WO2013122918A1 - Méthodes et compositions pour inhiber un mécanisme de transition mésenchymateuse multi-cancéreuse - Google Patents

Méthodes et compositions pour inhiber un mécanisme de transition mésenchymateuse multi-cancéreuse Download PDF

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WO2013122918A1
WO2013122918A1 PCT/US2013/025709 US2013025709W WO2013122918A1 WO 2013122918 A1 WO2013122918 A1 WO 2013122918A1 US 2013025709 W US2013025709 W US 2013025709W WO 2013122918 A1 WO2013122918 A1 WO 2013122918A1
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expression
activity
certain embodiments
coordinately
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Dimitris Anastassiou
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The Trustees Of Columbia University In The City Of New York
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links

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  • the present invention relates to the discovery that specific differentially-expressed genes in cancer cells are associated with epithelial- mesenchymal transition (EMT) and that, in certain instances, such EMT correlates with invasiveness, e.g., invasion of certain cells of primary tumors into adjacent connective tissue during the initial phase of metastasis.
  • EMT epithelial- mesenchymal transition
  • the identification of biomarkers associated with this mechanism can be used for identifying the initiation of EMT and, in certain instances, diagnosing and staging particular cancers, for monitoring cancer progress/regression, for developing therapeutics, e.g., the microRNA inhibitors disclosed herein, and for predicting the appropriateness of certain treatment strategies.
  • epithelial-mesenchymal transition relates to a biologic process that allows a cancer cell to undergo multiple biochemical changes enabling it to assume a mesenchymal cell phenotype, e.g., enhanced migratory capacity, invasiveness, elevated resistance to apoptosis, and greatly increased production of ECM components.
  • EMT refers to mesenchymal transitions generally and therefore is not limited to cells of epithelial origin, but includes non- epithelial cells, e.g., neuroblastoma cells.
  • the EMT signature As used herein, a gene expression signature correlating with the observed EMT is referred to as "the EMT signature.” There is currently great interest in characterizing and making use of the biological mechanism underlying EMT, as well as cancer invasion and subsequent metastasis, and this interest is addressed by the present invention. 3. SUMMARY OF THE INVENTION
  • the present invention relates to methods for inhibiting a mesenchymal transition in cell comprising: modulating the expression or activity in said cell of one or more microRNAs selected from the group consisting of miR-214, miR-199a, miR-199b, miR-409, miR-134, miR-200a, miR-200b, and miR- 192; and thereby inhibiting a mesenchymal transition in said cell.
  • the expression or activity of one or more of miR-214, miR-199a, miR- 199b, miR-409, and miR-134 is/are independently or coordinately reduced.
  • the expression or activity of one or more of miR-200a, miR-200b, and miR-192 is/are independently or coordinately increased. In certain embodiments, the expression or activity of one or more of miR-214, miR-199a, and miR-199b, is/are independently or coordinately reduced.
  • the present invention relates to methods for inhibition of a cancers cell acquiring a resistance to therapy or increased likelihood of recurrence as the cancer cell acquires properties of stem cells comprising: modulating the expression or activity in said cell of one or more microRNAs selected from the group consisting of miR-214, miR-199a, miR-199b, miR-409, miR-134, miR-200a, miR-200b, and miR-192; and thereby inhibiting the acquisition of resistance to therapy or increased likelihood of recurrence as the cancer cell acquires properties of stem cells in said cancer cell.
  • the expression or activity of one or more of miR-214, miR-199a, miR-199b, miR-409, and miR-134 is/are independently or coordinately reduced. In certain embodiments, the expression or activity of one or more of miR-200a, miR-200b, and miR-192 is/are independently or coordinately increased. In certain embodiments, the expression or activity of one or more of miR-214, miR-199a, and miR-199b, is/are independently or coordinately reduced.
  • the present invention relates to methods for inhibition of a cancer cell acquiring an invasive phenotype comprising: modulating the expression or activity in said cell of one or more microRNAs selected from the group consisting of miR-214, miR-199a, miR-199b, miR-409, miR-134, miR-200a, miR-200b, and miR-192; and thereby inhibiting the acquisition of an invasive phenotype in said cancer cell.
  • the expression or activity of one or more of miR-214, miR-199a, miR-199b, miR-409, and miR-134 is/are independently or coordinately reduced.
  • the expression or activity of one or more of miR-200a, miR-200b, and miR-192 is/are independently or coordinately increased. In certain embodiments, the expression or activity of one or more of miR-214, miR-199a, and miR-199b, is/are independently or coordinately reduced.
  • the present invention relates to the above- described methods wherein said reduction comprises administration of: (a) an antisense molecule targeted to said miRNA; (b) an RNAi molecule targeted to said miRNA; or (c) a catalytic RNA molecule targeted to said microRNA.
  • the present invention relates to the above- described methods wherein said increase comprises: (a) direct administration of said miRNA; (b) introduction of a transgene capable of expressing said miRNA; or (c) influencing the expression of the endogenous coding sequence for said miRNA.
  • the present invention relates to the above- described methods wherein the method comprises first performing a diagnostic step to identify the presence or absence of an EMT signature.
  • the present invention relates to the above- described methods wherein the method comprises a subsequent diagnostic step to identify the presence, absence, increase in, and/or reduction in an EMT signature.
  • the present invention relates to the above- described methods wherein the method comprises reducing the expression or activity of one or more of miR-214, miR-199a, miR-199b, miR-409, and miR-134, and increasing the expression or activity of one or more of miR-200a, miR-200b, and miR-192.
  • the present invention relates to the above- described methods wherein where the method comprises coordinately reducing the expression of miR-199a2 and miR-214.
  • the coordinated reduction of miR-199a2 and miR-214 comprises administration of an inhibitor of the expression of a transcript comprising both miR-199a2 and miR-214 sequences, such as the non-coding RNA DNM30S.
  • coordinated inhibitor of miR-199a2 and miR-214 is selected from an antisense oligonucleotide, a RNAi molecule, and a catalytic nucleic acid.
  • Figures 1(A)-(D) depict scatter plots for the coexpression of the EMT inducing transcription factor Slug (SNAI2) with the main signature genes COL11Al and THBS2, indicating the strong co-expression as well as continuity of the passing of cancer cells through a Slug-based EMT in solid tumors, and the total absence of the co-expression of these genes otherwise.
  • A, B and C plots from three solid tumor datasets.
  • D plot from a leukemia dataset.
  • Figures 2(A)-(C) depict scatter plots in human and mouse of the 18 samples for the expression of the EMT inducing transcription factor Slug (SNAI2) in terms of the expression of the main signature genes COL11 Al and THBS2.
  • A demonstration that this co-expression is present in the xenografted human cells.
  • B demonstration that this co-expression is absent in the peritumoral mouse cells.
  • C Bar diagram indicating that other EMT inducing transcription factors are not co- expressed.
  • Figure 3 depicts a heat map combining human and mouse genes.
  • the 29 human genes include many EMT factors and were found to be significantly co- expressed in the cancer cells.
  • the signature is not of a general fibroblastic nature, but rather has its own special characteristics, one of which is that genes COL1 1A1 and THBS2 have a prominent presence in all cases, and they are strongly co-expressed with a remarkably smooth continuous transition.
  • Collagen COL1 1A1 has been identified as a reliable proxy for the signature.
  • finding the list of genes whose expression is most correlated with that of COL1 1A1 consistently identifies the other genes of the signature.
  • the signature prominently contains only one of the known EMT inducing transcription factors, Slug (SNAI2). Furthermore, the signature contains numerous other EMT-associated genes.
