocellular carcinoma, prostate cancer, testicular tumor, multiple myeloma and various leukermas [see refs in Table 5] Similar to BcI-XL, high levels of McI- 1 is correlated with poor prognosis of patients with ovarian carcinoma and is indicative for leukemic relapse (Kaufmann et al , 1998, Shigemasa et al , 2002) RNA interference against McI-I induces a therapeutic response in gastπc and hepatocellular carcinoma cells (Schulze- Bergkamen et al , 2006, Zangemeister-Wittke and Huwiler, 2006)
Molecules regulated by hsa-miR-143 that function in intracellular signal transduction include the inflammatory mterleukin 8 (IL-8), transforming growth factor beta (TGF-β) receptor 2 (TGFBR2) and A-kinase anchor protein 12 (AKAP 12) IL-8 is frequently upregulated in various cancers and correlates with tumor vascularization, metastasis and poor prognosis (Rosenkilde and Schwartz, 2004, Sparmann and Bar-Sagi, 2004) TGFBR-2 forms a functional complex with TGFBR-I and is the primary receptor for TGF-β (Massague et al , 2000) Central role of TGF-β is inhibition of cellular growth of numerous cell types, such as epithelial, endothelial, hematopoietic neural and mesenchymal cells Many mammary and colorectal carcinomas with microsatellite instability harbor inactivating mutations of TGFBR-2, and therefore escape the growth-inhibitory function of TGF-β (Markowitz et al , 1995, Lucke et al , 2001) AKAP12, also referred to as gravin or SSeCKS (Src suppressed C kinase substrate), functions as a kinase scaffold protein that tethers the enzyme-substrate interaction (Nauert et al , 1997) Expression of AKAP 12 interferes with oncogenic cell transformation induced by the Src or Jun oncoproteins in vitro and is lost or reduced in numerous cancers, such as leukemia and carcinomas of the rectum, lung and stomach (Lm and Gelman, 1997, Cohen et al , 2001 , Xia et al , 2001 , Wikman et al , 2002, Boultwood et al , 2004, Choi et al , 2004, Moπ et al , 2006) An apparent anti-oncogemc activity of AKAP 12 in prostate and gastπc cancers marks this protein as a putative tumor suppressor (Xia et al , 2001 , Choi et al , 2004)
Based on the functions for most of these targets and how they are regulated by hsa- miR-143, hsa-miR-143 appears to have tumor suppressor potential This view is supported by our observation that most cancers show reduced expression of miR-143 However, hsa- miR-143 also regulates gene expression in a manner that suggests a role for hsa-miR-143 in the development or progression of disease For instance, hsa-miR-143 stimulates the expression of thioredoxin (TXN), a 12-kDa thiol reductase targeting various proteins and multiple pathways Thioredoxin modulates the activity of transcnption factors, induces the expression of angiogenic Hif-lα (hypoxia induced factor lα) as well as VEGF (vascular endothelial growth factor) and can act as a proliferative and anti-apoptotic agent (Marks, 2006) In accord, carcinomas of the lung, pancreas, cervix, and liver show increased levels of thioredoxin Thioredoxin expression is also correlated with aggressive tumor growth, poor prognosis, and chemoresistance (Marks, 2006) Therefore, a hsa-miR-143 antagonist may have therapeutic potential in cancers that show altered expression of thioredoxin
In summary and not intending to limit the invention by any particular theory, hsa- miR-143 governs the activity of proteins that are critical regulators of cell proliferation and survival These targets are frequently deregulated m human cancer Based on this review of the genes and related pathways that are regulated by miR-143, introduction of hsa-miR-143 or an anti-hsa-miR-143 into a variety of cancer cell types would likely result in a therapeutic response
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Claims

1. A method of modulating gene expression in a cell comprising administering to the cell an amount of an isolated nucleic acid comprising a miR-143 in an amount sufficient to modulate the expression of one or more genes identified in Table 1, 3, 4, or 5.
2. The method of claim 1, wherein the cell is in a subject having, suspected of having, or at risk of developing a metabolic, an immunologic, an infectious, a cardiovascular, a digestive, an endocrine, an ocular, a genitourinary, a blood, a musculoskeletal, a nervous system, a congenital, a respiratory, a skin, or a cancerous disease or condition.
3. The method of claim 2, wherein the infectious disease or condition is a parasitic, bacterial, viral, or fungal infection.
4. The method of claim 2, wherein the cancerous condition is astrocytoma, anaplastic large cell lymphoma, acute lymphoblastic leukemia, acute myelogenous leukemia, breast carcinoma, B-cell lymphoma, bladder carcinoma, cervical carcinoma, chronic lymphoblastic leukemia, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, leukemia, lung carcinoma, melanoma, medulloblastoma, mantle cell lymphoma, multiple myeloma, myeloma, non- Hodgkin lymphoma, non-small cell lung carcinoma, ovarian carcinoma, oligodendroglioma, oesophageal carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, renal cell carcinoma, squamous cell carcinoma of the head and neck, small cell lung carcinoma, thyroid carcinoma, testicular tumor wherein the modulation of one or more gene is sufficient for a therapeutic response.
5. The method of claim 1, wherein the expression of a gene is up-regulated.
6. The method of claim 1, wherein the cell is an epithelial, a stromal, or a mucosal cell.
7. The method of claim 1, wherein the cell is a brain, a neuronal, a blood, an esophageal, a lung, a cardiovascular, a liver, a breast, a bone, a thyroid, a glandular, an adrenal, a pancreatic, a stomach, an intestinal, a kidney, a bladder, a prostate, a cervical, a uterine, an ovarian, a testicular, a splenic, a skin, a smooth muscle, a cardiac muscle, a striated muscle cell.
