US 20090232893A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0232893 A1 Bader et al. (43) Pub. Date: Sep. 17, 2009

(54) MIR-143 REGULATED AND Related U.S. Application Data PATHWAYS AS TARGETS FOR (60) Provisional application No. 60/939,573, filed on May THERAPEUTIC INTERVENTION 22, 2007. (76) Inventors: Andreas G. Bader, Austin, TX Publication Classification (US); Mike W. Byrom, Austin, TX (51) Int. Cl. (US); Charles D. Johnson, Austin, A6IR 9/14 (2006.01) TX (US); David Brown, Austin, TX CI2N 5/02 (2006.01) (US) A63L/7088 (2006.01) CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl...... 424/489: 435/375; 514/44 R; 435/6 Fulbright & Jaworski L.L.P. 600 Congress Avenue, Suite 2400 (57) ABSTRACT Austin, TX 78701 (US) The present invention concerns methods and compositions for identifying genes or genetic pathways modulated by miR (21) Appl. No.: 12/125,412 143, using miR-143 to modulate a or gene pathway, using this profile in assessing the condition of a patient and/or (22) Filed: May 22, 2008 treating the patient with an appropriate miRNA. Patent Application Publication Sep. 17, 2009 US 2009/0232893 A1

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MR-143 REGULATED GENES AND sion is lower in many cancer tumor samples including PATHWAYS AS TARGETS FOR , colon, breast, bladder, and thyroid tumors, than in nor THERAPEUTIC INTERVENTION mal cells from the same patients. Overexpression of hsa-miR 143 in human leukemia cells (Jurkat) increased proliferation of those cells. The inventors also found hsa-miR-143 to be 0001. This application claims Priority to U.S. Provisional up-regulated in tissues of Alzheimer's patients. Other Patent Application Ser. No. 60/939,573, filed May 22, 2007 investigators have also observed that miR-143 is down-regu and PCT application No. PCT/US07/78859 filed Sep. 19, lated in colorectal tumors when compared with matched nor 2007, each of which are hereby incorporated by reference in mal samples (Michael et al., 2003: Akao et al., 2006) and that their entirety. miR-143 may be involved in the differentiation of human adipocytes (fat storage cells) (Esau et al., 2004). BACKGROUND OF THE INVENTION 0009 Bioinformatics analyses suggest that any given 0002 I. Field of the Invention miRNA may bind to and alter the expression of up to several 0003. The present invention relates to the fields of molecu hundred different genes. In addition, a single gene may be lar biology and medicine. More specifically, the invention regulated by several miRNAs. Thus, each miRNA may regu relates to methods and compositions for the treatment of late a complex interaction among genes, gene pathways, and diseases or conditions that are affected by miR-143 microR gene networks. Mis-regulation or alteration of these regula NAS, microRNA expression, and genes and cellular pathways tory pathways and networks, involving miRNAS, are likely to directly and indirectly modulated by such. contribute to the development of disorders and diseases such 0004 II. Background as cancer. Although bioinformatics tools are helpful in pre 0005. In 2001, several groups used a cloning method to dicting miRNA binding targets, all have limitations. Because isolate and identify a large group of “microRNAs (miRNAs) of the imperfect complementarity with their target binding from C. elegans, Drosophila, and (Lagos-Quintana et sites, it is difficult to accurately predict the mRNA targets of al., 2001; Lau et al., 2001; Lee and Ambros, 2001). Several miRNAs with bioinformatics tools alone. Furthermore, the hundred miRNAs have been identified in and ani complicated interactive regulatory networks among miRNAS mals—including humans—that do not appear to have endog and target genes make it difficult to accurately predict which enous siRNAs. Thus, while similar to siRNAs, miRNAs are genes will actually be mis-regulated in response to a given distinct. miRNA. 0006 miRNAs thus far observed have been approximately 0010 Correcting gene expression errors by manipulating 21-22 in length, and they arise from longer pre miRNA expression or by repairing miRNA mis-regulation cursors transcribed from non--encoding genes. See represent promising methods to repair genetic disorders and review of Carrington et al. (2003). The precursors form struc cure diseases like cancer. A current, disabling limitation of tures that fold back on themselves in self-complementary this approach is that, as mentioned above, the details of the regions; they are then processed by the nuclease Dicer (in regulatory pathways and networks that are affected by any animals) or DCL1 (in plants) to generate the short double given miRNA, including miR-143, remain largely unknown. stranded miRNA. One of the miRNA strands is incorporated This represents a significant limitation for treatment of can into a complex of and miRNA called the RNA cers in which miR-143 may play a role. A need exists to induced silencing complex (RISC). The miRNA guides the identify the genes, genetic pathways, and genetic networks RISC complex to a target mRNA, which is then cleaved or that are regulated by or that may regulate hsa-miR-143 translationally silenced, depending on the degree of sequence expression. complementarity of the miRNA to its target mRNA. Cur rently, it is believed that perfect or nearly perfect complemen SUMMARY OF THE INVENTION tarity leads to mRNA degradation, as is most commonly 0011. The present invention provides additional composi observed in plants. In contrast, imperfect base pairing, as is tions and methods by identifying genes that are direct targets primarily found in animals, leads to translational silencing. for miR-143 regulation or that are indirect or downstream However, recent data Suggest additional complexity (Bagga targets of regulation following the miR-143-mediated modi et al., 2005; Lim et al., 2005), and mechanisms of gene fication of another gene(s) expression. Furthermore, the silencing by miRNAS remain under intense study. invention describes gene, disease, and/or physiologic path 0007 Recent studies have shown that expression levels of ways and networks influenced by miR-143 and its family numerous miRNAS are associated with various cancers (re members. In certain aspects, compositions of the invention viewed in Esquela-Kerscher and Slack, 2006; Calin and are administered to a Subject having, Suspected of having, or Croce, 2006). miRNAs have also been implicated in regulat at risk of developing a metabolic, an immunologic, an infec ing cell growth and cell and tissue differentiation—cellular tious, a cardiovascular, a digestive, an endocrine, an ocular, a processes that are associated with the development of cancer. genitourinary, a blood, a musculoskeletal, a nervous system, 0008. The inventors previously demonstrated that hsa a congenital, a respiratory, a skin, or a cancerous disease or miR-143 is involved with the regulation of numerous cell condition. activities that represent intervention points for cancer therapy 0012. In particular aspects, a subject or patient may be and for therapy of other diseases and disorders (U.S. patent selected for treatment based on expression and/or aberrant application Ser. No. 1 1/141,707 filed May 31, 2005 and Ser. expression of one or more miRNA or mRNA. In a further No. 1 1/273,640 filed Nov. 14, 2005, each of which are incor aspect, a subject or patient may be selected for treatment porated herein by reference in their entirety). Upon evaluation based on aberrations in one or more biologic or physiologic of 24 different human tissues, hsa-miR-143 was found to be pathway(s), including aberrant expression of one or more preferentially expressed in human prostate and colon tissue gene associated with a pathway, or the aberrant expression of samples. The inventors observed that hsa-miR-143 expres one or more protein encoded by one or more gene associated US 2009/0232893 A1 Sep. 17, 2009 with a pathway. In still a further aspect, a Subject or patient miR-143 could be used as a therapeutic target for any of these may be selected based on aberrations in miRNA expression, diseases. In certain embodiments miR-143 can be used to or biologic and/or physiologic pathway(s). A subject may be modulate the activity of miR-143 in a Subject, organ, tissue, or assessed for sensitivity, resistance, and/or efficacy of a cell. therapy or treatment regime based on the evaluation and/or 0015. A cell, tissue, or subject may be a cancer cell, a analysis of miRNA or mRNA expression or lack thereof. A cancerous tissue, harbor cancerous tissue, or be a Subject or subject may be evaluated for amenability to certain therapy patient diagnosed or at risk of developing a disease or condi prior to, during, or after administration of one or therapy to a tion. In certain aspects a cancer cell is a neuronal, glial, lung, Subject or patient. Typically, evaluation or assessment may be , brain, breast, bladder, blood, leukemic, lymphoid, done by analysis of miRNA and/or mRNA, as well as com colon, endometrial, stomach, skin, ovarian, fat, bone, cervi bination of other assessment methods that include but are not cal, esophageal, pancreatic, prostate, kidney, testicular, intes limited to histology, immunohistochemistry, blood work, etc. tinal, colorectal, or thyroid cell. In still a further aspect cancer 0013. In some embodiments, an infectious disease or con includes, but is not limited to astrocytoma, acute myelog dition includes a bacterial, viral, parasite, or fungal infection. enous leukemia, acute lymphoblastic leukemia, anaplastic Many of these genes and pathways are associated with vari large cell lymphoma, B-cell lymphoma, breast carcinoma, ous cancers and other diseases. Cancerous conditions bladder carcinoma, cervical carcinoma, chronic lymphoblas include, but are not limited to astrocytoma, acute myelog tic leukemia, colorectal carcinoma, endometrial carcinoma, enous leukemia, acute lymphoblastic leukemia, anaplastic glioma, glioblastoma, gastric carcinoma, hepatocellular car large cell lymphoma, B-cell lymphoma, breast carcinoma, cinoma, Hodgkin lymphoma, leukemia, medulloblastoma, bladder carcinoma, cervical carcinoma, chronic lymphoblas melanoma, mantle cell lymphoma, multiple myeloma, tic leukemia, colorectal carcinoma, endometrial carcinoma, myeloma, non-Hodgkin lymphoma, lung carcinoma, non glioma, glioblastoma, gastric carcinoma, hepatocellular car Small cell lung carcinoma, oligodendroglioma, ovarian car cinoma, Hodgkin lymphoma, leukemia, medulloblastoma, cinoma, esophageal carcinoma, osteosarcoma, pancreatic melanoma, mantle cell lymphoma, multiple myeloma, carcinoma, prostate carcinoma, renal cell carcinoma, Small myeloma, non-Hodgkin lymphoma, lung carcinoma, non cell lung carcinoma, squamous cell carcinoma of the head and Small cell lung carcinoma, oligodendroglioma, ovarian car neck, thyroid carcinoma, or testicular tumor cinoma, esophageal carcinoma, osteosarcoma, pancreatic 0016 Embodiments of the invention include methods of carcinoma, prostate carcinoma, renal cell carcinoma, Small modulating gene expression, or biologic or physiologic path cell lung carcinoma, squamous cell carcinoma of the head and ways in a cell, a tissue, or a subject comprising administering neck, thyroid carcinoma, or testicular tumor wherein the to the cell, tissue, or Subject an amount of an isolated nucleic modulation of one or more gene is sufficient for a therapeutic acid or mimetic thereof comprising a miR-143 nucleic acid, response. Typically, a cancerous condition is an aberrant mimetic, or inhibitor in an amount Sufficient to modulate the hyperproliferative condition associated with the uncontrolled expression of a gene positively or negatively modulated by a growth or inability to undergo cell death, including apoptosis. miR-143 miRNA. A “miR-143 nucleic acid sequence' or In certain aspects the cancerous condition is lung carcinoma, “miR-143 inhibitor” includes the full length precursor of Such asadenocarcinoma, squamous cell carcinoma, large cell miR-143, or complement thereof, as well as 5, 6, 7, 8, 9, 10, carcinoma, or bronchioalveolar carcinoma. 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 0014. The present invention provides methods and com 28, 29 or more nucleotides of a precursor miRNA or its positions for identifying genes that are direct targets for miR processed sequence, or complement thereof, including all 143 regulation or that are downstream targets of regulation ranges and integers there between. In certain embodiments, following the miR-143-mediated modification of upstream the miR-143 nucleic acid sequence or miR-143 inhibitor con gene expression. Furthermore, the invention describes gene tains the full-length processed miRNA sequence or comple pathways and networks that are influenced by miR-143 ment thereof and is referred to as the “miR-143 full-length expression in biological samples. Many of these genes and processed nucleic acid sequence' or “miR-143 full-length pathways are associated with various cancers and other dis processed inhibitor sequence.” In still further aspects, the eases. The altered expression or function of miR-143 in cells miR-143 nucleic acid comprises at least 5, 6, 7, 8, 9, 10, 11, would lead to changes in the expression of these key genes 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 232, 24, 25, 50 and contribute to the development of disease. Introducing (including all ranges and integers there between) miR-143 (for diseases where the miRNA is down-regulated) segment or complementary segment of miR-143 that is at or a miR-143 inhibitor (for diseases where the miRNA is least 75, 80, 85,90, 95, 98.99 or 100% identical to SEQID up-regulated) into disease cells or tissues would result in a NO:1 to SEQID NO:13. The general term miR-143 includes therapeutic response. The identities of key genes that are all members of the miR-143 family that share at least part of regulated directly or indirectly by miR-143 and the disease a mature miR-143 sequence (UGAGAUGAAGCACU with which they are associated are provided herein. In certain GUAGCUCA (SEQ ID NO:1)) or a complement thereof. aspects a cell may be an endothelial, a mesothelial, an epithe 0017. A “miR-143 nucleic acid sequence' includes the lial, stromal, or mucosal cell. The cell can be, but is not full length precursor of miR-143 and other family members limited to brain, a neuronal, a blood, an esophageal, a lung, a that include cardiovascular, a liver, a breast, a bone, a thyroid, a glandular, an adrenal, a pancreatic, a stomach, a intestinal, a kidney, a bladder, a prostate, a , an ovarian, a testicular, a splenic, lla-mir-143 (MIOOO2552) (SEQ ID NO: 2) a skin, a smooth muscle, a cardiac muscle, or a striated muscle GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA cell. In certain aspects, the cell, tissue, or target may not be GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUC defective in miRNA expression yet may still respond thera UGCAGC; peutically to expression or over expression of a miRNA. US 2009/0232893 A1 Sep. 17, 2009

0018. In specific embodiments, a miR-143 or miR-143 - Continued inhibitor containing nucleic acid is hsa-miR-143 or hsa-miR 143 inhibitor, or a variation thereof. In a further aspect, a Xtr-mir-143 (MIOOO4937) miR-143 nucleic acid or miR-143 inhibitor can be adminis (SEQ ID NO : 3) UGUCUCCCAGCCCAAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGAGUCU tered with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more miRNAs or GAGAUGAAGCACUGUAGCUCGGGAAGGGGGAAU; miRNA inhibitors. miRNA or its complement can be admin ister concurrently, in sequence or in an ordered progression. dire-mir-143-2 (MIOOO2O08 (SEQ ID NO : 4) In certain aspects, a miR-143 or miR-143 inhibitor can be GAUCUACAGUCGUCUGGCCCGCGGUGCAGUGCUGCAUCUCUGGUCAACUG. administered in combination with one or more of let-7, miR GGAGUCUGAGAUGAAGCACUGUAGCUCGGGAGGACAACACUGUCAGCUC; 15a, miR-16, miR-20, miR-21, miR-26a, miR-31, miR-34a, miR-126, miR-145, miR-147, miR-188, miR-200b, miR rno-mir-143 (MIOOOO916) (SEO ID NO; 5) 200c, miR-215, miR-216, miR-292-3p, and/or miR-331. All GCGGAGCGCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAG or combinations of miRNAs or inhibitors thereof may be UUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGGGAGAAGAUGUUCU administered in a single formulation. Administration may be GCAGC; before, during or after a second therapy. ptir-mir-143 (MIOOO2549) 0019 miR-143 nucleic acids or complement thereof may (SEQ ID NO : 6) also include various heterologous nucleic acid sequence, i.e., GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA those sequences not typically found operatively coupled with GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUUUUC miR-143 in nature. Such as promoters, enhancers, and the UGCAGC; like. The miR-143 nucleic acid is a recombinant nucleic acid, ppy-mir-143 (MIOOO2551) and can be a ribonucleic acid or a deoxyribonucleic acid. The (SEO ID NO: 7) recombinant nucleic acid may comprise a miR-143 or miR GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA 143 inhibitor expression cassette, i.e., a nucleic acid segment GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUC that expresses a nucleic acid when introduce into an environ UGCAGC; ment containing components for nucleic acid synthesis. In a ggo-mir-143 (MIOOO2550) further aspect, the expression cassette is comprised in a viral, (SEQ ID NO: 8) GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA or plasmid DNA vector or other therapeutic nucleic acid GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUC vector or delivery vehicle, including liposomes and the like. UGCAGC; In certain aspects, viral vectors can be administered at 1x10, 1x10, 1x10, 1x10, 1x10°, 1x107, 1x10, 1x10, 1x109, dire-mir-143-1 (MIOOO2007 (SEO ID NO: 9) 1x10'', 1x10', 1x10", 1x10" pfu or viral particle (vp). GAUCUACAGUCGUCUGGCCCGCGGUGCAGUGCUGCAUCUCUGGUCAACUG. 0020. In a particular aspect, the miR-143 nucleic acid or GGAGUCUGAGAUGAAGCACUGUAGCUCGGGAGGACAACACUGUCAGCUC; miR-143 inhibitor is a synthetic nucleic acid. Moreover, nucleic acids of the invention may be fully or partially syn hisa-mir-143 (MIOOOO459) thetic. Instill further aspects, a nucleic acid of the invention or (SEQ ID NO: 10) a DNA encoding such can be administered at 0.001, 0.01, 0.1, GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA 1, 10, 20, 30, 40, 50, 100, 200, 400, 600, 800, 1000, 2000, to GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUC 4000 ug or mg, including all values and ranges there between. UGCAGC; In yet a further aspect, nucleic acids of the invention, includ ppa-mir-143 (MIOOO2553) ing synthetic nucleic acid, can be administered at 0.001, 0.01, (SEQ ID NO: 11) 0.1. 1, 10, 20, 30, 40, 50, 100, to 200 ug or mg per kilogram GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCA (kg) of body weight. Each of the amounts described herein GUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGAAGAGAGAAGUUUUUC may be administered over a period of time, including 0.5, 1,2, UGCAGC; 3, 4, 5, 6, 7, 8, 9, 10, minutes, hours, days, weeks, months or mdo-mir-143 (MIOOO5302) years, including all values and ranges there between. (SEQ ID NO: 12) 0021. In certain embodiments, administration of the com CCCGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGAGUCUGAGAUGAAGC position(s) can be enteral or parenteral. In certain aspects, ACUGUAGCUCGGG; enteral administration is oral. In further aspects, parenteral immu-mir-143 (MIOOOO257) administration is intralesional, intravascular, intracranial, (SEQ ID NO: 13) intrapleural, intratumoral, intraperitoneal, intramuscular, CCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGC intralymphatic, intraglandular, Subcutaneous, topical, intra ACUGUAGCUCAGG. bronchial, intratracheal, intranasal, inhaled, or instilled. Compositions of the invention may be administered region In certain aspects, a nucleic acid or mimetic of the present ally or locally and not necessarily directly into a lesion. invention will comprise 5, 6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 0022. In certain aspects, the gene or genes modulated 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more comprises 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, 15, 20, 25, nucleotides of the precursor miRNA or its processed 30, 35, 40, 45, 50, 100, 150, 200 or more genes or combina sequence, including all ranges and integers there between. In tions of genes identified in Tables 1, 3, 4, and/or 5. In still certain embodiments, the miR-143 nucleic acid sequence further aspects, the gene or genes modulated may exclude 1. contains the full-length processed miRNA sequence and is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, referred to as the “miR-143 full-length processed nucleic acid 45, 50, 100, 150, 175 or more genes or combinations of genes sequence.” In still further aspects, a miR-143 comprises at identified in Tables 1, 3, 4, and/or 5. Modulation includes least one 5, 6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, modulating , mRNA levels, mRNA translation, 21, 22, 23, 24, 25, 50 nucleotide (including all ranges and and/or protein levels in a cell, tissue, or organ. In certain integers there between) segment of miR-143 that is at least 75, aspects the expression of a gene or level of a gene product, 80, 85,90, 95, 98, 99 or 100% identical to SEQ ID NOs Such as mRNA or encoded protein, is down-regulated or provided herein. up-regulated. In a particular aspect the gene modulated com US 2009/0232893 A1 Sep. 17, 2009

prises or is selected from (and may even exclude) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, TABLE 1-continued 24, 25, 26.27, 28, or all of the genes identified in Tables 1, 3, 4, and/or 5, or any combinations thereof. In certain embodi Genes with increased (positive values) or decreased (negative values) ments a gene modulated or selected to be modulated is from expression following transfection of human cancer cells with Table 1. In further embodiments a gene modulated or selected pre-miRhsa-miR-143. to be modulated is from Table 3. In still further embodiments Gene a gene modulated or selected to be modulated is from Table 4. Symbol RefSeq, Transcript ID A log2 In yet further embodiments a gene modulated or selected to be modulated is from Table 5. Embodiments of the invention NM 148903 may also include obtaining or assessing a gene expression GREM1 NM 013372 1.OS1739161 HIPK2 NM O22740 -O.904313564 profile or miRNA profile of a target cell prior to selecting the HIPK3 NM OO5734 O.826433357 mode of treatment, e.g., administration of a miR-143 nucleic IFIH1 NM 022168 O.7O6653.845 acid, inhibitor of miR-143, or mimetics thereof. The database IGFBP3 NM 000598 NM 00101.3398 -O.8096O7512 content related to nucleic acids and genes designated by an IL32 NM 001012631 NM 001012632 O.7S7126883 accession number or a database Submission are incorporated NM 001012633 NM 001012634 herein by reference as of the filing date of this application. In NM 001012635 IL6ST NM 002184 NM 175767 O.7S1854.493 certain aspects of the invention one or more miRNA or IL8 NM 000584 1.104O16175 miRNA inhibitor may modulate a single gene. In a further INSIG1 NM OO5542 NM 198336 O.87SO27481 aspect, one or more genes in one or more genetic, cellular, or NM 198337 physiologic pathways can be modulated by one or more miR LEPR NM 001003679 NM 001003680 0.797930372 NAS or complements thereof, including miR-143 nucleic NM 002303 acids and miR-143 inhibitors in combination with other miR LMO4 NM OO6769 -1.O127O6499 NAS. LOC137886 XM 059929 -O.752855433 MCL1 NM O21960 NM 182763 0.761759353 0023 miR-143 nucleic acids may also include various MGCS618 0.797855581 heterologous nucleic acid sequence, i.e., those sequences not MTUS1 NM 001001924 NM OO1 OO1925 0.70655 typically found operatively coupled with miR-143 in nature, NM 001001927 NM 001001931 Such as promoters, enhancers, and the like. The miR-143 NM 020749 NID1 NM OO2508 1.09.097.6167 nucleic acid is a recombinant nucleic acid, and can be a NTSE NM OO2526 O.878O49429 ribonucleic acid or a deoxyribonucleic acid. The recombinant PDCD2 NM OO2598 NM 144781 -O.7234844O1 nucleic acid may comprise a miR-143 expression cassette. In PDCD4 NMO14456 if NM 145341 O.728228239 a further aspect, the expression cassette is comprised in a PDK4 NM 002612 O.961974975 PELI1 NM O2O651 O.768582.445 viral, or plasmid DNA vector or other therapeutic nucleic acid PMCH NM 002674 O.79.0936,704 vector or delivery vehicle, including liposomes and the like. PROSC NM 007198 -1.645677869 In a particular aspect, the miR-143 nucleic acid is a synthetic PTPN12 NM 002835 O.7698O8986 nucleic acid. Moreover, nucleic acids of the invention may be RAB11FIP1 NM OO1002233 NM OO10O2814 -0.83733308 NM O25151 fully or partially synthetic. RAB2 NM 002865 O.8273828OS RBL1 NM 002895 NM 1834.04 -1.3O2328.709 TABLE 1. RDX NM OO2906 O.760806942 RECK NM 021111 1.103484746 Genes with increased (positive values) or decreased (negative values) RHEB NM OO5614 O.825468322 expression following transfection of human cancer cells with RHOB NM OO4040 O.921813933 pre-miRhsa-miR-143. RHOBTB1 NM OO1032380 NM O14836 O.744478582 NM 198225 Gene RP2 NM OO6915 O.822851.399 Symbo RefSeq, Transcript ID A log2 SERPINE1 NM OOO602 -0.856846452 SLC11A2 NM 000617 O.7166827OS AKAP12 NM 005100 NM 144497 O.72S245496 SLC30A1 NM 021194 -0.841.163945 ANKRD46 NM 1984.01 O.791492237 SLC3SB1 NM OO5827 -107644709 ANXA6 NM 001155 NM OO4033 O.727214714 TAF10 NM OO6284 -1.695883S32 ARL2BP NM 012106 O.800772424 TBC1D2 NM 018421 -0.746279363 ASNA NM 004317 -107942093 TGFBR2 NM 001024847 NM OO3242 0.854SO9353 ATP6V1A NM OO1690 -1.126127932 TMEM45A NM 018004 -0.748492283 ATXN NM OOO332 O.8SO968582 TMF1 NM 007114 -O.939693594 AXL NM OO1699 NM O21913 1.1560396.98 TNC NM 002160 O.869011.83 BCL2L1 NM OO1191 NM 1385.78 -O.8.21265359 TNRC9 XM O49037 0.740367787 CCND NM O53056 -O.938O24465 TRA1 NM OO3299 O.875188144 CCNG NM 004060 NM 199246 O.862627632 TTMP NM O24616 O.84.4059608 CLIC4 NM O13943 O.82S614765 TXN NM OO3329 O.92S41735 CXCL NM OO1511 O.938115811 UGT1A8 NM O19076 NM 021027 -O.961897449 CXCL2 NM O02089 O.7O6326327 UGT1A9 DAZAP2 NM 014764 -O.916764957 WASPIP NM OO3387 1.041600SS DCP2 NM 152624 0.797770229 WDR50 NM 016001 -1.0491.52791 DDAH1 NM 012137 0.765730627 WEE1 NM OO3390 O.722369746 DDX3Y NM 004660 O.8486511 OS DICER1 NM 030621 NM 177438 O.929848609 DSC2 NM 004949 NM 024422 O.90283O281 0024. A further embodiment of the invention is directed to FLJ13910 NM O22780 O.866839.654 methods of modulating a cellular pathway comprising admin GALC NM OOO153 -11614321.75 GATM NM 001482 -1.97 OS48228 istering to the cell an amount of an isolated nucleic acid GOLPH2 NM O16548 NM 177937 -1.126884613 comprising a miR-143 nucleic acid sequence or a miR-143 GREB1 NM 014668 NM 03.3090 0.755673527 inhibitor. A cell, tissue, or Subject may be a cancer cell, a cancerous tissue or harbor cancerous tissue, or a cancer US 2009/0232893 A1 Sep. 17, 2009

