WO2010023658A2 - Compositions and methods for the treatment of glioblastoma - Google Patents

Abstract

The invention relates in general to microRNA molecules associated with glioblastoma, as well as various molecules relating thereto. More specifically, the invention relates to methods and compositions for the treatment of glioblastoma and for treatment by a combination of microRNA molecules and Imatinib mesylate.

Description

COMPOSITIONS AND METHODS FOR THE TREATMENT OF

GLIOBLASTOMA

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 61/136,318, filed August 28, 2008 and U.S. Provisional Application No. 61/167,166, filed April 7, 2009 which are herein incorporated by reference in their entirety.

FIELD OF THE INVENTION The invention relates in general to microRNA molecules associated with glioblastoma (GBM), as well as various molecules relating thereto. More specifically, the invention relates to methods and compositions for the treatment of glioblastoma.

BACKGROUND OF THE INVENTION

In recent years, microRNAs (miRs) have emerged as an important novel class of regulatory RNA, which have a profound impact on a wide array of biological processes.

These small (typically 18-24 nucleotides in length) non-coding RNA molecules can modulate protein expression patterns by promoting RNA degradation, inhibiting mRNA translation, and also affecting gene transcription. miRs play pivotal roles in diverse processes such as development and differentiation, control of cell proliferation, stress response and metabolism. The expression of many miRs was found to be altered in numerous types of human cancer, and in some cases strong evidence has been put forward in support of the conjecture that such alterations may play a causative role in tumor progression. There are currently about 885 known human miRs.

Glioblastoma multiforme (GBM) is the most common and most aggressive type of primary brain tumor, accounting for 52% of all primary brain tumor cases, and 20% of all intracranial tumors. Despite being the most prevalent form of primary brain tumor, GBMs occur in only 2-3 cases per 100,000 people in Europe and North America. The standard

WHO-2007 name for this brain tumor is "Glioblastoma". Treatment of glioblastoma can involve chemotherapy, radiotherapy, and surgery, all of which are acknowledged as palliative measures, meaning that they do not provide a cure. Even with complete surgical resection of the tumor, combined with the best available treatment, the survival rate for GBM remains very low. However, many advances in microsurgery techniques, radiotherapy and chemotherapy are slowly increasing the survival time of patients diagnosed with glioblastoma.

According to a current hypothesis, tumors contain a minor population of Cancer Stem Cells (CSCs) which maintain the proliferation of the tumor due to the self-renewal properties of these cells. Recently, identification of Glioblastoma-tumor initiating cells in human brain tumors has been reported, using CD 133 as a marker. It was demonstrated that as few as 100 CD 133+ cells isolated from high-grade GBM could initiate and propagate a tumor when re-introduced into the brain of immuno-deficient mice, whereas even a large number (10⁵) of CD133- cells can not transfer the tumor (S. K. Singh, et al, Nature 432

(2004) 396-401). The tumor initiating cells propagate in vitro as free floating neurosphere- like structures when cultured in serum free medium supplemented with growth factors.

There is an unmet need for a reliable method for the treatment of glioblastoma.

SUMMARY OF THE INVENTION

Comparison of the microRNA profiles of Cancer Stem Cells with that of the non- stem cell (CD 133-) population in GBM, showed overexpression of several miRs in the CD 133- population. Assuming that induction of miRs overexpression in the CD 133+ cells may drive these cells to differentiate and loose their stem cell character, these miRs were transfected to CD 133+ cells and their effect on the dispersion of the neurospheres and on the viability and proliferation capacity of the GBM stem cells was studied. At nanomolar concentrations, hsa-miR-425-5p (SEQ ID NO: 5), hsa-miR-486 (SEQ ID NO: 3) and particularly hsa-miR-451 (SEQ ID NO: 1), were found to inhibit the growth and neurosphere formation of A- 172 cells and to synergize with Imatinib mesylate in enhancing this effect. Similar results were also obtained with the CD 133+ cells derived from primary GBM. Additionally, two target sites for SMAD were identified in the upstream promoter region of miR-451. Transfection of the GBM cell line A- 172 with SMAD-containing plasmids inhibited their growth, similar to the effect of hsa-miR-451 (SEQ ID NO: 1).

The present invention provides specific nucleic acid sequences and variants thereof for use in the treatment of glioblastoma.

According to a first aspect, the present invention provides a method for treating or preventing a brain cancer comprising administering to a subject in need thereof an effective amount of a composition comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14, a fragment thereof, and sequences having at least 80% identity thereto. According to some embodiments the nucleic acid comprises a modified base. According to some embodiments the brain cancer is glioblastoma. According to some embodiments the subject is a human.

According to some embodiments, the administration comprises intratumoral administration, chemoemobilization, subcutaneous administration or intravenous administration. According to some embodiments the intratumoral administration is delivered through the blood brain barrier by a method selected from disruption of the blood brain barrier by osmotic means, use of vasoactive substances selected from the group comprising bradykinin, exposure to high intensity focused ultrasound, use of endogenous transport systems selected from the group comprising carrier-mediated glucose transporters and carrier-mediated amino acid carriers, use of receptor-mediated transcytosis selected from the group comprising receptor-mediated transcytosis of insulin and receptor-mediated transcytosis of transferrin, blocking of active efflux transporters selected from the group comprising p-glycoprotein, intracerebral implantation, convection-enhanced distribution, and use of an infusion pump.

According to some embodiments, the administered composition further comprises a pharmaceutically acceptable carrier. According to some embodiments the method further comprises administration of at least one additional therapy. According to some embodiments the at least one additional therapy is a tyrosine kinase inhibitor. According to some embodiments the tyrosine kinase inhibitor is Imatinib mesylate.

According to some embodiments, the administration results in one or more of inhibition of the formation of neurospheres, reduction in neurosphere size, neurosphere dispersion, reduction of number of tumor cells, reduction of tumor cell viability, and inhibition of tumor cell growth.

The use of a composition comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14, a fragment thereof, or a sequence having at least about 80% identity thereto for the manufacture of a medicament for the treatment or prevention of brain cancer is also provided.

According to some aspects, the invention further provides a method for initiating the differentiation of cancer stem cells comprising increasing, in said cells, the expression level of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14, a fragment thereof, and sequences having at least 80% identity to thereto. According to some embodiments, the cancer stem cells are glioblastoma stem cells.

According to other aspects, a method is provided for inhibiting the growth or viability of glioblastoma cells comprising increasing, in said cells, the expression level of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14, a fragment thereof, and sequences having at least 80% identity thereto.

According to some aspects, a method is provided for inhibiting the growth or viability of glioblastoma cells comprising administration to the cells an effective amount of a composition capable of binding to a sequence selected from the group consisting of SEQ ID NO: 17 and 18. According to some embodiments said composition is SMAD 3 or SMAD

4.

According to some aspects, a method is provided for determining the prognosis of glioblastoma in a subject comprising obtaining a biological sample from said subject, determining the expression level in said sample of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14 and sequences at least about 80% identical thereto; and comparing said expression level to a threshold expression level, wherein a relatively low expression level of said nucleic acids as compared to said threshold expression level is predictive of poor prognosis of said subject.

According to other aspects, also provided is a kit for determining the prognosis of glioblastoma in a subject, comprising a probe comprising a nucleic acid sequence that is complementary to a sequence selected from SEQ ID NOS: 1-14, a fragment thereof, or to a sequence at least about 80% identical thereto.

These and other embodiments of the present invention will become apparent in conjunction with the figures, description and claims that follow.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 demonstrates characterization of primary GBM by expression of CD 133. The expression of CD 133 in primary tumor cells obtained from six GBM patients (designated pl-p6). The percent of CD 133+ cells in the total population, prior (left number) and after magnetic sorting (right number), is indicated. The X-axis represents the fluorescence intensity of anti CD133/FITC and the Y-axis shows the cell count. Ml or MI marked the CD 133+ population. Figure 2 shows the neurosphere-like structures found in the CD133+ fractions of the primary GBM cells (top). The CD 133- fractions did not form neurospheres (bottom).

Figure 3 demonstrates miR expression in primary GBM cell fractions. Scatter plot of the Iog2 expression levels of miRs in the CD133+ cells (Y-axis) vs. the CD133- cells (X- axis) of a particular primary GBM tumor (pi). hsa-miR-451 (SEQ ID NO: 1), hsa-miR-486 (SEQ ID NO: 3), hsa-miR-425-5p (SEQ ID NO: 5), hsa-miR-16 (SEQ ID NO: 7), hsa-miR- 107 (SEQ ID NO: 9), hsa-miR-185 (SEQ ID NO: 11) and hsa-miR-103 (SEQ ID NO: 13) (marked as empty squares) showed apparent up-regulation in CD133- compared to the CD133+ expression with p-values of p<0.01, using t-test. These findings were consistent in the three GBM samples (pi, p2, p4) that were analyzed. RGM- 1491 is a probe that overlaps with hsa-miR-451 (SEQ ID NO: 1). The middle solid line represents the expected expression for non-differentially expressed miRNAs (same expression level in CDl 33- and CD 133+ samples), and the outer diagonal lines represent two fold change in expression which is in experimental error. Figures 4A-4C demonstrate the effect of miR plasmids on A- 172 growth and neurospheres

Figure 4A shows photographs of cells transfected with plasmids containing various miRs [hsa-miR-451 (SEQ ID NO: 1), hsa-miR-425-5p (SEQ ID NO: 5), hsa-miR-486 (SEQ ID NO: 3)] or with control GFP (lOOng) or Dharmafect (the transfection reagent), and subsequently transferred to 96-well plates with neurosphere medium. Neurosphere formation was apparent within 24-48h and visualized microscopically using 4X objective. Figure 4B shows photographs of cells transfected with mature hsa-miR-451 (SEQ ID NO: 1) or control oligonucleotide (2OnM) in 24-well plates and visualized microscopically after 2 days using 4X objective. Figure 4C shows growth curves of A- 172 transfected cells. A- 172 attached cells were transfected in 24-well plates and their viability was measured for 3 days. The experiments were repeated several times with similar results. The Y-axis represents the number of cells xlO⁵, and the X-axis represents days. The curve with the square symbols represents a control; the triangle symbols represents transfection with the transfection reagent only (Dharmafect), diamond symbols represent transfection with a control oligonucleotide, and the circle symbols represent transfection with 2OnM hsa-miR-451 (SEQ ID NO: 1).

Figures 5A-5B demonstrate the combined effect of hsa-miR-451 (SEQ ID NO: 1) and Imatinib Mesylate treatment on primary GBM and A- 172 cells. IM: Imatinib Mesylate, miR: hsa-miR-451 (SEQ ID NO: 1).

Figure 5A shows photographs of A- 172 treated cells. A- 172 cells were transfected with hsa-miR-451 (SEQ ID NO: 1) (5nM, 1OnM and 2OnM) and subsequently transferred to 96- well plates in serum free medium for neurosphere formation. Imatinib mesylate was added at concentrations of lμM and 2.5μM, 2 hours after transfer. Neurospheres were photographed 24hr later.

Figure 5B shows photographs of primary GBM cells transfected with hsa-miR-451 (SEQ ID NO: 1) and treated with Imatinib mesylate. Primary GBM cells were fractionated for CD 133+ stem cells and transfected with hsa-miR-451 (SEQ ID NO: 1) at 2OnM. Cells were then transferred to 96-well plates for neurosphere formation. Imatinib mesylate was added at lμM and 2.5μM (data not shown), 2 hours after transfer. Combination of hsa-miR-451 (SEQ ID NO: 1) (2OnM) and Imatinib mesylate (lμM) shows complete dispersion of neurospheres.

Figures 6A-6B demonstrate SMAD effect on the hsa-miR-451 promoter and on GBM A- 172 cell growth.

Figure 6 A shows a schematic view of hsa-miR-451 (SEQ ID NO: 1) and target sites (S3, S4) for SMAD.

Figure 6B demonstrates the results of a Luciferase assay. A- 172 cells were transfected with miR promoter-luciferase construct along with SMAD3 and SMAD4 plasmids. Luciferase assay showed activation of the hsa-miR-451 promoter by SMADs and particularly by combined SMAD3 and SMAD4, reaching up to 6 fold luciferase induction (Y-axis). miR-Luc: control transfection of miR-Luc alone. S: SMAD.