  • the previously-identified signature includes numerous EMT- associated genes expressed by cancer cells, it also includes genes that are not specifically expressed by cancer cells but which are expressed by other cells in the biopsy sample located in the adjacent microenvironment which participate in the EMT-inducing mechanism by interacting with the cancer cells. While a signature that takes into consideration the expression patterns of all cells obtained via a biopsy or other sampling technique can offer valuable information, a distinct signature that focuses specifically on the expression of cells undergoing an EMT, including, but not limited to, a cancer cells-specific EMT signature, is also useful as described herein. Many among the genes of the signature were found expressed by the cancer cells themselves in xenografts (Anastassiou et al., BMC Cancer, 1 1 :529 (201 1)).
  • SNAI2 and other EMT marker genes together with the signature genes COL1 1 Al and THBS2, among the 29 significantly overexpressed genes in the xenografted human cancer cells demonstrate that cancer cells themselves undergo SNAI2-based EMT and express COL11 Al and THBS2 in solid tumors. Indeed, in solid tumors, identifying the genes whose expression is most correlated with that of COL1 1 Al consistently reveals the other genes of the signature, including SNAI2. Although this is not observed for healthy samples or nonsolid tumors such as leukemia, such samples can still undergo some form of early or partial SNAI2-based EMT as outlined below.
  • genes of the signature consisting mainly of genes SNAI2, LUM, DCN, COL1 Al , COL3 Al and COL6A3 was found also coexpressed even in normal samples in a tissue-specific manner (Cheng and Anastassiou, available from Nature Precedings
  • SNAI2-based EMT which is not necessarily associated with cancer, but which can still play an important role when present in cancer, because the presence of an EMT, even in early or partial form, indicates that cells have acquired stem-like properties (Mani et al, Cell, 133, 704-715, 2008), and therefore can be resistant to therapy and/or more likely to cause recurrence following treatment and inducing the surviving cancer cells to evolve into aggressive invasive tumors. Therefore, the decision as to which therapy can be used can be influenced by the presence of even a partial EMT. Furthermore, any therapeutic intervention that inhibits even this early or partial EMT can render additional traditional therapies more effective.
  • genes SNAI2, LUM, DCN, COL1A1, COL3A1, COL6A3 can serve as important biomarkers for (at least the early or partial form of) the SNAI2 -based EMT by themselves.
  • the partial SNAI2- based EMT signature was found to be expressed in normal tissues (Cheng et al,
  • the present invention provides for methods of treating a subject, such as, but not limited to, methods comprising performing a diagnostic method and then, if an EMT signature is detected in a sample of the subject, recommending that the patient undergo a further diagnostic procedure (e.g. an imaging procedure such as X-ray, ultrasound, computerized axial tomography (CAT scan) or magnetic resonance imaging (M I)), and/or recommending that the subject be administered therapy with an agent that inhibits invasion and/or metastasis.
  • a further diagnostic procedure e.g. an imaging procedure such as X-ray, ultrasound, computerized axial tomography (CAT scan) or magnetic resonance imaging (M I)
  • a diagnostic method is performed and a therapeutic decision is made in light of the results of that assay.
  • a therapeutic decision such as whether to prescribe neoadjuvant chemo- and/or immunotherapy prior to surgical or radiologic anti-tumor treatment can be made in light of the results of a diagnostic method as set for the above.
  • the results of the diagnostic method are relevant to the therapeutic decision as the presence of the EMT signature or a subset of markers associated with it, in a sample from a subject indicates a decrease in the relative benefit conferred by the neoadjuvant therapy to the subject since the presence of the EMT signature, or a subset of markers associated with it, is indicative of a cancer that is not localized.
  • a diagnostic method is performed and a decision regarding whether to continue a particular therapeutic regimen is made in light of the results of that assay. For example, but not by way of limitation, a decision whether to continue a particular therapeutic regimen, such as whether to continue with a particular chemotherapeutic, radiation therapy, and/or molecular targeted therapy (e.g., a cancer cell-specific antibody therapeutic) can be made in light of the results of a diagnostic method as set for the above.
  • the results of the diagnostic method are relevant to the decision whether to continue a particular therapeutic regimen as the presence of the EMT signature or a subset of markers associated with it, in a sample from a subject can be indicative of the subject's responsiveness to that therapeutic.
  • the high-specificity invasion and/or metastasis-sensing biomarker assay methods to be employed in conjunction with treatment include, but are not limited: to, nucleic acid amplification assays; nucleic acid hybridization assays; and protein detection assays.
  • the assays of the present invention involve combinations of such detection techniques, e.g., but not limited to: assays that employ both amplification and hybridization to detect a change in the expression, such as overexpression or decreased expression, of a gene at the nucleic acid level; immunoassays that detect a change in the expression of a gene at the protein level; as well as combination assays comprising a nucleic acid-based detection step and a protein-based detection step.
  • “Overexpression”, as used herein, refers to an increase in expression of a gene product relative to a normal or control value, which, in non-limiting embodiments, is an increase of at least about 30% or at least about 40% or at least about 50%, or at least about 100%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500%, or at least 1000%.
  • Decreased expression refers to an decrease in expression of a gene product relative to a normal or control value, which, in non- limiting embodiments, is an decrease of at least about 30% or at least about 40% or at least about 50%, at least about 90%, or a decrease to a level where the expression is essentially undetectable using conventional methods.
  • gene product refers to any product of transcription and/or translation of a gene. Accordingly, gene products include, but are not limited to, pre-mRNA, mR A, and proteins.
  • the present invention provides compositions and methods for the detection of gene expression indicative of all or part of the EMT signature in a sample using nucleic acid hybridization and/or amplification-based assays.
  • the genes/proteins within the EMT signature set forth herein, e.g., in Section 5.1 constitute at least 10 percent, or at least 20 percent, or at least 30 percent, or at least 40 percent, or at least 50 percent, or at least 60 percent, or at least 70 percent, or at least 80 percent, or at least 90 percent, of the genes/proteins being evaluated in a given assay.
  • the present invention provides compositions and methods for the detection of gene expression indicative of all or part of the EMT signature in a sample using a nucleic acid hybridization assay, wherein nucleic acid from said sample, or amplification products thereof, are hybridized to an array of one or more nucleic acid probe sequences.
  • an "array” comprises a support, preferably solid, with one or more nucleic acid probes attached to the support.
  • Preferred arrays typically comprise a plurality of different nucleic acid probes that are coupled to a surface of a substrate in different, known locations.
  • Arrays may generally be produced using a variety of techniques, such as mechanical synthesis methods or light directed synthesis methods that incorporate a combination of photolithographic methods and solid phase synthesis methods. Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. Nos. 5,384,261, and 6,040,193, which are incorporated herein by reference in their entirety for all purposes. Although a planar array surface is preferred, the array may be fabricated on a surface of virtually any shape or even a multiplicity of surfaces. Arrays may be nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate. See U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992.
  • the arrays of the present invention can be packaged in such a manner as to allow for diagnostic, prognostic, and/or predictive use or can be an all-inclusive device; e.g., U.S. Pat. Nos. 5,856,174 and 5,922,591.
  • the hybridization assays of the present invention comprise a primer extension step.
  • Methods for extension of primers from solid supports have been disclosed, for example, in U.S. Pat. Nos. 5,547,839 and 6,770,751.
  • methods for genotyping a sample using primer extension have been disclosed, for example, in U.S. Pat. Nos. 5,888,819 and 5,981 ,176.
  • the methods for detection of all or a part of the EMT signature in a sample involves a nucleic acid amplification-based assay.