patient. The database content related to all nucleic acids and assessing the sensitivity of the Subject to therapy based on the genes designated by an accession number or a database Sub expression profile; (c) selecting a therapy based on the mission are incorporated herein by reference as of the filing assessed sensitivity; and (d) treating the Subject using a date of this application. In certain aspects, a composition of selected therapy. Typically, the disease or condition will have the invention is a pharmaceutical formulation Such a , as a component, indicator, or resulting mis-regulation of one nanoparticle, microparticle and the like that are typically or more gene of Table 1, 3, 4, and/or 5. biocompatible and/or biodegradable. 0029. In certain aspects, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more miRNA may be used in sequence or in combination. For 0025. A further embodiment of the invention is directed to instance, any combination of miR-143 or a miR-143 inhibitor methods of modulating a cellular pathway comprising admin with another miRNA Further embodiments include the iden istering to the cell an amount of an isolated nucleic acid tification and assessment of an expression profile indicative comprising a miR-143 nucleic acid sequence in an amount of miR-143 status in a cell or tissue comprising expression Sufficient to modulate the expression, function, status, or state assessment of one or more gene from Table 1, 3, 4, and/or 5. of a cellular pathway, in particular those pathways described or any combination thereof. in Table 2 or the pathways known to include one or more 0030 The term “miRNA is used according to its ordinary genes from Table 1, 3, 4, and/or 5. Modulation of a cellular and plain meaning and refers to a microRNA molecule found pathway includes, but is not limited to modulating the expres in eukaryotes that is involved in RNA-based gene regulation. sion of one or more gene(s). Modulation of a gene can include See, e.g., Carrington et al., 2003, which is hereby incorpo inhibiting the function of an endogenous miRNA or provid rated by reference. The term can be used to refer to the ing a functional miRNA to a cell, tissue, or subject. Modula single-stranded RNA molecule processed from a precursor or tion refers to the expression levels or activities of a gene or its in certain instances the precursor itself. related gene product (e.g., mRNA) or protein, e.g., the mRNA 0031. In some embodiments, it may be useful to know levels may be modulated or the translation of an mRNA may whether a cell expresses a particular miRNA endogenously or whether such expression is affected under particular condi be modulated. Modulation may increase or up regulate a gene tions or when it is in a particular disease state. Thus, in some or gene productor it may decrease or down regulate a gene or embodiments of the invention, methods include assaying a gene product (e.g., protein levels or activity). cell or a sample containing a cell for the presence of one or 0026. Still a further embodiment includes methods of more marker gene or mRNA or other analyte indicative of the administering an miRNA or mimic thereof, and/or treating a expression level of a gene of interest. Consequently, in some Subject or patient having, Suspected of having, or at risk of embodiments, methods include a step of generating an RNA developing a pathological condition comprising one or more profile for a sample. The term “RNA profile' or “gene expres of step (a) administering to a patient or Subject an amount of sion profile' refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample an isolated nucleic acid comprising a miR-143 nucleic acid (e.g., a plurality of nucleic acid probes that identify one or sequence or a miR-143 inhibitor in an amount Sufficient to more markers from Tables 1,3,4, and/or 5); it is contemplated modulate expression of a cellular pathway; and (b) adminis that the nucleic acid profile can be obtained using a set of tering a second therapy, wherein the modulation of the cellu , using for example nucleic acid amplification or lar pathway sensitizes the patient or Subject, or increases the hybridization techniques well know to one of ordinary skill in efficacy of a second therapy. An increase in efficacy can the art. The difference in the expression profile in the sample include a reduction in toxicity, a reduced dosage or duration from the patient and a reference expression profile, Such as an of the second therapy, or an additive or synergistic effect. A expression profile from a normal or non-pathologic sample, is cellular pathway may include, but is not limited to one or indicative of a pathologic, disease, or cancerous condition. A more pathway described in Table 2 below or a pathway that is nucleic acid or probe set comprising or inhibitor can be know to include one or more genes of Tables 1, 3, 4, and/or 5. selected based on observing two given miRNAs share a set of The second therapy may be administered before, during, and/ target genes or pathways listed in Tables 1, 2, 4 and/or 5 that or after the isolated nucleic acid or miRNA or inhibitor is are altered in a particular disease or condition. These two administered miRNAS may result in an improved therapy (e.g., reduced 0027. A second therapy can include administration of a toxicity, greater efficacy, prolong remission, or other second miRNA ortherapeutic nucleic acid such as a siRNA or improvements in a Subjects condition), result in an increased antisense oligonucleotide, or may include various standard efficacy, an additive efficacy, or a synergistic efficacy provid therapies, such as pharmaceuticals, chemotherapy, radiation ing an additional or an improved therapeutic response. With therapy, drug therapy, immunotherapy, and the like. Embodi out being bound by any particular theory, synergy of two ments of the invention may also include the determination or miRNA can be a consequence of regulating the same genes or assessment of gene expression or gene expression profile for related genes (related by a common pathway or biologic end the selection of an appropriate therapy. In a particular aspect, result) more effectively (e.g., due to distinct binding sites on a second therapy is a chemotherapy. A chemotherapy can the same target or related target(s)) and/or a consequence of include, but is not limited to paclitaxel, cisplatin, carboplatin, regulating different genes, but all of which have been impli doxorubicin, oxaliplatin, larotaxel, taxol, lapatinib, doc cated in a disease or condition. etaxel, methotrexate, capecitabine, Vinorelbine, cyclophos 0032. In certain aspects, miR-143 or a miR-143 inhibitor phamide, gemcitabine, amrubicin, cytarabine, etoposide, and let-7 can be administered to patients with acute myeloid camptothecin, dexamethasone, dasatinib, tipifarnib, bevaci leukemia, breast carcinoma, bladder carcinoma, cervical car Zumab, sirolimus, temsirolimus, everolimus, lonafarnib, cinoma, colorectal carcinoma, endometrial carcinoma, cetuximab, erlotinib, gefitinib, imatinib mesylate, rituximab, glioma, glioblastoma, gastric carcinoma, hepatocellular car trastuzumab, nocodazole, Sorafenib, Sunitinib, bortezomib, cinoma, Hodgkin lymphoma, leukemia, melanoma, myxofi alemtuzumab, gemtuzumab, to situmomab or ibritumomab. brosarcoma, multiple myeloma, neuroblastoma, non 0028 Embodiments of the invention include methods of Hodgkin lymphoma, non-small cell lung carcinoma, ovarian treating a Subject with a disease or condition comprising one carcinoma, esophageal carcinoma, pancreatic carcinoma, or more of the steps of (a) determining an expression profile prostate carcinoma, squamous cell carcinoma of the head and of one or more genes selected from Table 1, 3, 4, and/or 5; (b) neck, thyroid carcinoma, or urothelial carcinoma. US 2009/0232893 A1 Sep. 17, 2009

0033. Further aspects include administering miR-143 or a 0039. In certain aspects, miR-143 or a miR-143 inhibitor miR-143 inhibitor and miR-15 to patients with astrocytoma, and miR-126 are administered to patients with astrocytoma, acute myeloid leukemia, breast carcinoma, bladder carci acute myeloid leukemia, breast carcinoma, bladder carci noma, cervical carcinoma, colorectal carcinoma, endometrial noma, cervical carcinoma, colorectal carcinoma, endometrial carcinoma, glioma, glioblastoma, gastric carcinoma, hepato carcinoma, glioma, glioblastoma, gastric carcinoma, hepato cellular carcinoma, Hodgkin lymphoma, melanoma, mantle cellular carcinoma, Hodgkin lymphoma, leukemia, mela cell lymphoma, myxofibrosarcoma, multiple myeloma, neu noma, mantle cell lymphoma, non-Hodgkin lymphoma, non roblastoma, non-Hodgkin lymphoma, non-Small cell lung Small cell lung carcinoma, ovarian carcinoma, esophageal carcinoma, ovarian carcinoma, esophageal carcinoma, carcinoma, osteosarcoma, pancreatic carcinoma, prostate osteosarcoma, pancreatic carcinoma, prostate carcinoma, carcinoma, squamous cell carcinoma of the head and neck, or squamous cell carcinoma of the head and neck, or thyroid thyroid carcinoma. carcinoma. 0040. In still a further aspect, miR-143 or a miR-143 0034. In still further aspects, miR-143 or a miR-143 inhibitor and miR-147 are administered to patients with astro inhibitor and miR-16 are administered to patients with astro cytoma, breast carcinoma, bladder carcinoma, cervical carci cytoma, breast carcinoma, bladder carcinoma, colorectal car noma, colorectal carcinoma, endometrial carcinoma, esoph cinoma, endometrial carcinoma, glioblastoma, gastric carci ageal Squamous cell carcinoma, glioma, glioblastoma, gastric noma, hepatocellular carcinoma, Hodgkin lymphoma, carcinoma, hepatocellular carcinoma, Hodgkin lymphoma, melanoma, mantle cell lymphoma, myxofibrosarcoma, mul leukemia, lipoma, melanoma, mantle cell lymphoma, myx tiple myeloma, non-Small cell lung carcinoma, ovarian car ofibrosarcoma, multiple myeloma, non-Hodgkin lymphoma, cinoma, esophageal carcinoma, pancreatic carcinoma, pros non-Small cell lung carcinoma, ovarian carcinoma, esoph tate carcinoma, squamous cell carcinoma of the head and ageal carcinoma, osteosarcoma, pancreatic carcinoma, pros neck, or thyroid carcinoma. tate carcinoma, squamous cell carcinoma of the head and 0035 Aspects of the invention include methods where neck, or thyroid carcinoma. miR-143 or a miR-143 inhibitor and miR-20 are administered 0041. In yet another aspect, miR-143 or a miR-143 inhibi to patients with astrocytoma, acute myeloid leukemia, breast tor and miR-188 are administered to patients with astrocy carcinoma, bladder carcinoma, colorectal carcinoma, toma, acute myeloid leukemia, breast carcinoma, bladder endometrial carcinoma, glioma, glioblastoma, gastric carci carcinoma, cervical carcinoma, colorectal carcinoma, noma, hepatocellular carcinoma, melanoma, mantle cell lym endometrial carcinoma, esophageal squamous cell carci phoma, neuroblastoma, non-small cell lung carcinoma, ova noma, glioma, glioblastoma, gastric carcinoma, hepatocellu rian carcinoma, esophageal carcinoma, pancreatic lar carcinoma, leukemia, melanoma, multiple myeloma, non carcinoma, prostate carcinoma, or squamous cell carcinoma Hodgkin lymphoma, non-small cell lung carcinoma, ovarian of the head and neck. carcinoma, esophageal carcinoma, pancreatic carcinoma, 0036. In a further aspect, miR-143 or a miR-143 inhibitor prostate carcinoma, squamous cell carcinoma of the head and and miR-21 are administered to patients with astrocytoma, neck, or thyroid carcinoma. acute myeloid leukemia, breast carcinoma, bladder carci 0042. In other aspects, miR-143 or a miR-143 inhibitor noma, cervical carcinoma, colorectal carcinoma, endometrial and miR-215 are administered to patients with astrocytoma, carcinoma, glioma, glioblastoma, gastric carcinoma, hepato acute myeloid leukemia, breast carcinoma, bladder carci cellular carcinoma, Hodgkin lymphoma, leukemia, mela noma, cervical carcinoma, colorectal carcinoma, endometrial noma, mantle cell lymphoma, multiple myeloma, non carcinoma, esophageal Squamous cell carcinoma, glioma, Hodgkin lymphoma, non-small cell lung carcinoma, ovarian glioblastoma, gastric carcinoma, hepatocellular carcinoma, carcinoma, esophageal carcinoma, osteosarcoma, pancreatic Hodgkin lymphoma, leukemia, lipoma, melanoma, mantle carcinoma, prostate carcinoma, squamous cell carcinoma of cell lymphoma, myxofibrosarcoma, multiple myeloma, neu the head and neck, or thyroid carcinoma. roblastoma, non-Hodgkin lymphoma, non-Small cell lung 0037. In still further aspects, miR-143 or a miR-143 carcinoma, ovarian carcinoma, esophageal carcinoma, inhibitor and miR-26a are administered to patients with acute osteosarcoma, pancreatic carcinoma, prostate carcinoma, myeloid leukemia, breast carcinoma, bladder carcinoma, cer squamous cell carcinoma of the head and neck, thyroid car Vical carcinoma, colorectal carcinoma, glioma, glioblastoma, cinoma, or urothelial carcinoma. gastric carcinoma, hepatocellular carcinoma, leukemia, 0043. In certain aspects, miR-143 or a miR-143 inhibitor melanoma, multiple myeloma, neuroblastoma, non-Hodgkin and miR-216 are administered to patients with astrocytoma, lymphoma, non-Small cell lung carcinoma, ovarian carci breast carcinoma, cervical carcinoma, colorectal carcinoma, noma, esophageal carcinoma, osteosarcoma, pancreatic car endometrial carcinoma, glioma, glioblastoma, gastric carci cinoma, or prostate carcinoma. noma, hepatocellular carcinoma, Hodgkin lymphoma, leuke 0038. In yet further aspects, miR-143 or a miR-143 inhibi mia, non-Hodgkin lymphoma, non-Small cell lung carci tor and miR-34a are administered to patients with astrocy noma, ovarian carcinoma, esophageal carcinoma, toma, acute myeloid leukemia, breast carcinoma, bladder osteosarcoma, prostate carcinoma, or squamous cell carci carcinoma, cervical carcinoma, colorectal carcinoma, noma of the head and neck. endometrial carcinoma, glioma, glioblastoma, gastric carci 0044. In a further aspect, miR-143 or a miR-143 inhibitor noma, hepatocellular carcinoma, Hodgkin lymphoma, leuke and miR-292-3p are administered to patients with astrocy mia, melanoma, mantle cell lymphoma, multiple myeloma, toma, acute myeloid leukemia, breast carcinoma, bladder non-Hodgkin lymphoma, non-Small cell lung carcinoma, carcinoma, cervical carcinoma, colorectal carcinoma, ovarian carcinoma, esophageal carcinoma, osteosarcoma, endometrial carcinoma, glioma, glioblastoma, gastric carci pancreatic carcinoma, prostate carcinoma, squamous cell car noma, hepatocellular carcinoma, leukemia, lipoma, mela cinoma of the head and neck, thyroid carcinoma, or urothelial noma, myxofibrosarcoma, multiple myeloma, neuroblas carcinoma. toma, non-Hodgkin lymphoma, non-Small cell lung US 2009/0232893 A1 Sep. 17, 2009

carcinoma, ovarian carcinoma, esophageal carcinoma, niques well know to one of ordinary skill in the art. The osteosarcoma, pancreatic carcinoma, prostate carcinoma, difference in the expression profile in the sample from a squamous cell carcinoma of the head and neck, thyroid car patient and a reference expression profile, such as an expres cinoma, or urothelial carcinoma. sion profile from a normal or non-pathologic sample, or a 0045. In still a further aspect, miR-143 or a miR-143 digitized reference, is indicative of a pathologic, disease, or inhibitor and miR-331 are administered to patients with astro cancerous condition. In certain aspects the expression profile cytoma, acute myeloid leukemia, breast carcinoma, bladder is an indicator of a propensity to or probability of (i.e., risk carcinoma, cervical carcinoma, colorectal carcinoma, factor for a disease or condition) developing Such a condition endometrial carcinoma, glioma, glioblastoma, gastric carci (s). Such a risk or propensity may indicate a treatment, noma, hepatocellular carcinoma, leukemia, melanoma, myx increased monitoring, prophylactic measures, and the like. A ofibrosarcoma, multiple myeloma, neuroblastoma, non nucleic acid or probe set may comprise or identify a segment Hodgkin lymphoma, ovarian carcinoma, esophageal of a corresponding mRNA and may include all or part of 1, 2, carcinoma, osteosarcoma, pancreatic carcinoma, prostate 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, carcinoma, squamous cell carcinoma of the head and neck, or 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33,34, 35,36, 37,38, thyroid carcinoma. 39, 40, 41,42, 43,44, 45,46, 47, 48,49, 50, 51, 52,53,54, 55, 0046. In yet a further aspect, miR-143 or a miR-143 56, 57, 58, 59, 60, 61, 62, 100, 200, 500, or more segments, inhibitor and miR-200b/c are administered to patients with including any integer or range derivable there between, of a breast carcinoma, cervical carcinoma, colorectal carcinoma, glioma, glioblastoma, gastric carcinoma, hepatocellular car gene or genetic marker, or a nucleic acid, mRNA or a probe cinoma, leukemia, lipoma, multiple myeloma, non-small cell representative thereofthat is listed in Tables 1, 3, 4, and/or 5 lung carcinoma, ovarian carcinoma, esophageal carcinoma, or identified by the methods described herein. osteosarcoma, pancreatic carcinoma, prostate carcinoma, 0051 Certain embodiments of the invention are directed squamous cell carcinoma of the head and neck, or thyroid to compositions and methods for assessing, prognosing, or carcinoma. treatingapathological condition in a patient comprising mea 0047. It is contemplated that when miR-143 or a miR-143 Suring or determining an expression profile of one or more inhibitor is given in combination with one or more other miRNA or marker(s) in a sample from the patient, wherein a miRNA molecules, the two different miRNAs or inhibitors difference in the expression profile in the sample from the may be given at the same time or sequentially. In some patient and an expression profile of a normal sample or ref embodiments, therapy proceeds with one miRNA or inhibitor erence expression profile is indicative of pathological condi and that therapy is followed up with therapy with the other tion and particularly cancer (e.g., In certain aspects of the miRNA or inhibitor 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, invention, the miRNAs, cellular pathway, gene, or genetic 35, 40, 45, 50, 55 minutes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, marker is or is representative of one or more pathway or 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, 1, 2, 3, 4, marker described in Table 1, 2, 3, 4, and/or 5, including any 5, 6, 7 days, 1, 2, 3, 4, 5 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. combination thereof. 0052 Aspects of the invention include diagnosing, assess 11, or 12 months or any such combination later. ing, or treating a pathologic condition or preventing a patho 0.048. Further embodiments include the identification and logic condition from manifesting. For example, the methods assessment of an expression profile indicative of miR-143 can be used to screen for a pathological condition; assess status in a cell or tissue comprising expression assessment of prognosis of a pathological condition; stage a pathological one or more gene from Table 1, 3, 4, and/or 5, or any combi condition; assess response of a pathological condition to nation thereof. therapy, or to modulate the expression of a gene, genes, or 0049. The term “miRNA is used according to its ordinary related pathway as a first therapy or to render a Subject sen and plain meaning and refers to a microRNA molecule found sitive or more responsive to a second therapy. In particular in eukaryotes that is involved in RNA-based gene regulation. aspects, assessing the pathological condition of the patient See, e.g., Carrington et al., 2003, which is hereby incorpo can be assessing prognosis of the patient. Prognosis may rated by reference. The term can be used to refer to the include, but is not limited to an estimation of the time or single-stranded RNA molecule processed from a precursor or expected time of Survival, assessment of response to a in certain instances the precursor itself or a mimetic thereof. therapy, and the like. In certain aspects, the altered expression 0050. In some embodiments, it may be useful to know of one or more gene or marker is prognostic for a patient whether a cell expresses a particular miRNA endogenously or having a pathologic condition, wherein the marker is one or whether such expression is affected under particular condi more of Table 1, 3, 4, and/or 5, including any combination tions or when it is in a particular disease state. Thus, in some thereof. embodiments of the invention, methods include assaying a cell or a sample containing a cell for the presence of one or more miRNA marker gene or mRNA or other analyte indica TABLE 2 tive of the expression level of a gene of interest. Conse Significantly affected functional cellular pathways following quently, in some embodiments, methods include a step of hsa-miR-143 over-expression in human cancer cells. generating an RNA profile for a sample. The term “RNA profile' or “gene expression profile' refers to a set of data Number regarding the expression pattern for one or more gene or of Genes Pathway Functions genetic marker in the sample (e.g., a plurality of nucleic acid 9 Cellular Movement, Hematological System Development and Function, Immune Response probes that identify one or more markers or genes from Tables 2 Gene Expression, Cellular Growth and Proliferation, 1, 3, 4, and/or 5); it is contemplated that the nucleic acid Developmental Disorder profile can be obtained using a set of RNAs, using for example nucleic acid amplification or hybridization tech US 2009/0232893 A1 Sep. 17, 2009

TABLE 3 Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description 76P NM O14444 gamma ring complex protein (76p gene) AACS NM 023928 acetoacetyl-CoA synthetase AADACL1 NM O2O792 arylacetamide deacetylase-like 1 AARSL NM 020745 alanyl-tRNA synthetase like ABAT NM OOO663 4-aminobutyrate aminotransferase precursor ABCA1 NM OO55O2 ATP-binding cassette, Sub-family A member 1 ABCB11 NM 003742 ATP-binding cassette, Sub-family B (MDR/TAP), ABCB9 NM 203445 ATP-binding cassette, Sub-family B (MDR/TAP), ABCC1 NM 004996 ATP-binding cassette, Sub-family C, member 1 ABCC13 NM 172024 ATP-binding cassette protein C13 isoform b ABCC3 NM 020038 ATP-binding cassette, Sub-family C, member 3 ABCC4 NM 005845 ATP-binding cassette, Sub-family C, member 4 ABCG4 NM 0221.69 ATP-binding cassette, subfamily G, member 4 ABCGS NM 022436 sterolin 1 ABHD14A NM O15407 abhydrolase domain containing 14A ABHD14B NM 032750 abhydrolase domain containing 14B ABHD8 NM O24527 abhydrolase domain containing 8 ABLIM1 NM OO10O3407 -binding LIM protein 1 isoform b ABR NM 001092 active breakpoint cluster region-related ABTB2 NM 145804 repeat and BTB (POZ) domain containing ACACB NM 001093 acetyl-Coenzyme A carboxylase beta ACADSB NM OO1609 acyl-Coenzyme A dehydrogenase, short branched ACCN1 NM 001094 amiloride-sensitive cation channel 1, neuronal ACE NM 152831 angiotensin I converting isoform 3 ACE2 NM 021804 angiotensin I converting enzyme 2 precursor ACIN1 NM O14977 apoptotic chromatin condensation inducer 1 ACOXL NM 018308 acyl-Coenzyme A oxidase-like ACP1 NMOO4300 acid phosphatase 1 isoform c ACSL6 NM 0010091.85 acyl-CoA synthetase long-chain family member 6 ACTL8 NM O3O812 actin like protein ACTN2 NM 001103 , alpha 2 ACTR8 NM 022899 actin-related protein 8 ACVR1B NM 004302 activin A type IB receptor isoform a precursor ACY1L2 NM 00101.0853 hypothetical protein LOC135293 DAM10 NM 001110 DAM metallopeptidase domain 10 DAM12 NM OO3474 DAM metallopeptidase domain 12 isoform 1 DAM9 NM 001005845 DAM metallopeptidase domain 9 isoform 2 DAMTS1 NM OO6988 DAM metallopeptidase with thrombospondin type 1 DAMTS3 NM 014243 DAM metallopeptidase with thrombospondin type 1 DAMTS4 NM 005099 DAM metallopeptidase with thrombospondin type 1 DAMTSL1 NM 052866 DAMTS-like 1 isoform 2 DAR NM 001025107 enosine deaminase, RNA-specific isoform d DARB1 NM OO1033049 RNA-specific B1 isoform 4 DAT1 NM 012091 adenosine deaminase, tRNA-specific 1 DCY1 NM 021116 brain adenylate cyclase 1 DCY2 NM 020546 adenylate cyclase 2 DCY6 NM O15270 adenylate cyclase 6 isoform a DCY9 NM 001116 adenylate cyclase 9 DD2 NM OO1617 adducin 2 isoform a DD3 NM 001121 adducin 3 (gamma) isoform b DI1 NM 018269 membrane-type 1 matrix metalloproteinase DIPOQ NM OO4797 adiponectin precursor DORA3 NM OOO677 adenosine A3 receptor isoform 2 DRA2B NM OOO682 alpha-2B-adrenergic receptor DSSL1 NM 152328 adenylosuccinate synthase-like 1 isoform 2 FAP NM 021638 actin filament associated protein FF1 NM 005935 myeloid lymphoid or mixed-lineage leukemia FF2 NM 002025 fragile X mental retardation 2 FG3L2 NM OO6796 AFG3 ATPase family gene 3-like 2 AGBL4 NM 032785 hypothetical protein LOC84871 AGMAT NM O24758 agmatine () AGPAT1 NM 006411 1-acylglycerol-3-phosphate O- 1 AGPAT3 NM O2O132 1-acylglycerol-3-phosphate O-acyltransferase 3 AGPAT4 NM 001012733 1-acylglycerol-3-phosphate O-acyltransferase 4 AGR2 NM OO6408 anterior gradient 2 homolog AGRN NM 198576 agrin AHCTF1 NM 015446 ELYS AHCYL1 NM OO6621 S-adenosylhomocysteine -like 1 AICDA NM 020661 activation-induced AIF1 NM OO4847 allograft inflammatory factor 1 isoform 2 AIG1 NM 016108 androgen-induced 1 US 2009/0232893 A1 Sep. 17, 2009