Figure 6C demonstrates growth curves of A- 172 cells. A- 172 cells were transfected with either SMAD3, SMAD4 or both. Cells were grown for 4 days in multiple wells of 24 well plates and cell counts were taken in duplicates each day. The Y-axis represents the number of cells xlO , and the X-axis represents days. The curve with the square symbols represents a control, the circle symbols represent GFP, X symbols represent SMAD3, and the triangle symbols represent the combination of SMAD3 and SMAD4.

DETAILED DESCRIPTION OF THE INVENTION

The invention is based in part on the discovery that specific nucleic acid sequences (SEQ ID NOS: 1-14) or variants thereof can be used for the treatment of glioblastoma. Before the present compositions and methods are disclosed and described, it is to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise.

For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9 and 7.0 are explicitly contemplated.

1. Definitions aberrant proliferation

As used herein, the term "aberrant proliferation" means cell proliferation that deviates from the normal, proper, or expected course. For example, aberrant cell proliferation may include inappropriate proliferation of cells whose DNA or other cellular components have become damaged or defective. Aberrant cell proliferation may include cell proliferation whose characteristics are associated with an indication caused by, mediated by, or resulting in inappropriately high levels of cell division, inappropriately low levels of apoptosis, or both. Such indications may be characterized, for example, by single or multiple local abnormal proliferations of cells, groups of cells, or tissue(s), whether cancerous or noncancerous, benign or malignant. about

As used herein, the term "about" refers to +/-10%. administering "Administering" means providing a pharmaceutical agent or composition to a subject, and includes, but is not limited to, administering by a medical professional and self- administering.

"Parenteral administration," means administration through injection or infusion. Parenteral administration includes, but is not limited to, subcutaneous administration, intravenous administration, or intramuscular administration.

"Subcutaneous administration" means administration just below the skin. "Intravenous administration" means administration into a vein. "Intratumoral administration" means administration within a tumor.

"Chemoembolization" means a procedure in which the blood supply to a tumor is blocked surgically or mechanically and chemotherapeutic agents are administered directly into the tumor. amelioration

Amelioration as used herein, refers to a lessening of severity of at least one indicator of a condition or disease. In certain embodiments, amelioration includes a delay or slowing in the progression of one or more indicators of a condition or disease. The severity of indicators may be determined by subjective or objective measures which are known to those skilled in the art. antisense

The term "antisense," as used herein, refers to nucleotide sequences which are complementary to a specific DNA or RNA sequence. The term "antisense strand" is used in reference to a nucleic acid strand that is complementary to the "sense" strand. Antisense molecules may be produced by any method, including synthesis by ligating the gene(s) of interest in a reverse orientation to a viral promoter which permits the synthesis of a complementary strand. Once introduced into a cell, this transcribed strand combines with natural sequences produced by the cell to form duplexes. These duplexes then block either the further transcription or translation, hi this manner, mutant phenotypes may be generated. attached

"Attached" or "immobilized" as used herein refer to a probe and a solid support and may mean that the binding between the probe and the solid support is sufficient to be stable under conditions of binding, washing, analysis, and removal. The binding may be covalent or non-covalent. Covalent bonds may be formed directly between the probe and the solid support or may be formed by a cross linker or by inclusion of a specific reactive group on either the solid support or the probe, or both. Non-covalent binding may be one or more of electrostatic, hydrophilic, and hydrophobic interactions. Included in non-covalent binding is the covalent attachment of a molecule, such as streptavidin, to the support and the non- covalent binding of a biotinylated probe to the streptavidin. Immobilization may also involve a combination of covalent and non-covalent interactions. blood-brain barrier

The blood-brain barrier is a metabolic or cellular structure in the central nervous system that restricts the passage of various chemical substances and microscopic objects between the bloodstream and the neural tissue itself, while still allowing the passage of substances essential to metabolic function. blood tumor marker

Blood tumor marker as used herein means a biomarker that increases or decreases in the blood of a subject having a tumor. biological sample "Biological sample" as used herein means a sample of biological tissue or fluid that comprises nucleic acids. Such samples include, but are not limited to, tissue or fluid isolated from subjects. Biological samples may also include sections of tissues such as biopsy and autopsy samples, FFPE samples, frozen sections taken for histological purposes, blood, plasma, serum, sputum, stool, tears, mucus, hair, and skin. Biological samples also include explants and primary and/or transformed cell cultures derived from animal or patient tissues.

Biological samples may also be blood, a blood fraction, urine, effusions, ascitic fluid, saliva, cerebrospinal fluid, cervical secretions, vaginal secretions, endometrial secretions, gastrointestinal secretions, bronchial secretions, sputum, cell line, tissue sample, cellular content of fine needle aspiration (FNA) or secretions from the breast. A biological sample may be provided by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods described herein in vivo. Archival tissues, such as those having treatment or outcome history, may also be used. cancer The term "cancer" is meant to include all types of cancerous growths or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathologic type or stage of invasiveness. Examples of cancers include but are nor limited to solid tumors and leukemias, including: glioblastoma, apudoma, choristoma, branchioma, malignant carcinoid syndrome, carcinoid heart disease, carcinoma (e.g., Walker, basal cell, basosquamous, Brown-Pearce, ductal, Ehrlich tumor, small cell lung, non-small cell lung (e.g., lung squamous cell carcinoma, lung adenocarcinoma and lung undifferentiated large cell carcinoma), oat cell, papillary, bronchiolar, bronchogenic, squamous cell, and transitional cell), histiocytic disorders, leukemia (e.g., B cell, mixed cell, null cell, T cell, T-cell chronic, HTLV-II-associated, lymphocytic acute, lymphocytic chronic, mast cell, and myeloid), histiocytosis malignant, Hodgkin disease, immunoproliferative small, non-Hodgkin lymphoma, plasmacytoma, reticuloendotheliosis, melanoma, chondroblastoma, chondroma, chondrosarcoma, fibroma, fibrosarcoma, giant cell tumors, histiocytoma, lipoma, liposarcoma, mesothelioma, myxoma, myxosarcoma, osteoma, osteosarcoma, Ewing sarcoma, synovioma, adenofibroma, adenolymphoma, carcinosarcoma, chordoma, craniopharyngioma, dysgerminoma, hamartoma, mesenchymoma, mesonephroma, myosarcoma, ameloblastoma, cementoma, odontoma, teratoma, thymoma, trophoblastic tumor, adeno-carcinoma, adenoma, cholangioma, cholesteatoma, cylindroma, cystadenocarcinoma, cystadenoma, granulosa cell tumor, gynandroblastoma, hepatoma, hidradenoma, islet cell tumor, Leydig cell tumor, papilloma, Sertoli cell tumor, theca cell tumor, leiomyoma, leiomyosarcoma, myoblastoma, myosarcoma, rhabdomyoma, rhabdomyosarcoma, ependymoma, ganglioneuroma, glioma, medulloblastoma, meningioma, neurilemmoma, neuroblastoma, neuroepithelioma, neurofibroma, neuroma, paraganglioma, paraganglioma nonchromaffin, angiokeratoma, angiolymphoid hyperplasia with eosinophilia, angioma sclerosing, angiomatosis, glomangioma, hemangioendothelioma, hemangioma, hemangiopericytoma, hemangiosarcoma, lymphangioma, lymphangiomyoma, lymphangiosarcoma, pinealoma, carcinosarcoma, chondrosarcoma, cystosarcoma, phyllodes, fibrosarcoma, hemangiosarcoma, leimyosarcoma, leukosarcoma, liposarcoma, lymphangiosarcoma, myosarcoma, myxosarcoma, ovarian carcinoma, rhabdomyosarcoma, sarcoma (e.g., Ewing, experimental, Kaposi, and mast cell), neurofibromatosis, and cervical dysplasia, and other conditions in which cells have become immortalized or transformed. cancer prognosis

A forecast or prediction of the probable course or outcome of the cancer and response to its treatment. As used herein, cancer prognosis includes distinguishing between cancer stages and subtypes, and the forecast or prediction of any one or more of the following: duration of survival of a patient susceptible to or diagnosed with a cancer, duration of recurrence-free survival, duration of progression free survival of a patient susceptible to or diagnosed with a cancer, response rate in a group of patients susceptible to or diagnosed with a cancer, duration of response in a patient or a group of patients susceptible to or diagnosed with a cancer, and/or likelihood of metastasis in a patient susceptible to or diagnosed with a cancer. As used herein, "prognostic for cancer" means providing a forecast or prediction of the probable course or outcome of the cancer. In some embodiments, "prognostic for cancer" comprises providing the forecast or prediction of (prognostic for) any one or more of the following: duration of survival of a patient susceptible to or diagnosed with a cancer, duration of recurrence-free survival, duration of progression free survival of a patient susceptible to or diagnosed with a cancer, response rate in a group of patients susceptible to or diagnosed with a cancer, duration of response in a patient or a group of patients susceptible to or diagnosed with a cancer, and/or likelihood of metastasis in a patient susceptible to or diagnosed with a cancer. chemotherapeutic agent

A drug used to treat a disease, especially cancer. In relation to cancer the drugs typically target rapidly dividing cells, such as cancer cells. Non-limiting examples of chemotherapeutic agents include cisplatin, carboplatin, camptothecins, doxorubicin, cyclophosphamide, paclitaxel, etoposide, vinblastine, Actinomycin D and cloposide. classification

"Classification" as used herein refers to a procedure and/or algorithm in which individual items are placed into groups or classes based on quantitative information on one or more characteristics inherent in the items (referred to as traits, variables, characters, features, etc) and based on a statistical model and/or a training set of previously labeled items. According to one embodiment, classification means determination of the type of cancer. complement

"Complement" or "complementary" as used herein means Watson-Crick (e.g., A-T/U and C-G) or Hoogsteen base pairing between nucleotides or nucleotide analogs of nucleic acid molecules. A full complement or fully complementary may mean 100% complementary base pairing between nucleotides or nucleotide analogs of nucleic acid molecules.

Ct

"Ct" as used herein refers to Cycle Threshold of qRT-PCR, which is the fractional cycle number at which the fluorescence crosses the threshold. detection

"Detection" means detecting the presence of a component in a sample. Detection also means detecting the absence of a component. Detection also means measuring the level of a component, either quantitatively or qualitatively. differential expression

"Differential expression" means qualitative or quantitative differences in the temporal and/or cellular gene expression patterns within and among cells and tissue. Thus, a differentially expressed gene may qualitatively have its expression altered, including an activation or inactivation, in, e.g., normal versus disease tissue. Genes may be turned on or turned off in a particular state, relative to another state thus permitting comparison of two or more states. A qualitatively regulated gene may exhibit an expression pattern within a state or cell type which may be detectable by standard techniques. Some genes may be expressed in one state or cell type, but not in both. Alternatively, the difference in expression may be quantitative, e.g., in that expression is modulated, either up-regulated- resulting in an increased amount of transcript, or down-regulated- resulting in a decreased amount of transcript. The degree to which expression differs need only be large enough to quantify via standard characterization techniques such as expression arrays, quantitative reverse transcriptase PCR, northern analysis, real-time PCR, in situ hybridization and RNase protection. dose

"Dose" as used herein means a specified quantity of a pharmaceutical agent provided in a single administration. In certain embodiments, a dose may be administered in two or more boluses, tablets, or injections. For example, in certain embodiments, where subcutaneous administration is desired, the desired dose requires a volume not easily accommodated by a single injection. In such embodiments, two or more injections may be used to achieve the desired dose. In certain embodiments, a dose may be administered in two or more injections to minimize injection site reaction in an individual. dosage unit

"Dosage unit" as used herein means a form in which a pharmaceutical agent is provided. In certain embodiments, a dosage unit is a vial containing lyophilized oligonucleotide. In certain embodiments, a dosage unit is a vial containing reconstituted oligonucleotide. expression profile

"Expression profile" as used herein may mean a genomic expression profile, e.g., an expression profile of microKNAs. Profiles may be generated by any convenient means for determining a level of a nucleic acid sequence e.g. quantitative hybridization of microRNA, labeled microRNA, amplified microRNA, cRNA, etc., quantitative PCR, ELISA for quantitation, and the like, and allow the analysis of differential gene expression between two samples. A subject or patient tumor sample, e.g., cells or collections thereof, e.g., tissues, is assayed. Samples are collected by any convenient method, as known in the art. Nucleic acid sequences of interest are nucleic acid sequences that are found to be predictive, including the nucleic acid sequences provided above, where the expression profile may include expression data for 5, 10, 20, 25, 50, 100 or more of, including all of the listed nucleic acid sequences. The term "expression profile" may also mean measuring the abundance of the nucleic acid sequences in the measured samples. expression ratio "Expression ratio" as used herein refers to relative expression levels of two or more nucleic acids as determined by detecting the relative expression levels of the corresponding nucleic acids in a biological sample.