8. The method of claim 1 , wherein the cell is a cancer cell.
9. The method of claim 8, wherein the cancer cell is a neuronal, glial, lung, liver, brain, breast, bladder, blood, leukemic, colon, endometrial, stomach, skin, ovarian, fat, bone, cervical, esophageal, pancreatic, prostate, kidney, or thyroid cell.
10. The method of claim 1, wherein the isolated miR-143 is a recombinant nucleic acid.
11. The method of claim 10, wherein the recombinant nucleic acid is RNA.
12. The method of claim 10, wherein the recombinant nucleic acid is DNA.
13. The method of claim 12, wherein the recombinant nucleic acid comprises a miR-143 inhibitor expression cassette.
14. The method of claim 13, wherein the expression cassette is comprised in a viral vector, or plasmid DNA vector.
15. The method of claim 14, wherein the viral vector is administered at a dose of 1x105 to IxIO14 viral particles per dose or the plasmid DNA vector is administered at a dose of 100 mg per patient to 4000 mg per patient.
16. The method of claim 1, wherein the miR-143 nucleic acid is a synthetic nucleic acid.
17. The method of claim 16, wherein the nucleic acid is administered at a dose of 0.01 mg/kg of body weight to 10 mg/kg of body weight.
18. The method of claim 1, wherein the miR-143 is a hsa-miR-143.
19. The method of claim 1, wherein the nucleic acid is administered enterally or parenterally.
20. The method of claim 19, wherein enteral administration is orally.
21. The method of claim 19, wherein parenteral administration is intravascular, intracranial, intrapleural, intratumoral, intraperitoneal, intramuscular, intralymphatic, intraglandular, subcutaneous, topical, intrabronchial, intratracheal, intranasal, inhaled, or instilled.
22. The method of claim 1, wherein the nucleic acid is comprised in a pharmaceutical formulation.
23. The method of claim 22, wherein the pharmaceutical formulation is a lipid composition.
24. A method of modulating a cellular pathway or a physiologic pathway comprising administering to a cell an amount of an isolated nucleic acid comprising a miR-143 inhibitor in an amount sufficient to modulate the cellular pathway or physiologic pathway that includes one or more genes identified or gene products related to one or more genes identified in Table 1, 3, 4, or 5.
25. The method of claim 24, further comprising administering 2, 3, 4, 5, 6, or more miRNAs.
26. The method claim 25 wherein the miRNAs are comprised in a single composition.
27. The method of 23, wherein at least two cellular pathways or physiologic pathways are modulated.
28. The method of claim 25, wherein at least one gene is modulated by multiple miRNAs.
29. The method of claim 24, wherein the expression of a gene or a gene product is down- regulated.
30. The method of claim 24, wherein the expression of a gene or a gene product is up- regulated.
31. The method of claim 24, wherein the cell is a cancer cell.
32. The method of claim 31, wherein viability of the cell is reduced, proliferation of the cell is reduced, metastasis of the cell is reduced, or the cell's sensitivity to therapy is increased.
33. The method of claim 31, wherein the cancer cell is a neuronal, glial, lung, liver, brain, breast, bladder, blood, leukemic, colon, endometrial, stomach, intestinal, skin, ovarian, fat, bone, cervical, esophageal, pancreatic, prostate, kidney, testicular, or thyroid cell.
34. The method of claim 24, wherein the miR-143 is a recombinant nucleic acid.
35. The method of claim 34, wherein the recombinant nucleic acid is DNA.
36. The method of claim 35, wherein the recombinant nucleic acid is a viral vector or a plasmid DNA vector.
37. A method of treating a patient diagnosed with or suspected of having or suspected of developing a pathological condition or disease related to a gene modulated by a miRNA comprising the steps of:
(a) administering to the patient an amount of an isolated nucleic acid comprising a miR-143 in an amount sufficient to modulate a cellular pathway or a physiologic pathway; and
(b) administering a second therapy, wherein the modulation of the cellular pathway or physiologic pathway sensitizes the patient to the second therapy.
38. The method of claim 37, wherein one or more cellular pathway or physiologic pathway includes one or more genes identified in Table 1, 3, 4, or 5.
39. A method of selecting a miRNA to be administered to a subject with, suspected of having, or having a propensity for developing a pathological condition or disease comprising:
(a) determining an expression profile of one or more genes selected from Table 1, 3,
4, or 5;
(b) assessing the sensitivity of the subject to miRNA therapy based on the expression profile; and
(c) selecting one or more miRNA based on the assessed sensitivity.
40. The method of claim 39 further comprising treating the subject with 1, 2, 4, 5, 6, 7, 8, 9, 10, or more miRNAs.
41. The method of claim 40, wherein each miRNA is administered individually or one or more combinations.
42. The method of claim 41 , wherein the miRNAs are in a single composition.
43. A method of assessing a cell, tissue, or subject comprising assessing expression of miR-143 in combination with assessing expression of one or more gene from Table 1, 3, 4, or 5 in at least one sample.
44. A method of assessing miR-143 status in a sample comprising the steps of: (a) assessing expression of one or more genes from Table 1, 3, 4, or 5 in a sample; and
(b) determining miR-143 status based on level of miR-143 expression in the sample.
EP07842750A 2006-09-19 2007-09-19 Mir-143 regulated genes and pathways as targets for therapeutic intervention Withdrawn EP2094848A2 (en)

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