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description AIPL1 NM OO1033054 aryl hydrocarbon receptor interacting AIRE NM OOO383 autoimmune regulator AIRE isoform 1 AK1 NM 000476 adenylate kinase 1 AK3 NM 016282 adenylate kinase 3 AKAP11 NM 144490 A-kinase anchor protein 11 isoform 2 AKAP13 NM OO6738 A-kinase anchor protein 13 isoform 1 AKAP6 NM OO4274 A-kinase anchor protein 6 AKT1 NM 001014431 V-akt murine thymoma viral oncogene homolog 1 ALB NM 000477 albumin precursor ALDH3A2 NM OOO382 aldehyde dehydrogenase 3A2 isoform 2 ALDHSA1 NM 001080 aldehyde dehydrogenase 5A1 precursor, isoform 2 ALKBH4 NM O17621 hypothetical protein LOC54784 ALPL NM 000478 tissue non-specific alkaline phosphatase ALS2 NM 020919 alsin ALX3 NM OO6492 aristaless-like homeobox 3 AMDHD1 NM 152435 hypothetical protein LOC144193 AMFR NM 001144 autocrine motility factor receptor AMICA1 NM 1532O6 adhesion molecule, interacts with CXADR antigen AMMECR1 NM 001025580 AMMECR1 2 AMOTL1 NM 130847 angiomotin like 1 AMPD2 NM 004037 adenosine monophosphate deaminase 2 (isoform L) AMT NM 000481 aminomethyltransferase (glycine cleavage system AMZ1. NM 133463 archaemetZincin-1 ANGEL.1 NM O15305 angelhomolog 1 ANGPTL1 NM 004673 angiopoietin-like 1 precursor ANGPTL2 NM 012098 angiopoietin-like 2 precursor ANGPTL7 NM 021146 angiopoietin-like 7 ANKH NMO54027 ankylosis, progressive homolog ANKRD12 NM O15208 ankyrin repeat domain 12 ANKRD13 NM 033121 ankyrin repeat domain 13 ANKRD2OA3 NM 00101.2419 hypothetical protein LOC441425 ANKRD25 NM O15493 ankyrin repeat domain 25 ANKRD28 NM O15199 ankyrin repeat domain 28 ANKRD29 NM 173505 ankyrin repeat domain 29 ANKRD41 NM 152363 ankyrin repeat domain 41 ANKRDSO NM 020337 ankyrin repeat domain 50 ANKS6 NM 173551 sterile alpha motif domain containing 6 ANXA3 NM OO5139 annexin A3 ANXA9 NM 003568 annexin A9 AOC2 NM 001158 amine oxidase, copper containing 2 isoform a AP2B1 NM OO 1030006 adaptor-related protein complex 2, beta 1 AP3D1 NM OO3938 adaptor-related protein complex 3, delta 1 AP3M1 NM 012095 adaptor-related protein complex 3, mu 1 subunit APAF1 NM 001160 apoptotic protease activating factor isoform b APOA1BP NM 144772 apolipoprotein A-I binding protein precursor APOAS NM 052968 apolipoprotein AV APOBEC3A NM 145699 phorbolin APOBEC3F NM 145298 apolipoprotein B mRNA editing enzyme, catalytic APOBEC4 NM 203454 apolipoprotein B mRNA editing enzyme, catalytic APOL1 NM OO3661 apolipoprotein isoform a precursor APOL6 NM 030641 apolipoprotein L6 APOLD1 NM O3O817 apolipoprotein L. domain containing 1 APPL NM 012096 adaptor protein containing pH domain, PTB domain APTX NM 175069 aprataxin isoform b AQP10 NM 08.0429 aquaporin 10 AQP2 NM 000486 aquaporin 2 AQP3 NM 004925 aquaporin 3 ARCN1 NM OO1655 archain ARFGAP3 NM 014570 ADP-ribosylation factor GTPase activating ARFIP2 NM 012402 ADP-ribosylation factor interacting protein 2 ARHGAP18. NM 033515 Rho GTPase activating protein 18 ARHGAP2O NM 020809 Rho GTPase activating protein 20 ARHGAP2S NM OO1007231 Rho GTPase activating protein 25 isoform a ARHGAP26 NM O15071 GTPase regulator associated with the focal ARHGAP28 NM 001010000 Rho GTPase activating protein 28 isoform a ARHGAP9 NM 032496 Rho GTPase activating protein 9 ARHGDIB NM 001175 Rho GDP dissociation inhibitor (GDI) beta ARHGEF1 NM 004706 Rho guanine nucleotide exchange factor 1 isoform ARHGEF7 NM OO3899 Rho guanine nucleotide exchange factor 7 isoform ARID3B NM OO6465 AT rich interactive domain 3B (BRIGHT-like) ARIDSB NM 032199 AT rich interactive domain 5B (MRF1-like) US 2009/0232893 A1 Sep. 17, 2009 10

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description ARL15 NM O19087 ADP-ribosylation factor related protein 2 ARL3 NM 004311 ADP-ribosylation factor-like 3 ARL6 NM 032146 ADP-ribosylation factor-like 6 ARL6IP2 NM 022374 ADP-ribosylation factor-like 6 interacting ARMCS NM O24742 armadillo repeat containing 5 ARMC8 NM 014154 armadillo repeat containing 8 isoform 1 ARNT NM OO1668 aryl hydrocarbon receptor nuclear translocator ARRDC4 NM 183376 domain containing 4 ARSD NM OO1669 arylsulfatase D isoform a precursor ARTS-1 NM 016442 type 1 tumor necrosis factor receptor shedding ASAM NM O24769 adipocyte-specific adhesion molecule ASB4 NM 145872 ankyrin repeat and SOCS box-containing protein 4 ASB6 NM O17873 ankyrin repeat and SOCS box-containing 6 isoform ASCC3 NM OO6828 activating signal cointegrator 1 complex subunit ASL NM 000048 argininosuccinate isoform 1 ASPH NM 004318 aspartate beta-hydroxylase isoform a ASTN NM 004319 astrotactin isoform 1 ASXL1 NM O15338 additional sex combs like 1 ASXL2 NM 018263 additional sex combs like 2 ATCAY NM 033064 caytaxin ATF3 NM OO1030287 activating transcription factor 3 isoform 1 ATG10 NM 031482 APG10 autophagy 10-like ATG12 NM 004707 APG12 autophagy 12-like ATG9A NM 024085 APG9 autophagy 9-like 1 ATG9B NM 173681 nitric oxide synthase 3 antisense ATHL1 NM O25092 hypothetical protein LOC80162 ATM NM 000051 ataxiatelangiectasia mutated protein isoform 1 ATOH8 NM 032827 atonal homolog 8 ATP10A NM 024490 ATPase, Class V, type 10A ATP11B NM 014616 ATPase, Class VI, type 11B ATP11C NM 00101.0986 ATPase, Class VI, type 11C isoform b ATP1A2 NM 000702 Na+K+-ATPase alpha 2 subunit proprotein ATP1A3 NM 152296 Na+K+-ATPase alpha 3 subunit ATP2B2 NM OO1 OO1331 plasma membrane calcium ATPase 2 isoform a ATP6AP1 NM 001183 ATPase, H+ transporting, lysosomal accessory ATP6VOE NM OO3945 ATPase, H+ transporting, lysosomal, VO subunit ATP6V1A NM OO1690 ATPase, H+ transporting, lysosomal 70 kD, V1 ATP6V1 C2 NM 144583 vacuolar H--ATPase C2 isoform b ATP6V1F NM 004231 ATPase, H+ transporting, lysosomal 14 kD, V1 ATP8A1 NM OO6095 ATPase, aminophospholipid transporter (APLT), ATPBD4 NM 080650 ATP binding domain 4 ATPIF1 NM 178191 ATPase inhibitory factor 1 isoform 3 precursor ATXN1 NM OOO332 ataxin 1 AVPR1B NM 000707 arginine vasopressin receptor 1B AZGP1 NM 001185 alpha-2-glycoprotein 1, B3GNT6 NM 1387O6 UDP-GlcNAc:beta,Gal B4GALT1 NM OO1497 UDP-Gal:betaGlcNAc beta 14 B4GALTS NM 004776 UDP-Gal:betaGlcNAc beta 14 BAAT NM OO1701 bile acid Coenzyme A: BACE NM 012104 beta-site APP-cleaving enzyme 1 isoform A BACH1 NM 00101.1545 BTB and CNC 1 isoform b BACH2 NM 021813 BTB and CNC homology 1, basic leucine zipper BAG NM 004323 BCL2-associated athanogene isoform 1L. BAG3 NM 004281 BCL2-associated athanogene 3 BAGS NM 00101504.8 BCL2-associated athanogene 5 isoform b BAGE4 NM 181704 B melanoma antigen family, member 4 BARHL2 NM O2O063 Bar-like 2 BAT2D1 NM O15172 HBXAg transactivated protein 2 BATF2 NM 138456 basic leucine Zipper transcription factor, BAZ2A NM 013449 bromodomain adjacent to domain, 2A BBC3 NM O14417 BCL2 binding component 3 BBS1 NM O24649 Bardet-Biedl syndrome 1 BBSS NM 152384 Bardet-Biedl syndrome 5 BCAN NM 198427 brevican isoform 2 BCAP29 NM 0010084.06 B-cell receptor-associated protein BAP29 isoform BCAP31 NM OO5745 B-cell receptor-associated protein 31 BCL2 NM 000633 B-cell lymphoma protein 2 alpha isoform BCL3 NM OO5178 B-cell CLL/lymphoma 3 BCORL1 NM 021946 BCL6 co-repressor-like 1 BCR NM 004327 breakpoint cluster region isoform 1 BDH2 NM O2O139 3-hydroxybutyrate dehydrogenase, type 2 US 2009/0232893 A1 Sep. 17, 2009 11

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description BET1L. NM O16526 blocked early in transport 1 homolog (S. BFAR NM O16561 apoptosis regulator BGN NM OO1711 biglycan preproprotein BHLHB9 NM 030639 basic helix-loop-helix domain containing, class BHMT2 NM O17614 betaine-homocysteine methyltransferase 2 BICD1 NM 001003398 bicaudal Dhomolog 1 isoform 2 BIRC1 NM OO4536 baculoviral IAP repeat-containing 1 BIRC2 NM 001166 baculoviral IAP repeat-containing protein 2 BIRC4 NM 001167 baculoviral IAP repeat-containing protein 4 BIRC4BP NM 017523 XIAP associated factor-1 isoform 1 BIRCS NM 00101.2270 baculoviral IAP repeat-containing protein 5 BLMH NM 000386 bleomycin hydrolase BLOC1S2 NM 001001342 biogenesis of lysosome-related organelles BLR1 NM OO1716 Burkitt lymphoma receptor 1 isoform 1 BLZF1 NM OO3666 basic leucine Zipper nuclear factor 1 BMPR1A NM 004329 bone morphogenetic protein receptor, type IA BMPR2 NM 001204 bone morphogenetic protein receptor type II BOK NM 032515 BCL2-related ovarian killer BOLA2 NM OO1031833 BolA-like protein 2 isoform b BOLL NM 033030 boule isoform 2 BPNT1 NM OO6085 3'(2), 5'-bisphosphate nucleotidase 1 BRCA1 NM OO7306 breast cancer 1, early onset isoform BRD2 NM 005104 bromodomain containing protein 2 BRD4. NM O14299 bromodomain-containing protein 4 isoform short BSN NM OO3458 bassoon protein BTBD14B NM 052876 transcriptional repressor NAC1 BTBD15 NM 014155 BTB (POZ) domain containing 15 BTBD4 NMO25224 BTB (POZ) domain containing 4 BTBD6 NM 033271 BTB domain protein BDPL BTF3L4 NM 152265 transcription factor BTF3-like BTG2 NM OO6763 B-cell translocation gene 2 BTN1A1 NM OO1732 butyrophilin, subfamily 1, member A1 BTN2A1 NM 007049 butyrophilin, subfamily 2, member A1 isoform 1 BTN2A2 NM O06995 butyrophilin, subfamily 2, member A2 isoform a BTN3A2 NM 007047 butyrophilin, subfamily 3, member A2 precursor BTNL8 NM O24850 butyrophilin-like 8 short form BTRC NM OO3939 beta-transducin repeat containing protein BVES NM 007073 blood vessel epicardial Substance Oorf10 NM 007021 asting induced gene Oorf104 NM 173473 hypothetical protein LOC119504 Oorf111 NM 153244 hypothetical protein LOC221060 Oorf114 NM 00101.0911 hypothetical protein LOC399726 Oorf12 NM O15652 hypothetical protein LOC26148 Oorf129 NM 207321 hypothetical protein LOC142827 Oorf38 NM 001010924 hypothetical protein LOC221061 Oorf39 NM 194303 hypothetical protein LOC282973 Oorf242 NM 138357 hypothetical protein LOC90550 Oorf246 NM 153810 hypothetical protein LOC143384 Oorf53 NM 182554 hypothetical protein LOC282966 Oorf54 hypothetical protein LOC64115 Oorf56 hypothetical protein LOC219.654 OOrf6S hypothetical protein LOC112817 Oorf33 hypothetical protein LOC118812 Oorf 9 hypothetical protein LOC387695 1or hypothetical protein LOC64776 1orf17 11 open reading frame 17 1orf245 hypothetical protein LOC219833 1orf246 hypothetical protein LOC120534 1orf249 hypothetical protein LOC79096 isoform 1 1orf54 hypothetical protein LOC28970 1orf55 hypothetical protein LOC399879 1orf69 NM 152314 hypothetical protein LOC120196 2Orf22 NM 03.08.09 TGF-beta induced apoptosis protein 12 2Orf29 NM 0010098.94 hypothetical protein LOC91298 2Orf31 NM 032338 hypothetical protein LOC84298 2Orfa-1 NM 017822 hypothetical protein LOC54934 2Orfs NM O2O375 open reading frame 5 2Orfs9 NM 153022 hypothetical protein LOC120939 3orf NM 145061 hypothetical protein LOC221 150 4orf103 NM 018036 hypothetical protein LOC55102 4orf11 NM 018453 hypothetical protein LOC55837 US 2009/0232893 A1 Sep. 17, 2009 12

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description C14orf115 NM 018228 hypothetical protein LOC55237 C14orf143 NM 145231 hypothetical protein LOC90141 C14orf150 NM OO10O8726 hypothetical protein LOC112840 C14orf162 NM O2O181 chromosome 14 open reading frame 162 C14orf243 NM 194278 hypothetical protein LOC91748 C14orf58 NM O17791 hypothetical protein LOC55640 C14or NM 173846 chromosome 14 open reading frame 8 C1 Sorf15 NM 016304 ribosomal protein L24-like C15 orf2O NM O25049 DNA helicase homolog PIF1 C15 orf27 NM 152335 hypothetical protein LOC123591 C15Crf38 NM 182616 hypothetical protein LOC348110 C15Crf39 NM O15492 hypothetical protein LOC56905 C15Crfa2 NM 152259 eucine-rich repeat kinase 1 C16orf53 NM O24516 hypothetical protein LOC79447 C16orf54 NM 175900 hypothetical protein LOC283897 C16orf58 NM 022744 hypothetical protein LOC64755 C17orf28 NM 030630 hypothetical protein LOC283987 C17orfa2 NM O24683 hypothetical protein LOC79736 C17orfas NM 152350 hypothetical protein LOC125144 C17orf53 NM 024032 hypothetical protein LOC78995 C17orf56 NM 1446.79 hypothetical protein LOC146705 C17orf59 NM O17622 hypothetical protein LOC54785 C17orf69 NM 152466 hypothetical protein LOC147081 C18or NM 001003674 hypothetical protein LOC753 isoform gamma 1 C18orf24 NM 145060 hypothetical protein LOC220134 C18orf25 NM OO10O8239 chromosome 18 open reading frame 25 isoform b C18Orfals NM 032933 hypothetical protein LOC85019 C19Corf10 NM O19107 chromosome 19 open reading frame 10 C19Crf23 NM 152480 hypothetical protein LOC148046 C19Crf3S NM 198532 hypothetical protein LOC374872 C19Crf39 NM 175871 hypothetical protein LOC126074 C19Corfa. NM 012109 brain-specific membrane-anchored protein C1orf106 NM 018265 hypothetical protein LOC55765 C1orf107 NM 014388 hypothetical protein LOC27042 C1orf108 NM O24595 hypothetical protein LOC79647 C1orf109 NM O17850 hypothetical protein LOC54955 C1orf115 NM O24709 hypothetical protein LOC79762 C1orf116 NM O23938 specifically androgen-regulated protein C1orf117 NM 182623 hypothetical protein LOC348487 C1orf119 NM 020141 hypothetical protein LOC56900 C1orf130 NM 00101.0980 hypothetical protein LOC400746 C1orf13S NM 024037 hypothetical protein LOC79000 C1orf140 NM 001010913 hypothetical protein LOC400804 C1orf144 NM O15609 putative MAPK activating protein PM20, PM21 C1orf145 NM 001025495 hypothetical protein LOC574407 C1orf149 NM O22756 hypothetical protein LOC64769 C1orf151 NM OO1032363 open reading frame 151 protein C1orf157 NM 182579 hypothetical protein LOC284573 C1orf162 NM 174896 hypothetical protein LOC128346 C1orf166 NM 024544 hypothetical protein LOC79594 C1orf172 NM 152365 hypothetical protein LOC126695 C1orf173 NM OO10O2912 hypothetical protein LOC127254 C1orf183 NM O19099 hypothetical protein LOC55924 isoform 1 C1orf187 NM 1985.45 chromosome 1 open reading frame 187 C1orf21 NM 030806 chromosome 1 open reading frame 21 C1orf56 NM 183059 chromosome 1 open reading frame 36 C1orf58 NM 004848 -induced gene isoform 1 C1orf245 NM 001025231 hypothetical protein LOC448834 C1orf249 NM 03.2126 hypothetical protein LOC84.066 C1orf52 NM 198077 hypothetical protein LOC148423 C1orf53 NM 001024594 hypothetical protein LOC388722 C1orf56 NM O17860 hypothetical protein LOC54964 C1orf61 NM OO6365 transcriptional activator of the c-fos C1orf66 NM O15997 hypothetical protein LOC51093 C1orf69 NM 001010867 hypothetical protein LOC200205 C1orf74 NM 152485 hypothetical protein LOC148304 C1orf76 NM 173509 hypothetical protein MGC16664 C1orf&O NM O22831 hypothetical protein LOC64853 C1orf33 NM 153035 hypothetical protein LOC127428 C1orf5 NM 001003665 hypothetical protein LOC375057 C1orf6 NM 145257 hypothetical protein LOC126731 US 2009/0232893 A1 Sep. 17, 2009 13

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description C1OTNF1 NM 030968 C1q and tumor necrosis factor related protein 1 C1RL NM O16546 complement component 1, r Subcomponent-like C20orf108 NM 080821 hypothetical protein LOC116151 C20orf11 NM O17896 chromosome 20 open reading frame 11 C20orf111 NM 016470 oxidative stress responsive 1 C20orf12 NM 018152 hypothetical protein LOC55184 C20orf28 NM O15417 hypothetical protein LOC25876 C20orf29 NM 018347 hypothetical protein LOC55317 C20orf24 NM O15511 hypothetical protein LOC25.980 C20orf242 NM O17671 chromosome 20 open reading frame 42 C20orf243 NM 016407 hypothetical protein LOC51507 C20orf244 NM 018244 basic FGF-repressed Zic binding protein isoform C20orf3 NM O24958 hypothetical protein LOC80023 C21orf114 NM 001012707 hypothetical protein LOC378826 C21orf24 NM 001001789 hypothetical protein LOC400866 C21orf29 NM 144991 chromosome 21 open reading frame 29 C21orf62 NM 019596 hypothetical protein LOC56245 C21orf69 NM 0581.89 chromosome 21 open reading frame 69 C21orf3 NM 145179 hypothetical protein LOC246.704 C22Orf13 NM 031444 open reading frame 13 C22Orf18 NM OO1002876 proliferation associated nuclear element 1 C22Orf25 NM 152906 hypothetical protein LOC128989 C22Orf NM 00100988O hypothetical protein LOC23313 isoform b C2Orf11 NM 144629 hypothetical protein LOC130132 C2Orf15 NM 144706 hypothetical protein LOC150590 C2Orf17 NM O24293 hypothetical protein LOC79137 C2Orf18 NM O17877 hypothetical protein LOC54978 C2Orf27 NMO13310 hypothetical protein LOC29798 C2Orf37 NM O25000 hypothetical protein LOC80067 C3orf17 NM 001025072 hypothetical protein LOC25871 isoform b C3orf21 NM 152531 hypothetical protein LOC152002 C3orf23 NM 0010298.39 hypothetical protein LOC285343 isoform 2 C3orf54 NM 032898 hypothetical protein LOC84984 C4orf13 NM OO1030316 hypothetical protein LOC84068 isoform a CSOrf21 NM 032042 hypothetical protein LOC83989 CSorf24 NM 1524.09 hypothetical protein LOC134553 CSOrfa. NM 016348 hypothetical protein LOC10826 isoform 1 C6orf130 NM 145063 hypothetical protein LOC221443 C6orf149 NM 020408 hypothetical protein LOC57128 C6orf15 NM O14070 STG protein C6orf15S NM O24882 hypothetical protein LOC79940 C6orf157 NM 198920 hypothetical protein LOC90025 C6orf16S NM 178823 hypothetical protein LOC154313 isoform 2 C6orf2O1 NM 206834 hypothetical protein LOC404220 C6orf2OS NM 001010909 hypothetical protein LOC394263 C6orf69 NM 173562 hypothetical protein LOC222658 C6orf26 NM O17909 hypothetical protein LOC55005 C6orf7 NM O25059 hypothetical protein LOC80129 C7 NM OOO587 complement component 7 precursor C7orf4 NM 178829 hypothetical protein LOC135927 C7orf58 NM 145111 hypothetical protein LOC221786 C8or NM 004337 hypothetical protein LOC734 C8orf17 NM O2O237 MOST-1 protein C8orf244 NM 019607 hypothetical protein LOC56260 C8orf51 NM 024035 hypothetical protein LOC78998 C9Crf106 NM 001012715 hypothetical protein LOC414318 C9orf128 NM 001012446 hypothetical protein LOC392307 C9Crf140 NM 178448 hypothetical protein LOC89958 C9orf152 NM 001012993 hypothetical protein LOC401546 C9orf163 NM 152571 hypothetical protein LOC158055 C9orf25 NM 1472O2 hypothetical protein LOC203259 C9orf27 NM 021208 open reading frame 27 C9Crfa2 NM 138333 hypothetical protein LOC116224 C9orfs NM 032012 hypothetical protein LOC23731 C9orf SO NM 1993.50 hypothetical protein LOC375759 C9orf58 NM OO10O2260 chromosome 9 open reading frame 58 isoform 2 C9orf6S NM 1388.18 hypothetical protein LOC158471 C9orf39 NM 032310 chromosome 9 open reading frame 89 C9orf1 NM 153045 hypothetical protein LOC203197 CA12 NM OO1218 carbonic anhydrase XII isoform 1 precursor CA2 NM OOOO67 carbonic anhydrase I US 2009/0232893 A1 Sep. 17, 2009 14