FDR

When performing multiple statistical tests, for example in comparing the signal between two groups in multiple data features, there is an increasingly high probability of obtaining false positive results, by random differences between the groups that can reach levels that would otherwise be considered as statistically significant. In order to limit the proportion of such false discoveries, statistical significance is defined only for data features in which the differences reached a p-value (by two-sided t-test) below a threshold, which is dependent on the number of tests performed and the distribution of p-values obtained in these tests. fragment

"Fragment" is used herein to indicate a non-full length part of a nucleic acid or polypeptide. Thus, a fragment is itself also a nucleic acid or polypeptide, respectively. gene

"Gene" as used herein may be a natural (e.g., genomic) or synthetic gene comprising transcriptional and/or translational regulatory sequences and/or a coding region and/or non- translated sequences (e.g., introns, 5'- and 3 '-untranslated sequences). The coding region of a gene may be a nucleotide sequence coding for an amino acid sequence or a functional RNA, such as tRNA, rRNA, catalytic RNA, siRNA, miRNA or antisense RNA. A gene may also be an mRNA or cDNA corresponding to the coding regions (e.g., exons and miRNA) optionally comprising 5'- or 3 '-untranslated sequences linked thereto. A gene may also be an amplified nucleic acid molecule produced in vitro comprising all or a part of the coding region and/or 5'- or 3'-untranslated sequences linked thereto.

Groove binder/minor groove binder (MGB) "Groove binder" and/or "minor groove binder" may be used interchangeably and refer to small molecules that fit into the minor groove of double-stranded DNA, typically in a sequence-specific manner. Minor groove binders may be long, flat molecules that can adopt a crescent-like shape and thus, fit snugly into the minor groove of a double helix, often displacing water. Minor groove binding molecules may typically comprise several aromatic rings connected by bonds with torsional freedom such as furan, benzene, or pyrrole rings. Minor groove binders may be antibiotics such as netropsin, distamycin, berenil, pentamidine and other aromatic diamidines, Hoechst 33258, SN 6999, aureolic anti-tumor drugs such as chromomycin and mithramycin, CC- 1065, dihydrocyclopyrroloindole tripeptide (DPI₃), l,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI₃), and related compounds and analogues, including those described in Nucleic Acids in Chemistry and Biology, 2d ed., Blackburn and Gait, eds., Oxford University Press, 1996, and PCT Published Application No. WO 03/078450, the contents of which are incorporated herein by reference. A minor groove binder may be a component of a primer, a probe, a hybridization tag complement, or combinations thereof. Minor groove binders may increase the T_m of the primer or a probe to which they are attached, allowing such primers or probes to effectively hybridize at higher temperatures. host cell

"Host cell" as used herein may be a naturally occurring cell or a transformed cell that may contain a vector and may support replication of the vector. identity

"Identical" or "identity" as used herein in the context of two or more nucleic acids or polypeptide sequences mean that the sequences have a specified percentage of residues that are the same over a specified region. The percentage may be calculated by optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity, hi cases where the two sequences are of different lengths or the alignment produces one or more staggered ends and the specified region of comparison includes only a single sequence, the residues of the single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and RNA, thymine (T) and uracil (U) may be considered equivalent. Identity may be performed manually or by using a computer sequence algorithm such as BLAST or BLAST 2.0. in situ detection

"In situ detection" as used herein means the detection of expression or expression levels in the original site hereby meaning in a tissue sample such as biopsy. inhibit

"Inhibit" as used herein may mean prevent, suppress, repress, reduce or eliminate. label

"Label" as used herein means a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include ³²P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and other entities which can be made detectable. A label may be incorporated into nucleic acids and proteins at any position. metastasis "Metastasis" as used herein means the process by which cancer spreads from the place at which it first arose as a primary tumor to other locations in the body. The metastatic progression of a primary tumor reflects multiple stages, including dissociation from neighboring primary tumor cells, survival in the circulation, and growth in a secondary location. mismatch

"Mismatch" means a nucleobase of a first nucleic acid that is not capable of pairing with a nucleobase at a corresponding position of a second nucleic acid.

modified oligonucleotide

"Modified oligonucleotide" as used herein means an oligonucleotide having one or more modifications relative to a naturally occurring terminus, sugar, nucleobase, and/or internucleoside linkage. According to one embodiment, the modified oligonucleotide is a miRNA comprising a modification (e.g. labeled). modulation

"Modulation" as used herein means a perturbation of function or activity. In certain embodiments, modulation means an increase in gene expression. In certain embodiments, modulation means a decrease in gene expression. nucleic acid "Nucleic acid" or "oligonucleotide" or "polynucleotide" as used herein mean at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid may be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. A single strand provides a probe that may hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions.

Nucleic acids may be single stranded or double stranded, or may contain portions of both double stranded and single stranded sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine and isoguanine. Nucleic acids may be obtained by chemical synthesis methods or by recombinant methods. A nucleic acid will generally contain phosphodiester bonds, although nucleic acid analogs may be included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite linkages and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, which are incorporated by reference. Nucleic acids containing one or more non-naturally occurring or modified nucleotides are also included within one definition of nucleic acids. The modified nucleotide analog may be located for example at the 5'-end and/or the 3'-end of the nucleic acid molecule. Representative examples of nucleotide analogs may be selected from sugar- or backbone-modified ribonucleotides. It should be noted, however, that also nucleobase-modified ribonucleotides, i.e. ribonucleotides, containing a non-naturally occurring nucleobase instead of a naturally occurring nucleobase such as uridines or cytidines modified at the 5-position, e.g. 5-(2- amino) propyl uridine, 5-bromo undine; adenosines and guanosines modified at the 8- position, e.g. 8-bromo guanosine; deaza nucleotides, e.g. 7-deaza-adenosine; O- and N- alkylated nucleotides, e.g. N6-methyl adenosine are suitable. The 2'-OH-group may be replaced by a group selected from H, OR, R, halo, SH, SR, NH₂, NHR, NR₂ or CN, wherein R is C₁-C₆ alkyl, alkenyl or alkynyl and halo is F, Cl, Br or I. Modified nucleotides also include nucleotides conjugated with cholesterol through, e.g., a hydroxyprolinol linkage as described in Krutzfeldt et al., Nature 438:685-689 (2005) and Soutschek et al., Nature 432:173-178 (2004), which are incorporated herein by reference. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments, to enhance diffusion across cell membranes, or as probes on a biochip. The backbone modification may also enhance resistance to degradation, such as in the harsh endocytic environment of cells. The backbone modification may also reduce nucleic acid clearance by hepatocytes, such as in the liver. Mixtures of naturally occurring nucleic acids and analogs may be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made. overall survival time

"Overall survival time" or "survival time", as used herein means the time period for which a subject survives after diagnosis of or treatment for a disease. In certain embodiments, the disease is cancer. pharmaceutical agent

Pharmaceutical agent as used herein means a substance that provides a therapeutic effect when administered to a subject. "Pharmaceutical composition" means a mixture of substances suitable for administering to an individual that includes a pharmaceutical agent. For example, a pharmaceutical composition may comprise a modified oligonucleotide and a sterile aqueous solution. "Active pharmaceutical ingredient" means the substance in a pharmaceutical composition that provides a desired effect. prevention

Prevention as used herein means delaying or forestalling the onset or development or progression of a condition or disease for a period of time, including weeks, months, or years. progression-free survival

"Progression-free survival" means the time period for which a subject having a disease survives, without the disease getting worse. In certain embodiments, progression- free survival is assessed by staging or scoring the disease. In certain embodiments, progression-free survival of a subject having cancer is assessed by evaluating tumor size, tumor number, and/or metastasis. probe

"Probe" as used herein means an oligonucleotide capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation.

Probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. There may be any number of base pair mismatches which will interfere with hybridization between the target sequence and the single stranded nucleic acids described herein. However, if the number of mutations is so great that no hybridization can occur under even the least stringent of hybridization conditions, the sequence is not a complementary target sequence. A probe may be single stranded or partially single and partially double stranded. The strandedness of the probe is dictated by the structure, composition, and properties of the target sequence. Probes may be directly labeled or indirectly labeled such as with biotin to which a streptavidin complex may later bind. promoter

"Promoter" as used herein means a synthetic or naturally-derived molecule which is capable of conferring, activating or enhancing expression of a nucleic acid in a cell. A promoter may comprise one or more specific transcriptional regulatory sequences to further enhance expression and/or to alter the spatial expression and/or temporal expression of same. A promoter may also comprise distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A promoter may be derived from sources including viral, bacterial, fungal, plants, insects, and animals. A promoter may regulate the expression of a gene component constitutively, or differentially with respect to cell, the tissue or organ in which expression occurs or, with respect to the developmental stage at which expression occurs, or in response to external stimuli such as physiological stresses, pathogens, metal ions, or inducing agents.

Representative examples of promoters include the bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter, lac operator-promoter, tac promoter, SV40 late promoter, SV40 early promoter, RSV-LTR promoter, CMV IE promoter, SV40 early promoter or SV40 late promoter and the CMV IE promoter. reduced tumorigenicity

"Reduced tumorigenicity" as used herein refers to the conversion of hyperproliferative (e.g., neoplastic) cells to a less proliferative state. In the case of tumor cells, "reduced tumorigenicity" is intended to mean tumor cells that have become less tumorigenic or non-tumorigenic or non-tumor cells whose ability to convert into tumor cells is reduced or eliminated. Cells with reduced tumorigenicity either form no tumors in vivo or have an extended lag time of weeks to months before the appearance of in vivo tumor growth. Cells with reduced tumorigenicity may also result in slower growing three dimensional tumor mass compared to the same type of cells having fully inactivated or nonfunctional tumor suppressor gene growing in the same physiological milieu (e.g., tissue, organism age, organism sex, time in menstrual cycle, etc.). side effect

Side effect as used herein means a physiological response attributable to a treatment other than desired effects. selectable marker

"Selectable marker" as used herein means any gene which confers a phenotype on a host cell in which it is expressed to facilitate the identification and/or selection of cells which are transfected or transformed with a genetic construct. Representative examples of selectable markers include the ampicillin-resistance gene (Amp¹), tetracycline-resistance gene (Tc¹), bacterial kanamycin-resistance gene (Kan¹), zeocin resistance gene, the AURI-C gene which confers resistance to the antibiotic aureobasidin A, phosphinothricin-resistance gene, neomycin phosphotransferase gene (nptll), hygromycin-resistance gene, beta- glucuronidase (GUS) gene, chloramphenicol acetyltransferase (CAT) gene, green fluorescent protein (GFP)-encoding gene and luciferase gene. stringent hybridization conditions "Stringent hybridization conditions" as used herein mean conditions under which a first nucleic acid sequence (e.g., probe) will hybridize to a second nucleic acid sequence (e.g., target), such as in a complex mixture of nucleic acids. Stringent conditions are sequence-dependent and will be different in different circumstances. Stringent conditions may be selected to be about 5-10°C lower than the thermal melting point (T_1n) for the specific sequence at a defined ionic strength pH. The T_m may be the temperature (under defined ionic strength, pH, and nucleic acid concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_m, 50% of the probes are occupied at equilibrium).