  • assays include, but are not limited to: real-time PCR (for example see Mackay, Clin. Microbiol. Infect. 10(3): 190-212, 2004), Strand Displacement Amplification (SDA) (for example see Jolley and Nasir, Comb. Chem. High Throughput Screen. 6(3):235-44, 2003), self-sustained sequence replication reaction (3SR) (for example see Mueller et al., Histochem. Cell. Biol.
  • a PCR-based assay such as, but not limited to, real time PCR is used to detect the presence of an EMT signature in a test sample.
  • EMT signature-specific PCR primer sets are used to amplify EMT signature associated RNA and/or DNA targets.
  • Signal for such targets can be generated, for example, with fluorescence-labeled probes.
  • the fluorescence emission of the fluorophore can be, in certain embodiments, eliminated by a quenching molecule also operably linked to the probe nucleic acid.
  • probe binds to template strand during primer extension step and the nuclease activity of the polymerase catalyzing the primer extension step results in the release of the fluorophore and production of a detectable signal as the fluorophore is no longer linked to the quenching molecule.
  • fluorophore e.g., FAM, TET, or Cy5
  • quenching molecule e.g. BHQ1 or BHQ2
  • the present invention provides compositions and methods for the detection of gene expression indicative of all or part of the EMT signature in a sample by employing high throughput sequencing techniques, such as RNA-seq.
  • high throughput sequencing techniques such as RNA-seq.
  • Each of the adaptor-tagged molecules, with or without amplification, can then be sequenced in a high-throughput manner to obtain short sequences.
  • Virtually any high-throughput sequencing technology can be used for the sequencing step, including, but not limited to the Ulumina IG ® , Applied Biosystems SOLiD ® , Roche 454 Life Science ® , and Helicos Biosciences tSMS ® systems.
  • bioinformatics techniques can be used to either align there results against a reference genome or to assemble the results de novo. Such analysis is capable of identifying both the level of expression for each gene as well as the sequence of particular expressed genes.
  • the present invention provides compositions and methods for the detection of gene expression indicative of all or part of the EMT signature in a sample by detecting changes in concentration of the protein, or proteins, encoded by the genes of interest.
  • the present invention relates to the use of immunoassays to detect modulation of gene expression by detecting changes in the concentration of proteins expressed by a gene of interest. Numerous techniques are known in the art for detecting changes in protein expression via immunoassays.
  • antibody reagents capable of specifically interacting with a protein of interest are covalently or non-covalently attached to a solid phase.
  • Linking agents for covalent attachment are known and may be part of the solid phase or derivatized to it prior to coating.
  • solid phases used in immunoassays are porous and non-porous materials, latex particles, magnetic particles, microparticles, strips, beads, membranes, microliter wells and plastic tubes. The choice of solid phase material and method of labeling the antibody reagent are determined based upon desired assay format performance characteristics.
  • the antibody reagent used in an immunoassay is attached to a signal-generating compound or "label".
  • This signal- generating compound or "label” is in itself detectable or may be reacted with one or more additional compounds to generate a detectable product (see also U.S. Patent No. 6,395,472 Bl).
  • signal generating compounds include chromogens, radioisotopes ⁇ e.g., i25 L, m I, 32 P, 3 H, 3S S, and 14 C), fluorescent compounds ⁇ e.g., fluorescein and rhodamine), chemiluminescent compounds, particles (visible or fluorescent), nucleic acids, complexing agents, or catalysts such as enzymes ⁇ e.g., alkaline phosphatase, acid phosphatase, horseradish peroxidase, beta-galactosidase, and ribonuclease).
  • enzymes ⁇ e.g., alkaline phosphatase, acid phosphatase, horseradish peroxidase, beta-galactosidase, and ribonuclease.
  • enzymes ⁇ e.g., alkaline phosphatase, acid phosphatase, horseradish peroxidase, beta-galactosidase, and
  • sample from a subject to be tested according to one of the assay methods described herein may be at least a portion of a tissue, at least a portion of a tumor, a cell, a collection of cells, or a fluid (e.g., blood, cerebrospinal fluid, urine, expressed prostatic fluid, peritoneal fluid, a pleural effusion, peritoneal fluid, etc.).
  • a biopsy may be done by an open or percutaneous technique. Open biopsy is conventionally performed with a scalpel and can involve removal of the entire tumor mass (excisional biopsy) or a part of the tumor mass (incisional biopsy).
  • Percutaneous biopsy in contrast, is commonly performed with a needle-like instrument either blindly or with the aid of an imaging device, and may be either a fine needle aspiration (FNA) or a core biopsy.
  • FNA biopsy individual cells or clusters of cells are obtained for cytologic examination.
  • core biopsy a core or fragment of tissue is obtained for histologic examination which may be done via a frozen section or paraffin section.
  • the assay methods described herein can be employed to detect the presence of the EMT signature in cancer and non-cancer cells.
  • the assay methods described herein can be employed to detect the presence of the EMT signature in cancer.
  • such cancers can include those involving the presence of solid tumors.
  • such cancers can include epithelial cancers.
  • such cancers can include non-epithelial cancers.
  • such epithelial and non-epithelial cancers can include, for example, but not by way of limitation, cancers of the ovary, stomach, pancreas, duodenum, liver, colon, breast, vagina, cervix, prostate, lung, testicle, oral cavity, esophagus, as well as neuroblastoma and Ewing's sarcoma.
  • the present invention is directed to assay methods allowing for diagnostic, prognostic, and/or predictive use of the EMT signature.
  • the assay methods described herein can be used in a diagnostic context, e.g., where a cell undergoing an EMT can be identified or where invasive cancer can be diagnosed by detecting all or part of the EMT signature in a sample.
  • the assay methods described herein can be used in a prognostic context, e.g., where detection of all or part of the EMT signature allows for an assessment of the likelihood of future EMT or future metastasis, including in those situations where such metastasis is not yet identified.
  • the assay methods described herein can be used in predictive context, e.g., where detection of all or part of the EMT signature allows for an assessment of the likely benefit of certain types of therapy, such as, but not limited to, neoadjuvant therapy, surgical resection, and/or chemotherapy.
  • the markers and assay methods of the present invention can be used to determine whether a cancer in a subject has progressed to a invasive and/or metastatic form, or has remitted (for example, in response to treatment).
  • the markers and assay methods of the present invention can be used to stage a cancer (where clinical staging considers whether invasion has occurred). Such multi-cancer staging is possible due to the fact that the EMT signature is present in a variety of cancers as a marker of invasion and the acquisition of such invasive quality correlates with the cancer having achieved a particular stage.
  • the markers and assay methods of the present invention can be used to identify when breast carcinoma in situ becomes invasive, which correlates with the carcinoma achieving stage I.
  • the markers and assay methods of the present invention can be used to identify when ovarian cancer becomes invasive, which correlates with the cancer achieving stage ⁇ , and more particularly, stage nic.
  • the markers and assay methods of the present invention can be used to identify when colorectal cancer becomes invasive, which correlates with the cancer achieving stage ⁇ . In alternative embodiments, the markers and assay methods of the present invention can be used to identify when a neuroblastoma becomes invasive, which correlates with the neuroblastoma having progressed beyond stage I.
  • the EMT signature, or a subset of markers associated with it can be used to evaluate the contextual (relative) benefit of a therapy in a subject. For example, if a therapeutic decision is based on an assumption that a cancer is localized in a subject, the presence of the EMT signature, or a subset of markers associated with it, would suggest that the cancer is invasive.
  • the relative benefit, to a subject with a malignant tumor, of neoadjuvant chemo- and/or immuno-therapy prior to surgical or radiologic anti-tumor treatment can be assessed by detennining the presence of the EMT signature or a subset of markers associated with it, where the presence of the EMT signature or a subset of markers associated with it, is indicative of a decrease in the relative benefit conferred by the neoadjuvant therapy to the subject.