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description CABLES2 NM 03.1215 CdkS and Ablenzyme substrate 2 CACHD1 NM 020925 cache domain containing 1 CACNA1E NM 000721 calcium channel, Voltage-dependent, alpha 1E CACNA2D2 NM 001005505 calcium channel, Voltage-dependent, alpha CACNA2D3 NM 018398 calcium channel, Voltage-dependent, alpha CACNG4 NM O14405 voltage-dependent calcium channel gamma-4 CALCB NM 000728 calcitonin-related polypeptide, beta CALD1 NM 004342 caldesmon 1 isoform 2 CALM3 NM 005184 calmodulin 3 CALML4 NM 033429 calmodulin-like 4 isoform 2 CALN1 NM 001017440 calneuron 1 CALR NM 004343 calreticulin precursor CAMK2A NM O15981 calcium calmodulin-dependent protein kinase IIA CAMK2D NM 172127 calcium calmodulin-dependent protein kinase II CAMK2G NM OO1222 calcium calmodulin-dependent protein kinase II CAMKK1 NM 032294 calcium calmodulin-dependent protein kinase 1 CAMKK2 NM OO6549 calcium calmodulin-dependent protein kinase CAMLG NM OO1745 calcium modulating ligand CAMSAP1 NM 015447 calmodulin regulated -associated protein CAND1 NM 018448 TIP120 protein CAPN11 NM 007058 calpain 11 CAPN3 NM 212464 calpain 3 isoform g CAPZB NM OO4930 F-actin capping protein beta Subunit CARKL NM 013276 carbohydrate kinase-like CASC2 NM 178816 cancer Susceptibility candidate 2 isoform 1 CASC3 NM OO7359 cancer Susceptibility candidate 3 CASKIN2 NM 020753 cask-interacting protein 2 CASP2 NMO32982 caspase 2 isoform 1 preproprotein CASP8 NM OO1228 caspase 8 isoform A CASQ2 NM OO1232 cardiac callsequestrin 2 CAST NM O15576 cytomatrix protein p110 CBFA2T2 NM OO1032999 core-binding factor, runt domain, alpha subunit CBFB NM OO1755 core-binding factor, beta Subunit isoform 2 CBL NM 00518.8 Cas-Br-M (murine) ecotropic retroviral CBLL NM 024814 Cas-Br-M (murine) ecotropic retroviral CBXT NM 175709 chromobox homolog 7 CC2D1B NM 032449 coiled-coil and C2 domain containing 1B CCBL NM 004.059 cytoplasmic conjugate-beta lyase CCBP2 NM 001296 chemokine binding protein 2 CCDC102B NM O24781 hypothetical protein LOC79839 CCDC14 NM 022757 coiled-coil domain containing 14 CCDC21 NM O2.2778 coiled-coil domain containing 21 CCDC25 NM OO1031708 coiled-coil domain containing 25 isoform 1 CCDC33 NM 1827.91 hypothetical protein LOC80125 CCDC49 NM O17748 hypothetical protein LOC54883 CCDC58 NM 001017928 hypothetical protein LOC131076 CCDC68 NM O25214 CTCL tumor antigen se57-1 CCDC72 NM O15933 hypothetical protein LOC51372 CCDC93 NM O19044 hypothetical protein LOC54520 CCDC94 NM 018074 hypothetical protein LOC55702 CCDC97 NM 052848 hypothetical protein LOC90324 CCDC98 NM 139076 coiled-coil domain containing 98 CCKAR NM OOO730 cholecystokinin A receptor CCL18 NM OO2988 Small inducible cytokine A18 precursor CCL22 NM OO2990 Small inducible cytokine A22 precursor CCL4L1 NM 001001435 chemokine (C-C motif) ligand 4-like 1 precursor CCL4L2 NM 207007 chemokine (C-C motif) ligand 4-like 2 precursor CCL7 NM OO6273 chemokine (C-C motif) ligand 7 precursor CCND1 NM 053056 cyclin D1 CCND2 NM OO1759 cyclin D2 CCNT2 NM OO1241 cyclin T2 isoform a CCPG1 NM 004748 cell cycle progression 1 isoform 1 CCR1 NM 001295 chemokine (C-C motif) receptor 1 CCR2 NM OOO647 chemokine (C-C motif) receptor 2 isoform A CCR6 NM 004367 chemokine (C-C motif) receptor 6 CCT5 NM 012073 chaperonin containing TCP1, Subunit 5 (epsilon) CD109 NM 133493 CD109 CD164L2 NM 207397 CD164 sialomucin-like 2 CD22 NM OO1771 CD22 antigen CD244 NM 016382 CD244 natural killer cell receptor 2B4 CD276 NM 001024736 CD276 antigen isoform a US 2009/0232893 A1 Sep. 17, 2009 15

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description CD28 NM OO6139 CD28 antigen CD3OOC NM OO6678 CD300C antigen CD3OOLG NM 145273 triggering receptor expressed on myeloid cells CD34 NM 001025109 CD34 antigen isoform a CD3D NM OOO732 CD3D antigen, delta polypeptide (TIT3 complex) CD4 NM 000616 CD4 antigen precursor CD40 NM 152854 CD40 antigen isoform 2 precursor CD44 NM 000610 CD44 antigen isoform 1 precursor CD47 NM 001025079 CD47 molecule isoform 3 precursor CD53 NM OOO560 CD53 antigen CD8O NM 005191 CD80 antigen (CD28 antigen ligand 1, B7-1 CD82 NM 001024844 CD82 antigen isoform 2 CD84 NM OO3874 CD84 antigen (leukocyte antigen) CD8A NM OO1768 CD8 antigen alpha polypeptide isoform 1 CD93 NM 012072 CD93 antigen precursor CDAN1 NM 138477 codanin CDC25A NM OO1789 cell division cycle 25A isoform a CDC25B NM 004358 cell division cycle 25B isoform 2 CDC42BPA NM OO3607 CDC42-binding protein kinase alpha isoform B CDC42SE1 NM O2O239 CDC42 Small effector 1 CDCAS NM 080668 cell division cycle associated 5 CDGAP NM 020754 Cdc42 GTPase-activating protein CDH1 NM 004360 cadherin 1, type 1 preproprotein CDH17 NM 004O63 cadherin 17 precursor CDH3 NM OO1793 cadherin 3, type 1 preproprotein CDHS NM OO1795 cadherin 5, type 2 preproprotein CDK2AP1 NM 004642 CDK2-associated protein 1 CDKSR2 NMOO3936 cyclin-dependent kinase 5, regulatory subunit 2 CDK5RAP3 NM O25197 CDK5 regulatory subunit associated protein 3 CDK6 NM OO1259 cyclin-dependent kinase 6 CDKAL1 NM O17774 CDK5 regulatory subunit associated protein CDON NM 016952 Surface glycoprotein, Ig Superfamily member CDR2L NM 014603 paraneoplastic antigen CDRT1 NM OO6382 CMT1A duplicated region transcript 1 CDRT4 NM 173622 hypothetical protein LOC284040 CDX1 NM 001804 caudal type homeo box transcription factor 1 CEACAMS NM 0043.63 -related cell adhesion CELSR1 NM 014246 cadherin EGF LAG seven-pass G-type receptor 1 CELSR2 NM OO1408 cadherin EGF LAG seven-pass G-type receptor 2 CELSR3 NM OO1407 cadherin EGF LAG seven-pass G-type receptor 3 CENTA2 NM 018.404 centaurin-alpha 2 protein CENTD1 NM O15230 centaurin delta 1 isoform a CENTO1 NM 014770 centaurin, gamma 1 CEP135 NM O25009 centrosome protein 4 CEP192 NM 018069 hypothetical protein LOC55125 isoform 2 CEP350 NM O14810 centrosome-associated protein 350 CFD NM OO1928 complement factor D preproprotein CGO18 NM 052818 hypothetical protein LOC90634 CGN NM 020770 cingulin CGNL1 NM 032866 cingulin-like 1 CHDS NM O15557 chromodomain helicase DNA binding protein 5 CHD6 NM 032221 chromodomain helicase DNA binding protein 6 CHKA NM OO1277 choline kinase alpha isoform a CHKB NM 152253 choline? ethanolamine kinase isoform b CHML NM OO1821 choroideremia-like Rab escort protein 2 CHPF NM O24536 chondroitin polymerizing factor CHRNB1 NM OOO747 nicotinic acetylcholine receptor beta 1 subunit CHRNB2 NM OOO748 cholinergic receptor, nicotinic, beta CHRNG NM 005199 cholinergic receptor, nicotinic, gamma CHST10 NM 004854 HNK-1 sulfotransferase CHST13 NM 152889 carbohydrate (chondroitin 4) sulfotransferase CHST3 NM OO4273 carbohydrate (chondroitin 6) sulfotransferase 3 CHST4 NM OO5769 carbohydrate (N-acetylglucosamine 6-O) CHURC1 NM 145165 churchill domain containing 1 CIAPIN1 NM 020313 cytokine induced apoptosis inhibitor 1 CLAS1 NM 004.895 cryopyrin isoform a CIDEA NM OO1279 cell death-inducing DFFA-like effectora isoform CIR NM 004882 CBF1 interacting corepressor CIT NM 007174 citron CITED4 NM 133467 Cbp/p300-interacting transactivator, with C LASP1 NM O15282 CLIP-associating protein 1 US 2009/0232893 A1 Sep. 17, 2009 16

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description CLCN6 NM 001286 chloride channel 6 isoform CC-6a CLEC12A NM 138337 myeloid inhibitory C-type lectin-like receptor CLEC12B NM 205852 macrophage antigenh CLEC4E NM O14358 C-type lectin domain family 4, member E CLEC4F NM 173535 C-type lectin, Superfamily member 13 CLECSA NM 013252 C-type lectin, Superfamily member 5 CLIC4 NM O13943 chloride intracellular channel 4 CLNS NM OO6493 ceroid-lipofuscinosis, neuronal 5 CLN6 NM O17882 CLN6 protein CLN8 NM 018941 CLN8 protein CLPS NM OO1832 colipase preproprotein CLYBL NM 13828O citrate lyase beta like CMYA5 NM 153610 cardiomyopathy associated 5 CNDP2 NM 018235 CNDP dipeptidase 2 (metallopeptidase M20 CNGA2 NM OO5140 cyclic nucleotide gated channel alpha 2 CNGA3 NM 001298 cyclic nucleotide gated channel alpha 3 CNGB1 NM 001297 cyclic nucleotide gated channel beta 1 CNNM1 NM O2O348 cyclin M1 CNNM3 NM O17623 cyclin M3 isoform 1 CNOT4 NM 013316 CCR4-NOT transcription complex, Subunit 4 CNP NM 033133 2',3'-cyclic nucleotide 3' phosphodiesterase CNTD1 NM 173478 hypothetical protein LOC124817 CNTD2 NM O24877 hypothetical protein LOC79935 CNTNAP2 NM 014141 cell recognition molecule Caspir2 precursor COG4 NM O15386 component of oligomeric golgi complex 4 COGS NM OO6348 component of oligomeric golgi complex 5 isoform COL12A1 NM 004370 , type XII, alpha 1 long isoform COL18A1 NM O30582 alpha 1 type XVIII collagen isoform 1 precursor COL1A1 NM OOOO88 alpha 1 preproprotein COL21A1 NM O3O820 collagen, type XXI, alpha 1 precursor COL24A1 NM 152890 collagen, type XXIV, alpha 1 COL4A4 NM 000092 alpha 4 type IV collagen precursor COL4A5 NM 000495 alpha 5 type IV collagen isoform 1, precursor COLSA2 NM OOO393 alpha 2 preproprotein COLSA3 NM O15719 collagen, type V, alpha 3 preproprotein COL9A1 NM OO1851 alpha 1 type IX collagen isoform 1 precursor COL9A2 NM OO1852 alpha 2 type IX collagen COMMD2 NM 016094 COMM domain containing 2 COMMDS NM 014066 hypertension-related calcium-regulated gene COMMD7 NM 053041 COMM domain containing 7 COPA NM 0043.71 coatomer protein complex, Subunit alpha COPZ1 NM 016057 coatomer protein complex, Subunit Zeta 1 COQ5 NM 032314 hypothetical protein LOC84274 COQ9 NM 020312 hypothetical protein LOC57017 CORIN NM OO6587 corin CORO1B NM 001018070 coronin, actin binding protein, 1B CORO2B NM OO6091 coronin, actin binding protein, 2B COTL1 NM 021149 coactosin-like 1 COVA1 NM OO6375 cytosolic ovarian carcinoma antigen 1 isoform a COX4NB NM OO6067 neighbor of COX4 COX7A2L NM 004718 cytochrome c oxidase subunit VIIa polypeptide 2 P110 NM 014711 CP110 protein PAMD8 NM O15692 C3 and PZP-like, alpha-2-macroglobulin domain PB2 NM OO1872 plasma carboxypeptidase B2 isoform a PD NM OO1304 carboxypeptidase D precursor PLX2 NM OO10O8220 complexin 2 PM NM 0010055O2 carboxypeptidase M precursor PNE3 NM OO3909 copine III POX NM OOOO97 coproporphyrinogen oxidase PSF2 NM O17437 cleavage and polyadenylation specific factor 2 PSF3L NM 032179 related to CPSF subunits 68 kDa isoform 2 RAMP1L, NM 020825 Crm, cramped-like EB1 NM 004379 cAMP responsive element binding protein 1 EB3L2 NM 194O71 cAMP responsive element binding protein 3-like EB5 NM 001011666 cAMP responsive element binding protein 5 EBL2 NM 001310 cAMP responsive element binding protein-like 2 EG2 NM 153836 cellular repressor of E1A-stimulated genes 2 ELD1 NM OO 1031717 cysteine-rich with EGF-like domains 1 isoform 1 SPLD2 NM 031476 cysteine-rich Secretory protein LCCL domain K NM OO52O6 v-crk sarcoma virus CT10 oncogene homolog LF3 NM O15986 cytokine receptor-like factor 3 US 2009/0232893 A1 Sep. 17, 2009 17

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description CRNKL1 NM 016652 crooked neck-like 1 protein CRSP2 NM 004229 required for Sp1 transcriptional CRSP7 NM 004831 cofactor required for Sp1 transcriptional CRTC3 NM O22769 transducer of regulated CREB protein 3 CRX NM 000554 cone-rod homeobox protein CSDC2 NM O14460 RNA-binding protein pippin CSF NM 172212 colony stimulating factor 1 isoform a precursor CSF2RA NM 006140 colony stimulating factor 2 receptor alpha chain CSMD1 NM 033225 CUB and Sushi multiple domains 1 CSNK1 G1 NM 001011664 casein kinase 1, gamma 1 isoform L. CSNK1G3 NM OO1031812 casein kinase 1, gamma 3 isoform 2 CSNK2A1 NM OO1895 casein kinase II alpha 1 subunit isoform a CSPG3 NM 004386 chondroitin Sulfate proteoglycan 3 (neurocan) CSRP3 NM OO3476 cysteine and glycine-rich protein 3 CSTB NM OOO100 cystatin B CTAGE1 NM 172241 cutaneous T-cell lymphoma-associated antigen 1 CTDSP2 NM OO5730 nuclear LIM interactor-interacting factor 2 CTF NM OO1330 cardiotrophin 1 CTGF NM OO1901 connective tissue growth factor CTH NM OO1902 cystathionase isoform 1 CTLA4 NM OO5214 cytotoxic T-lymphocyte-associated protein 4 CTNNBIP1 NM 00101.2329 , beta interacting protein 1 CTNND1 NM OO1331 catenin (cadherin-associated protein), delta 1 CTSB NM OO1908 cathepsin B preproprotein CTSC NM 148170 cathepsin C isoform b precursor CTSD NM OO1909 cathepsin D preproprotein CTSS NM 004079 cathepsin Spreproprotein CTTN NMOO5231 cortactin isoform a CTXN1 NM 206833 cortexin 1 CUBN NM 001081 cubilin CUGBP2 NM 001025076 CUG triplet repeat, RNA binding protein 2 CUL3 NM 003590 cullin 3 CUL5 NM OO3478 Vasopressin-activated calcium-mobilizing CWF19L1 NM 018294 CWF19-like 1, cell cycle control CX3CL1 NM OO2996 chemokine (C-X3—C motif) ligand 1 CXCL12 NM OOO609 chemokine (C X-C motif) ligand 12 (stromal CXCL14 NM OO4887 Small inducible cytokine B14 precursor CXCL9 NM 002416 Small inducible cytokine B9 precursor CXorf21 NM O251.59 hypothetical protein LOC80231 CXorf23 NM 1982.79 hypothetical protein LOC256643 CXorf34 NM O24917 hypothetical protein LOC79979 CXorf38 NM 144970 hypothetical protein LOC159013 CXorf53 NM 001018055 BRCA1/BRCA2-containing complex subunit 36 CXXC5 NM 016463 CXXC finger 5 CXXC6 NM 03.0625 CXXC finger 6 CYB561D1 NM 182580 cytochrome b-561 domain containing 1 CYB5B NM O30579 cytochrome b5 outer mitochondrial membrane CYB5D1 NM 144607 hypothetical protein LOC124637 CYBRD1 NM 024843 cytochrome b reductase 1 CYCS NM 018947 cytochromec CYFIP2 NM O14376 cytoplasmic FMR1 interacting protein 2 CYLC2 NM 001340 cylicin 2 CYLD NM O15247 carboxyl-terminal hydrolase CYLD CYLN2 NM OO3388 cytoplasmic linker 2 isoform 1 CYP11B1 NM 000497 cytochrome P450, family 11, subfamily B, CYP11B2 NM 000498 cytochrome P450, subfamily XIB polypeptide 2 CYP1A2 NM 000761 cytochrome P450, family 1, Subfamily A, CYP26B1 NM 019885 cytochrome P450, family 26, subfamily b, CYP2B6 NM 000767 cytochrome P450, family 2, Subfamily B, CYP2C9 NM 000771 cytochrome P450, family 2, Subfamily C, CYP8B1 NM 004391 cytochrome P450, family 8, Subfamily B, D2HGDH NM 152783 D-2-hydroxyglutarate dehydrogenase DAB2 NM OO1343 disabled homolog 2 DAPK1 NM OO4938 death-associated protein kinase 1 DAPK2 NM O14326 death-associated protein kinase 2 DBF NM OO6716 activator of S phase kinase DBT NM OO1918 dihydrolipoamide branched chain transacylase DCAKD NM O24819 dephospho-CoA kinase domain containing DCAMKL1 NM OO4734 doublecortin and CaM kinase-like 1 DCLRE1C NM OO1033855 artemis protein isoform a DCST2 NM 144622 hypothetical protein LOC127579 US 2009/0232893 A1 Sep. 17, 2009 18

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description DCTD NM 00101.2732 CMP deaminase isoform a DCTN4 NM 016221 ynactin 4 (p62) DCTNS NM 032486 ynactin 4 X NM 000555 oublecortin isoform a DAH1 NM 012137 imethylarginine dimethylaminohydrolase 1 EFL1 NM O17707 evelopment and differentiation enhancing 1 NM 001001711 hypothetical protein LOC414301 2 NM 032341 DNA-damage inducible protein 2 T4L NM 145244 DNA-damage-inducible transcript 4-like R1 NM OO1954 iscoidin domain receptor family, member 1 X11 NM 004399 DEAD H (Asp-Glu-Ala-Asp/His) box polypeptide 11 X17 NM OO6386 DEAD box polypeptide 17 isoform p82 X23 NM 004.818 DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 NM 133328 eath effector domain-containing DNA binding NM O05217 efensin, alpha 3 preproprotein NM OO1926 efensin, alpha 6 preproprotein :s NM OO3676 egenerative spermatocyte homolog 1, lipid NND1C NM O24898 hypothetical protein LOC79958 E NND2C NM 198459 DENN/MADD domain containing 2C NM O15954 2-deoxyribose-5-phosphate aldolase homolog NM OO10O2862 erlin-3 protein isoform b NM 213566 DNA fragmentation factor, 45 kDa, alpha B NM OO1004285 DNA fragmentation factor, 40 kD, beta NM 004080 iacylglycerol kinase, beta isoform 1 NM OO1347 iacylglycerol kinase, theta NM 014762 24-dehydrocholesterol reductase precursor NM O24887 ehydrodolichyl diphosphate synthase isoform a NMOOO791 ihydrofolate reductase NM O15510 hypothetical protein LOC25979 NM O05771 NADP-dependent retinol dehydrogenase/reductase T K D 1 NM 0187O6 ehydrogenase E1 and transketolase domain NM 138614 DEAH (Asp-Glu-Ala-His) box polypeptide 30 NM 032656 DEAH (Asp-Glu-Ala-His) box polypeptide 37 NM OO5219 iaphanous 1 NM 033081 eath inducer-obliterator 1 isoform c NM 018171 DIP13 beta NM 173602 hypothetical protein LOC576.09 NM O14974 hypothetical protein LOC22982 NM 145173 Small GTP-binding tumor suppressor 1 NM 017594 NM 052952 hypothetical protein LOC116093 NM 001012957 disrupted in schizophrenia 1 isoform LV NM 033425 DIX domain containing 1 isoform b NM 020466 hypothetical protein LOC57226 NM O15395 hypothetical protein LOC25851 NM 194295 hypothetical protein LOC196968 NM 02O161 hypothetical protein LOC56918 NM 0321.21 implantation-associated protein NM 001012987 hypothetical protein LOC388957 NM 0010099.13 hypothetical protein LOC374383 NM 173463 hypothetical protein LOC91050 NM 138368 hypothetical protein LOC91056 NM 001010903 hypothetical protein LOC38.9384 NM OO6094 eleted in liver cancer 1 isoform 2 LEC1 NM OO7335 eleted in lung and esophageal cancer 1 isoform NM 021120 synapse-associated protein 102 LGAP2 NM 004745 iscs large-associated protein 2 NM 178120 istal-less homeobox 1 isoform 1 DMBX1 NM 147192 iencephalon mesencephalon homeobox. 1 isoform b DMTF1 NM 021145 cyclin D binding myb-like transcription factor DNAH11 NM 003777 ynein, axonemal, heavy polypeptide 11 DNAJA4 NM 018602 DnaJ (Hsp40) homolog, subfamily A, member 4 DNAJC11 NM 018198 DnaJ (Hsp40) homolog, subfamily C, member 11 DNAJC14 NM 032364 opamine receptor interacting protein DNAJC18 NM 152686 DnaJ (Hsp40) homolog, subfamily C, member 18 DNAL4 NM OO5740 ynein chain 4, axonemal DNASE1L1 NM 001009932 eoxyribonuclease I-like 1 precursor DNASE2 NM OO1375 eoxyribonuclease II, lysosomal precursor DNMT3A NM O22552 DNA methyltransferase 3alpha isoform DOC2B NM 003585 ouble C2-like domains, beta DOCK1 NM OO1380 edicator of cytokinesis 1 US 2009/0232893 A1 Sep. 17, 2009 19