Stringent conditions may be those in which the salt concentration is less than about 1.0 M sodium ion, such as about 0.01-1.0 M sodium ion concentration (or other salts) at pH

7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g., about 10-50 nucleotides) and at least about 60°C for long probes (e.g., greater than about 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal may be at least 2 to 10 times background hybridization. Exemplary stringent hybridization conditions include the following: 50% formamide, 5x SSC, and 1% SDS, incubating at

42°C, or, 5x SSC, 1% SDS, incubating at 65°C, with wash in 0.2x SSC, and 0.1% SDS at

65°C. substantially complementary "Substantially complementary" as used herein means that a first sequence is at least

60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the complement of a second sequence over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more nucleotides, or that the two sequences hybridize under stringent hybridization conditions. substantially identical

"Substantially identical" as used herein means that a first and a second sequence are at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more nucleotides or amino acids, or with respect to nucleic acids, if the first sequence is substantially complementary to the complement of the second sequence. subject

As used herein, the term "subject" refers to a human or non-human animal selected for treatment or therapy. The methods of the present invention are preferably applied to human subjects. "Subject in need thereof refers to a subject identified as in need of a therapy or treatment. In certain embodiments, a subject is in need of treatment for glioblastoma. In such embodiments, a subject has one or more clinical indications of glioblastoma or is at risk for developing glioblastoma. target nucleic acid

"Target nucleic acid" as used herein means a nucleic acid or variant thereof that may be bound by another nucleic acid. A target nucleic acid may be a DNA sequence. The target nucleic acid may be RNA. The target nucleic acid may comprise a mRNA, tRNA, shRNA, siRNA or Piwi-interacting RNA, or a pri-miRNA, pre-miRNA, miRNA, or anti-miRNA.

The target nucleic acid may comprise a target miRNA binding site or a variant thereof. One or more probes may bind the target nucleic acid. The target binding site may comprise 5-100 or 10-60 nucleotides. The target binding site may comprise a total of 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, 30-40, 40-50, 50-60, 61, 62 or 63 nucleotides. The target site sequence may comprise at least 5 nucleotides of the sequence of a target miRNA binding site disclosed in U.S. Patent Application Nos. 11/384,049, 11/418,870 or 11/429,720, the contents of which are incorporated herein. therapy "Therapy" as used herein means a disease treatment method. In certain embodiments, therapy includes, but is not limited to, modified oligonucleotide therapy, tyrosine kinase inhibition therapy, chemotherapy, surgical resection, transplant, and/or chemoembolization. "Therapeutic agent" means a pharmaceutical agent used for the cure, amelioration or prevention of a disease. "Recommended therapy" means a treatment recommended by a medical professional for the treatment, amelioration, or prevention of a disease. therapeutically effective amount

"Therapeutically effective amount" or "therapeutically efficient" used herein as to a drug dosage, refer to dosage that provides the specific pharmacological response for which the drug is administered in a significant number of subjects in need of such treatment. The "therapeutically effective amount" may vary according, for example, the physical condition of the patient, the age of the patient and the severity of the disease. threshold expression level

As used herein, the phrase "threshold expression level" refers to a reference expression value. Measured values are compared to a corresponding threshold expression level to determine the prognosis of a subject. tissue sample

As used herein, a tissue sample is tissue obtained from a tissue biopsy using methods well known to those of ordinary skill in the related medical arts. The phrase "suspected of being cancerous" as used herein means a cancer tissue sample believed by one of ordinary skill in the medical arts to contain cancerous cells. Methods for obtaining the sample from the biopsy include gross apportioning of a mass, microdissection, laser-based microdissection, or other art-known cell-separation methods. transcription factor

As used herein, a transcription factor (sometimes called a sequence-specific DNA binding factor) is a protein that binds to specific DNA sequences and thereby controls the transfer (or transcription) of genetic information. Transcription factors perform this function alone, or with other proteins in a complex, by promoting, or blocking the recruitment of

RNA polymerase to specific genes.

A defining feature of transcription factors is that they contain one or more DNA binding site (or binding domains) which attach to specific sequences of DNA adjacent to the genes that they regulate. treat

"Treat" or "treating" used herein when referring to protection of a subject from a condition may mean preventing, suppressing, repressing, or eliminating the condition.

Preventing the condition involves administering a composition described herein to a subject prior to onset of the condition. Suppressing the condition involves administering the composition to a subject after induction of the condition but before its clinical appearance.

Repressing the condition involves administering the composition to a subject after clinical appearance of the condition such that the condition is reduced or prevented from worsening.

Elimination of the condition involves administering the composition to a subject after clinical appearance of the condition such that the subject no longer suffers from the condition. tyrosine kinase inhibitor

A Tyrosine kinase inhibitor is an enzyme inhibitor which specifically blocks the action of tyrosine kinase enzymes. Imatinib mesylate is an example of a Tyrosine kinase inhibitor. unit dosage form

"Unit dosage form," used herein may refer to a physically discrete unit suitable as a unitary dosage for a human or animal subject. Each unit may contain a predetermined quantity of a composition described herein, calculated in an amount sufficient to produce a desired effect in association with a pharmaceutically acceptable diluent, carrier or vehicle. The specifications for a unit dosage form may depend on the particular composition employed and the effect to be achieved, and the pharmacodynamics associated with the composition in the host. variant "Variant" as used herein referring to a nucleic acid means (i) a portion of a referenced nucleotide sequence; (ii) the complement of a referenced nucleotide sequence or portion thereof; (iii) a nucleic acid that is substantially identical to a referenced nucleic acid or the complement thereof; or (iv) a nucleic acid that hybridizes under stringent conditions to the referenced nucleic acid, complement thereof, or a sequence substantially identical thereto. vector

"Vector" as used herein means a nucleic acid sequence containing an origin of replication. A vector may be a plasmid, bacteriophage, bacterial artificial chromosome or yeast artificial chromosome. A vector may be a DNA or RNA vector. A vector may be either a self-replicating extrachromosomal vector or a vector which integrates into a host genome. wild type

As used herein, the term "wild type" sequence refers to a coding, a non-coding or an interface sequence which is an allelic form of sequence that performs the natural or normal function for that sequence. Wild type sequences include multiple allelic forms of a cognate sequence, for example, multiple alleles of a wild type sequence may encode silent or conservative changes to the protein sequence that a coding sequence encodes.

2. MicroRNAs and their processing

A gene coding for a microRNA (miRNA) may be transcribed leading to production of an miRNA precursor known as the pri-miRNA. The pri-miRNA may be part of a polycistronic RNA comprising multiple pri-miRNAs. The pri-miRNA may form a hairpin structure with a stem and loop. The stem may comprise mismatched bases.

The hairpin structure of the pri-miRNA may be recognized by Drosha, which is an RNase III endonuclease. Drosha may recognize terminal loops in the pri-miRNA and cleave approximately two helical turns into the stem to produce a 60-70 nucleotide precursor known as the pre-miRNA. Drosha may cleave the pri-miRNA with a staggered cut typical of RNase III endonucleases yielding a pre-miRNA stem loop with a 5' phosphate and ~2 nucleotide 3¹ overhang. Approximately one helical turn of the stem (~10 nucleotides) extending beyond the Drosha cleavage site may be essential for efficient processing. The pre-miRNA may then be actively transported from the nucleus to the cytoplasm by Ran- GTP and the export receptor Ex-portin-5.

The pre-miRNA may be recognized by Dicer, which is also an RNase III endonuclease. Dicer may recognize the double-stranded stem of the pre-miRNA. Dicer may also recognize the 5' phosphate and 3' overhang at the base of the stem loop. Dicer may cleave off the terminal loop two helical turns away from the base of the stem loop leaving an additional 5' phosphate and ~2 nucleotide 3' overhang. The resulting siRNA-like duplex, which may comprise mismatches, comprises the mature miRNA and a similar-sized fragment known as the miRNA*. The miRNA and miRNA* may be derived from opposing arms of the pri-miRNA and pre-miRNA. MiRNA* sequences may be found in libraries of cloned miRNAs but typically at lower frequency than the miRNAs.

Although initially present as a double-stranded species with rm^'RNA*, the miRNA may eventually become incorporated as a single-stranded RNA into a ribonucleoprotein complex known as the RNA-induced silencing complex (RISC). Various proteins can form the RISC, which can lead to variability in specificity for miRNA/miRNA* duplexes, binding site of the target gene, activity of miRNA (repression or activation), and which strand of the miRNA/miRNA* duplex is loaded in to the RISC.

When the miRNA strand of the miRNA:miRNA* duplex is loaded into the RISC, the miRNA* may be removed and degraded. The strand of the miRNA:miRNA* duplex that is loaded into the RISC may be the strand whose 5' end is less tightly paired. In cases where both ends of the miRNA:miRNA* have roughly equivalent 5' pairing, both miRNA and miRNA* may have gene silencing activity.

The RISC may identify target nucleic acids based on high levels of complementarity between the miRNA and the niRNA, especially by nucleotides 2-7 of the miRNA. Only one case has been reported in animals where the interaction between the miRNA and its target was along the entire length of the miRNA. This was shown for mir-196 and Hox B8 and it was further shown that mir-196 mediates the cleavage of the Hox B 8 mRNA (Yekta et al

2004, Science 304-594). Otherwise, such interactions are known only in plants (Bartel & Bartel 2003, Plant Physiol 132-709).

A number of studies have studied the base-pairing requirement between miRNA and its mRNA target for achieving efficient inhibition of translation (reviewed by Bartel 2004, Cell 116-281). In mammalian cells, the first 8 nucleotides of the miRNA may be important (Doench & Sharp 2004 GenesDev 2004-504). However, other parts of the microRNA may also participate in mRNA binding. Moreover, sufficient base pairing at the 3' can compensate for insufficient pairing at the 5' (Brennecke et al, 2005 PLoS 3-e85).

Computation studies, analyzing miRNA binding on whole genomes have suggested a specific role for bases 2-7 at the 5' of the miRNA in target binding but the role of the first nucleotide, found usually to be "A" was also recognized (Lewis et at 2005 Cell 120-15). Similarly, nucleotides 1-7 or 2-8 were used to identify and validate targets by Krek et al

(2005, Nat Genet 37-495).

The target sites in the mRNA may be in the 5' UTR, the 3' UTR or in the coding region. Interestingly, multiple miRNAs may regulate the same mRNA target by recognizing the same or multiple sites. The presence of multiple miRNA binding sites in most genetically identified targets may indicate that the cooperative action of multiple RISCs provides the most efficient translational inhibition. miRNAs may direct the RISC to downregulate gene expression by either of two mechanisms: mRNA cleavage or translational repression. The miRNA may specify cleavage of the mRNA if the mRNA has a certain degree of complementarity to the miRNA. When a miRNA guides cleavage, the cut may be between the nucleotides pairing to residues 10 and 11 of the miRNA. Alternatively, the miRNA may repress translation if the miRNA does not have the requisite degree of complementarity to the miRNA. Translational repression may be more prevalent in animals since animals may have a lower degree of complementarity between the miRNA and the binding site.

It should be noted that there may be variability in the 5' and 3' ends of any pair of miRNA and miRNA*. This variability may be due to variability in the enzymatic processing of Drosha and Dicer with respect to the site of cleavage. Variability at the 5' and 3' ends of miRNA and miRNA* may also be due to mismatches in the stem structures of the pri- miRNA and pre-miRNA. The mismatches of the stem strands may lead to a population of different hairpin structures. Variability in the stem structures may also lead to variability in the products of cleavage by Drosha and Dicer. 3. Nucleic Acids

Nucleic acids are provided herein. The nucleic acids comprise the sequence of SEQ ID NOS: 1-18 detailed below in tables 1-3, or variants thereof. The variant may be a complement of the referenced nucleotide sequence. The variant may also be a nucleotide sequence that is substantially identical to the referenced nucleotide sequence or the complement thereof. The variant may also be a nucleotide sequence which hybridizes under stringent conditions to the referenced nucleotide sequence, complements thereof, or nucleotide sequences substantially identical thereto.

The nucleic acid may have a length of from 10 to 250 nucleotides. The nucleic acid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200 or 250 nucleotides.

The nucleic acid may be synthesized or expressed in a cell (in vitro or in vivo) using a synthetic gene described herein. The nucleic acid may be synthesized as a single strand molecule and hybridized to a substantially complementary nucleic acid to form a duplex. The nucleic acid may be introduced to a cell, tissue or organ in a single- or double-stranded form or capable of being expressed by a synthetic gene using methods well known to those skilled in the art, including as described in U.S. Patent No. 6,506,559 which is incorporated by reference.

3 a. Nucleic acid complexes

The nucleic acid may further comprise one or more of the following: a peptide, a protein, a RNA-DNA hybrid, an antibody, an antibody fragment, a Fab fragment, and an aptamer.

3b. Pri-miRNA The nucleic acid may comprise a sequence of a pri-miRNA or a variant thereof. The pri-miRNA sequence may comprise from 45-30,000, 50-25,000, 100-20,000, 1,000-1,500 or 80-100 nucleotides. The sequence of the pri-miRNA may comprise a pre-miRNA, miRNA and miRNA*, as set forth herein, and variants thereof.