  • the assays of the present invention are capable of detecting coordinated modulation of expression, for example, but not limited to, overexpression, of the genes associated with the EMT signature.
  • detection involves, but is not limited to, detection of the expression of SNAI2, LUM, and DCN.
  • detection involves, but is not limited to, detection of the expression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following proteins: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3.
  • the method further comprises a step of detecting FABP4 expression, wherein altered FABP4 expression, i.e., either an increase or decrease in FABP4 expression, is indicative of EMT.
  • a sample from a subject either diagnosed with a cancer or who is being evaluated for the presence or stage of cancer may be tested for the presence of EMT genes and/or overexpression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3; as well as one or more or two or more or three or more of the following: COL1 1 Al, THBS2, COL5A2, COL5A1, VCAN, FN1, SULF1, FBN1, ASPN, SPARC, CTSK, MMP2, BGN, LO
  • SNAI1 expression is not altered (in addition, in certain non-limiting embodiments, the SNAI1 gene is methylated).
  • overexpression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following proteins: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3, but not SNAI1, is indicative of a diagnosis of cancer having invasive and/or metastatic progression.
  • the method further comprises a step of detecting FABP4 expression, wherein altered FABP4 expression, i.e., either an increase or decrease in FABP4 expression, is indicative of EMT.
  • a high-specificity invasion-sensing biomarker assay of the present invention detects overexpression of SNAI2.
  • the high-specificity invasion-sensing biomarker assay detects coordinated overexpression of SNAI2, LUM, and DCN. In certain embodiments the high-specificity invasion-sensing biomarker assay detects coordinated overexpression of SNAI2, LUM, DCN, COL1A1 , COL1A2, COL3A1, and COL6A3.
  • the high-specificity invasion-sensing biomarker assay detects coordinated overexpression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following proteins: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3, but not SNAI1 ; as well as one or more or two or more or three or more of the following: COL11A1, THBS2, COL5A2, COL5A1 , VCAN, FN1 , SULF1, FBN1, ASPN, SPARC, CTSK, MMP2, BGN, LOXL2, ⁇ 3, CDH11, SERPINF1, EDNRA, ACTA2, PDGFRB, LGALS1, GLT8D2, NID2, PRRX1, and VIM.
  • the high-specificity invasion-sensing biomarker assay detects coordinated overexpression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following proteins: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3, in combination with differential expression of one or more microR As selected from the group consisting of: miR-214, miR-199a, and miR-199b.
  • the high-specificity invasion-sensing biomarker assay detects coordinated overexpression of at least one of, at least two of, at least three of, at least four of, or at least five, at least six, or at least all seven of the following proteins: SNAI2, LUM, DCN, COL1A1, COL1A2, COL3A1, and COL6A3, in combination with differential expression of one or more microRNAs selected from the group consisting of: hsa-miR-22; hsa-miR-514-l/hsa-miR-514- 2
  • the present invention also relates to the discovery that the modulation of particular microRNAs can be employed to inhibit a mesenchymal transition that, in certain instances, correlates with resistance to therapy and recurrence as the corresponding cells acquire properties of stem cells as they start undergoing this transition, as well as with invasiveness, e.g., invasion of certain cells of primary tumors into adjacent connective tissue during the initial phase of metastasis.
  • the identification inhibitors of this mechanism such as inhibitors of certain microRNAs, disclosed herein, can be used for inhibiting the mesenchymal transition to reduce the invasive nature of certain cells of primary cancerous tumors and, in certain instances, to prevent the recurrence of cancer by inhibiting the induction of stem cell-like features in certain cancer cells.
  • EMT signature (as being strongly correlated with COL1 1A1 in solid cancers) were investigated in the presence of additional publicly available cancer datasets, and are shown to correlate with the expression of SNAI2 and the other genes of the signature even in nonsolid cancers. Indeed, the following microRNAs: miR-214, miR-199a, miR-199b, miR-409, and miR-134 were found to be consistently positively co- expressed with the genes of the signature, while miR-200a, miR-200b, and miR-192 were found to be consistently negatively associated with the genes of the signature.
  • micro RNAs can not only serve as biomarkers for, in certain embodiments, the full or partial form of the SNAI2-based EMT by themselves, but also, as disclosed herein, as targets for therapeutic intervention.
  • MicroR As, such as miR-214, miR-199a, miR-199b, miR-409, miR-
  • miR-200a, miR-200b, and miR-192 are produced, depending on the specific species of microRNA, from either their own genes or from introns.
  • MicroRNAs are initially transcribed as either a pri-miRNA (when transcribed from their own genes) or as pre-mRNA (when present in an intron of a pre-mRNA molecule) molecules. These miRNA-containing molecules are first processed to produce a pre-miRNA hairpin precursor molecule, which is further processed to produce mature microRNA molecules, including the mature microRNA sequences identified in Table 1.
  • microRNA is intended to encompass pri-miRNA, pre-miRNA, and mature microRNAs
  • miR-214 is intended to encompass miR-214 in all of its precursor and mature forms, including, but not limited to pre-miR-214, miR- 214-5p and miR-214-3p.
  • therapeutic interventions that modulate the expression and/or activity of microRNAs may exert their effect by modulating the expression and/or activity at any level (e.g., pri-miRNA, pre-miRNA, and/or mature microRNA).
  • the present invention is directed to the inhibition of a mesenchymal transition that correlates with the expression of the EMT signature described herein, wherein such inhibition is achieved by appropriately modulating the expression and/or activity of one or more of the following microRNAs: miR-214, miR-199a, miR-199b, miR-409, miR-134, miR-200a, miR- 200b, and miR-192.
  • the expression and/or activity of the following microRNAs would be independently or coordinately reduced: miR-214, miR-199a, miR-199b, miR-409, and miR-134, while the expression and/or activity of the following microRNAs would be independently or coordinately increased: miR-200a, miR-200b, and miR-192.
  • such inhibition can be achieved by independently or coordinately reducing the expression and/or activity of miR-214, miR-199a, and miR-199b.
  • the present invention is directed to the inhibition of cancers cells acquiring a resistance to therapy and/or increased likelihood of recurrence as the cancer cells acquire properties of stem cells, where the acquisition of such properties correlates with the expression the EMT signature described herein.
  • such inhibition can be achieved by appropriately modulating the expression and/or activity of one or more of the following microRNAs: miR-214, miR-199a, miR-199b, miR-409, miR-134, miR- 200a, miR-200b, and miR-192.
  • the expression and/or activity of the following microRNAs would be independently or coordinately reduced: miR-214, miR-199a, miR-199b, miR-409, and miR-134, while the expression and/or activity of the following microRNAs would be independently or coordinately increased: miR-200a, miR-200b, and miR-192.
  • such inhibition can be achieved by independently or coordinately reducing the expression and/or activity of miR-214, miR-199a, and miR-199b.
  • the present invention is directed to the inhibition of invasiveness, e.g., invasion of certain cells of primary tumors into adjacent connective tissue during the initial phase of metastasis, which correlates with the expression of the EMT signature described herein.
  • invasiveness e.g., invasion of certain cells of primary tumors into adjacent connective tissue during the initial phase of metastasis
  • such inhibition can be achieved by appropriately modulating the expression and/or activity of one or more of the following microRNAs: miR-214, miR-199a, miR-199b, miR-409, miR-134, miR-200a, miR-200b, and miR-192.