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description DOCK2 NM 004946 edicator of cytokinesis 2 DOCK3 NM OO4947 edicator of cytokinesis 3 DOCK9 NM O15296 edicator of cytokinesis 9 DPCR1 NM 080870 iffuse panbronchiolitis critical region 1 DPF3 NM 012074 D4, zinc and double PHD fingers, family 3 DPY19L2 NM 173812 hypothetical protein LOC2834.17 DPYSL3 NM OO1387 ihydropyrimidinase-like 3 DQX1 NM 133637 DEAQ box polypeptide 1 (RNA-dependent ATPase) DSCAM NM 206887 Down syndrome cell adhesion molecule isoform DTNA NM 001390 ystrobrevin alpha isoform 1 DTNB NM O21907 ystrobrevin, beta isoform 1 DTWD2 NM 173666 DTW domain containing 2 DTX1 NM 004416 eltex homolog DTX3L NM 138287 eltex 3-like DUSP13 NM OO1007271 muscle-restricted dual specificity phosphatase DUSP4 NM 001394 ual specificity phosphatase 4 isoform 1 DUT NM 001025248 UTP pyrophosphatase isoform 1 precursor DUX1 NM 012146 ouble homeobox, 1 DUXA NM 001012729 hypothetical protein LOC503835 DVL3 NM 004423 ishevelled 3 DYNC2LI1 NM 016008 ynein 2 light intermediate chain isoform 1 DYRK1B NM 004714 ual-specificity tyrosine-(Y)-phosphorylation DZIP1 NM O14934 DAZ interacting protein 1 isoform 1 E2F2 NM 004.091 E2F transcription factor 2 E2F3 NM OO1949 E2F transcription factor 3 EAF1 NM 033083 ELL associated factor 1 EARS2 NM 133451 hypothetical protein LOC124.454 EBI3 NMOO5755 Epstein-Barr virus induced gene 3 precursor ECM2 NM 001393 extracellular matrix protein 2 precursor ECOP NM 030796 EGFR-coamplified and overexpressed protein E NM 021783 X-linked ectodysplasin receptor NM 080738 EDAR-associated death domain isoform B NM 014674 ER degradation enhancer, mannosidase alpha-like NM 004.720 endothelial differentiation, lysophosphatidic NM 000114 endothelin 3 isoform 1 preproprotein NM 013302 elongation factor-2 kinase NM OO 1033562 EF-hand calcium binding domain 5 isoform 2 NM OO4105 EGF-containing fibulin-like extracellular matrix NM 004428 ephrin A1 isoform a precursor NM OO4952 ephrin A3 NM OO1406 ephrin-B3 precursor NM OO5864 embryonal Fyn-associated Substrate isoform 1 E NM 201284 epidermal growth factor receptor isoform d E NM O22051 egl nine homolog 1 E NM OO1964 early growth response 1 E NM 014601 EH-domain containing 2 E NM OO2759 eukaryotic translation initiation factor 2-alpha E NM 004.836 eukaryotic translation initiation factor 2-alpha E NM 001013703 eukaryotic translation initiation factor 2 alpha EIF2C1 NM 012199 eukaryotic translation initiation factor 2C, 1 EIF4EBP2 NM 004.096 eukaryotic translation initiation factor 4E EIF4ENIF1 NM 019843 eukaryotic translation initiation factor 4E EIF5 NM OO1969 eukaryotic translation initiation factor 5 E NM 018696 elaChomolog 1 NM 001421 E74-like factor 4 (ets domain transcription NM 001422 E74-like factor SESE-2b NM OO5229 ELK1 protein NM 021795 ELK4 protein isoform b NM 014800 engulfment and cell motility 1 isoform 1 NM 133171 engulfment and cell motility 2 NM 018712 ELMO domain containing 1 NM 032377 elongation factor 1 homolog (ELF1, S. NM 021814 homolog of yeast long chain polyunsaturated NM 024090 ELOVL family member 6, elongation of long chain NM 152463 essential meiotic endonuclease 1 homolog 1 NM 133455 EMI domain containing 1 NM 001423 epithelial 1 NM 013447 egf-like module containing, mucin-like, hormone NM OO1008493 enabled homolog isoform a NM 031889 enamelin NM 001428 enolase 1 US 2009/0232893 A1 Sep. 17, 2009 20

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description ENPP1 NM OO6208 ectonucleotide pyrophosphatase/phosphodiesterase ENPP5 NM 021572 ectonucleotide pyrophosphatase/phosphodiesterase ENPP6 NM 153343 ectonucleotide pyrophosphatase/phosphodiesterase ENSA NM 207043 endosulfine alpha isoform 2 ENTPD3 NM OO1248 ectonucleoside triphosphate diphosphohydrolase EP4OO NM O15409 E1A binding protein p400 EPB41 NM OO4437 erythrocyte membrane protein band 4.1 EPB41LS NM 020909 erythrocyte membrane protein band 4.1 like 5 EPHA2 NM 004431 ephrin receptor Eph A2 EPHA3 NM OO5233 ephrin receptor EphA3 isoform a precursor EPHB4 NM 004444 ephrin receptor EphB4 precursor EPM2AIP1 NM O14805 EPM2A interacting protein 1 EPO NM 000799 erythropoietin precursor ERBB3 NM OO1982 erbB-3 isoform 1 precursor ERGIC1 NM 020462 -golgi intermediate ESAM NM 138961 endothelial cell adhesion molecule ESRRG NM 001438 estrogen-related receptor gamma isoform 1 ET NM 024311 hypothetical protein LOC79157 ETV1 NM OO4956 ets variant gene 1 ETV3 NM OO5240 ets variant gene 3 ETV6 NM OO1987 ets variant gene 6 EVC NM 153717 Ellis van Creveld syndrome protein EXOC2 NM 018303 Sec5 protein EXOC4 NM O21807 SEC8 protein isoform a EXTL3 NM OO1440 Reg receptor EYA2 NM 005.244 eyes absent 2 isoform a 1 NM OO1991 enhancer of Zeste homolog 1 NMO16946 isoform a precursor NM 000129 coagulation factor XIII A1 subunit precursor NM OO1992 coagulation factor II receptor precursor F2RL1 NM OO5242 coagulation factor II (thrombin) receptor-like 1 F2RL3 NM OO3950 coagulation factor II (thrombin) receptor-like 3 FADS2 NM OO4265 atty acid desaturase 2 FADS6 NM 178128 atty acid desaturase domain family, member 6 FAIM2 NM 012306 Fas apoptotic inhibitory molecule 2 FAM1 OOB NM 182565 hypothetical protein LOC283991 FAM102A NM 203305 early estrogen-induced gene 1 protein isoform b FAM102B NM 00101.0883 hypothetical protein LOC284611 FAM104A NM 032837 hypothetical protein LOC84923 FAM106A NM O24974 hypothetical protein LOC80039 FAM107A NM 007177 downregulated in renal cell carcinoma FAM107B NM 031453 hypothetical protein LOC83641 FAM111A NM O22074 hypothetical protein LOC63901 FAM117A NM O3O802 C/EBP-induced protein FAM11A NM 032508 amily with sequence similarity 11, member A FAM19A1 NM 213609 amily with sequence similarity 19 (chemokine FAM2OB NM O14864 amily with sequence similarity 20, member B FAM36A NM 198076 amily with sequence similarity 36, member A FAM3B amily with sequence similarity 3, member B FAM40A hypothetical protein LOC85369 FAM43A hypothetical protein LOC131583 FAMS3B hypothetical protein LOC9679 FAMSSC hypothetical protein LOC91775 FAMSB BMP retinoic acid-inducible neural-specific FAM60A amily with sequence similarity 60, member A FAM62C amily with sequence similarity 62 (C2 domain FAM71C hypothetical protein LOC196472 FAM81A hypothetical protein LOC145773 FAM83E hypothetical protein LOC54854 FAM83F hypothetical protein LOC113828 FAM83H hypothetical protein LOC286.077 FAM89B Mammary Turmor Virus Receptor homolog 1 FAM98B NM 173611 hypothetical protein LOC283742 EANCC NM OOO136 Fanconi anemia, complementation group C EANCD2 NM 033084 Fanconi anemia complementation group D2 isoform FATE1 NM 033085 etal and adult testis expressed transcript FBS1 NM O224.52 fibrosin 1 FBXL11 NM 012308 F-box and leucine-rich repeat protein 11 FBXO16 NM 172366 F-box only protein 16 FBXO21 NM O15002 F-box only protein 21 isoform 2 FBXO27 NM 178820 F-box protein 27 US 2009/0232893 A1 Sep. 17, 2009 21

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description NM O24735 F-box protein 31 NM O17943 F-box only protein 34 NM 001014765 F-box protein 44 iso orm 1 NM 012347 F-box only protein 9 isoform 1 NM 012300 F-box and WD-40 domain protein 1B isoform C NM 012174 F-box and WD-40 domain protein 8 isoform 2 NM OO2002 Fc fragment of IgE, ow affinity II, receptor NM OOO569 Fc fragment of IgG, ow affinity IIIa, receptor NM 000570 ow affinity immunoglobulingamma Fc region NM 033449 FCH and double SH3 domains 1 NM OO6731 ukutin NM O2O177 eminization 1 homo Oga NM O21871 fibrinogen, alpha polypeptide isoform alpha NM 018351 FYVE, RhoGEF and PH domain containing 6 NM 000800 fibroblast growth fac or 1 (acidic) isoform 1 NM OO5117 fibroblast growth fac or 19 precursor NM 023107 fibroblast growth fac or receptor 1 isoform 5 T NM OO2012 ragile triad gene 's NM 175616 hypothetical protein LOC202299 BP10 NM O21939 FK506 binding prote in 10, 65 kDa BP1A NM 000801 FK506-binding protein 1A BP5 NM OO4117 FK506 binding protein 5 BP9 NM OO7270 FK506 binding protein 9 BP9L. NM 182827 FK506 binding protein 9-like RP NM 024301 ukutin-related protein SG44 NM 03.1904 FKSG44 protein O159 NM 018013 hypothetical protein LOCSSO84 O324 NM 018059 hypothetical protein LOCSS698 L10357 NM 018071 hypothetical protein LOC55701 LJ10490 NM 018111 hypothetical protein LOC55150 LJ108O3 NM 018224 hypothetical protein LOCSS744 LJ10815 NM 018231 amino acid transporter LJ11021 NM 023012 hypothetical protein LOC65117 isoform a L11151 NM 018340 hypothetical protein LOC55313 L11171 NM 018348 hypothetical protein LOC55.783 LJ11259 NM 018370 hypothetical protein LOC55332 LJ11292 NM 018382 hypothetical protein LOCSS338 LJ11806 NM 024824 nuclear protein UKp68 isoform 1 LJ12SOS NM O24749 hypothetical protein LOC798OS LJ12681 NM O22773 hypothetical protein LOC64788 LJ12700 NM 024910 hypothetical protein LOC79970 LJ12949 NM 023008 hypothetical protein LOC65095 isoform 1 LJ13197 NM O24614 hypothetical protein LOC79667 L14001 NM O24677 hypothetical protein LOC7973O LJ14213 NM 024841 hypothetical protein LOC798.99 L14397 NM 032779 hypothetical protein LOC8486S LJ14816 NM 032845 hypothetical protein LOC84931 LJ14834 NM 032849 hypothetical protein LOC84935 20032 NM O17628 hypothetical protein LOCS4790 2003S NM O17631 hypothetical protein LOCSS6O1 LJ2O160 NM O17694 hypothetical protein LOCS4.842 LJ2O186 NM 207514 differentially expressed in FDCP8 isoform 1 LJ2O297 NM O17751 hypothetical protein LOC55627 isoform 1 20581 NM O17888 hypothetical protein LOCS4988 LJ2O582 NM 014106 hypothetical protein LOCS4989 LJ2O628 NM O17910 hypothetical protein LOCSSOO6 20701 NM O17933 hypothetical protein LOCSSO22 LI2O758 NM O17952 hypothetical protein LOC55037 LJ2O972 NM O25030 hypothetical protein LOC80098 21865 NM O22759 endo-beta-N-acetylg lucosaminidase LJ21963 NM O24560 hypothetical protein LOC796.11 LJ22795 NM O25084 hypothetical protein LOC8O154 LJ23322 NM O24955 hypothetical protein LOC80O2O LJ23834 NM 152750 hypothetical protein LOC222256 LJ25996 NM 001001699 hypothetical protein LOC4O1109 LJ261.75 NM 001001668 hypothetical protein LOC38.8566 LT27365 NM 207477 hypothetical protein LOC4OO931 LJ31222 NM 207388 hypothetical protein LOC388387 LJ31568 NM 152509 hypothetical protein LOC150244 LJ31875 NM 182531 hypothetical protein LOC197320 LJ32O11 NM 182516 hypothetical protein LOC14893O US 2009/0232893 A1 Sep. 17, 2009 22

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. RefSeq, Transcript ID Description NM 152458 hypothetical protein LOC146540 NM 144709 hypothetical protein LOC150962 NM 153038 hypothetical protein LOC151278 NM 152491 hypothetical protein LOC148811 NM 144667 hypothetical protein LOC144360 NM 144577 hypothetical protein LOC93233 NM 153041 hypothetical protein LOC150596 hypothetical protein LOC161145 hypothetical protein LOC2847S6 hypothetical protein LOC388.939 hypothetical protein LOC4OO765 hypothetical protein LOC285830 FLJ35740 protein hypothetical protein LOC162387 hypothetical protein LOC2S6O76 hypothetical protein LOC4O1563 hypothetical protein LOC284.047 hypothetical protein LOC219988 hypothetical protein LOC166979 hypothetical protein LOC284309 hypothetical protein LOC91574 hypothetical protein LOC205327 mitochondrial COX1 8 isoform 5 hypothetical protein LOC13272O hypothetical protein LOC4OO360 hypothetical protein LOC283777 hypothetical protein LOC4OOO73 hypothetical protein LOC28S962 hypothetical protein LOC399886 hypothetical protein LOC40O870 hypothetical protein LOC4O1263 hypothetical protein LOC4OO935 hypothetical protein LOC399923 hypothetical protein LOC4OO941 hypothetical protein LOC40O892 hypothetical protein LOC388,115 hypothetical protein LOC40O823 hypothetical protein LOC389649 hypothetical protein LOC4O1039 hypothetical protein LOC124149 hypothetical protein LOC3451.93 hypothetical protein LOC4OO624 hypothetical protein LOC4OOSS6 hypothetical protein LOC40O867 hypothetical protein LOC4O1508 NM 001004349 hypothetical protein LOC441140 NM 198557 hypothetical protein LOC375287 NM 207462 hypothetical protein LOC4OO666 NM 001001684 hypothetical protein LOC400576 NM 207395 hypothetical protein LOC38.8569 NM 1984.45 hypothetical protein LOC126432 NM 207390 hypothetical protein LOC388512 NM 207483 hypothetical protein LOC4O1040 NM 001001703 hypothetical protein LOC4O1.191 NM 207458 hypothetical protein LOC4OO627 NM 1984.62 FLJ46154 protein NM 207463 hypothetical protein LOC4OO679 NM 001001693 hypothetical protein LOC4OO932 NM 207430 hypothetical protein LOC399949 NM 001005303 hypothetical protein LOC389.064 NM 207434 hypothetical protein LOC4OOOO2 NM 207504 hypothetical protein LOC4O1459 NM 207405 hypothetical protein LOC3891.97 NM OO1004330 hypothetical protein LOC44O107 NM 207426 orkhead box I2 NM OO1.007546 hypothetical protein LOC44086S NM OO1004336 hypothetical protein LOC440465 NM OO5803 NM 004475 NM OO2019 ms-related tyrosine kinase 1 (vascular NM 182925 ms-related tyrosine kinase 4 isoform 1 US 2009/0232893 A1 Sep. 17, 2009 23

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description FLYWCH1 NM 032296 FLYWCH-type zinc finger 1 isoform a FMNL3 NM 175736 ormin-like 3 isoform 1 FMO4 NM 002022 flavin containing monooxygenase 4 FMOD NM 002023 fibromodulin precursor FN1 NM 002026 fibronectin 1 isoform 3 preproprotein FNDC1 NM 032532 fibronectin type III domain containing 1 FNDC5 NM 153756 fibronectin type III domain containing 5 FNDC8 NM 017559 hypothetical protein LOC54752 FNTB NM 002028 arnesyltransferase, CAAXbox, beta FOSB NM OO6732 FBJ murine osteosarcoma viral oncogene homolog FOSL2 NM O05253 FOS-like antigen 2 FOXJ2 NM 018416 orkhead box J2 FOXJ3 NM O14947 orkhead box J3 FOXK2 NM 181430 orkhead box K2 isoform 2 FOXO1A NM OO2015 orkhead box O1A FOXP1 NM 032682 orkhead box P1 isoform 1 FRMD1 NM 024919 FERM domain containing 1 FRMPD2 NM 001017929 FERM and PDZ domain containing 2 isoform 2 FSCN1 NM OO3O88 ascin 1 FSD1 L, NM 207647 fibronectin type III and SPRY domain containing FST NM OO6350 ollistatin isoform FST317 precursor FSTL4 NM O15082 ollistatin-like 4 FTSJ1 NM 012280 FtsJ homolog 1 isoform a FUNDC2 NM O23934 FUN14 domain containing 2 FUSIP NM O06625 FUS interacting protein (serine-arginine rich) 1 FUT2 NM 000511 lucosyltransferase 2 (secretor status included) FUT4 NM 002033 lucosyltransferase 4 FUT6 NMOOO150 lucosyltransferase 6 (alpha (1,3) FXYD3 NM OO5971 FXYD domain containing ion transport regulator 3 FYCO NM O24513 FYVE and coiled-coil domain containing 1 FZD1 NM 003505 rizzled 1 GAB2 NM 012296 GRB2-associated binding protein 2 isoform b GABARAPL1 NM 031412 GABA(A) receptor-associated protein like 1 GABBR1 NM OO1470 gamma-aminobu yric acid (GABA) B receptor 1 GABRA4 NM 000809 gamma-aminobu yric acid A receptor, alpha 4 GABRB3 NM 000814 gamma-aminobu yric acid (GABA) A receptor, beta GABRE NM 004961 gamma-aminobu yric acid (GABA) A receptor, GABRG1 NM 173536 gamma-aminobu yric acid A receptor, gamma 1 GABRG2 NM 000816 gamma-aminobu yric acid A receptor, gamma 2 GABRR2 NM 002043 gamma-aminobu yric acid (GABA) receptor, rho 2 GALC NM OOO153 galactosylceramidase isoform a precursor GALM NM 1388O1 galactose mutaro ase (aldose 1-epimerase) GALNT13 NM 052917 UDP-N-acetyl-al pha-D-galactosamine:polypeptide GALNT3 NM 004482 polypeptide N-ac etylgalactosaminyltransferase 3 GALNT6 NM 007210 polypeptide N-ac etylgalactosaminyltransferase 6 GALNTL2 NM 054110 UDP-N-acetyl-al pha-D-galactosamine:polypeptide GALT NM OOO155 galactose-1-phos phate uridylyltransferase NM O15635 GTPase activating protein and VPS9 domains 1 NM O14990 GTPase activating Rap/RangAP domain-like 1 NM O15085 GTPase activating Rap/RangAP domain-like 4 NM 152237 growth arrest-specific 2 like 1 isoform b NM 003644 growth arrest-specific 7 isoform a GATA4 NM 002052 GATA binding protein 4 GATAD1 NM 021167 GATA zinc finger domain containing 1 GATM NM 001482 glycine amidinotransferase (L-arginine:glycine GATS NM 178831 opposite strand transcription unit to STAG3 GCLM NM 002061 glutamate-cysteine regulatory protein GCM1 NM OO3643 glial cells missing homolog a GCNT1 NM OO1490 beta-1,3-galactosyl-O-glycosyl-glycoprotein GCNT2 NM OO1491 glucosaminyl (N-acetyl) 2, Gcom1 NM 001018097 GRINL1A combined protein isoform 8 GDAP2 NM O17686 ganglioside induced differentiation associated GDF10 NM 004962 growth differentiation factor 10 precursor GDF6 NM 001001557 growth differentiation factor 6 GDPD4 NM 182833 glycerophosphodiester phosphodiesterase domain Gene symbol hsa-miR-143 targets Gene name GFOD1 NM 018988 glucose-fructose domain GFOD2 NM O3O819 hypothetical protein LOC81577 GFPT1 NM 002056 glucosamine-fructose-6-phosphate GFPT2 NM OO5110 glutamine-fructose-6-phosphate transaminase 2 GGA2 NM O15044 ADP-ribosylation factor binding protein 2 US 2009/0232893 A1 Sep. 17, 2009 24

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description GGT6 NM 153338 gamma-glutamyltransferase 6 homolog GGTL3 NM 178025 gamma-glutamyltransferase-like 3 isoform b GHR NM OOO163 growth hormone receptor precursor GIF NM OO5142 gastric intrinsic factor (vitamin B synthesis) GIMAP6 NM OO1007224 GTPase, IMAP family member 6 isoform 3 GIT2 NM 014776 G protein-coupled receptor kinase-interactor 2 GJC1 NM 152219 gap junction protein, chi 1, 31.9 kDa (connexin GLB1L, NM 024506 galactosidase, beta 1-like GLDC NM OOO170 glycine dehydrogenase (decarboxylating; glycine GLI3 NM OOO168 GLI-Kruppel family member GLI3 GLP1R NM 002062 glucagon-like peptide 1 receptor GLT2SD2 NM O15101 glycosyltransferase 25 domain containing 2 GLYATL2 NM 145016 hypothetical protein LOC219970 GMEB2 NM 012384 modulatory element binding GMFB NM 004124 glia maturation factor, beta GNA15 NM 002068 guanine nucleotide binding protein (G protein), GNAI1 NM 002069 guanine nucleotide binding protein (G protein), GNAL NM OO2O71 guanine nucleotide binding protein (G protein), GNAS NM O16592 guanine nucleotide binding protein, alpha GNB3 NM 002075 guanine nucleotide-binding protein, beta-3 GNB4 NM 021629 guanine nucleotide-binding protein, beta-4 GNBS NM OO6578 guanine nucleotide-binding protein, beta-5 GNG12 NM 018841 G-protein gamma-12 subunit GNG4 NM 004485 guanine nucleotide binding protein (G protein), GNG7 NM 052847 guanine nucleotide binding protein (G protein), GNL3 NM O14366 guanine nucleotide binding protein-like 3 GNPNAT1 NM 198066 glucosamine-phosphate N- 1 GNS NMOO2O76 glucosamine (N-acetyl)-6-sulfatase precursor GOLGA NM 018652 golgin-like protein GOLGA1 NM OO2O77 golgin 97 GOLGA4 NM 002078 golgi autoantigen, golgin subfamily a 4 GOLPH2 NM O16548 golgi phosphoprotein 2 GORASP1 NM 031899 Golgi reassembly stacking protein 1 GOSR1 NM OO1007024 golgi SNAP receptor complex member 1 isoform 3 GOT1 NM 002079 aspartate aminotransferase 1 GOT2 NM O02080 aspartate aminotransferase 2 precursor GP5 NM 004488 glycoprotein V (platelet) GP6 NM 016363 glycoprotein VI (platelet) GPA33 NM OO5814 transmembrane glycoprotein A33 precursor GPC1 NM O02081 glypican 1 precursor GPC2 NM 152742 glypican 2 GPIAP1 NM OO5898 membrane component chromosome 11 Surface marker GPR109A NM 177551 G protein-coupled receptor 109A GPR109B NM OO6018 G protein-coupled receptor 109B GPR135 NM O22571 G protein-coupled receptor 135 GPR176 NM OO7223 putative G protein coupled receptor GPR18O NM 180989 G protein-coupled receptor 180 precursor GPR26 NM 153442 G protein-coupled receptor 26 GPR62 NM 08O865 G protein-coupled receptor 62 GPR83 NM O16540 G protein-coupled receptor 83 GPRCSA NM OO3979 G protein-coupled receptor, family C, group 5, GPRCSB NM O16235 G protein-coupled receptor, family C, group 5, GPSM3 NM 022107 G-protein signalling modulator 3 (AGS3-like, C. GPX3 NM 002084 plasma glutathione peroxidase 3 precursor GRAMD1A NM 020895 hypothetical protein LOC57655 GRAMD2 NM 001012642 hypothetical protein LOC196996 GRHL2 NM O24915 transcription factor CP2-like 3 GRLA2 NM OOO826 glutamate receptor, ionotropic, AMPA2 GRIN2B NM 000834 N-methyl-D-aspartate receptor subunit 2B GRINL1A NM 0010181.03 glutamate receptor, ionotropic, N-methyl GRIPAP1 NM O2O137 GRIP1 associated protein 1 isoform 1 GRK1 NM OO2929 rhodopsin kinase GSDMDC1 NM O24736 gasdermin domain containing 1 GSTA4 NM OO1512 glutathione S-transferase A4 GSTM4 NM 147149 glutathione S-transferase M4 isoform 3 GTF2I NM OO1518 general transcription factor II, i isoform 4 GTPBP1 NM 004286 GTP binding protein 1 GTPBP3 NM 032620 GTP binding protein 3 (mitochondrial) isoform V GUSBL2 NM 206910 hypothetical protein LOC375513 isoform 2 H2AFY2 NM 018649 core histone macroH2A2.2 H2BFWT NM OO10O2916 H2B histone family, member W, testis-specific US 2009/0232893 A1 Sep. 17, 2009 25

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. RefSeq, Transcript ID Description