The pri-miRNA may form a hairpin structure. The hairpin may comprise a first and a second nucleic acid sequence that are substantially complimentary. The first and second nucleic acid sequence may be from 37-50 nucleotides. The first and second nucleic acid sequence may be separated by a third sequence of from 8-12 nucleotides. The hairpin structure may have a free energy of less than -25 Kcal/mole, as calculated by the Vienna algorithm, with default parameters as described in Hofacker et al., Monatshefte f. Chemie 125: 167-188 (1994), the contents of which are incorporated herein. The hairpin may comprise a terminal loop of 4-20, 8-12 or 10 nucleotides. The pri-miRNA may comprise at least 19% adenosine nucleotides, at least 16% cytosine nucleotides, at least 23% thymine nucleotides and at least 19% guanine nucleotides.

3c. Pre-miRNA The nucleic acid may also comprise a sequence of a pre-miRNA or a variant thereof.

The pre-miRNA sequence may comprise from 45-90, 60-80 or 60-70 nucleotides. The sequence of the pre-miRNA may comprise a miRNA and a miRNA* as set forth herein. The sequence of the pre-miRNA may also be that of a pri-miRNA excluding from 0-160 nucleotides from the 5' and 3' ends of the pri-miRNA. The sequence of the pre-miRNA may comprise the sequence of SEQ ID NOS: 2, 4, 6, 8, 10, 12 and 14 or variants thereof. 3d. miRNA

The nucleic acid may also comprise a sequence of a miRNA (including miRNA*) or a variant thereof. The miRNA sequence may comprise from 13-33, 18-24 or 21-23 nucleotides. The miRNA may also comprise a total of at least 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 nucleotides. The sequence of the miRNA may be the first 13-33 nucleotides of the pre-miRNA. The sequence of the miRNA may also be the last 13-33 nucleotides of the pre-miRNA. The sequence of the miRNA may comprise the sequence of SEQ ID NOS: 1, 3, 5, 7, 9, 11, and 13 or variants thereof. 3e. Anti-miRNA

The nucleic acid may also comprise a sequence of an anti-miRNA capable of blocking the activity of a miRNA or miRNA*, such as by binding to the pri-miRNA, pre- miRNA, miRNA or miRNA* (e.g. antisense or RNA silencing), or by binding to the target binding site. The anti-miRNA may comprise a total of 5-100 or 10-60 nucleotides. The anti- miRNA may also comprise a total of at least 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 nucleotides. The sequence of the anti-miRNA may comprise (a) at least 5 nucleotides that are substantially identical or complimentary to the 5' of a miRNA and at least 5-12 nucleotides that are substantially complimentary to the flanking regions of the target site from the 5' end of the miRNA, or (b) at least 5-12 nucleotides that are substantially identical or complimentary to the 3' of a miRNA and at least 5 nucleotide that are substantially complimentary to the flanking region of the target site from the 3' end of the miRNA.

3f. microRNA Binding Site of Target

The nucleic acid may also comprise a sequence of a target binding site or a variant thereof. The target site sequence may comprise a total of 5-100 or 10-60 nucleotides. The target site sequence may also comprise a total of at least 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 or 63 nucleotides. 4. Synthetic Gene

A synthetic gene is also provided comprising a nucleic acid described herein operably linked to a transcriptional and/or translational regulatory sequence. The synthetic gene may be capable of modifying the expression of a target gene with a binding site for a nucleic acid described herein. Expression of the target gene may be modified in a cell, tissue or organ. The synthetic gene may be synthesized or derived from naturally-occurring genes by standard recombinant techniques. The synthetic gene may also comprise terminators at the 3 '-end of the transcriptional unit of the synthetic gene sequence. The synthetic gene may also comprise a selectable marker.

5. Vector

A vector is also provided comprising a synthetic gene described herein. The vector may be an expression vector. An expression vector may comprise additional elements. For example, the expression vector may have two replication systems allowing it to be maintained in two organisms, e.g., in one host cell for expression and in a second host cell (e.g., bacteria) for cloning and amplification. For integrating expression vectors, the expression vector may contain at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. The vector may also comprise a selectable marker gene to allow the selection of transformed host cells.

6. Host Cell

A host cell is also provided comprising a vector, synthetic gene or nucleic acid described herein. The cell may be a bacterial, fungal, plant, insect or animal cell. For example, the host cell line may be DG44 and DUXBIl (Chinese Hamster Ovary lines,

DHFR minus), HELA (human cervical carcinoma), CVI (monkey kidney line), COS (a derivative of CVI with SV40 T antigen), R1610 (Chinese hamster fibroblast) BALBC/3T3

(mouse fibroblast), HAK (hamster kidney line), SP2/O (mouse myeloma), P3x63-Ag3.653 (mouse myeloma), BFA-IcIBPT (bovine endothelial cells), RAJI (human lymphocyte) and

293 (human kidney). Host cell lines may be available from commercial services, the

American Tissue Culture Collection or from published literature.

7. Probes

A probe is provided herein. A probe may comprise a nucleic acid. The probe may have a length of from 8 to 500, 10 to 100 or 20 to 60 nucleotides. The probe may also have a length of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280 or 300 nucleotides. The probe may comprise a nucleic acid of 18-25 nucleotides.

A probe may be capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. Probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. A probe may be single stranded or partially single and partially double stranded. The strandedness of the probe is dictated by the structure, composition, and properties of the target sequence. Probes may be directly labeled or indirectly labeled.

The probe may be a test probe. The test probe may comprise a nucleic acid sequence that is complementary to a miRNA, a miRNA*, a pre-miRNA, or a pri-miRNA. The probe may further comprise a linker. The linker may be 10-60 nucleotides in length. The linker may be 20-27 nucleotides in length. The linker may be of sufficient length to allow the probe to be a total length of 45-60 nucleotides. The linker may not be capable of forming a stable secondary structure, or may not be capable of folding on itself, or may not be capable of folding on a non-linker portion of a nucleic acid contained in the probe. The sequence of the linker may not appear in the genome of the animal from which the probe non-linker nucleic acid is derived. 8. Reverse Transcription

Target sequences of a cDNA may be generated by reverse transcription of the target RNA. Methods for generating cDNA may be reverse transcribing polyadenylated RNA or alternatively, RNA with a ligated adaptor sequence.

The RNA may be ligated to an adapter sequence prior to reverse transcription. A ligation reaction may be performed by T4 RNA ligase to ligate an adaptor sequence at the 3 ' end of the RNA. Reverse transcription (RT) reaction may then be performed using a primer comprising a sequence that is complementary to the 3' end of the adaptor sequence.

Polyadenylated RNA may be used in a reverse transcription (RT) reaction using a poly(T) primer comprising a 5' adaptor sequence. The poly(T) sequence may comprise 8, 9, 10, 11, 12, 13, or 14 consecutive thymines.

The reverse transcript of the RNA may be amplified by real time PCR, using a specific forward primer comprising at least 15 nucleic acids complementary to the target nucleic acid and a 5' tail sequence; a reverse primer that is complementary to the 3' end of the adaptor sequence; and a probe comprising at least 8 nucleic acids complementary to the target nucleic acid. The probe may be partially complementary to the 5' end of the adaptor sequence. Methods of amplifying target nucleic acids are described herein. The amplification may be by a method comprising PCR. The first cycles of the PCR reaction may have an annealing temp of 56°C, 57°C, 58⁰C, 59⁰C, or 60°C. The first cycles may comprise 1-10 cycles. The remaining cycles of the PCR reaction may be 60°C. The remaining cycles may comprise 2-40 cycles. The annealing temperature may cause the PCR to be more sensitive. The PCR may generate longer products that can serve as higher stringency PCR templates.

The PCR reaction may comprise a forward primer. The forward primer may comprise 15, 16, 17, 18, 19, 20, or 21 nucleotides identical to the target nucleic acid.

The 3' end of the forward primer may be sensitive to differences in sequence between a target nucleic acid and a sibling nucleic acid. The forward primer may also comprise a 5' overhanging tail. The 5' tail may increase the melting temperature of the forward primer. The sequence of the 5' tail may comprise a sequence that is non-identical to the genome of the animal from which the target nucleic acid is isolated. The sequence of the 5' tail may also be synthetic. The 5' tail may comprise 8, 9, 10, 11, 12, 13, 14, 15, or 16 nucleotides. The PCR reaction may comprise a reverse primer. The reverse primer may be complementary to a target nucleic acid. The reverse primer may also comprise a sequence complementary to an adaptor sequence. The sequence complementary to an adaptor sequence may comprise 12-24 nucleotides.

9. Biochip A biochip is also provided. The biochip may comprise a solid substrate comprising an attached probe or plurality of probes described herein. The probes may be capable of hybridizing to a target sequence under stringent hybridization conditions. The probes may be attached at spatially defined locations on the substrate. More than one probe per target sequence may be used, with either overlapping probes or probes to different sections of a particular target sequence. The probes may be capable of hybridizing to target sequences associated with a single disorder appreciated by those in the art. The probes may either be synthesized first, with subsequent attachment to the biochip, or may be directly synthesized on the biochip.

The solid substrate may be a material that may be modified to contain discrete individual sites appropriate for the attachment or association of the probes and is amenable to at least one detection method. Representative examples of substrate materials include glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica- based materials including silicon and modified silicon, carbon, metals, inorganic glasses and plastics. The substrates may allow optical detection without appreciably fluorescing. The substrate may be planar, although other configurations of substrates may be used as well. For example, probes may be placed on the inside surface of a tube, for flow- through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as flexible foam, including closed cell foams made of particular plastics.

The substrate of the biochip and the probe may be derivatized with chemical functional groups for subsequent attachment of the two. For example, the biochip may be derivatized with a chemical functional group including, but not limited to, amino groups, carboxyl groups, oxo groups or thiol groups. Using these functional groups, the probes may be attached using functional groups on the probes either directly or indirectly using a linker.

The probes may be attached to the solid support by either the 5' terminus, 3' terminus, or via an internal nucleotide.

The probe may also be attached to the solid support non-covalently. For example, biotinylated oligonucleotides can be made, which may bind to surfaces covalently coated with streptavidin, resulting in attachment. Alternatively, probes may be synthesized on the surface using techniques such as photopolymerization and photolithography. 10. Diagnostics

A method of diagnosis is also provided. The method comprises detecting a differential expression level of glioblastoma-associated nucleic acids in a biological sample. The sample may be derived from a patient. Diagnosis of a cancer state, and its histological type, in a patient may allow for prognosis and selection of therapeutic strategy. Further, the developmental stage of cells may be classified by determining temporarily expressed cancer-associated nucleic acids. In situ hybridization of labeled probes to tissue arrays may be performed. When comparing the fingerprints between an individual and a standard, the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may differ from those which indicate the prognosis and molecular profiling of the condition of the cells may lead to distinctions between responsive or refractory conditions or may be predictive of outcomes.

11. Kits

A kit is also provided and may comprise a nucleic acid described herein together with any or all of the following: assay reagents, buffers, probes and/or primers, and sterile saline or another pharmaceutically acceptable emulsion and suspension base. In addition, the kits may include instructional materials containing directions (e.g., protocols) for the practice of the methods described herein.

For example, the kit may be used for the amplification, detection, identification or quantification of a target nucleic acid sequence. The kit may comprise a poly(T) primer, a forward primer, a reverse primer, and a probe.

Any of the compositions described herein may be comprised in a kit. In a non- limiting example, reagents for isolating miRNA, labeling miRNA, and/or evaluating a miRNA population using an array are included in a kit. The kit may further include reagents for creating or synthesizing miRNA probes. The kits will thus comprise, in suitable container means, an enzyme for labeling the miRNA by incorporating labeled nucleotide or unlabeled nucleotides that are subsequently labeled. 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, components for in situ hybridization 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.