  • the expression and/or activity of the following microRNAs would be independently or coordinately reduced: miR-214, miR-199a, miR-199b, miR-409, and miR-134, while the expression and/or activity of the following microRNAs would be independently or coordinately increased: miR- 200a, miR-200b, and miR-192.
  • such inhibition can be achieved by independently or coordinately reducing the expression and/or activity of miR-214, miR-199a, and miR-l99b.
  • microRNA expression and/or activity can be reduced by administration of antisense molecules capable of binding to the miRNA of interest and thereby inhibiting the activity of the microRNA.
  • RNAi or catalytic RNA molecules can be designed such that they are capable of specifically binding the microRNA of interest and thereby inducing the destruction of that microRNA.
  • Exemplary techniques for increasing expression and/or activity of microRNAs include, but are not limited to, direct administration of the microRNA of interest, the introduction of a transgene capable of expressing the microRNA of interest, and influencing the expression and/or activity of the endogenous microRNA coding sequence.
  • Certain embodiments of the present invention comprise coupling one or more of the above-described techniques for modulating microRNA expression and/or activity with an initial diagnostic step whereby the above-described EMT signature is identified.
  • the technique for modulation microRNA expression and/or activity is followed by one or more subsequent diagnostic steps to monitor an increase or decrease in the presence of the EMT signature.
  • an initial diagnostic step is not performed, and only the one or more subsequent diagnostic steps are performed.
  • Certain embodiments of the present invention comprise coupling one or more of the above-described techniques for modulating microRNA expression and/or activity with an one or more additional techniques for modulating microRNA expression and/or activity.
  • a techniques for reducing the expression and/or activity for one or more of miR-214, miR-199a, miR- 199b, miR-409, and miR-134 can be coupled to a technique for increasing the expression and/or activity of one or more of miR-200a, miR-200b, and miR-192.
  • such combinations of techniques for modulating the expression and/or activity of the specified microRNAs can be practiced in concert with an initial diagnostic step whereby the above-described EMT signature is identified.
  • the techniques for modulation microRNA expression and/or activity is followed by one or more subsequent diagnostic steps to monitor an increase or decrease in the presence of the EMT signature.
  • an initial diagnostic step is not performed, and only the one or more subsequent diagnostic steps are performed.
  • the methods of the instant invention will make use of the fact that certain microRNAs are coordinately expressed via their genomic locations.
  • miR-199a2 and miR-214 are located in the same transcript within an intron of a protein coding gene (dynamin-3), while miR-199al and miR-199b are located in other genomic regions, but still within introns of the protein coding genes of the dynamin family, although not necessarily on the coding strand (i.e., microRNAs may be present on non-coding, opposite strand, sequences).
  • the miR-199a2/214 cluster has previously been associated with the EMT-inducing transcription factor Twist and these two microRNAs are regulated as a cluster within the human DNM30S gene (Lee et al, Nucleic Acids
  • microRNAs e.g., miR-199a2 and miR-214 can be achieved in a coordinated manner by inhibiting the expression and/or activity of the single transcript containing both sequences. In certain of such embodiments such inhibition is achieved via the introduction of antisense, RNAi, and/or catalytic nucleic acid inhibitors of one or more of the dynamin family coding sequences.
  • the present invention relates to methods of inhibiting the expression and/or activity of certain microRNAs, including miR-214, miR-199a, miR-199b, miR-409, and miR-134 using antisense oligonucleotides.
  • the miR-214, miR-199a, miR-199b, miR-409, and miR-134 inhibitors are antisense oligonucleotides targeting the mature miR-214, miR- 199a, miR-199b, miR-409, and miR-134 sequences.
  • the antisense oligonucleotides can be ribonucleotides or deoxyribonucleotides.
  • the antisense oligonucleotides have at least one chemical modification.
  • suitable antisense oligonucleotides can be comprised of one or more "conformationaUy constrained” or bicyclic sugar nucleoside modifications, for example, “locked nucleic acids” (LNAs).
  • LNAs are modified ribonucleotides that contain a bridge between the 2' and 4' carbons of the ribose sugar moiety resulting in a "locked” conformation that confers enhanced thermal stability to oligonucleotides containing the LNAs.
  • the antisense oligonucleotides targeting miR-214, miR-199a, miR- 199b, miR-409, and miR-134 can contain combinations of LNAs or other modified nucleotides and ribonucleotides or deoxyribonucleotides.
  • the antisense oligonucleotides can comprise peptide nucleic acids (PNAs), which contain a peptide- based backbone rather than a sugar-phosphate backbone.
  • PNAs peptide nucleic acids
  • Other chemical modifications that the antisense oligonucleotides can contain include, but are not limited to, sugar modifications, such as 2'-0-alkyl (e.g.
  • antisense oligonucleotides particularly those of shorter lengths (e.g., less than 15 nucleotides) can comprise one or more affinity enhancing modifications, such as, but not limited to, LNAs, bicyclic nucleosides, phosphonoformates, 2' O alkyl and the like.
  • antisense oligonucleotides useful in connection with the instant invention are 2'-0-methoxyethyl "gapmers" which contain 2'-0-methoxyethyl- modified ribonucleotides on both 5' and 3' ends with at least ten deoxyribonucleotides in the center. These "gapmers” are capable of triggering R ase H-dependent degradation mechanisms of RNA targets.
  • Other modifications of antisense oligonucleotides to enhance stability and improve efficacy such as those described in U.S. Pat. No. 6,838,283, which is herein incorporated by reference in its entirety, are known in the art and are suitable for use in the methods of the invention.
  • the antisense oligonucleotides useful for inhibiting the activity of miRNAs miR-214, miR-199a, miR-199b, miR-409, and miR-134 are about 5 to about 50 nucleotides in length, about 10 to about 30 nucleotides in length, or about 20 to about 25 nucleotides in length. In certain embodiments, antisense oligonucleotides targeting miR-214, miR-199a, miR-199b, miR-409, and miR-134 are about 8 to about 18 nucleotides in length, and in other embodiments about 12 to 16 nucleotides in length.
  • any 8-mer or longer that is complementary to miR-214, miR-199a, miR- 199b, miR-409, or miR-134 can be used, i.e., any antimir sequence that is complementary to any consecutive sequence in miR-214, miR-199a, miR-199b, miR- 409, or miR-134, starting from the 5' end of the miR to the 3' end of the mature sequence.
  • Antisense oligonucleotides can, in certain non-limiting cases, comprise a sequence that is at least partially complementary to a mature miRNA sequence, e.g.
  • the antisense oligonucleotide can be substantially complementary to a mature miRNA sequence, that is at least about 95%, 96%, 97%, 98%, or 99% complementary to a target sequence. In certain embodiments, the antisense oligonucleotide comprises a sequence that is 100% complementary to a mature miRNA sequence.
  • the antisense oligonucleotides useful in the instant methods can comprise a sequence that is substantially complementary to a precursor miRNA sequence (pre-miR A) for miR-214, miR-199a, miR-199b, miR- 409, or miR-134.
  • the antisense oligonucleotide comprises a sequence that is substantially complementary to a sequence located outside the stem- loop regions of the miR-214, miR-199a, miR-199b, miR-409, or miR-134 pre-miRNA sequences.
  • any of the inhibitors of miR-214, miR-199a, miR-199b, miR-409, and miR-134 described herein can be delivered to the target cell by delivering to the cell one or more expression vectors encoding one or more of the miR-214, miR-199a, miR-199b, miR-409, and miR-134 inhibitors.
  • a "vector” is a composition of matter which can be used to deliver a nucleic acid of interest to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses.
  • the term “vector” includes an autonomously replicating plasmid or a virus.
  • viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and the like.