NM OO4285 hexose-6-phosphate dehydrogenase precursor NM 004132 hyaluronan binding protein 2 NM 207112 hydroxyacylglutathione hydrolase-like isoform 1 NM 0230O2 brain link protein 2 NM 005329 hyaluronan synthase 3 isoform a NM O06620 HBS1-like NM 152299 kleisin beta isoform 2 NM 005333 holocytochrome c synthase (cytochrome c NM 005844 hypothetical protein LOC10255 NM 080669 heme carrier protein 1 NM OO6037 4 NM O15401 histone deacetylase 7A isoform a NM O16217 headcase NM O15382 HECT domain containing 1 NM 020760 HECT, C2 and WW domain containing E3 ubiquitin NM O16173 HemK methyltransferase family member 1 NM O19089 hairy and enhancer of split homolog 2 NM 000410 hemochromatosis protein isoform 1 precursor NM 001010934 hepatocyte growth factor isoform 5 precursor NM 004712 hepatocyte growth factor-regulated tyrosine HHAT NM 018194 hedgehog acyltransferase HHLA2 NM 007072 HERV-H LTR-associating 2 HIATL1 NM 032558 hypothetical protein LOC84641 HIG2 NM 013332 hypoxia-inducible protein 2 HIGD2A NM 138820 HIG1 domain family, member 2A HIP1 NM 005338 huntingtin interacting protein 1 HIPK1 NM 181358 homeodomain-interacting protein kinase 1 isoform HIST1H4E NM 003545 H4 histone family, member J HK2 89 hexokinase 2 HKDC1 30 hexokinase domain containing 1 HKR2 NM 181846 GLI-Kruppel family member HKR2 HLA-A NM 002 16 major histocompatibility complex, class I, A HLA-B major histocompatibility complex, class I, B HLA-C NM 002 17 major histocompatibility complex, class I, C HLA-DOA NM 002 19 major histocompatibility complex, class II, DO HLA-DPA1 NM 033554 major histocompatibility complex, class II, DP HLA-DPB1 NM 002 21 major histocompatibility complex, class II, DP HLA-DQA2 NM 020056 major histocompatibility complex, class II, DQ HLA-DQB1 NM 002 23 major histocompatibility complex, class II, DQ HLA-E major histocompatibility complex, class I, E HLF NM 002 26 hepatic leukemia factor HMBS NM OOO 90 hydroxymethylbilane synthase isoform 1 HMG2L1 NM 001003681 high-mobility group protein 2-like 1 isoform b HMGA1 NM 002 31 high mobility group AT-hook 1 isoform b HMGA2 NM 001015886 high mobility group AT-hook 2 isoform c HMGB1 NM 002 28 high-mobility group box 1 HMGCS2 NM OO5518 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 HMMR NM 012484 hyaluronan-mediated motility receptor isoform a HN1 NM OO1002033 hematological and neurological expressed 1 HNF4A NM 000457 hepatocyte nuclear factor 4 alpha isoform b HNMT NM 001024.074 histamine N-methyltransferase isoform 2 HNRPAO NM OO6805 heterogeneous nuclear ribonucleoprotein AO HOXAS NM 019102 homeobox A5 HOXB13 NM OO6361 homeobox B13 HOXB9 NM 024017 homeobox B9 HOXCS NM 018953 homeobox C5 HPCAL4 NM O16257 hippocalcin-like protein 4 HPS5 NM 007216 Hermansky-Pudlak syndrome 5 isoform b HPSE NM OO6665 heparanase HR NM 005144 hairless protein isoform a NM 004.504 HIV-1 Rev binding protein NM 021624 histamine H4 receptor NM 012262 heparan sulfate 2-O-sulfotransferase 1 NM OO6043 heparan Sulfate D-glucosaminyl NM OO1537 heat shock factor binding protein 1 NM 000413 hydroxysteroid (17-beta) dehydrogenase 1 NM 032303 hydroxysteroid dehydrogenase like 2 NM 032855 hematopoietic SH2 domain containing NM O14424 heat shock 27 kDa , member 7 NM 012267 hsp70-interacting protein NM 014157 hypothetical protein LOC29070 US 2009/0232893 A1 Sep. 17, 2009 26

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description HTR2C NM OOO868 5-hydroxytryptamine (serotonin) receptor 2C HTR3A NM OOO869 5-hydroxytryptamine (serotonin) receptor 3A HTR3B NM OO6028 5-hydroxytryptamine (serotonin) receptor 3B HTR4 NM OOO870 serotonin 5-HT4 receptor isoform b HTR6 NM OOO871 5-hydroxytryptamine (serotonin) receptor 6 HTR7 NM OOO872 5-hydroxytryptamine receptor 7 isoform a HUNK NM 014586 hormonally upregulated Neu-associated kinase HYOU1 NM OO6389 oxygen regulated protein precursor HYPK NM 016400 Huntingtin interacting protein K APP NM 000415 islet amyloid polypeptide precursor BRDC1 NM 152553 IBR domain contai ning 1 CA1 NM 0223O8 islet cell autoantigen 1 isoform 3 D4 NM OO1546 inhibitor of DNA binding 4., dominant negative NM OO3897 immediate early response 3 isoform short FIT3 NM OO1031683 -induce protein with FITS NM 012420 interferon-induce protein with FNA14 NM 002172 interferon, alpha 14 FNA16 NM 002173 interferon, alpha 16 FNA7 NM 021057 interferon, alpha 7 NM 000618 insulin-like growth factor 1 (Somatomedin C) NM OO6546 insulin-like growth factor 2 mRNA binding NM OOO876 insulin-like growth factor 2 receptor NM 000598 insulin-like growth factor binding protein 3 NM 000599 insulin-like growth factor binding protein 5 NM 198541 insulin growth factor-like family member 1 NM 153184 immunoglobulin Superfamily, member 4D NM OO1 OO6115 inositol hexaphosp hate kinase 1 isoform 2 NM 001005910 inositol hexaphosp hate kinase 2 isoform b NM 054111 inositol hexaphosp hate kinase 3 NM OO1558 interleukin 10 rece ptor, alpha precursor NM 000628 interleukin 10 rece ptor, beta precursor NM 147162 interleukin 11 rece ptor, alpha isoform 2 NM 153701 interleukin 12 rece ptor, beta 1 isoform 2 NM OO1559 interleukin 12 rece ptor, beta 2 precursor NM OO1560 interleukin 13 rece ptor, alpha 1 precursor NM OO4513 interleukin 16 isoform 1 precursor NM 013278 interleukin 17C NM 017563 interleukin 17 rece btor D NM OO1562 interleukin 18 proprotein NM 012275 interleukin 1 family, member 5 NM 019618 in Clel kin family, member 9 NM 002182 in Clel kin receptor accessory protein isoform NM OO3856 in Clel kin receptor-like 1 isoform 2 NM 000577 in Clel kin receptor antagonist isoform 3 NM 052962 in Clel kin 22-bin ing protein isoform 1 NM 004.843 class I cytokine receptor NM 170743 in Clel kin 28 rece ptor, alpha isoform 1 NM 000417 in Clel kin 2 recep or, alpha chain precursor NM OOO588 in Clel kin 3 precursor L6R NM 181359 in Clel kin 6 recep or isoform 2 precursor L8RA NM 000634 in Clel kin 8 receptor alpha NCA1 NM 213726 in hibitor of CDK interacting with cyclin A1 NG5 NM 032329 in hibitor of growth family, member 5 NOC1 NM 017553 INO80 complex homolog 1 NPP5E NM 019892 inositol polyphosp hate-5-phosphatase E NSL4 NM 002195 insulin-like 4 precursor NTS2 NM 020748 in egrator complex subunit 2 QCC NM 018134 IQ motif containing C QCE NM 152558 IQ motif containing E RAK1 NM 001025242 in erleukin-1 receptor-associated kinase 1 RF5 NM OO2200 in erferon regulatory factor 5 isoform a RF8 NM 002163 in erferon regulatory factor 8 RX6 NM O24335 iroquois homeobox protein 6 TGA11 NM 001004439 in egrin, alpha 11 precursor TGA3 NM 002.204 in egrin alpha 3 isoform a precursor TGAS NM OO2205 in egrin alpha 5 precursor TGA6 NM 000210 in egrin alpha chain, alpha 6 TGAM NM OOO632 in egrin alpha M precursor TGAV NM OO2210 in egrin alpha-V precursor TM2B NM O21999 in egral membrane protein 2B TPR1 NM O02222 inositol 14,5-triphosphate receptor, type 1 US 2009/0232893 A1 Sep. 17, 2009 27

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description AG1 NM 000214 jagged 1 precursor AGN1 NM 032492 jagunal homolog 1 M11 NM 033626 hypothetical protein LOC90060 MD2B NM O15O15 jumonji domain containing 2B MD2C NM O15061 jumonji domain containing 2C OSD1 NM O14876 osephin domain containing 1 OSD3 NM 024116 osephin domain containing 3 PH1 NM 020647 junctophilin 1 PH3 NM O2O655 junctophilin 3 RK NM 003724 jerky homolog K6IRS4 NM 175053 6 irs4 KA36 NM 182497 type I KA36 KAL1 NM 000216 Kallmann syndrome 1 protein KATNAL1 NM 001014380 katanin p60 subunit A-like 1 KBTBD3 NM 152433 BTB and kelch domain containing 3 KBTBD6 NM 152903 kelch repeat and BTB (POZ) domain-containing 6 KBTBD8 NM 032505 T-cell activation kelch repeat protein KCNA7 NM 031886 potassium voltage-gated channe , shaker-related KCNB1 NM OO4975 potassium voltage-gated channe , Shab-related KCND1 NM OO4979 potassium voltage-gated channe , Shal-related KCND2 NM 012281 potassium voltage-gated channe , Shal-related KCND3 NM OO498O potassium voltage-gated channe , Shal-related KCNE1L, NM 012282 potassium voltage-gated channe , Isk-related KCNE3 NM 005472 potassium voltage-gated channe , Isk-related KCNHS NM 172375 potassium voltage-gated channe , subfamily H, KCNH6 NM 173092 potassium voltage-gated channe , subfamily H, KCNH7 NM 033272 potassium voltage-gated channe , subfamily H, KCNH8 NM 144633 potassium voltage-gated channe , subfamily H, KCNIP1 NM 014592 KV channel interacting protein 1 isoform 2 KCNIP2 NM 014591 KV channel interacting protein 2 isoform 1 KCNJ 10 NM 002241 potassium inwardly-rectifying c hannel, Subfamily KCNJ13 NM 002242 potassium inwardly-rectifying c hannel J13 KCN4 NM 004981 potassium inwardly-rectifying c hannel J4 KCNJS NM OOO890 potassium inwardly-rectifying c hannel J5 KCNJ8 NM 004982 potassium inwardly-rectifying c hannel J8 KCNK2 NM 001017424 potassium channel, Subfamily K , member 2 isoform KCNK3 NM 002246 potassium channel, Subfamily K , member 3 KCNMA1 NM 001014797 arge conductance calcium-activated potassium KCNS2 NM 020697 potassium voltage-gated channe KCTD10 NM 031954 potassium channel tetramerisation domain DELC2 NM 153705 KDEL (Lys-Asp-Glu-Leu) containing 2 EAP1 NM 012289 kelch-like ECH-associated protein 1 ENAE NM 176816 hypothetical protein LOC202243 AAO125 NM 014792 hypothetical protein LOC9834 AAO232 NM 014743 hypothetical protein LOC9778 AAO256 NM 014701 hypothetical protein LOC9728 AAO265 NM O14997 hypothetical protein LOC23008 AAO286 NM O15257 hypothetical protein LOC23306 AAO319 NM O14809 KIAAO319 AAO319L. NM O24874 polycystic kidney disease 1-like isoform a AAO329 NM 014844 hypothetical protein LOC9895 AAO3SO NM O15226 hypothetical protein LOC23274 AAO3SS NM 014686 hypothetical protein LOC9710 AAO427 NM 014772 hypothetical protein LOC9811 AA0446 NM 014655 hypothetical protein LOC9673 AAO467 NM O15284 KIAAO467 protein AAO494 NM 014774 hypothetical protein LOC9813 AAO495 NM 207306 KIAAO495 AAOS13 NM 014732 hypothetical protein LOC9764 AAOS14 NM 014696 hypothetical protein LOC9721 AAOS23 NM O15253 hypothetical protein LOC23302 AAOSS3 NM OO10O2909 hypothetical protein LOC23131 AAO644 NM O14817 hypothetical protein LOC9865 AAO652 NM 014741 hypothetical protein LOC9776 AAO676 NM O15043 hypothetical protein LOC23061 isoform b AAO701 NM OO1 OO6947 hypothetical protein LOC23074 isoform b AAO703 NM O14861 calcium-transporting ATPase 2C2 AAO738 NM 014719 hypothetical protein LOC9747 AAO773 NM OO1031690 hypothetical protein LOC9715 AAO789 NM 014653 hypothetical protein LOC9671 AAO804 NM 001009921 hypothetical protein LOC23355 isoform a US 2009/0232893 A1 Sep. 17, 2009 28

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description AAO831 NM O14924 hypothetical protein LOC22863 AAO889 NM 152257 hypothetical protein LOC25781 AAO892 NM O15329 hypothetical protein LOC23383 O08 NM O14953 KIAA1008 O12 NM O14939 hypothetical protein LOC22878 O24 NM O15206 hypothetical protein LOC23251 128 NM 018999 granule cell antiserum positive 14 161 NM 020702 hypothetical protein LOC57462 166 NM 018684 hepatocellular carcinoma-associated antigen 127 189 NM OO1.009959 hypothetical protein LOC57471 isoform a 267 NM 015443 hypothetical protein LOC284.058 274 NM O14431 KIAA1274 328 NM 020776 hypothetical protein LOC57536 333 NM O17769 hypothetical protein LOC55632 446 NM 020836 ikely ortholog of rat brain-enriched guanylate 456 NM 020844 hypothetical protein LOC57604 467 NM 020853 hypothetical protein LOC57613 522 NM 020888 hypothetical protein LOC57648 576 NM 020927 hypothetical protein LOC57687 604 NM 020943 hypothetical protein LOC57703 622 NM 020958 HEAT-like repeat-containing protein isoform 2 641 NM 020970 hypothetical protein LOC57730 706 NM 030636 hypothetical protein LOC80820 715 NM 030650 Lll88k 727 NM 03.3393 hypothetical protein LOC85462 729 NM O53042 hypothetical protein LOC85460 737 NM 033426 KIAA1737 protein 853 NM194286 KIAA1853 protein 875 NM 032529 KIAA1875 protein 909 NM 052909 hypothetical protein LOC153478 914 NM 001001936 KIAA1914 protein isoform 1 920 NM 052919 hypothetical protein LOC114817 AA2022 NM OO10O8537 hypothetical protein LOC340533 F1B NM O15074 family member 1B isoform b NM OO4798 kinesin family member 3B NM OO2254 kinesin family member 3C NM 012310 kinesin family member 4 F9 NM 022342 kinesin family member 9 isoform 1 RREL NM 018240 kin of IRRE like NM 022822 ikely ortholog of kinesin light chain 2 NM 177417 kinesin light chain 3 NM OO7249 Kruppel-like factor 12 isoform a : NM O15995 Kruppel-like factor 13 7 NM 173484 Zinc finger protein 393 NM OO1730 Kruppel-like factor 5 NM 207335 hypothetical protein LOC166348 NM O14458 kelch-like 20 NM O14851 kelch-like 21 NM 032775 kelch-like NM 017644 DRE1 protein NM 022480 BTB/POZ KELCH domain protein NM 018316 hypothetical protein LOC55295 NM 130446 kelch-like 6 NM OO1031710 SBBI26 protein isoform 1 NM O15596 kallikrein 13 precursor NM 012427 kallikrein 5 preproprotein RG1 NM OO5810 killer cell lectin-like receptor subfamily G, -HN-1 NM 1527.75 KM-HN-1 protein DC1 NM 152643 kinase non-catalytic C-lobe domain (KIND) PNA1 NM 002264 karyopherin alpha 1 PNA6 NM 012316 karyopherin alpha 6 RAS NM OO4985 c-K-ras2 protein isoform b REMEN2 NM 024507 kringle-containing transmembrane protein 2 RIT1 NM 001013406 krew interaction trapped 1 isoform 2 RT2SA NM 181534 keratin 25A RT2A NM 000423 RT2B NM O15848 2 RT4 NM OO2272 RTAP1-1 NM 030967 keratin associated protein 1-1 RTAP4-14 NM 033059 keratin associated protein 4-14 RTAP4-4 NM 032524 keratin associated protein 4.4 US 2009/0232893 A1 Sep. 17, 2009 29

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description KRTAP9-2 NM 03.1961 keratin associated protein 9.2 KRTAP9-3 NM 031962 keratin associated protein 9.3 L3MBTL4 NM 173464 hypothetical protein LOC91133 LACE1 NM 145315 actation elevated 1 LAMB3 NM 000228 aminin Subunit beta 3 precursor LAMC1 NM 002293 aminin, gamma 1 precursor LANCL2 NM 018697 Lanc lantibiotic synthetase component C-like 2 LARP1 NM O15315 a related protein isoform 1 LARP4 NM 052879 c-Mplbinding protein isoform a LARPS NM O15155 La ribonucleoprotein domain family, member 5 LASP1 NM 006148 LIM and SH3 protein 1 LASS3 NM 178842 hypothetical protein LOC204219 NM 030915 hypothetical protein DKFZp566J091 NM 002299 actase-phlorizin hydrolase preproprotein B3 NM 007078 LIM domain binding 3 NM 000527 ow density lipoprotein receptor precursor NM O15627 ow density lipoprotein receptor adaptor protein NM 032287 hypothetical protein LOC84247 E NM 002302 eukocyte cell-derived chemotaxin 2 precursor NM 018655 ens epithelial protein NM 018471 erythropoietin 4 immediate early response NM 012318 eucine Zipper-EF-hand containing transmembrane NM OO6499 galectin 8 isoform a NM OO5779 ipoma HMGIC fusion partner-like 2 NM 199000 ipoma HMGIC fusion partner-like 3 NM 182548 ipoma HMGIC fusion partner-like 5 NM 014564 LIM homeobox protein 3 isoform b NMO33343 LIM homeobox protein 4 NM OO6859 ipoic acid synthetase isoform 1 precursor NM 002309 eukemia inhibitory factor (cholinergic NM 002310 eukemia inhibitory factor receptor precursor NM OO6669 eukocyte immunoglobulin-like receptor, NM OO6847 eukocyte immunoglobulin-like receptor, NM 014240 LIM domains containing 1 NM O30576 LIM domain containing 2 NM 002314 LIM domain kinase 1 NM 005569 LIM domain kinase 2 isoform 2a NM O1798O LIM and Senescent cell antigen-like domains 2 NM 033514 LIM and Senescent cell antigen-like domains 3 NM O24674 in-28 homolog NM 173083 in-9 homolog NM 153234 imb expression 1 NM 004140 ethalgiant larvae homolog 1 NM 032737 NM OO6769 LIM domain only 4 NM OO5358 LIM domain only 7 NM 1982.71 eiomodin 3 (fetal) 16236 NM 198147 hypothetical protein LOC116236 24491 NM 145254 hypothetical protein LOC124491 291.38 hypothetical protein LOC129138 296O7 hymidylate kinase family LPS-inducible member 30576 hypothetical protein LOC130576 33619 hypothetical protein LOC133619 445O1 hypothetical protein LOC144501 S1194 hypothetical protein LOC151194 52485 hypothetical protein LOC152485 53561 hypothetical protein LOC153561 S8318 hypothetical protein LOC158318 62427 hypothetical protein LOC162427 96463 hypothetical protein LOC196463 96752 hypothetical protein LOC196752 LOC 97.322 hypothetical protein LOC197322 LOC2O1164 hypothetical protein LOC201164 LOC2O3427 mitochondrial Solute carrier protein LOC221091 hypothetical protein LOC221091 LOC222967 hypothetical protein LOC222967 LOC2832.19 hypothetical protein LOC2832.19 LOC283537 hypothetical protein LOC283537 LOC283SS1 hypothetical protein LOC283551 LOC284296 NM 175908 hypothetical protein LOC284296 LOC284434 NM OO1.0075.25 hypothetical protein LOC284434 US 2009/0232893 A1 Sep. 17, 2009 30

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description LOC2847S7 NM OO1004305 hypone ical protein LOC284757 LOC286O76 NM 001024610 hypone ical protein LOC286O76 LOC339524 NM 207357 hypone ical protein LOC339524 LOC34O156 NM 001012418 hypone ical protein LOC34.0156 LOC342897 NM 001001414 similar to F-box only protein 2 LOC345222 NM 001012982 hypone ical protein LOC345222 LOC348262 NM 207368 hypone ical protein LOC348262 LOC387856 NM 001013635 hypone ical protein LOC387856 LOC388503 NM 001013640 hypone ical protein LOC388503 LOC3891.18 NM OO1.007540 hypone ical protein LOC389118 LOC3891.99 NM 203423 hypone ical protein LOC389199 LOC389791 NM 001013652 hypone ical protein LOC389791 LOC389834 NM 001013655 hypone ical protein LOC389834 LOC392,395 NM 001013664 hypone ical protein LOC392,395 LOC3997O6 NM 001010910 hypone ical protein LOC3997O6 LOC399898 NM 001013666 hypone ical protein LOC399898 LOC4OO145 NM 001013669 hypone ical protein LOC400145 LOC4OO499 NM 001013671 hypone ical protein LOC400499 LOC4OO657 NM OO10O8234 hypone ical protein LOC400657 LOC40O891 NM 001013675 hypone ical protein LOC400891 LOC4OO924 NM 001013676 hypone ical protein LOC400924 LOC4OO96S NM 001013677 hypone ical protein LOC400965 LOC4O1137 NM 214711 hypone ical protein LOC4O1137 LOC4O1398 NM 001023566 hypone ical protein LOC4O1398 LOC4O1431 NM OO10O8745 hypone ical protein LOC4.01431 LOC4O1507 NM 001012278 hypone ical protein LOC4O1507 LOC4O1589 NM 001013687 hypone ical protein LOC4O1589 LOC4O162O NMOO1013688 hypotne ical protein LOC4O1620 LOC4O1720 NM 001013690 hypone ical protein LOC401720 LOC440313 NM 001013704 hypone ical protein LOC440313 LOC440337 NM 001013705 hypone ical protein LOC440337 LOC44.0570 NM 001013708 hypone ical protein LOC440570 LOC44O742 NM 001013710 hypone ical protein LOC440742 LOC44O925 NM 001013712 hypone ical protein LOC440925 LOC440944 NM 001013713 hypone ical protein LOC440944 LOC441070 NM 001013715 hypone ical protein LOC441070 LOC441136 NM 001013719 hypone ical protein LOC441136 LOC441268 NM 001013725 hypone ical protein LOC441268 LOC441459 NM 001013728 hypone ical protein LOC441459 LOC442247 NM 001013734 hypone ical protein LOC442247 LOCSO4.188 NM 001013404 hypone ical protein LOC504.188 LOCS4103 NM O17439 hypone ical protein LOC54103 LOCS41473 NM 001013748 FKBP6 ike LOCSS4251 NM 001024680 hypone ical protein LOC554251 LOCSS908 NM 018687 hepatocellular carcinoma-associated gene TD26 LOC6132O6 NM OO1033016 myeloproliferative disease associated tumor LOC613266 NM OO1033516 hypone ical protein LOC613266 LOC63928 NM O22097 hepatocellular carcinoma antigen gene 520 LOC90167 NM 194277 hypone cal protein LOC90167 LOC90639 NM OO1031617 hypone ical protein LOC90639 LOH12CR1 NM 058169 LOH1C R12 LOXL4 NM 032211 ysyl oxidase-like 4 precursor LPIN3 NM O22896 ipin 3 LPP NM OO5578 LIM domain containing preferred translocation LRAT NM 004744 ecithin retinol acyltransferase LRBA NM OO6726 LPS-responsive vesicle trafficking, beach and LRCH4 NM 002319 eucine-rich repeats and calponin homology (CH) LRP11 NM 032832 ow density lipoprotein receptor-related protein LRP12 NM 013437 Suppression of tumorigenicity LRP2BP NM 018409 LRP2 binding protein LRRC14 NM 014665 eucine rich repeat containing 14 LRRC2 NM O24512 eucine rich repeat containing 2 LRRC2O NM 018205 eucine rich repeat containing 20 isoform 3 LRRC27 NM 030626 eucine rich repeat containing 27 LRRC3B NM 052953 eucine rich repeat containing 3B LRRC48 NM 031294 eucine rich repeat containing 48 LRRCS4 NM O15516 Sukushi LRRIQ2 NM 024548 eucine-rich repeats and IQ motif containing 2 LRRNS NM OO6338 eucine rich repeat neuronal 5 precursor LRRTM3 NM 178011 eucine rich repeat transmembrane neuronal 3 LSM12 NM 152344 hypothetical protein LOC124801 US 2009/0232893 A1 Sep. 17, 2009 31