12. Compositions

A pharmaceutical composition is also provided. The composition may comprise a nucleic acid described herein and optionally a pharmaceutically acceptable carrier. The composition may encompass modified oligonucleotides that are identical, substantially identical, substantially complementary or complementary to any nucleobase sequence version of the miRNAs described herein or a precursor thereof. In certain embodiments, a nucleobase sequence of a modified oligonucleotide is fully identical or complementary to a miRNA nucleobase sequence listed herein, or a precursor thereof. In certain embodiments, a modified oligonucleotide has a nucleobase sequence having one mismatch with respect to the nucleobase sequence of the mature miRNA, or a precursor thereof. In certain embodiments, a modified oligonucleotide has a nucleobase sequence having two mismatches with respect to the nucleobase sequence of the miRNA, or a precursor thereof. In certain such embodiments, a modified oligonucleotide has a nucleobase sequence having no more than two mismatches with respect to the nucleobase sequence of the mature miRNA, or a precursor thereof. In certain such embodiments, the mismatched nucleobases are contiguous, hi certain such embodiments, the mismatched nucleobases are not contiguous. hi certain embodiments, a modified oligonucleotide consists of a number of linked nucleosides that is equal to the length of the mature miRNA. hi certain embodiments, the number of linked nucleosides of a modified oligonucleotide is less than the length of the mature miRNA. hi certain such embodiments, the number of linked nucleosides of a modified oligonucleotide is one less than the length of the mature miRNA. hi certain such embodiments, a modified oligonucleotide has one less nucleoside at the 5' terminus, hi certain such embodiments, a modified oligonucleotide has one less nucleoside at the 3' terminus. Li certain such embodiments, a modified oligonucleotide has two fewer nucleosides at the 5' terminus. Li certain such embodiments, a modified oligonucleotide has two fewer nucleosides at the 3' terminus. A modified oligonucleotide having a number of linked nucleosides that is less than the length of the miRNA, wherein each nucleobase of a modified oligonucleotide is complementary to each nucleobase at a corresponding position in a miRNA, is considered to be a modified oligonucleotide having a nucleobase sequence that is fully complementary to a portion of a miRNA sequence.

In certain embodiments, a modified oligonucleotide consists of 15 to 30 linked nucleosides. Li certain embodiments, a modified oligonucleotide consists of 19 to 24 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 21 to 24 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 15 linked nucleosides. Li certain embodiments, a modified oligonucleotide consists of 16 linked nucleosides. Li certain embodiments, a modified oligonucleotide consists of 17 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 18 linked nucleosides. Li certain embodiments, a modified oligonucleotide consists of 19 linked nucleosides. Li certain embodiments, a modified oligonucleotide consists of 20 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 21 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 22 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 23 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 24 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 25 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 26 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 27 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 28 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 29 linked nucleosides. In certain embodiments, a modified oligonucleotide consists of 30 linked nucleosides.

Modified oligonucleotides of the present invention may comprise one or more modifications to a nucleobase, sugar, and/or internucleoside linkage. A modified nucleobase, sugar, and/or internucleoside linkage may be selected over an unmodified form because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for other oligonucleotides or nucleic acid targets and increased stability in the presence of nucleases. hi certain embodiments, a modified oligonucleotide of the present invention comprises one or more modified nucleosides, hi certain such embodiments, a modified nucleoside is a stabilizing nucleoside. An example of a stabilizing nucleoside is a sugar- modified nucleoside. hi certain embodiments, a modified nucleoside is a sugar-modified nucleoside, hi certain such embodiments, the sugar-modified nucleosides can further comprise a natural or modified heterocyclic base moiety and/or a natural or modified internucleoside linkage and may include further modifications independent from the sugar modification, hi certain embodiments, a sugar modified nucleoside is a 2 '-modified nucleoside, wherein the sugar ring is modified at the 2' carbon from natural ribose or 2'-deoxy-ribose. hi certain embodiments, 2'-O-methyl group is present in the sugar residue.

The modified oligonucleotides designed according to the teachings of the present invention can be generated according to any oligonucleotide synthesis method known in the art, including both enzymatic syntheses or solid-phase syntheses. Equipment and reagents for executing solid-phase synthesis are commercially available from, for example, Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the capabilities of one skilled in the art and can be accomplished via established methodologies as detailed in, for example: Sambrook, J. and Russell, D. W. (2001), "Molecular Cloning: A Laboratory Manual"; Ausubel, R. M. et al., eds. (1994, 1989), "Current Protocols in Molecular Biology," Volumes I-III, John Wiley & Sons, Baltimore, Md.; Perbal, B. (1988), "A Practical Guide to Molecular Cloning," John Wiley & Sons, New York; and Gait, M. J., ed. (1984), "Oligonucleotide Synthesis"; utilizing solid-phase chemistry, e.g. cyanoethyl phosphoramidite followed by deprotection, desalting, and purification by, for example, an automated trityl-on method or HPLC. It will be appreciated that an oligonucleotide comprising an RNA molecule can be also generated using an expression vector as is further described hereinbelow. The compositions may be used for therapeutic applications. The pharmaceutical composition may be administered by known methods, including wherein a nucleic acid is introduced into a desired target cell in vitro or in vivo.

Methods for the delivery of nucleic acid molecules are described in Akhtar et al., (Trends Cell Bio. 2, 139, 1992). WO 94/02595 describes general methods for delivery of RNA molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres. Alternatively, the nucleic acid/vehicle combination is locally delivered by direct injection or by use of an infusion pump. Other routes of delivery include, but are not limited to oral (tablet or pill form) and/or intrathecal delivery (Gold, 1997, Neuroscience, 76, 1153-1158). Other approaches include the use of various transport and carrier systems, for example, through the use of conjugates and biodegradable polymers. More detailed descriptions of nucleic acid delivery and administration are provided for example in WO93/23569, WO99/05094, and WO99/04819.

The nucleic acids can be introduced into tissues or host cells by any number of routes, including viral infection, microinjection, or fusion of vesicles. Jet injection may also be used for intra-muscular administration, as described by Furth et al. (Anal Biochem 115 205:365-368, 1992). The nucleic acids can be coated onto gold microparticles, and delivered intradermally by a particle bombardment device, or "gene gun" as described in the literature (see, for example, Tang et al. Nature 356:152-154, 1992), where gold microprojectiles are coated with the DNA, then bombarded into skin cells. The compositions of the present invention can be formulated into pharmaceutical compositions by combination with appropriate, pharmaceutically acceptable carriers or diluents, and can be formulated into preparations in solid, semi-solid, liquid or gaseous forms, such as tablets, capsules, powders, granules, ointments, solutions, suppositories, injections, inhalants and aerosols. As such, administration of the agents can be achieved in various ways, including oral, buccal, rectal, parenteral, intraperitoneal, intradermal, transdermal, intracheal, etc.

13. Treatments

A method of treatment is also provided. A subject may be diagnosed with glioblastoma following the administration of medical tests well-known to those in the medical profession. In certain embodiments, the present invention provides methods for the treatment of glioblastoma comprising administering to a subject in need thereof a pharmaceutical composition. Administration of a pharmaceutical composition of the present invention to a subject having glioblastoma may result in one or more clinically desirable outcomes. Such clinically desirable outcomes include reduction of tumor number or reduction of tumor size. Additional clinically desirable outcomes include the extension of overall survival time of the subject, and/or extension of progression-free survival time of the subject. In certain embodiments, administration of a pharmaceutical composition of the invention prevents an increase in tumor size and/or tumor number. In certain embodiments, administration of a pharmaceutical composition of the invention prevents the recurrence of tumors. Administration of a pharmaceutical composition of the present invention results in desirable phenotypic effects. A subject's response to treatment may be evaluated by tests similar to those used to diagnosis the glioblastoma. Response to treatment may also be assessed by measuring biomarkers in blood, for comparison to pre-treatment levels of biomarkers.

The compounds provided herein maybe useful for the treatment of glioblastoma.

Tumor treatments often comprise more than one therapy. As such, in certain embodiments the present invention provides methods for treating glioblastoma comprising administering to a subject in need thereof a pharmaceutical composition of the present invention, and further comprising administering at least one additional therapy.

In certain embodiments, an additional therapy may also be designed to treat glioblastoma. An additional therapy may be a chemotherapeutic agent. An additional therapy may be surgery. In certain embodiments, an additional therapy may be a pharmaceutical agent that enhances the body's immune system, including low-dose cyclophosphamide, thymostimulin, vitamins and nutritional supplements (e.g., antioxidants, including vitamins A, C, E, beta- carotene, zinc, selenium, glutathione, coenzyme Q-IO and echinacea), and vaccines, e.g., the immunostimulating complex (ISCOM), which comprises a vaccine formulation that combines a multimeric presentation of antigen and an adjuvant. hi certain such embodiments, the additional therapy is selected to treat or ameliorate a side effect of one or more pharmaceutical compositions of the present invention. Such side effects include, without limitation, injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity and central nervous system abnormalities. hi certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at the same time, hi certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are administered at different times, hi certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared together in a single formulation. In certain embodiments, one or more pharmaceutical compositions of the present invention and one or more other pharmaceutical agents are prepared separately. hi certain embodiments, suitable administration routes of a pharmaceutical composition for the treatment of glioblastoma include, but are not limited to, oral, rectal, transmucosal, intestinal, enteral, topical, suppository, through inhalation, intrathecal, intraventricular, intraperitoneal, intranasal, intraocular, intratumoral, and parenteral (e.g., intravenous, intramuscular, intramedullary, and subcutaneous). An additional suitable administration route includes chemoembolization. hi certain embodiments, pharmaceutical intrathecals are administered to achieve local rather than systemic exposures. For example, pharmaceutical compositions may be injected directly in the area of desired effect (e.g., into a tumor). hi certain embodiments, a pharmaceutical composition of the present invention is administered in the form of a dosage unit (e.g., tablet, capsule, bolus, etc.). hi certain embodiments, such pharmaceutical compositions comprise a dose selected from 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 55 mg, 60 mg, 65 mg, 70 mg, 75 mg, 80 mg, 85 mg, 90 mg, 95 mg, 100 mg, 105 mg, 110 mg, 115 mg, 120 mg, 125 mg, 130 mg, 135 mg, 140 mg, 145 mg, 150 mg, 155 mg, 160 mg, 165 mg, 170 mg, 175 mg, 180 mg, 185 mg, 190 mg, 195 mg, 200 mg, 205 mg, 210 mg, 215 mg, 220 mg, 225 mg, 230 mg, 235 mg, 240 mg, 245 mg, 250 mg, 255 mg, 260 mg, 265 mg, 270 mg, 270 mg, 280 mg, 285 mg, 290 mg, 295 mg, 300 mg, 305 mg, 310 mg, 315 mg, 320 mg, 325 mg, 330 mg, 335 mg, 340 mg, 345 mg, 350 mg, 355 mg, 360 mg, 365 mg, 370 mg, 375 mg, 380 mg, 385 mg, 390 mg, 395 mg, 400 mg, 405 mg, 410 mg, 415 mg, 420 mg, 425 mg, 430 mg, 435 mg, 440 mg, 445 mg, 450 mg, 455 mg, 460 mg, 465 mg, 470 mg, 475 mg, 480 mg, 485 mg, 490 mg, 495 mg, 500 mg, 505 mg, 510 mg, 515 mg, 520 mg, 525 mg, 530 mg, 535 mg, 540 mg, 545 mg, 550 mg, 555 mg, 560 mg, 565 mg, 570 mg, 575 mg, 580 mg, 585 mg, 590 mg, 595 mg, 600 mg, 605 mg, 610 mg, 615 mg, 620 mg, 625 mg, 630 mg, 635 mg, 640 mg, 645 mg, 650 mg, 655 mg, 660 mg, 665 mg, 670 mg, 675 mg, 680 mg, 685 mg, 690 mg, 695 mg, 700 mg, 705 mg, 710 mg, 715 mg, 720 mg, 725 mg, 730 mg, 735 mg, 740 mg, 745 mg, 750 mg, 755 mg, 760 mg, 765 mg, 770 mg, 775 mg, 780 mg, 785 mg, 790 mg, 795 mg, and 800 mg. In certain such embodiments, a pharmaceutical composition of the present invention comprises a dose selected from 25 mg, 50 mg, 75 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 500 mg, 600 mg, 700 mg, and 800mg.

In certain embodiments, the compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the formulation. In certain embodiments, pharmaceutical compositions of the present invention comprise one or more excipients. In certain such embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulosem and polyvinylpyrrolidone.

In certain embodiments, a pharmaceutical composition of the present invention is prepared using known techniques, including, but not limited to mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or tabletting processes.