  • An expression construct can be replicated in a living cell, or it can be made synthetically.
  • the terms "expression construct,” “expression vector,” and “vector,” are used interchangeably to demonstrate the application of the invention in a general, illustrative sense, and are not intended to limit the invention.
  • the expression vector is suitable for gene therapy of mammals, including gene therapy of humans.
  • the nucleic acid construct according to the invention is a viral gene therapy vector.
  • Viral gene therapy vectors are well known in the art and e.g. include vectors based on an adenovirus, and members of the Parvoviridae family, such as an adeno-associated virus (AAV), or a herpes virus, pox virus or retrovirus.
  • AAV adeno-associated virus
  • the viral gene therapy vector is an AAV, adenoviral or a lentiviral vector (see e.g., Gentner et al., Nature Methods 6, 63 - 66 (2009)).
  • RNA interference refers to the biological process of inhibiting or down regulating gene expression and/or activity in a cell, as is generally known in the art, and which is mediated by short interfering nucleic acid molecules, (see e.g., example Zamore and Haley, 2005, Science, 309, 1519-1524; Vaughn and Martienssen, 2005, Science, 309, 1525-1526; Zamore et al., 2000, Cell, 101, 25-33; Bass, 2001, Nature, 41 1 , 428-429; Elbashir et al., 2001, Nature, 41 1, 494-498; and reutzer et al., International PCT Publication No.
  • RNAi is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, transcriptional inhibition, or epigenetics.
  • siRNA molecules of the invention can be used to epigenetically silence genes at either the post-transcriptional level or the pre- transcriptional level.
  • epigenetic modulation of gene expression by siRNA molecules of the invention can result from siRNA mediated modification of chromatin structure or methylation patterns to alter gene expression (see, for example, Verdel et al., 2004, Science, 303, 672-676; Pal-Bhadra et al., 2004, Science, 303, 669-672; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237).
  • modulation of gene expression and/or activity by siRNA molecules of the invention can result from siRNA mediated cleavage of RNA (either coding or non-coding RNA) via RISC, or via translational inhibition, as is known in the art or modulation can result from transcriptional inhibition (see. e.g., Janowski et al., 2005, Nature Chemical Biology, 1, 216-222).
  • the phrase "short interfering RNA" or “siRNA” refer to any nucleic acid molecule capable of inhibiting or down regulating gene expression and/or activity by mediating RNA interference "RNAi" or gene silencing in a sequence- specific manner.
  • the siRNA can be a double-stranded nucleic acid molecule comprising self-complementary sense and antisense strands, wherein the antisense strand comprises a nucleotide sequence that is complementary to a nucleotide sequence of miR-214, miR-199a, miR-199b, miR-409, or miR-134 or a portion thereof and the sense strand comprises a nucleotide sequence corresponding to the miR-214, miR-199a, miR-199b, miR-409, or miR-134 sequence or a portion thereof.
  • the siRNA can be a polynucleotide with a duplex, asymmetric duplex, hairpin or asymmetric hairpin secondary structure, having self- complementary sense and antisense regions, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of miR-214, miR-199a, miR-199b, miR-409, or miR-134 or a portion thereof and the sense region comprises a nucleotide sequence corresponding to the sequence of miR-214, miR- 199a, miR-199b, miR-409, or miR-134 or a portion thereof.
  • each strand, the sense strand and antisense strand are independently about 15 to about 40 (e.g., about 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 in length.
  • the antisense region or strand of the molecule is about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length, wherein the sense region is about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, or 25) nucleotides in length.
  • siRNA molecules of the invention have 100% complementarity between the sense strand or sense region and the antisense strand or antisense region of the siRNA molecule.
  • siNA molecules of the invention are perfectly complementary to the sequence of miR-214, miR-199a, miR-199b, miR-409, or miR-134 or a portion thereof.
  • the siRNA molecules of the invention have partial complementarity (i.e., less than 100% complementarity) between the sense strand or sense region and the antisense strand or antisense region of the siR A molecule or between the antisense strand or antisense region of the siRNA molecule and the sequence of miR- 214, miR-199a, miR-199b, miR-409, or miR-134 or a portion thereof.
  • the double-stranded nucleic acid molecules of the invention have between about 15 to about 40 (e.g., about 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 in one strand that are complementary to the nucleotides of the other strand.
  • about 15 to about 40 e.g., about 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
  • the molecules have between about 15 to about 40 (e.g., about 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 in the sense region that are complementary to the nucleotides of the antisense region of the double-stranded nucleic acid molecule.
  • the double- stranded nucleic acid molecules of the invention have between about 15 to about 40 (e.g., about 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 in the antisense strand that are complementary to a nucleotide sequence of the sequence of miR-214, miR-199a, miR-199b, miR-409, or miR-134 or a portion thereof.
  • the siRNA molecules of the instant invention can comprise one or more modified nucleotides.
  • the modified siRNA molecules of the invention can comprise modifications at various locations within the siRNA molecule.
  • the double-stranded siRNA molecule of the invention comprises modified nucleotides at internal base paired positions within the siRNA duplex.
  • a double-stranded siRNA molecule of the invention comprises modified nucleotides at non-base paired or overhang regions of the siRNA molecule.
  • a double-stranded siRNA molecule of the invention comprises modified nucleotides at terminal positions of the siRNA molecule.
  • such terminal regions include the 3'-position and/or 5 1 - position of the sense and/or antisense strand or region of the siRNA molecule.
  • any of the modified siRNA molecules of the invention can have a modification in one or both oligonucleotide strands of the siRNA duplex, for example in the sense strand, the antisense strand, or both strands.
  • each strand of the double-stranded siRNA molecules of the invention can have one or more chemical modifications, such that each strand comprises a different pattern of chemical modifications.
  • the present invention relates to methods of inhibiting the expression and/or activity of certain microRNAs, including miR-214, miR-199a, miR-199b, miR-409, and miR-134, using catalytic nucleic acids.
  • catalytic nucleic acids includes DNA and RNA molecules that have complementarity in a target-binding region to a specified oligonucleotide target, such as miR-214, miR-199a, miR-199b, miR-409, and/or miR-134, and an enzymatic activity which is active to specifically cleave the oligonucleotide target.
  • catalytic nucleic acids molecules are capable of cleaving the oligonucleotide target, such as miR-214, miR-199a, miR-199b, miR-409, and/or miR-134, intermolecularly.
  • This complementarity functions to allow sufficient hybridization of the catalytic nucleic acid to the target to allow the intermolecular cleavage of the target to occur.
  • catalytic nucleic acid encompasses enzymatic RNA or DNA molecules, enzymatic RNA-DNA polymers, and enzymatically active portions or derivatives thereof.
  • the catalytic nucleic acid molecules of the present invention can be of varying lengths and folding patterns, as appropriate, depending on the type and function of the molecule.
  • catalytic nucleic acid molecules may be about 15 to about 400 or more nucleotides in length.
  • the catalytic nucleic acid molecule of the present invention is between about 20 and 100 nucleotides, or 20 and 50 nucleotides, or 25 and 45 nucleotides in length.
  • the catalytic nucleic acid molecules of the instant invention can comprise one or more modified nucleotides.
  • the target-binding or "recognition" domain of a catalytic nucleic acid molecule of the present invention typically comprises two nucleotide sequences flanking a catalytic domain, and typically contains a sequence of at least about 3 to about 30 bases, or about 6 to about 15 bases, which are capable of hybridizing to a complementary sequence of bases within the target nucleic acid giving the enzymatic DNA molecule its high sequence specificity. Modification or mutation of the recognition site via well-known methods allows one to alter the sequence specificity of an enzymatic nucleic acid molecule. (See Joyce et al, Nucleic Acids Res., 17:71 1-712, (1989), which is hereby incorporated by reference in its entirety).