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description LSM16 NM O25083 LSM16 homolog (EDC3, S. cerevisiae) LTBP2 NM 000428 latent transforming growth factor beta binding LUZP1 NM 033631 leucine Zipper protein 1 LY6E NM 002347 lymphocyte antigen 6 complex, H LY86 NM OO4271 MD-1, RP105-associated LYCAT NM OO10O2257 lysocardiolipin acyltransferase isoform 2 LYPLA3 NM 012320 lysophospholipase 3 (lysosomal phospholipase LYSMD1 NM 212551 LysM, putative peptidoglycan-binding, domain LYSMD4 NM 152449 hypothetical protein LOC145748 LYZ NM OOO239 lysozyme precursor LZTR2 NM 033127 regucalcin gene promotor region related protein LZTS1 NM 021020 leucine Zipper, putative tumor Suppressor 1 M6PR NM 002355 cation-dependent mannose-6-phosphate receptor M6PRBP1 NM OO5817 mannose 6 phosphate receptor binding protein 1 MAB21L1 NM OO5584 mab-21-like protein 1 MAF NM OO1031804 V-maf musculoaponeurotic fibrosarcoma oncogene MAGEA8 NM OO5364 melanoma antigen family A, 8 MAGEA9 NM OO5365 melanoma antigen family A, 9 MAGEL2 NM O19066 MAGE-like protein 2 MAGI2 NM 012301 membrane associated guanylate kinase, WW and PDZ MALL NM 005434 mal, T-cell differentiation protein-like MAN1C1 NM O2O379 mannosidase, alpha, class 1C, member 1 MANEA NM O24641 mannosidase, endo-alpha MAP1B NM OO5909 -associated protein 1B isoform 1 MAP3K3 NM 002401 mitogen-activated protein kinase kinase kinase 3 MAP3K7 NM OO3188 mitogen-activated protein kinase kinase kinase 7 MAP4K1 NM 007181 mitogen-activated protein kinase kinase kinase MAPK1 NMOO2745 mitogen-activated protein kinase 1 MAPK14 NM 001315 mitogen-activated protein kinase 14 isoform 1 MAPK3 NM OO2746 mitogen-activated protein kinase 3 isoform 1 MAPK7 NM OO2749 mitogen-activated protein kinase 7 isoform 1 MAPKAPK2 NM OO4759 mitogen-activated protein kinase-activated MAPKBP1 NM 014994 mitogen-activated protein kinase binding protein MAPT NM 005910 microtubule-associated protein tau isoform 2 MARCH3 NM 178450 membrane-associated ring finger (C3HC4)3 MARCHS NM 017824 ring finger protein 153 MARCKS NM 002356 myristoylated alanine-rich protein kinase C MARK3 NM 002376 MAP microtubule affinity-regulating kinase 3 MARVELD1 NM 031484 MARVEL domain containing 1 MARVELD3 NM 052858 MARVEL domain containing 3 isoform 2 MAS NM 002377 MAS1 oncogene MASP1 NM OO1879 mannan-binding lectin serine protease 1 isoform MAT1A NM 000429 methionine adenosyltransferase I, alpha MATN2 NM 002380 matrilin 2 isoform a precursor MBD3 NM OO3926 methyl-CpG binding domain protein 3 MBNL3 NM 018388 muscleblind-like 3 isoform G MCART6 NM 001012755 hypothetical protein LOC4O1612 MCCC2 NM 022132 methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCF2 NM OO5369 MCF.2 cell line derived transforming sequence MCFD2 NM 139279 multiple coagulation factor deficiency 2 MCL NM O21960 myeloid cell leukemia sequence 1 isoform 1 MCM4 NM 005914 minichromosome maintenance protein 4 MCM8 NM 032485 minichromosome maintenance protein 8 isoform 1 MDFIC NM 199072 MyoD family inhibitor domain containing isoform MDGA1 NM 153487 MAM domain containing MECP2 NM OO4992 methyl CpG binding protein 2 MED12L NM 053002 mediator of RNA polymerase II transcription, MEF2C NM 002397 MADS box transcription enhancer factor 2, MEF2D NM O05920 MADS box transcription enhancer factor 2, MEGF10 NM 0324.46 MEGF10 protein MEP1A NM OO5588 meprin A, alpha (PABA peptide hydrolase) METTSD1 NM 152636 methyltransferase 5 domain containing 1 METTL5 NM 014168 methyltransferase like 5 MFAP3 NM OO5927 microfibrillar-associated protein 3 MFI2 NM 033316 melanoma-associated antigen p97 isoform 2, MFN2 NM O14874 mitofusin 2 MFSD4 NM 181644 hypothetical protein DKFZp761N1114 MGAM NM 004668 maltase-glucoamylase MGC10334 NM 001029885 hypothetical protein LOC80772 MGC11102 NM 032325 hypothetical protein LOC84285 MGC13379 NM 016499 hypothetical protein LOC51259 US 2009/0232893 A1 Sep. 17, 2009 32

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description MGC15875 NM 032921 hypothetical protein LOC85007 isoform 1 MGC16028 NM 052873 hypothetical protein LOC112752 MGC16703 NM 45042 hypothetical protein LOC113691 MGC2O470 NM 45053 hypothetical protein LOC143630 MGC2328O NM 44683 hypothetical protein LOC147015 MGC24039 NM 44973 hypothetical protein LOC160518 MGC26694 hypothetical protein LOC284439 MGC26718 hypothetical protein LOC440482 MGC26733 hypothetical protein LOC200403 MGC27121 hypothetical protein LOC408263 MGC2752 hypothetical protein LOC65996 MGC298.91 GA repeat binding protein, beta 2 MGC29898 hypothetical protein LOC133015 MGC32O7 hypothetical protein LOC84245 isoform 1 MGC33214 hypothetical protein LOC153396 MGC33S30 hypothetical protein LOC222008 MGC34646 hypothetical protein LOC157807 MGC35295 hypothetical protein LOC219995 MGC39900 hypothetical protein LOC286527 MGC4562 hypothetical protein LOC115752 hypothetical protein LOC84752 MGCSO273 hypothetical protein LOC408029 NM 52689 hypothetical protein LOC202915 NM 001003794 monoglyceride lipase isoform 2 NM 020774 mind bomb homolog 1 NM 014632 microtubule associated monoxygenase, calponin NM 03.3386 molecule interacting with Rab13 NM021242 MID1 interacting G12-like protein NM 152622 hypothetical protein LOC166968 NM 138731 mirror-image polydactyly 1 NM 020831 megakaryoblastic leukemia 1 protein NM 014048 megakaryoblastic leukemia 2 protein NM 013255 muskelin 1, intracellular mediator containing NM OO5664 makorin, ring finger protein, 3 NM O15166 megalencephalic leukoencephalopathy with NM 014727 myeloid lymphoid or mixed-lineage leukemia 4 NM OO4529 myeloid lymphoid or mixed-lineage leukemia NM 032228 malesterility domain containing 2 NM 170607 transcription factor-like protein 4 isoform NM 032.951 Williams Beuren syndrome chromosome region 14 NM 1984.03 monocyte-to-macrophage differentiation factor 2 MMP14 NM OO4995 matrix metalloproteinase 14 preproprotein MMP17 NM O16155 matrix metalloproteinase 17 preproprotein MMP19 NM OO1032360 matrix metalloproteinase 19 isoform 2 precursor MMP2 NM 004530 matrix metalloproteinase 2 preproprotein MMP8 NM 002424 matrix metalloproteinase 8 preproprotein MN1 NM OO2430 meningioma 1 MOBKL2A NM 130807 MOB-LAK MOBKL2B NM O24761 MOB1, Mps One Binder kinase activator-like 2B MOCS1 NM OO5942 molybdenum cofactor synthesis-step 1 protein MOCS2 NM 1768.06 molybdopterin synthase Small subunit MOCS2A MOG NM OO10O8228 oligodendrocyte glycoprotein isoform MON1B NM O14940 MON1 homolog B MOSPD1 NM O19556 motile sperm domain containing 1 MPP2 NM OO5374 palmitoylated membrane protein 2 MPPED1 NM OO1585 hypothetical protein LOC758 MPST NM 001013436 3-mercaptopyruvate Sulfurtransferase MRAS NM 012219 muscle RAS oncogene homolog MRO NM 031939 maestro MRP63 NM 024026 mitochondrial ribosomal protein 63 MRPL30 NM 145212 mitochondrial ribosomal protein L30 MRPL41 NM 032477 mitochondrial ribosomal protein L41 MRPL52 NM 178336 mitochondrial ribosomal protein L52 isoform a MRPS11 NM O22839 mitochondrial ribosomal protein S11 isoform a MRPS26 NM 030811 mitochondrial ribosomal protein S26 MRPS33 NM 016071 mitochondrial ribosomal protein S33 MS4A10 NM 206893 membrane-spanning 4-domains, subfamily A, member MS4A2 NM 000139 membrane-spanning 4-domains, subfamily A, member MS4A4A NM 024021 membrane-spanning 4-domains, subfamily A, member MS4A7 NM 021201 membrane-spanning 4-domains, subfamily A, member MSH3 NM OO2439 mutS homolog 3 US 2009/0232893 A1 Sep. 17, 2009 33

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description MSI2 NM 138962 musashi 2 isoform a MSL3L1 NM O78628 male-specific lethal 3-like 1 isoform d MSR1 NM OO2445 macrophage scavenger receptor 1 isoform type 2 MSRB3 NM OO1031679 methionine sulfoxide reductase B3 isoform 2 MTAC2D1 NM 152332 membrane targeting (tandem) C2 domain containing MTHFR NM OO5957 5,10-methylenetetrahydrofolate reductase MTHFSD NM O22764 hypothetical protein LOC64779 MTM1 NM OOO252 myotubularin MTMR12 NM O19061 myotubularin related protein 12 MTMR2 NM O16156 myotubularin-related protein 2 isoform 1 MTMR3 NM 021090 myotubularin-related protein 3 isoform c MTMR9 NM O15458 myotubularin-related protein 9 MTPN NM 145808 myotrophin MTRR NM 002454 methionine synthase reductase isoform 1 MUCDHL NM 03.1265 mu-protocadherin isoform 4 MUM1L1 NM 152423 melanoma associated antigen (mutated) 1-like 1 MUTED NM 201280 muted MX2 NM 002463 myxovirus resistance protein 2 MXD1 NM 002357 MAX dimerization protein 1 MXD4 NM OO6454 MAD4 MYADM NM 001020818 myeloid-associated differentiation marker MYBBP1A NM 014520 MYB binding protein 1a MYBL2 NM 002466 MYB-related protein B MYCL1 NM OO1033081 1-myc-1 proto-oncogene isoform 1 MYD88 NM 002468 myeloid differentiation primary response gene MYL2 NM OOO432 light chain 2 MYL3 NM OOO258 3 MYO18A NM O78471 myosin 18A isoform a MYO1B NM 012223 myosin IB MYO1E NM 004998 myosin IE MYO3A NM O17433 myosin IIIA MYOSC NM 018728 myosin VC MYO6 NM OO4999 myosin VI MYO7A NM 000260 myosin VIIA MYOM2 NM OO3970 myomesin 2 MYST2 NM 007067 MYST histone acetyltransferase 2 MYST3 NM OO6766 MYST histone acetyltransferase (monocytic MYT1L. NM O15025 myelin transcription factor 1-like N4BP1 NM 153029 Nedd4 binding protein 1 NAALADL2 NM 207015 N-acetylated alpha-linked acidic dipeptidase 2 NAG6 NM O22742 hypothetical protein DKFZp434G156 NAG8 NM O14411 nasopharyngeal carcinoma associated gene NALP1 NM O14922 death effector filament-forming Ced-4-like NALP12 NM 144687 PYRIN-containing APAF1-like protein 7 isoform 2 NANOS1 NM 199461 nanos homolog 1 isoform 1 NANP NM 152667 haloacid dehalogenase-like hydrolase domain NAP1L4 NM 005969 nucleosome assembly protein 1-like 4 NAPE-PLD NM 1989.90 N-acyl-phosphatidylethanolamine-hydrolyzing NARG1 NM 057175 NMDA receptor regulated 1 NARG1L, NM O24561 NMDA receptor regulated 1-like protein isoform NARG2 NM 001018089 NMDA receptor regulated 2 isoform b NAT10 NM 024662 N-acetyltransferase-like protein NAT12 NM 001011713 hypothetical protein LOC122830 NAV3 NM O14903 neuron navigator 3 NCAM1 NM 181351 neural cell adhesion molecule 1 isoform 2 NCOA1 NM 003743 nuclear receptor coactivator 1 isoform 1 NCOA6IP NM O24831 PRIP-interacting protein PIPMT NCOA7 NM 181782 nuclear receptor coactivator 7 NCR1 NM 004.829 natural cytotoxicity triggering receptor 1 NCSTN NM O15331 nicastrin precursor NDE1 NM O17668 nuclear distribution gene E homolog 1 NDEL1 NM 001025579 nudE nuclear distribution gene E homolog like 1 NDFIP1 NM O30571 Nedd4 family interacting protein 1 NDRG4 NM 020465 NDRG family member 4 NDST1 NM OO1543 N-deacetylase/N-sulfotransferase (heparan NEBL NM OO6393 nebullette sarcomeric isoform NECAP1 NM O15509 adaptin-ear-binding coat-associated protein 1 NECAP2 NM 018090 adaptin-ear-binding coat-associated protein 2 NEDD4. NM OO6154 neural precursor cell expressed, developmentally NEDD9 NM 182966 neural precursor cell expressed, developmentally NEIL2 NM 145043 nei-like 2 US 2009/0232893 A1 Sep. 17, 2009 34

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description EK8 NM 178170 NIMA-related kinase 8 NM OO6617 ETO1 NM 138999 - and tolloid-like protein 1 isoform 1 ETO2 NM 018092 neuropilin- and tolloid-like protein 2 EURL NM 004210 neuralized-like NM 024019 neurogenin 2 NM 000268 neurofibromin 2 isoform 1 NM 145912 NFAT activation molecule 1 precursor NM O15090 neurofascin precursor NM OO6599 nuclear factor of activated T-cells 5 isoform c NM OO6162 nuclear factor of activated T-cells, cytosolic IC NM OO5597 nuclear factor IC isoform 1 NM 005.007 nuclear factor of kappa light polypeptide gene NM 152995 nuclear transcription factor, X-box binding-like NM OO2505 nuclear transcription factor Y, alpha isoform 1 NM OO6166 nuclear transcription factorY., beta NM OO2507 nerve growth factor receptor precursor NM OO5598 nescient helix loop helix 1 NM 144599 non-imprinted in Prader-Willi/Angelman syndrome NM 003634 nipSnap homolog 1 NM 001001349 NFKB inhibitor interacting Ras-like 2 NM 001012651 natural killer-tumor recognition sequence NM 020795 neuroligin 2 NM O22787 nicotinamide nucleotide adenylyltransferase 1 NM 021079 N-myristoyltransferase 1 NM OO4808 glycylpeptide N-tetradecanoyltransferase 2 NM OO5386 neuronatin isoform alpha NMO14062 nin one binding protein NM O15462 nucleolar protein 11 NM 022917 nucleolar RNA-associated protein alpha isoform NM 138400 nucleolar protein with MIF4G domain 1 NM OO2515 neuro-oncological ventral antigen 1 isoform 1 NM 007052 NADPH oxidase 1 isoform long NPAL3 NM 020448 NIPA-like domain containing 3 NPAS2 NM OO2518 neuronal PAS domain protein 2 NPC1 NM 000271 Niemann-Pick disease, type C1 NPHP1 NM 000272 nephrocystin isoform 1 NPLOC4 NM O17921 nuclear protein localization 4 NPR3 NM OOO908 natriuretic peptide receptor Ciguanylate cyclase NPTX1 NM OO2522 neuronal pentraxin I precursor NPTXR NM O14293 neuronal pentraxin receptor isoform 1 NQO1 NM OOO903 NAD(P)H menadione oxidoreductase 1, NR3C1 NM OOO176 nuclear receptor Subfamily 3, group C, member 1 NRG1 NM O13958 neuregulin 1 isoform HRG-beta3 NRIP1 NM OO3489 receptor interacting protein 140 NRIP2 NM 031474 nuclear receptor interacting protein 2 NRP2 NM OO3872 neuropilin 2 isoform 2 precursor NSF NM OO6178 N-ethylmaleimide-sensitive factor NTSC2 NM 012229 5'-nucleotidase, cytosolic II NTRK2 NM OO1007097 neurotrophic tyrosine kinase, receptor, type 2 NUAK2 NM 030952 NUAK family, SNF1-like kinase, 2 NUCB1 NM 006184 nucleobindin 1 NUDT10 NM 1531.83 nudix-type motif 10 NUDT12 NM 031438 nudix-type motif 12 NUDT15 NM 018283 nudix-type motif 15 NUDT16 NM 152395 nudix-type motif 16 NUDT16L1 NM 032349 Syndesmos NUDT18 NM O24815 nudix (nucleoside diphosphate linked moiety NUDT4 NM O19094 nudix-type motif 4 isoform alpha NM 001005743 numb homolog isoform 1 NM OO4756 numb homolog (Drosophila)-like NM OO10O8544 nucleoporin 35 kDa isoform b NM 198887 nucleoporin 43 kDa NM OO6362 nuclear RNA export factor 1 NM 032599 testes development-related NYD-SP18 NM 173663 hypothetical protein LOC285596 NM 138799 O-acyltransferase (membrane bound) domain NM OO5768 gene rich cluster, C3f gene NM 178507 hypothetical protein LOC220323 NM OO61.87 2'-5"oligoadenylate synthetase 3 NM 004152 ornithine decarboxylase antizyme 1 US 2009/0232893 A1 Sep. 17, 2009 35

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description OBFC2B NM 024068 hypothetical protein LOC79035 OCRL NM 000276 phosphatidylinositol polyphosphate 5-phosphatase OLIG1 NM 138983 oligodendrocyte transcription factor 1 OPCML NM 00101.2393 opioid binding protein cell adhesion OPRD1 NM 000911 opioid receptor, delta 1 OPTC NM O14359 opticin precursor OR2H1 NM O3O883 olfactory receptor, family 2, Subfamily H, ORS1E2 NM 030774 olfactory receptor, family 51, subfamily E, OR7D2 NM 175883 hypothetical protein LOC162998 ORAOV1 NM 153451 oral cancer overexpressed 1 ORC2L NM O06190 origin recognition complex, Subunit 2 OSBP2 NM 030758 oxysterol binding protein 2 isoform a OSBPL2 NM O14835 oxysterol-binding protein-like protein 2 isoform OSBPL3 NM O15550 oxysterol-binding protein-like protein 3 isoform OSBPL7 NM 145798 oxysterol-binding protein-like protein 7 OSCAR NM 206817 Osteoclast-associated receptor isoform 2 OTUD4 NM 199324 OTU domain containing 4 protein isoform 1 OTUD6B NM 016023 OTU domain containing 6B OXGR1 NM 080818 oxoglutarate (alpha-ketoglutarate) receptor 1 P2RX2 NM 012226 purinergic receptor P2X2 isoform I P2RX7 NM OO2562 purinergic receptor P2X7 P2RY13 NM O23914 purinergic receptor P2Y, G-protein coupled, 13 P2RY14 NM O14879 purinergic receptor P2Y, G-protein coupled, 14 P2RY4. NM OO2565 pyrimidinergic receptor P2Y4 P2RY8 NM 178129 G-protein coupled purinergic receptor P2Y8 P4HA1 NM 000917 prolyl 4-hydroxylase, alpha I subunit isoform 1 P4HA3 NM 182904 prolyl 4-hydroxylase, alpha III subunit P53AIP1 NMO22112 p53-regulated apoptosis-inducing protein 1 PACRG NM 152410 PARK2 co-regulated PACS1 NM 018026 phosphofurin acidic cluster sorting protein 1 PAFAH1B2 NM OO2572 platelet-activating factor acetylhydrolase, PAG1 NM 018440 phosphoprotein associated with glycosphingolipid PAICS NM OO6452 phosphoribosylaminoimidazole carboxylase PALMD NM O17734 palmdelphin PAN3 NM 175854 PABP1-dependent poly A-specific ribonuclease PAP2D NM 001010861 phosphatidic acid phosphatase type 2d isoform 2 PAPLN NM 173462 papilin PAPOLB NM 02014.4 poly(A) polymerase beta (testis specific) PAPPA NM OO2581 pregnancy-associated plasma protein A PAQR5 NM O17705 membrane progestin receptor gamma PAQR6 NM 198406 progestin and adipoCR receptor family member VI PARD6G NM 032510 PAR-6 gamma protein PARP6 NM 020213 poly (ADP-ribose) polymerase family, member 6 PARVA NM 018222 parvin, alpha PATE NM 138294 expressed in prostate and testis PAX5 NM O16734 paired box 5 PBK NM 018492 T-LAK cell-originated protein kinase PC NM 000920 pyruvate carboxylase precursor PCDH11X NM 032967 protocadherin 11 X-linked isoform b precursor PCDH11 Y NM 032971 protocadherin 11 Y-linked isoform a PCDH21 NM 033100 protocadherin 21 precursor PCDHA9 NM O14005 protocadherin alpha 9 isoform 2 precursor PCDHB10 NM 018930 protocadherin beta 10 precursor PCGF3 NM OO6315 ring finger protein 3 PCGF6 NM 001011663 polycomb group ring finger 6 isoform a PCMT1 NM OO5389 protein-L-isoaspartate (D-aspartate) PCNXL2 NM O14801 pecanex-like 2 PCQAP NM 001003891 positive cofactor 2, glutamine, Q-rich-associated PCSK2 NM OO2594 proprotein convertase Subtilisinkexin type 2 PCSK6 NM 138323 paired basic amino acid cleaving system 4 PCSK7 NM 004716 proprotein convertase subtilisin?kexin type 7 PCSK9 NM 174936 proprotein convertase subtilisin?kexin type 9 PCYOX1 NM O16297 prenylcysteine oxidase 1 PDAP1 NM O14891 PDGFA associated protein 1 PDCD6IP NM 013374 programmed cell death 6 interacting protein PDCL NM OO5388 phosducin-like PDDC1 NM 182612 hypothetical protein LOC347862 PDE11A NM 016953 phosphodiesterase 11A PDE1B NM 000924 phosphodiesterase 1B, calmodulin-dependent PDE4DIP NM OO10O2811 phosphodiesterase 4D interacting protein isoform PDE5A NM 001083 phosphodiesterase 5A isoform 1 US 2009/0232893 A1 Sep. 17, 2009 36

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description DE7A NM 002604 phosphodiesterase 7A isoform b DE8B NM 001029851 phosphodiesterase 8B isoform 3 DGFB NM 002608 platelet-derived growth factor beta isoform 1, DGF NM OO62O6 platelet-derived growth factor receptor alpha DGFRB NM 002609 platelet-derived growth factor receptor beta DIA6 NM OO5742 protein disulfide -associated 6 DK1 NM 0026 O pyruvate dehydrogenase kinase, isozyme 1 DLIM2 NM 176871 PDZ and LIM domain 2 isoform 1 DLIMS NM 0010 1513 PDZ and LIM domain 5 isoform b DP2 NM 020786 pyruvate dehydrogenase phosphatase isoenzyme 2 DPK1 NM 0026 3 3-phosphoinositide dependent protein kinase-1 DPR NM O17990 pyruvate dehydrogenase phosphatase regulatory NM OO3681 pyridoxal kinase NM 0244 1 beta-neoendorphin-dynorphin preproprotein NM 178140 PDZ domain containing 2 NM 0325 2 PDZ domain containing 4 NM OO2567 prostatic binding protein NM 018441 peroxisomal trans-2-enoyl-CoA reductase NM OO62 O paternally expressed 3 NM 0228 7 period 2 isoform 1 NM 0026 7 peroxisome biogenesis factor 10 isoform 2 NM OOO3 9 peroxisomal biogenesis factor 5 NM 0010 8053 6-phosphofructo-2-kinase/fructose-2, NM O24989 GPI deacylase NM 152595 piggyBac transposable element derived 4 NM 002631 phosphogluconate dehydrogenase NM 000291 phosphoglycerate kinase 1 NM 138733 phosphoglycerate kinase 2 NM 052890 peptidoglycan recognition protein L precursor NM O2O393 peptidoglycan recognition protein-I-beta NM 173582 phosphoglucomutase 2-like 1 NM OO6320 progesterone membrane binding protein NM OO4427 olyhomeotic 2-like isoform b NM 016119 HD finger protein 11 NM 153812 HD finger protein 13 NM 016436 HD finger protein 20 NM 016018 HD finger protein 20-like 1 isoform 1 NM 001015877 HD finger protein 6 isoform 1 NM O15107 HD finger protein 8 NM 177967 hypothetical protein LOC337867 NM O15157 pleckstrin homology-like domain, family B, NM 020432 putative homeodomain transcription factor 2 NM 018425 phosphatidylinositol 4-kinase type II NM OO6099 protein inhibitor of activated STAT, 3 NM 004204 hosphatidylinositol glycan, class Q isoform 2 NM 178517 hosphatidylinositol glycan, class W NM 002649 hosphoinositide-3-kinase, catalytic, gamma NM 181504 hosphoinositide-3-kinase, regulatory Subunit, NM OO3629 hosphoinositide-3-kinase, regulatory Subunit 3 NM 013439 aired immunoglobulin-like type 2 receptor alpha NM O15553 hosphoinositide-binding protein PIP3-E NM 012398 hosphatidylinositol-4-phosphate 5-kinase, type NM 003559 hosphatidylinositol-4-phosphate 5-kinase type NM 173492 hosphatidylinositol-4-phosphate 5-kinase-like NM OO6224 hosphatidylinositol transfer protein, alpha NM 002653 aired-like homeodomain transcription factor 1 NM OOO297 polycystin 2 NM 004571 PBX knotted 1 homeobox 1 isoform 1 NM OOO299 1 isoform 1b NM OOO928 phospholipase A2, group IB NM 012400 phospholipase A2, group IID NM 178034 hospholipase A2, group IVD NM 002657 eiomorphic adenoma gene-like 2 NM 002658 urokinase plasminogen activator preproprotein NM 001005376 plasminogen activator, NM OOO933 phospholipase C beta 4 isoform a NM 133373 phospholipase C delta 3 NM 001005473 phosphatidylinositol-specific phospholipase C, X NM 152666 hospholipase D family, member 5 NM OO1 OO1974 eckstrin homology domain containing, family A NM O14935 hosphoinositol 3-phosphate-binding protein-3 US 2009/0232893 A1 Sep. 17, 2009 37