In certain embodiments, a pharmaceutical composition of the present invention is a liquid (e.g., a suspension, elixir and/or solution). In certain of such embodiments, a liquid pharmaceutical composition is prepared using ingredients known in the art, including, but not limited to, water, glycols, oils, alcohols, flavoring agents, preservatives, and coloring agents.

In certain embodiments, a pharmaceutical composition of the present invention is a solid (e.g., a powder, tablet, and/or capsule). In certain of such embodiments, a solid pharmaceutical composition is prepared using ingredients known in the art, including, but not limited to, starches, sugars, diluents, granulating agents, lubricants, binders, and disintegrating agents.

In certain embodiments, a pharmaceutical composition of the present invention is formulated as a depot preparation. Certain such depot preparations are typically longer acting than non-depot preparations. In certain embodiments, such preparations are administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. In certain embodiments, depot preparations are prepared using suitable polymeric or hydrophobic materials (for example an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt. In certain embodiments, a pharmaceutical composition of the present invention comprises a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds, hi certain embodiments, certain organic solvents such as dimethylsulfoxide are used. In certain embodiments, a pharmaceutical composition of the present invention comprises one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.

In certain embodiments, a pharmaceutical composition of the present invention comprises a co-solvent system. Certain of such co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase, hi certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80™ and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80™; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.

In certain embodiments, a pharmaceutical composition of the present invention comprises a sustained-release system. A non-limiting example of such a sustained-release system is a semi-permeable matrix of solid hydrophobic polymers, hi certain embodiments, sustained-release systems may, depending on their chemical nature, release pharmaceutical agents over a period of hours, days, weeks or months. hi certain embodiments, a pharmaceutical composition of the present invention is prepared for oral administration. In certain of such embodiments, a pharmaceutical composition is formulated by combining one or more compounds with one or more pharmaceutically acceptable carriers. Certain of such carriers enable pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject, hi certain embodiments, pharmaceutical compositions for oral use are obtained by mixing oligonucleotide and one or more solid excipient. Suitable excipients include, but are not limited to, fillers, such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). hi certain embodiments, such a mixture is optionally ground and auxiliaries are optionally added, hi certain embodiments, pharmaceutical compositions are formed to obtain tablets or dragee cores. In certain embodiments, disintegrating agents (e.g., cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof, such as sodium alginate) are added.

Ih certain embodiments, dragee cores are provided with coatings. In certain such embodiments, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to tablets or dragee coatings. hi certain embodiments, pharmaceutical compositions for oral administration are push-fit capsules made of gelatin. Certain of such push-fit capsules comprise one or more pharmaceutical agents of the present invention in admixture with one or more filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers, hi certain embodiments, pharmaceutical compositions for oral administration are soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol, hi certain soft capsules, one or more pharmaceutical agents of the present invention are be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. hi certain embodiments, pharmaceutical compositions are prepared for buccal administration. Certain of such pharmaceutical compositions are tablets or lozenges formulated in conventional manner. hi certain embodiments, a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, etc.). hi certain of such embodiments, a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer, hi certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives), hi certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multi-dose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, such suspensions may also contain suitable stabilizers or agents that increase the solubility of the pharmaceutical agents to allow for the preparation of highly concentrated solutions.

In certain embodiments, a pharmaceutical composition is prepared for transmucosal administration, hi certain of such embodiments penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. hi certain embodiments, a pharmaceutical composition is prepared for administration by inhalation. Certain of such pharmaceutical compositions for inhalation are prepared in the form of an aerosol spray in a pressurized pack or a nebulizer. Certain of such pharmaceutical compositions comprise a propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In certain embodiments using a pressurized aerosol, the dosage unit may be determined with a valve that delivers a metered amount, hi certain embodiments, capsules and cartridges for use in an inhaler or insufflator may be formulated. Certain of such formulations comprise a powder mixture of a pharmaceutical agent of the invention and a suitable powder base such as lactose or starch. hi certain embodiments, a pharmaceutical composition is prepared for rectal administration, such as a suppositories or retention enema. Certain of such pharmaceutical compositions comprise known ingredients, such as cocoa butter and/or other glycerides. hi certain embodiments, a pharmaceutical composition is prepared for topical administration. Certain of such pharmaceutical compositions comprise bland moisturizing bases, such as ointments or creams. Exemplary suitable ointment bases include, but are not limited to, petrolatum, petrolatum plus volatile silicones, and lanolin and water in oil emulsions. Exemplary suitable cream bases include, but are not limited to, cold cream and hydrophilic ointment. hi certain embodiments, the therapeutically effective amount of the pharmaceutical composition of the present invention is sufficient to prevent, alleviate or ameliorate symptoms of a disease or to prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art. In certain embodiments, the pharmaceutical composition of the present invention is formulated as a prodrug, hi certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically more active form of the composition. In certain embodiments, prodrugs are useful because they are easier to administer than the corresponding active form. For example, in certain instances, a prodrug may be more bioavailable (e.g., through oral administration) than is the corresponding active form, hi certain instances, a prodrug may have improved solubility compared to the corresponding active form, hi certain embodiments, prodrugs are less water soluble than the corresponding active form, hi certain instances, such prodrugs possess superior transmittal across cell membranes, where water solubility is detrimental to mobility, hi certain embodiments, a prodrug is an ester. In certain such embodiments, the ester is metabolically hydrolyzed to carboxylic acid upon administration, hi certain instances the carboxylic acid containing compound is the corresponding active form, hi certain embodiments, a prodrug comprises a short peptide (polyaminoacid) bound to an acid group, hi certain of such embodiments, the peptide is cleaved upon administration to form the corresponding active form.

In certain embodiments, a prodrug is produced by modifying a pharmaceutically active compound such that the active compound will be regenerated upon in vivo administration. The prodrug can be designed to alter the metabolic stability or the transport characteristics of a drug, to mask side effects or toxicity, to improve the flavor of a drug or to alter other characteristics or properties of a drug. By virtue of knowledge of pharmacodynamic processes and drug metabolism in vivo, those of skill in this art, once a pharmaceutically active compound is known, can design prodrugs of the compound (see, e.g., Nogrady (1985) Medicinal Chemistry A Biochemical Approach, Oxford University Press, New York, pages 388-392).

Mechanisms for drug targeting in the brain involve going either "through" or "behind" the blood-brain barrier. Modalities for drug delivery through the blood-brain barrier entail its disruption by osmotic means, biochemically by the use of vasoactive substances such as bradykinin, or even by localized exposure to high intensity focused ultrasound (HIFU). Other strategies to go through the blood brain barrier may entail the use of endogenous transport systems, including carrier-mediated transporters such as glucose and amino acid carriers; receptor-mediated transcytosis for insulin or transferrin; and blocking of active efflux transporters such as p-glycoprotein. Strategies for drug delivery behind the blood-brain barrier include intracerebral implantation and convection-enhanced distribution. In some embodiments the compounds may be administered by infusion pump to be delivered to the blood brain barrier.

The following examples are presented in order to more fully illustrate some embodiments of the invention. They should, in no way be construed, however, as limiting the broad scope of the invention.

EXAMPLES

Example 1 Materials and Methods 1. 1 GBM samples, isolation of stem cells and cell culture

Tumor samples were obtained from surgical resection of adult GBM patients after informed consent at the Tel-Aviv Souraski Medical Center (Tel-Aviv, Israel). Cells were prepared and subjected to magnetic bead isolation using the CD133 Cell Isolation Kit (Miltenyi Biotec). Cells were labeled with anti-human CD 133-2 Phycoerythrin (PE) and control IgG isotype monoclonal antibodies (Miltenyi Biotec, Auburn, CA, USA) and analyzed for purity by flow cytometry with the FACS-Calibur machine (Becton Dickinson, Franklin Lakes, NJ, USA). For sample fractionation CD 133/1 Microbeads were used (Miltenyi Biotec) and Cell separation was carried out on the autoMACS machine (Miltenyi Biotec). Data acquisition and analysis were performed with CellQuest software (Becton Dickinson).

For neurosphere formation the GBM CD133+ and CD133- cell populations or GBM cell line A- 172 cells were resuspended in a defined serum-free tumor sphere medium (TSM), containing DMEM/F12, B27 (1:50; Gibco-Invitrogen), Fibroblast growth factor (bFGF, Peprotech, Rocky Hill, NJ, USA), Epidermal growth factor (EGF, Peprotech) Leukemia Inhibitory Factor (LIF, Chemicon), each 20ng/ml and Heparin (5 μg/ml) and plated in 96 well at 20,000 cell per well. Neurospheres were observed after 24-36 hr.

1. 2 Expression profiling of miRs

For microRNA analysis, total RNA was isolated from three GBM patients using TRTZOL according to the manufacturer's instructions. Custom microarrays were produced using the Rosetta Genomics microRNA microarray platform and contained DNA oligonucleotide probes representing 688 miRNAs. microRNA was labeled in total RNA (l-5ug) by ligation of an RNA-linker, p-rCrU-

Cy/dye (Eurogentec), to the 3' end with Cy3 or Cy5 at 4°C for 1 h followed by 1 h at 37 C. The labeled RNA was mixed with 3X hybridization buffer (Ambion), heated to 95⁰C for 3 min and then added on top of the microRNA array. Slides were hybridized for 12-16 h at 42⁰C, followed by two washes in room temperature (25⁰C) with IXSSC, 0.2% SDS and a final wash with 0.1X SSC.

Arrays were scanned using an Agilent Microarray Scanner Bundle G2565BA (resolution of 10 mm at 100% power). The data was analyzed using the SpotReader software (Niles Scientific) and triplicate spots were combined. Differentially expressed miRs were identified by using a filter based on a fold change of 2 combined with t-test (ρ<0.01) for CD133+ versus CD133- comparisons. The differentially expressed miRs are listed in table 1 below.

Table 1; Differentially expressed miRs and their hairpins

The miR name is the miRBase registry name (release 8).

1. 3 Transfection of A-172 and primary GBM tumors with microRNAs

Stability-enhanced hsa-miR-451 (SEQ ID NO: 1) and control oligo-ribonucleotides were from Dharmacon. Transfection was carried out using Dharmafect (Dharmacon), according to the manufacturer's instructions. Additionally, plasmids containing hsa-miR- 451 (SEQ ID NO: 1), hsa-miR-425-5p (SEQ ID NO: 5), hsa-miR-486 (SEQ ID NO: 3) and pGFP were from Dr. R. Agami's lab (R.Nagel and C.LeSage). A- 172 cells were plated in

24-well plates, (12xlO⁵ cells/well) in antibiotic-free medium one day prior to transfection. Transfection with miR-containing plasmids hsa-miR-451 (SEQ ID NO: 1), lisa-miR-425-5p (SEQ ID NO: 5) and hsa-miR-486 (SEQ ID NO: 3) was performed with 100-300ng and after 24h fresh medium was added for additional 24h. For GBM primary tumor cells, transfection was for 4hr without further incubations. A- 172 cells and GBM primary cells were then transferred to 96- well plates at 6x10⁴ cells/well with TSM medium for neurosphere formation. Neurosphere growth was determined 3 days after transfer, viewed and photographed microscopically (Olympus CK2) using a 4X objective. The assay was repeated several times.

1. 4 Lu cif erase assay

Specific primers (SEQ ID NOS: 15 and 16) were used to amplify the hsa-miR-451 putative promoter from human DNA, with added sites of Xhol and HindBI, and cloned into pGEMT vector (Promega, Madison, Wisconsin), denoted pGEMTl-miR 451. The sequences of the primers are detailed in table 2:

Table 2: Sequences used in the PCR amplification of the hsa-miR-451 putative promoter

The miR promoter was released from the upstream region of miR451 in pGEMTl- miR 451 vector (see Fig.6A) with Xhol and HindBI and cloned into pGL3-bαsic vector at the corresponding sites, denoted pGL3-miR451. A-172, H1299 and HCTl 16 cells were plated in 24 well dishes at 6X10⁴ cells/well.