  • Non-limiting examples of catalytic domains that can be used in the context of the catalytic nucleic acid molecules of the instant invention include catalytic domains derived from hairpin ribozymes, hammerhead ribozymes, group I intron ribozymes, ribonuclease P and hepatitis delta virus ribozymes.
  • Specific catalytic domain sequences and techniques for incorporation of such domains into catalytic nucleic acid molecules are well known in the art. (See, e.g., Sun et ah, Therapeutic Use Of Catalytic RNA And DNA, Pharmacol Rev, 52:325-347, (2000), which is hereby incorporated by reference in its entirety.)
  • the present invention relates to methods of increasing the expression and/or activity of certain microRNAs, including: miR-200a, miR-200b, and/or miR-192.
  • the agonist of miR- 200a, miR-200b, and/or miR-192 are polynucleotides encoding a mature miR-200a, miR-200b, and/or miR-192 sequences.
  • the agonist of miR- 200a, miR-200b, and/or miR-192 can be a polynucleotide comprising the pre-miRNA sequence for miR-200a, miR-200b, and/or miR-192.
  • the agonist of miR-200a, miR-200b, and/or miR-192 can be separate polynucleotides each comprising a mature sequence or pre-miRNA sequence of the miRNA.
  • the polynucleotide comprising the mature miR-200a, miR-200b, and/or miR-192 sequence can be single stranded or double stranded.
  • the polynucleotides can contain one or more chemical modifications, such as locked nucleic acids, peptide nucleic acids, sugar modifications, such as 2 -O-alkyl (e.g.
  • the polynucleotide comprising a miR-200a, miR-200b, and/or miR-192 sequence is conjugated to another moiety, such as, but not limited to, cholesterol.
  • the agonist of miR-200a, miR-200b, and/or miR-192 can be encoded on an expression vector.
  • An expression vector for expressing miR-200a, miR-200b, and/or miR-192 comprises at least one promoter operably linked to a polynucleotide encoding miR-200a, miR-200b, and/or miR-192.
  • the polynucleotides encoding the one or more miRNA sequences can encode pre- miRNA or mature rniRNA sequence(s).
  • a nucleic acid construct such as an expression vector, comprising a microRNA agonist of the invention is operably linked to a mammalian cell-compatible expression control sequence, e.g., a promoter.
  • a mammalian cell-compatible expression control sequence e.g., a promoter.
  • a promoter e.g., a promoter that are known in the art.
  • Constitutive promoters that are broadly expressed in many cell types, such as the CMV promoter can be used.
  • promoters that are inducible, tissue-specific, cell-type-specific, or cell cycle-specific can also be used.
  • the present invention relates to nucleic acid constructs comprising a nucleotide sequence encoding an microRNA agonist operably linked to an expression control sequence as defined herein above, wherein the construct is an expression vector that is suitable for gene therapy of mammals, including gene therapy of humans.
  • the nucleic acid construct according to the invention is a viral gene therapy vector.
  • Viral gene therapy vectors are well known in the art and e.g. include vectors based on an adenovirus, and members of the Parvoviridae family, such as an adeno-associated virus (AAV), or a herpes virus, pox virus or retrovirus.
  • the viral gene therapy vector is an AAV, adenoviral or a lentiviral vector, (see e.g., Gentner et al., Nature Methods 6, 63 - 66 (2009). 5.2.3 Pharmaceutical Compositions For Modulating EMT-Related microRNA Activity
  • the present invention also includes pharmaceutical compositions comprising an inhibitor of miR-214, miR-199a, miR-199b, miR-409, or miR-134 or agonist of miR-200a, miR-200b, or miR-192.
  • pharmaceutical compositions will be prepared in a form appropriate for the intended application. Generally, this will entail preparing compositions that are essentially free of pyrogens, as well as other impurities that could be harmful to humans or animals.
  • the pharmaceutical composition comprises an effective dose of a miR-214, miR-199a, miR-199b, miR-409, or miR-134 inhibitor. In another embodiment, the pharmaceutical composition comprises an effective dose of a miR-200a, miR-200b, and/or miR-1 2 agonist.
  • An "effective dose” is an amount sufficient to effect a beneficial or desired clinical result.
  • An effective dose of an miRNA inhibitor or miRNA agonist of the invention can be about 1 mg/kg to about 200 mg/kg, about 20 mg/kg to about 160 mg/kg, or about 40 mg/kg to about 100 mg/kg.
  • the inhibitor of miR-214, miR-199a, miR-199b, miR-409, or miR-134 is administered each at a dosage of about 20 mg/kg to about 200 mg/kg. In another embodiment, the inhibitor of miR-214, miR-199a, miR-199b, miR-409, or miR-134 is administered each at a dosage of about 80 mg/kg. In another embodiment, the agonist of miR-200a, miR-200b, or miR-192 is administered each at a dosage of about 20 mg/kg to about 200 mg/kg. In still another embodiment, the agonist of miR- 200a, miR-200b, or miR-192 is administered each at a dosage of about 80 mg/kg.
  • Colloidal dispersion systems such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes, can be used as delivery vehicles for the oligonucleotide inhibitors of miRNA function, polynucleotides encoding miRNA agonists, or constructs expressing particular miRNA inhibitors or agonists.
  • Commercially available fat emulsions that are suitable for delivering the nucleic acids of the invention include IntralipidTM, LiposynTM, LiposynTM ⁇ , LiposynTM III, Nutrilipid, and other similar lipid emulsions.
  • a preferred colloidal system for use as a delivery vehicle in vivo is a liposome (i.e., an artificial membrane vesicle).
  • a liposome i.e., an artificial membrane vesicle.
  • the preparation and use of such systems is well known in the art.
  • Exemplary formulations are also disclosed in U.S. Pat. No. 5,981,505; U.S. Pat. No. 6,217,900; U.S. Pat. No. 6,383,512; U.S. Pat. No. 5,783,565; U.S. Pat. No. 7,202,227; U.S. Pat. No. 6,379,965; U.S. Pat. No. 6,127,170; U.S. Pat. No. 5,837,533; U.S. Pat. No. 6,747,014; and WO03/093449, which are herein incorporated by reference in their entireties.
  • Aqueous compositions of the present invention comprise an effective amount of the delivery vehicle comprising the inhibitor polynucleotides or miRNA polynucleotide sequences (e.g. liposomes or other complexes or expression vectors) dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium.
  • pharmaceutically acceptable or “pharmacologically acceptable” refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human.
  • pharmaceutically acceptable carrier includes solvents, buffers, solutions, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like acceptable for use in formulating pharmaceuticals, such as pharmaceuticals suitable for administration to humans.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredients of the present invention, its use in therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions, provided they do not inactivate the vectors or polynucleotides of the compositions.
  • the active compositions of the present invention can include classic pharmaceutical preparations. Administration of these compositions according to the present invention can be via any common route so long as the target tissue is available via that route. This includes oral, nasal, or buccal. Alternatively, administration can be by intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. Pharmaceutical compositions comprising miRNA inhibitors, polynucleotides encoding miRNA sequence or expression constructs comprising miRNA sequences can also be administered by catheter systems. The active compounds can also be administered parenterally or intraperitoneally. By way of illustration, solutions of the active compounds as free base or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose.
  • a surfactant such as hydroxypropylcellulose.
  • Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations generally contain a preservative to prevent the growth of microorganisms.
  • the pharmaceutical forms suitable for injectable use or catheter delivery include, for example, sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. Generally, these preparations are sterile and fluid to the extent that easy injectability exists. Preparations should be stable under the conditions of manufacture and storage and should be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • Appropriate solvents or dispersion media can contain, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • the prevention of the action of microorganisms can be brought about by various antibacterial an antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compounds in an appropriate amount into a solvent along with any other ingredients (for example as enumerated above) as desired, followed by filtered sterilization.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the desired other ingredients, e.g., as enumerated above.
  • the preferred methods of preparation include vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient(s) plus any additional desired ingredient from a previously sterile- filtered solution thereof.
  • compositions of the present invention generally can be formulated in a neutral or salt form.
  • Pharmaceutically-acceptable salts include, for example, acid addition salts (formed with the free amino groups of the protein) derived from inorganic acids ⁇ e.g., hydrochloric or phosphoric acids, or from organic acids ⁇ e.g., acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups of the protein can also be derived from inorganic bases (e.g., sodium, potassium, ammonium, calcium, or ferric hydroxides) or from organic bases (e.g., isopropylamine, trimethylamine, histidine, procaine and the like. 5.2.4. Assays For Use In Connection With Anti-microRNA
  • the present invention provides for methods of treating a subject, such as, but not limited to, methods comprising performing a diagnostic method as set forth herein and then, if an EMT signature is detected in a sample of the subject, and administering therapy with a microRNA expression/activity modulator.
  • one or more of the diagnostic methods set forth above, in Section 5.2.1 is performed and a therapeutic decision concerning the use of an anti-microRNA therapeutic approach is made in light of the results of that assay.
  • a therapeutic decision such as whether to prescribe a therapeutic such as those outlined in Sections 5.2.2. - 5.2.3.
  • the results of the diagnostic method are relevant to the therapeutic decision as the presence of the EMT signature or a subset of markers associated with it, in a sample from a subject can, in certain embodiments, indicate a decrease in the relative benefit conferred by a particular therapeutic intervention
  • the high-specificity invasion and/or metastasis-sensing biomarker assay methods for use in connection with the therapeutic interventions discussed herein include, but are not limited to, the nucleic acid amplification assays; nucleic acid hybridization assays; and protein detection assays that employ the EMT biomarkers discussed in detail in Section 5.2.1.
  • the assays of the present invention involve combinations of such detection techniques, e.g., but not limited to: assays that employ both amplification and hybridization to detect a change in the expression, such as overexpression or decreased expression, of a gene at the nucleic acid level; immunoassays that detect a change in the expression of a gene at the protein level; as well as combination assays comprising a nucleic acid-based detection step and a protein-based detection step.
  • Example 1 The aim of the following work is to exemplify that modulation of the expression and/or activity of certain microRNAs can inhibit EMT.
  • xenograft models employing human cancer cell lines are implanted into NCR nude mice. Certain of the implanted cancer cell lines are in their original form, while others are engineered to express specific microRNAs (thereby increasing the expression and/or activity of such microRNAs), and still others are engineered to express antisense oligonucleotides targeted to specific microRNAs (thereby decreasing the expression and/or activity of such microRNAs).
  • Each of the resulting growing tumors is harvested and profiled for gene expression using microarrays, as outlined below.
  • NGP neuroblastoma cells are stably co-transfected with one or more expression vectors capable of independently or coordinately expressing one or more of miR-200a, miR-200b, and/or miR-192.
  • NGP neuroblastoma cells are stably co-transfected with one or more expression vectors capable of independently or coordinately expressing one or more antisense oligonucleotides capable of inhibiting the expression and/or activity of miR-214, miR-199a, miR-199b, miR-409, and/or miR-134.
  • the left flank of each mouse is prepared in a sterile manner after anesthetizing the mice with intraperitoneal ketamine (50 mg/kg) and xylazine (5 mg/kg).
  • An incision is made exposing the left kidney, and an inoculum of 10 6 NGP tumor cells expressing the particular microR A or antisense molecule or control NGP cells suspended in 0.1 mL of phosphate-buffered saline (PBS) is injected with a 25- gauge needle.
  • PBS phosphate-buffered saline
  • the fascia is closed with a single 4-0 polysorb suture (US Surgical Corp, Norwalk, CT). Mice are sacrificed when estimated tumor weight reaches 1.5 g followed by collection of contralateral kidney and tumor.
  • Tumor tissue is either snap frozen for RNA isolation or fixed in freshly prepared 4% paraformaldehyde for histology. Paraformaldehyde-fixed specimens are subsequently embedded in paraffin blocks and sectioned. Slides are stained with H&E and examined microscopically.
  • Gene Chips (Affymetrix, Santa Clara, CA) are used to investigate gene expression of biomarkers of EMT in xenograft tumors and cRNA probes are synthesized as recommended by Affymetrix.
  • the cRNA is purified using RNeasy and fragmented according to the Affymetrix protocol, and 15 Ag of biotinylated cRNA are hybridized to the microarrays (Affymetrix). After scanning, expression values for each gene are determined using Affymetrix Gene Chip software version 4.0.
  • Gene Spring Silicon Genetics, Redwood City, CA).
  • RNA is isolated from tumors by the acid/guanidinium
  • Agilent human microRNA microarrays were employed to profile the following seven xenograft samples, which had been implanted in mice, as described in the Methods section of the paper (Anastassiou et al, BMC Cancer, 11 :529 (2011)):

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Abstract

L'invention concerne la découverte que la modulation de micro-ARN particuliers peut être utilisée pour inhiber une transition mésenchymateuse qui, dans certains cas, est une corrélation avec la résistance à une thérapie et à une récurrence lorsque les cellules correspondantes acquièrent des propriétés de cellules souches lorsqu'elles commencent à subir cette transition, ainsi qu'avec le pouvoir envahissant, par exemple l'invasion de certaines cellules de tumeurs primaires dans un tissu conjonctif adjacent pendant la phase initiale de métastase. En conséquence, les inhibiteurs d'identification de ce mécanisme, tels que les inhibiteurs de certains micro-ARN précités peuvent être utilisés pour inhiber la transition mésenchymateuse afin de réduire la nature invasive des certaines cellules de tumeurs cancéreuses primaires et, dans certains cas, d'empêcher la récurrence du cancer par inhibition de l'induction de caractéristiques de type cellules souches dans certaines cellules cancéreuses.
PCT/US2013/025709 2012-02-14 2013-02-12 Méthodes et compositions pour inhiber un mécanisme de transition mésenchymateuse multi-cancéreuse WO2013122918A1 (fr)

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Citations (2)

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Publication number Priority date Publication date Assignee Title
US20100088775A1 (en) * 2006-05-26 2010-04-08 Medvet Science Pty. Ltd. Methods of modulating epithelial-mesenchymal transition and mesenchymal-epithelial transition in cells and agents useful for the same
US20110190378A1 (en) * 2008-08-27 2011-08-04 Usdh, Nih Mir 204, mir 211, their anti-mirs, and therapeutic uses of same

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100088775A1 (en) * 2006-05-26 2010-04-08 Medvet Science Pty. Ltd. Methods of modulating epithelial-mesenchymal transition and mesenchymal-epithelial transition in cells and agents useful for the same
US20110190378A1 (en) * 2008-08-27 2011-08-04 Usdh, Nih Mir 204, mir 211, their anti-mirs, and therapeutic uses of same

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DENBY ET AL.: "MiR-21 and miR-214 Are Consistently Modulated during Renal Injury in Rodent Models.", THE AMERICAN JOURNAL OF PATHOLOGY, vol. 179, no. 2, August 2011 (2011-08-01), pages 661 - 672., XP055080332 *

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