All transfections included pGL3-miR451, and the SMAD containing plasmids, pFLAG- SMAD3 or pMyc-SMAD4, or both, at 100- 300 ng/well and a constant amount of Renillα luciferase plasmid (lOOng) for internal control. Twenty four hours post-transfection, cells were incubated for 30 minutes with 100 μl/well lysis buffer (Amersham) and 35 μl of each lysate was subjected to a dual luciferase assay (Promega) using a Luminoskan Ascent apparatus (Thermo lab systems). Results of triplicate transfection are presented after normalization to Renillα luciferase activity. Values are shown in Figure 6B as mean ±SEM. Renilla plasmid was from Promega and the SMAD plasmids were a gift of Dr. Y. Shaul. Example 2 Isolation of CD133+ and CD133- fractions from primary GBM and miRNA expression profiling

Antibody coated magnetic beads (Miltenyi) were used to fractionate primary GBM samples to CD133+ and CD133- cells. GBM samples derived from six patients (pl-p6) were sorted for stem cells (CD133+) and for CD133- cell fractions by one passage through the antibody coated beads (Figure 1). After sorting, the content of the CD 133+ fraction was enriched up to 89% and each fraction formed neurosphere-like structures within 24-48h, in the appropriate serum-free medium, whereas the CD 133- fraction did not exhibit neurosphere formation (Figure 2). Total RNA was isolated from the cells of the GBM fractions and the RNA was analyzed for miR expression, using Rosetta Genomics microarrays for three out of six GBM tumors. Figure 3 shows the differentially expressed miRs in the CD133+ and CD133- fractions of the pi GBM sample. Interestingly, the modulated miRs were not found to be over-expressed in the CD 133+ cells, but rather several miRs were over expressed in the CD133- fraction of all samples. These include hsa-miR-451 (SEQ ID NO: 1), hsa-miR-486 (SEQ ID NO: 3), has-miR-425-5p (SEQ ID NO: 5), lisa-miR-16 (SEQ ID NO: 7), hsa-miR- 107 (SEQ ID NO: 9), hsa-miR-185 (SEQ ID NO: 11) and hsa-miR-103 (SEQ ID NO: 13). Similar results were obtained for the other two GBM samples.

Example 3 hsa-miR-451 (SEQ ID NO: 1) and Imatinib Mesylate cooperate in targeting GBM stem cells for neurosphere dispersion

A- 172 cells were used to study the effect of over-expression of miRs on neurosphere formation. As apparent in Figure 4A, transfection with plasmids containing miRs: hsa-miR- 451 (SEQ ID NO: 1), hsa-miR-425-5p (SEQ ID NO: 5) and hsa-miR-486 (SEQ ID NO: 3) inhibited the formation of neurospheres in A- 172 cells. hsa-miR-451 (SEQ ID NO: 1) in particular, showed a considerable neurosphere inhibition effect. In order to study the effect of miR expression on the growth of GBM cells, plastic-attached A- 172 glioma cells were transfected with either the 22-mer olignucleotide of hsa-miR-451 (SEQ ID NO: 1) or with a control-miR, and assayed for viability for several days (Figure 4B). As indicated in Figure 4C, transfection of hsa-miR-451 (SEQ ID NO: 1) caused a significant drop in cell number, depressing cell viability by more than 80% and inhibited cell growth. hnatinib mesylate at 2.5μM has previously been shown to inhibit neurosphere formation and cause neurosphere dispersion (H. Gal, A. Makovitzki, N. Amariglio, G. Rechavi, Z. Ram, D. Givol, Biochem Biophys Res Commun 358 (2007) 908-913.). To evaluate the combined effect of hsa-miR-451 (SEQ. ID. NO: 1) and Imatinib mesylate, A- 172 cells were transfected with hsa-miR-451 (SEQ ID NO: 1) followed by neurosphere formation and the addition of Imatinib mesylate at concentrations of lμM and 2.5μM. Cells were evaluated for neurosphere formation and growth 3 days later.

As apparent in Figure 5A, middle, transfection of hsa-miR-451 (SEQ ID NO: 1) at concentrations of 5nM, 1OnM and 2OnM showed a reduction in neurosphere size and number. Dispersion of neurospheres was observed at miR concentrations of 1OnM and 2OnM, whereas Imatinib mesylate showed partial dispersion of the neurospheres and reduction in sphere size at IuM and the effect was pronounced at 2.5μM (Figure 5A, top). The combination of hsa-miR-451 and Imatinib mesylate led to complete dispersion of the neuropheres at lower concentrations of both reagents (Figure 5A, bottom). This assay was also performed on primary GBM stem cells within 24h of surgical resection and with similar results, as indicated in Figure 5B. The fractionated CD 133+ cells were transfected with hsa-miR-451 (SEQ ID NO: 1) and Imatinib mesylate was added as described above for the A- 172 cells. Figure 5B shows the response of the transfection with hsa-miR-451 (SEQ. ID NO: 1), Imatinib mesylate treatment and their combination on a particular GBM tumor. As indicated, the combination of hsa-miR-451 (SEQ ID NO: 1) and Imatinib mesylate was demonstrated to disperse the spheres at 2OnM hsa-miR-451 (SEQ ID NO: 1) and lμM Imatinib mesylate. Although the dispersion of neurospheres is not complete, the effect is similar to that obtained with A- 172 cells. Furthermore, inhibition of cell growth and reduction in cell viability was observed on attached A- 172 cells that were transfected with hsa-miR-451 (SEQ ID NO: 1) (2OnM), followed by the addition of Imatinib mesylate (2.5μM) 12 hr later (data not shown).

Example 4 Regulation of hsa-miR-451 by SMAD hsa-miR-451 is located on chromosome 17qll.2, a region known to be amplified in certain types of cancers, and is in close proximity to HER2 (17ql2). To better understand the potential role of hsa-miR-451 (SEQ ID NO: 1) in cell signaling, its upstream regions were examined, using the Genomatix software, for transcription factor targets. Binding sites for SMAD3 (GenBank accession AAL68976.1) and SMAD4 (GenBank accession

BAB40977.1), separated by 157bp and beginning 1135 bp upstream to the hsa-miR-451 sequence were identified, as presented schematically in Figure 6A, and as detailed in table 3 below.

Table 3^ Transcription factors SMAD3 and SMAD4, and their binding sites

Transcription factor Sequence of Binding Site SEQ. ID. NO.

SMAD3 GTCTGGCCT 17

SMAD4 GTCTAGTCT 18

To explore whether these target sites respond to SMAD by PCR amplification, the hsa-miR-451 putative promoter that contained the SMAD targets was cloned fused to firefly-luciferase, to generate the pGL3-miR451 vector. SMAD3 and SMAD4 containing plasmids and the pGL3-miR451 or appropriate controls were co-transfected to A- 172 cells and assayed for luciferase activity. As indicated in Figure 6B, the results showed increased luciferase activity in the presence of SMAD3 or SMAD4, and when both activators were used, 6 fold luciferase inductions were observed. Similar results were obtained with H 1299 or HCTl 16 cell lines (data not shown), suggesting that hsa-miR-451 transcription is enhanced by SMAD.

To investigate the effect of SMAD3 and SMAD4 on the growth of A- 172 glioma cell lines, these cells were transfected with SMAD plasmids (as described in Example 1). As shown in Figure 6C, cells transfected with SMAD3 or SMAD4 showed a much slower growth rate in comparison to control or GFP transected cells, whereas their combination induced a more profound growth inhibition. This is in line with the results of the luciferase assay presented in Figure 6B, suggesting that SMAD3 and SMAD4 may enhance the hsa- miR-451 transcription and induce inhibition of cell growth and proliferation.

Example 5 In vivo model of human glioblastoma

To determine the effect of miR-451 over-expression on the growth of GBM cells in vivo, matrigel and orthotopic (intracranial) implantation techniques are used. Equal volumes of matrigel are mixed with T98G cell suspensions, tumors are developed at both flank and orthotopic locations. Four groups of nude mice (each group contained 10 mice) are inoculated into the flanks with 4xlO⁵ T98G cells (2 groups with miR-451 transfected cells and 2 groups with mocked transfected control) in a 150 μl total volume with Matrigel (BD Biosciences). Tumors are developed 15 weeks, following inoculation. Tumor size is monitored with calipers. Tumor volume is calculated as (L * W²)/2, where L = length (mm) and W = width (mm). Mean tumor volumes for miR-451 transfected cells treated groups are compared to mean tumor volumes for control treated groups.

The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying current knowledge, readily modify and/or adapt for various applications such specific embodiments without undue experimentation and without departing from the generic concept, and, therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art.

Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

It should be understood that the detailed description and specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

Claims

1. A method for treating or preventing a brain cancer, comprising administering to a subject in need thereof an effective amount of a composition comprising a nucleic acid sequence selected from the group consisting of:

(a) SEQ ID NOS: 1-14,

(b) a fragment of (a),

(c) sequences having at least 80% identity to (a) or (b), and

(d) a vector comprising any of (a), (b) or (c).

2. The method of claim 1, wherein the nucleic acid comprises a modified base.

3. The method of any of claims 1 and 2, wherein the brain cancer is glioblastoma.

4. The method of any of claims 1-3, wherein the subject is a human.

5. The method of any of claims 1-4, wherein the administering comprises intratumoral administration, chemoembolization, subcutaneous administration or intravenous administration.

6. The method of any of claims 1-5, wherein said intratumoral administration is delivered through the blood brain barrier by a method selected from: disruption of the blood brain barrier by osmotic means,

(a) use of vasoactive substances, selected from the group comprising bradykinin,

(b) exposure to high intensity focused ultrasound,

(c) use of endogenous transport systems, selected from the group comprising carrier-mediated glucose transporters and carrier-mediated amino acid carriers;

(d) use of receptor-mediated transcytosis, selected from the group comprising receptor-mediated transcytosis of insulin and receptor-mediated transcytosis of transferrin;

(e) blocking of active efflux transporters selected from the group comprising p- glycoprotein;

(f) intracerebral implantation,

(g) convection-enhanced distribution, and (h) use of an infusion pump.

7. The method of any of claims 1-6, wherein the administered composition further comprises a pharmaceutically acceptable carrier.

8. The method of any of claims 1-6, further comprising administering at least one additional therapy.

9. The method of claim 8, wherein the at least one additional therapy is a tyrosine kinase inhibitor.

10. The method of claim 9, wherein said tyrosine kinase inhibitor is Imatinib mesylate.

11. The method of any of claims 1-10, wherein the administering results in one or more of:

(a) inhibition of the formation of neurospheres,

(b) reduction in neurosphere size,

(c) neurosphere dispersion,

(d) reduction of number of tumor cells,

(e) reduction of tumor cell viability, and

(f) inhibition of tumor cell growth.

12. A method for initiating the differentiation of cancer stem cells comprising increasing, in said cells, the level of a nucleic acid sequence selected from the group consisting of:

(a) SEQ ID NOS: 1-14,

(b) a fragment of (a), and.

(c) sequences having at least 80% identity to (a) or (b).

13. The method of claim 12, wherein said cancer stem cells are glioblastoma stem cells.

14. A method for inhibiting the growth or viability of glioblastoma cells comprising increasing, in said cells, the level of a nucleic acid sequence selected from the group consisting of:

(a) SEQ ID NOS: 1-14,

(b) a fragment of (a), and

(c) sequences having at least 80% identity to (a) or (b).

15. A method for inhibiting the growth or viability of glioblastoma cells comprising administering to the cells an effective amount of a composition capable of binding to a sequence selected from the group consisting of SEQ ID NO: 17 and 18.

16. The method of claim 15, wherein the composition is selected from the group consisting of SMAD 3 and SMAD 4.

17. A method for determining the prognosis of glioblastoma in a subject comprising:

(a) obtaining a biological sample from said subject;

(b) determining the expression level in said sample of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-14 and sequences at least about 80% identical thereto; and

(c) comparing said expression level to a threshold expression level,

(d) wherein a relatively low expression level of said nucleic acids as compared to said threshold expression level is predictive of poor prognosis of said subject.

18. A kit for determining the prognosis of glioblastoma in a subject, comprising a probe comprising a nucleic acid sequence that is complementary to a sequence selected from SEQ ID NOS: 1-14, a fragment thereof, or to a sequence at least about 80% identical thereto.

19. Use of a nucleic acid comprising a nucleic acid sequence selected from the group consisting of:

(a) SEQ ID NOS: 1-14,

(b) a fragment of (a),

(c) sequences having at least 80% identity to (a) or (b), and

(d) a vector comprising any of (a), (b) or (c) for the preparation of a medicament for the treatment or prevention of a brain cancer.