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description PLEKHB2 NM O 7958 pleckstrin homology domain containing, family B PLEKHQ1 NM O252O1 PH domain-containing protein PLIN NM 002666 perilipin PLXNA1 NM 032242 plexin A1 PML NM 033238 promyelocytic leukemia protein isoform 1 PNKD NM O S488 myofibrillogenesis regulator 1 isoform 1 PNMA2 NM 007257 paraneoplastic antigen MA2 PNPLA1 NM 173676 patatin-like phospholipase domain containing 1 PNPO 8129 pyridoxine 5'-phosphate oxidase PNRC1 proline-rich nuclear receptor coactivator 1 PODXL NM 001018111 podocalyxin-like precursor isoform 1 PO UT1 NM O 5352 protein O-fucosyltransferase 1 isoform 1 PO UT2 NM O 5227 protein O-fucosyltransferase 2 isoform A POGK NM O 7542 pogo transposable element with KRAB domain POGZ. NM 145796 pogo transposable element with ZNF domain POLDIP2 SS84 DNA polymerase delta interacting protein 2 POLDIP3 DNA polymerase delta interacting protein 3 POLH polymerase (DNA directed), eta POLR1B 9014 RNA polymerase I polypeptide B POLR1E NM 022490 RNA polymerase I associated factor 53 POLR2L NM 021128 DNA directed RNA polymerase II polypeptide L. POLR3E 8119 polymerase (RNA) III (DNA directed) polypeptide POLR3GL NM 032305 polymerase (RNA) III (DNA directed) polypeptide POM121 NM 172020 nuclear pore membrane protein 121 POU2F2 NM 002698 POU domain, class 2, transcription factor 2 POU2F3 4352 POU transcription factor PAPDC2 NM 203453 phosphatidic acid phosphatase type 2 domain PARA NMOO1001928 peroxisome proliferative activated receptor, PCDC NM O21823 phosphopantothenoylcysteine decarboxylase EF2 NM 152933 serine threonine protein phosphatase with FIBP2 NM OO3621 PTPRF interacting protein, binding protein 2 NM O14337 peptidylprolyl isomerase-like 2 isoform a NM 139126 peptidylprolyl isomerase-like 4 NM OO2705 NM 177968 protein phosphatase 1B isoform 2 NM O14906 protein phosphatase 1E NM 018444 pyruvate dehydrogenase phosphatase precursor NM 002481 protein phosphatase 1, regulatory (inhibitor) NM O17607 protein phosphatase 1, regulatory subunit 12C NM OO6663 protein phosphatase 1, regulatory (inhibitor) NM 032833 protein phosphatase 1, regulatory subunit 15B P1 NM O15568 protein phosphatase 1 regulatory inhibitor NM 002711 protein phosphatase 1 glycogen-binding s NM O24607 protein phosphatase 1, regulatory (inhibitor) NM 001009552 protein phosphatase 2, catalytic Subunit, beta NM 002716 beta isoform of regulatory subunit A, protein NM 002717 alpha isoform of regulatory subunit B55, protein NM 002718 protein phosphatase 2, regulatory subunit B", NM 021131 protein phosphatase 2A, regulatory Subunit B' NM 002719 gamma isoform of regulatory subunit B56, protein NM 018498 hypothetical protein LOC55370 NM OO5155 palmitoyl-protein thioesterase 2 isoform a C1 NM OO3981 protein regulator of cytokinesis 1 isoform 1 NM 021619 PR domain containing 12 NM 022114 PR domain containing 16 isoform 1 NM 020227 PR domain containing 9 NM 013388 prolactin regulatory element binding protein NM 002725 proline arginine-rich end leucine-rich repeat NM OO6036 prolyl endopeptidase-like NM 198859 prickle-like 2 NM OO6252 AMP-activated protein kinase alpha 2 catalytic KC A. NM OO2737 protein kinase C, alpha NM OO5400 protein kinase C, epsilon NM 016457 protein kinase D2 NM O24653 PRKR interacting protein 1 (IL11 inducible) NM 004705 protein-kinase, interferon-inducible double NM 005044 protein kinase, X-linked NM 002760 protein kinase, Y-linked NM 012409 prion-like protein doppel preproprotein S. NM 007198 proline synthetase co-transcribed homolog NM 0145O2 PRP19/PSO4 pre-mRNA processing factor 19 US 2009/0232893 A1 Sep. 17, 2009 38

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description PRPF4 NM 004697 PRP4 pre-mRNA processing factor 4 homolog PRRG4 NM 024081 proline rich Gla (G-carboxyglutamic acid) 4 PRRT2 NM 145239 hypothetical protein LOC112476 PRRX1 NM OO6902 paired mesoderm homeobox. 1 isoform pmX-1a PRSS23 NM 007173 protease, serine, 23 precursor PRX NM 020956 periaxin isoform 1 PRY NM 004676 PTPN13-lilce, Y-linked PRY2 NM OO1002758 PTPN13-like, Y-linked 2 PSCD1 NM 004762 pleckstrin homology, Sect and coiled coil PSCD4 NM 013385 pleckstrin homology, Sect and coiled coil PSD3 NM O15310 ADP-ribosylation factor guanine nucleotide PSG4 NM OO2780 pregnancy specific beta-1-glycoprotein 4 isoform PSG7 NM OO2783 pregnancy specific beta-1-glycoprotein 7 PSMD5 NM 005047 proteasome 26S non-ATPase subunit 5 PSME4 NM 014614 proteasome (prosome, macropain) activator PTAFR NM OOO952 platelet-activating factor receptor PTCH NM 000264 patched PTDOO4 NM 001011708 GTP-binding protein PTD004 isoform 2 PTDSS2 NM 030783 phosphatidylserine synthase 2 PTGDR NM OOO953 prostaglandin D2 receptor PTGER3 NM 198718 prostaglandin E receptor 3, Subtype EP3 isoform PTGES2 NM O25072 prostaglandin E synthase 2 isoform 1 PTGES3 NM OO66O1 unactive progesterone receptor, 23 kD PTGIS NM OOO961 prostaglandin I2 (prostacyclin) synthase PTHB1 NM OO1033604 parathyroid hormone-responsive B1 isoform 3 PTK6 NM OO5975 PTK6 protein tyrosine kinase 6 PTK7 NM 002821 PTK7 protein tyrosine kinase 7 isoform a PTK9L. NMOO7284 twinfilin-like protein PTPDC1 NM 152422 protein tyrosine phosphatase domain containing 1 PTPLB NM 1984O2 protein tyrosine phosphatase-like (proline PTPN11 NM 002834 protein tyrosine phosphatase, non-receptor type PTPN2 NM 002828 protein tyrosine phosphatase, non-receptor type PTPN23 NM 015466 protein tyrosine phosphatase, non-receptor type PTPN4 NM 002830 protein tyrosine phosphatase, non-receptor type PTPN7 NM 002832 protein tyrosine phosphatase, non-receptor type PTPRE NM O06504 protein tyrosine phosphatase, receptor type, E PTPRN NM 002846 protein tyrosine phosphatase, receptor type, N PTPRT NM 007050 protein tyrosine phosphatase, receptor type, T PTRF NM 012232 polymerase I and transcript release factor PTTG1IP NM 004339 pituitary tumor-transforming gene 1 C XMP4 NM 183397 peroxisomal membrane protein 4 isoform b C XT1 NM 152990 peroxisomal, testis specific 1 C YCRL NM 023078 pyrroline-5-carboxylate reductase-like NM OOO320 quinoid dihydropteridine reductase NM OO6775 quaking homolog, KH domain RNA binding isoform PC T NM O17659 glutaminyl-peptide cyclotransferase-like NM O14298 quinolinate phosphoribosyltransferase NM 018292 glutaminyl-tRNA synthase NM 002826 quiescin Q6 isoform a NM 181701 quiescin Q6-like 1 NM 004663 Ras-related protein Rab-1 1A NM 0010O2814 Rab coupling protein isoform 3 NM 032932 RAB11 family interacting protein 4 (class II) NM 198686 Ras-related protein Rab-15 NM O2O673 RAS-related protein RAB-22A NM O16277 Ras-related protein Rab-23 NM OO4580 Ras-related protein Rab-27A NM 001017979 RAB28, member RAS oncogene family isoform 1 NM 031296 RAB33B, member RAS oncogene family NM OO1OO6638 RAB37, member RAS oncogene family isoform 2 NM OO6822 RAB40B, member RAS oncogene family OC NM 021168 RAR (RAS like GTPASE) like NM OO1032726 RAB41, member RAS homolog family NM 198490 RAB43 protein NM O16577 RAB6B, member RAS oncogene family NM O15064 RAB6-interacting protein 2 isoform alpha NM 004637 RAB7, member RAS oncogene family NM OO3929 RAB7, member RAS oncogene family-like 1 NM 004703 rabaptin, RAB GTPase binding effector protein 1 NM 002871 RAB-interacting factor NM O22777 RAB, member RAS oncogene family-like 5 US 2009/0232893 A1 Sep. 17, 2009 39

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description RAD1 NM 002853 RAD1 homolog isoform 1 RAD23B NM 002874 UV excision repair protein RAD23 homolog B RADS NM 002875 RAD51 homolog protein isoform 1 RADS1L3 NM 002878 RAD51-like 3 isoform 1 RAE NM 001015885 RAE1 (RNA export 1, S. pombe) homolog RAF NM 002880 v-raf-1 murine leukemia viral oncogene homolog RAI17 NM 020338 retinoic acid induced 17 RALBP1 NM OO6788 ralAbinding protein 1 RALGPS1 NM 014636 Ral GEF with PH domain and SH3 binding motif 1 RANBP10 NM 020850 RAN binding protein 10 RAP2B NM 002886 RAP2B, member of RAS oncogene family RAPGEF1 NM 005312 guanine nucleotide-releasing factor 2 isoform a RAPGEF6 NM 016340 PDZ domain-containing guanine nucleotide RARG NM OOO966 retinoic acid receptor, gamma RARRES1 NM 206963 retinoic acid receptor responder (tazaroteine RASD2 NM 014310 RASD family, member 2 RASGEF1B NM 1525.45 RasGEF domain family, member 1B RASGRP1 NM OO5739 RAS guanyl releasing protein 1 RASGRP4 NM 052949 RAS guanyl releasing protein 4 isoform 3 RASL1 OB NM 033315 RAS-like, family 10, member B RASSF2 NM 014737 Ras association domain family 2 RASSF4 NM 032023 Ras association domain family 4 isoform a RASSFS NM 031437 Ras association (RalGDSAF-6) domain family 5 RASSF6 NM 177532 Ras association (RalGDSAF-6) domain family 6 RASSF8 NM 007211 Ras association (RalGDSAF-6) domain family 8 RAVER1 NM 1334.52 RAVER1 RAXLX NM 001008494 hypothetical protein LOC91464 RB1 NMOOO321 retinoblastoma 1 RBBP9 NM OO6606 retinoblastoma binding protein 9 RBL1 NM 002895 retinoblastoma-like protein 1 isoform a RBM14 NM OO6328 RNA binding motif protein 14 RBM16 NM O14892 RNA-binding motif protein 16 RBM17 NM 032.905 RNA binding motif protein 17 RBM19 NM 0161.96 RNA binding motif protein 19 RBM24 NM 153020 hypothetical protein LOC221662 RBM3 NM 001017430 RNA binding motif protein 3 isoform b RBM33 NM OO10084.08 hypothetical protein LOC155435 RBMS NM OO5778 RNA binding motif protein 5 RCC2 NM 018715 RCC1-like RCD-8 NM O14329 autoantigen RCD8 RCHY1 NM OO10O8925 ring finger and CHY Zinc finger domain RDBP NM 002904 RD RNA-binding protein RDH12 NM 152443 retinol dehydrogenase 12 (all-trans and 9-cis) RECQL5 NM 001003715 RecQ protein-like 5 isoform 2 REEP1 NM 022912 receptor expression enhancing protein 1 REEP3 NM OO1 OO1330 receptor expression enhancing protein 3 REG4 NM 032044 regenerating islet-derived family, member 4 REPS1 NM 03.1922 RALBP1 associated Eps domain containing 1 RER1 NM 007033 RER1 retention in endoplasmic reticulum 1 RETNLB NM 032579 colon and Small intestine-specific cysteine-rich REXO1L1 NM 172239 exonuclease GOR REXO2 NM O15523 Small fragment nuclease RFC3 NM 181558 replication factor C3 isoform 2 RFK NM 018339 riboflavin kinase RFNG NM OO2917 radical fringe homolog RFWD3 NM 018124 ring finger and WD repeat domain 3 RFX2 NM OOO635 regulatory factor X2 isoform a RG9MTD3 NM 144964 RNA (guanine-9-) methyltransferase domain RGAG1 NM 020769 gag domain containing 1 RGL1 NM O15149 ral guanine nucleotide dissociation RGMB NM 001012761 RGM domain family, member B isoform 1 precursor RGS11 NM OO3834 regulator of G-protein signalling 11 isoform 2 RGS12 NM 198432 regulator of G-protein signalling 12 isoform 5 RGS18 NM 130782 regulator of G-protein signalling 18 RGS3 NM O17790 regulator of G-protein signalling 3 isoform 3 RGSL1 NM 181572 regulator of G-protein signalling like 1 RHBDD1 NM 032276 rhomboid domain containing 1 RHBDL3 NM 138328 rhomboid, veinlet-like 3 RHCG NM 016321 Rhesus blood group, C glycoprotein RHOBTB1 NM OO1032380 Rho-related BTB domain containing 1 RHOG NM OO1665 ras homolog , member G US 2009/0232893 A1 Sep. 17, 2009 40

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description RHOJ NM 020663 TC10-like Rho GTPase RHOU NM 021205 ras homolog gene family, member U. RIC8A NM O21932 resistance to inhibitors of cholinesterase 8 RICTOR NM 152756 rapamycin-insensitive companion of mTOR RIMBP2 NM O15347 RIM-binding protein 2 RIMS3 NM 014747 regulating synaptic membrane exocytosis 3 RIN2 NM 018993 RAB5 interacting protein 2 NM 024832 Ras and Rab interactor 3 NM O15375 receptor interacting protein kinase 5 isoform 1 NM 016626 ring finger and KH domain containing 2 NM 005059 relaxin 2 isoform 2 NM O22780 hypothetical protein LOC64795 NM 032572 ribonuclease 7 NM OO5440 Rho family GTPase 2 NM O14868 ring finger protein 10 NM O14372 ring finger protein 11 NM 018320 ring finger protein 121 isoform 1 NM O17831 ring finger protein 125 NM 197939 ring finger protein 135 isoform 2 NM O16271 ring finger protein 138 isoform 1 NM 014746 ring finger protein 144 NM 152470 ring finger protein 165 NM 152267 ring finger protein 185 NM 007212 ring finger protein 2 NM 007219 ring finger protein 24 NM 032015 ring finger protein 26 NM OO2938 ring finger protein 4 NM 014771 ring finger protein 40 NM OO5977 ring finger protein 6 isoform 1 NM OO3958 ring finger protein 8 isoform 1 NM OO3800 RNA guanylyltransferase and 5'-phosphatase NM 003799 RNA (guanine-7-) methyltransferase NM 004902 RNA-binding region containing protein 2 isoform ROBO4 NM O19055 roundabout homolog 4, magic roundabout ROD1 NM OO5156 ROD1 regulator of differentiation 1 RORC NM 001001523 RAR-related orphan receptor C isoform b P11-193.3 NM 001012267 hypothetical protein LOC401541 P11-311P8.3 NM 145052 hypothetical protein LOC139596 P13-1SM17.2 NM 001010866 hypothetical protein LOC199953 PA1 NM OO2945 replication protein A1, 70 kDa L28 NM OOO991 ribosomal protein L28 NM OOO994 ribosomal protein L32 NM OOO995 ribosomal protein L34 NM OOO997 ribosomal protein L37 NM 198486 ribosomal protein L7-like 1 NM 001004 ribosomal protein P2 P25 NM O17793 ribonuclease P 25 kDa subunit S27 NM OO1030 ribosomal protein S27 PS6KA3 NM OO4586 ribosomal protein S6 kinase, 90 kDa, polypeptide RAS2 NM 012250 related RAS viral (r-ras) oncogene homolog 2 NM OO6583 peropsin NM 001034 ribonucleotide reductase M2 polypeptide NM O15713 ribonucleotide reductase M2 B (TP53 inducible) NM OO1007279 RAS-related on chromosome 22 isoform b NM OOO330 X-linked juvenile retinoschisis protein SAD1 NM 018346 radical S-adenosyl methionine domain containing EL1 NM 032957 regulator of telomere elongation helicase 1 F1 NM O15138 Paf1/RNA polymerase II complex component RTN2 NM 206902 reticulon 2 isoform D RTN4RL1 NM 178568 reticulon 4 receptor-like 1 RUNDC1 NM 173079 RUN domain containing 1 RUNX3 NM OO1031680 runt-related transcription factor 3 isoform 1 RWDD4A NM 152682 RWD domain containing 4A S100A11 NM OO5620 S100 calcium binding protein A11 (calgizZarin) S100A14 NM O2O672 S100 calcium binding protein A14 S100A7L1 NM 1768.23 S100 calcium binding protein A7-like 1 S1OOPBP NM O22753 S100P binding protein Riken isoform a SALL4 NM 020436 sal-like 4 SAMD13 NM 001010971 -like protein SAP130 NM 024545 mSin3A-associated protein 130 SAP3 OBP NM 013260 transcriptional regulator protein US 2009/0232893 A1 Sep. 17, 2009 41

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description SARM1 NM O15.077 sterile alpha and TIR motif containing 1 SART1 NM OO5146 Squamous cell carcinoma antigen recognized by T SASH1 NM O15278 SAM and SH3 domain containing 1 SATL1 NM 00101.2980 spermidine?spermine N1-acetyltransferase-like SAV1 NM 021818 WW45 protein SC65 NM OO6455 synaptonemal complex protein SC65 SCAMP1 NM 004.866 Secretory carrier membrane protein 1 isoform 1 SCAMP4 NM O79834 Secretory carrier membrane protein 4 SCAMPS NM 138967 secretory carrier membrane protein 5 SCAND2 NM O22050 SCAN domain-containing protein 2 isoform 1 SCAP2 NM OO3930 Src family associated phosphoprotein 2 SCC-112 NM O15200 SCC-112 protein SCG3 NM 013243 Secretogranin III SCML.1 NM OO6746 sex comb on midleg-like 1 isoform b SCML4 NM 198O81 sex comb on midleg-like 4 NM 014139 Sodium channel, voltage-gated, type XI, alpha NM OO4588 Sodium channel, voltage-gated, type II, beta NM OOO334 voltage-gated sodium channel type 4 alpha NM 174934 Sodium channel, voltage-gated, type IV, beta NM 032547 short coiled-coil protein NM 031309 Scratch NM O2O680 SCY1-like 1 NM O16176 calcium binding protein Cab45 precursor NM OO6843 serine dehydratase NM OO3003 SEC14 (S. cerevisiae)-like 1 isoform a NM 174977 SEC14p-like protein TAP3 NM 005065 sel-1 Suppressor of lin-12-like NM 033505 selenoprotein I NM OOO655 L. ELP NM OO3005 selectin P precursor ELT NM O16275 selenoprotein T EMA3E NM 012431 semaphorin 3E EMA3G NM O2O163 Semaphorin Sem2 EMA4F NM 004263 semaphorin W EMASA NM OO3966 Semaphorin 5A EMA7A NM OO3612 Semaphorin 7A EPT10 NM 144710 septin 10 isoform 1 EPT11 NM 018243 Septin 11 EPT3 NM 019106 septin 3 isoform B EPT4 NM 080417 Septin 4 isoform 4 EPT6 NM 145799 septin 6 isoform A EPT9 NM O06640 septin 9 EPX1 NM 016332 Selenoprotein X, 1 ERF1A NM O21967 Small EDRK-rich factor 1A, telomeric ERF1B NM O22978 Small EDRK-rich factor 1B, centromeric ERPINB13 NM 012397 serine (or cysteine) proteinase inhibitor, clade ERPINB8 NM 002640 serine (or cysteine) proteinase inhibitor, clade ERPINC1 NM 000488 serine (or cysteine) proteinase inhibitor, clade ERPINE1 NM OOO602 plasminogen activator inhibitor-1 ETD1A NM 014712 SET domain containing 1A F1 NM 004630 splicing factor 1 isoform 1 NM 001005409 splicing factor 3a, Subunit 1, 120 kDa isoform 2 NM OO6802 splicing factor 3a, Subunit 3 F4 NM 182812 splicing factor 4 isoform c FMBT1 NM 001005158 Scm-like with four mbt domains 1 FMBT2 NM 00102988O Scm-like with four mbt domains 2 FRP4 NM 003.014 secreted frizzled-related protein 4 FRS11 NM 004768 splicing factor p54 FRS1.4 NM 001017392 splicing factor, arginine?serine-rich 14 FTPB NM 1988.43 Surfactant, pulmonary-associated protein B FXN1 NM O22754 sideroflexin 1 S NM 144579 sideroflexin 5 NM OOO232 sarcoglycan, beta (43 kDa -associated NM O15595 Src homology 3 domain-containing guanine NM O16276 serum glucocorticoid regulated kinase 2 isoform NM OO1033578 serum glucocorticoid regulated kinase 3 isoform NM 014633 SH2 domain binding protein 1 NM OO5490 SH2 domain containing 3A NM 170600 SH2 domain containing 3C isoform 2 NM O22071 SH2 domain containing 4A NM 207372 SH2 domain containing 4B US 2009/0232893 A1 Sep. 17, 2009 42

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description NM 031469 SH3 domain binding -rich protein NM OO3O23 SH3-domain binding protein 2 NM OO3O26 SH3-domain GRB2-like 2 NM 153271 SH3 and PX domain containing 3 NM 014631 SH3 multiple domains 1 NM 001017995 SH3 and PX domains 2B NM 012309 SH3 and multiple ankyrin repeat domains 2 NM 001010846 Src homology 2 domain containing E NM O17699 SID1 transmembrane family, member 1 NM 052884 sialic acid binding Ig-like lectin 11 NM 198846 sialic acid binding Ig-like lectin 6 isoform 3 NM O15073 signal-induced proliferation-associated 1 like NM 080792 signal-regulatory protein alpha precursor NM OO6065 signal-regulatory protein beta 1 precursor NM 018556 signal-regulatory protein gamma isoform 1 NM 012237 2 isoform 1 NM 031244 sirtuin 5 isoform 2 NM O14450 SHP2-interacting transmembrane adaptor protein NM O16581 evolutionarily conserved signaling intermediate NM O17420 sine oculis homeobox homolog 4 NM O16532 skeletal muscle and kidney enriched inositol NM 021181 SLAM family member 7 NM 020708 solute carrier family 12 member 5 NM 177550 solute carrier family 13 (sodium-dependent NM 007163 Solute carrier family 14 (urea transporter), NM 145648 solute carrier family 15, member 4 NM 213606 Solute carrier family 16 (monocarboxylic acid NM 152527 solute carrier family 16 (monocarboxylic acid NM O06517 solute carrier family 16, member 2 NM 012434 Solute carrier family 17 (anion sugar NM 020346 differentiation-associated Na-dependent NM 020309 solute carrier family 17, member 7 NM OO4170 solute carrier family 1, member 1 NM OO4171 solute carrier family 1, member 2 NM OO4172 Solute carrier family 1 (glial high affinity NM 018420 Solute carrier family 22 (organic cation NM 033125 solute carrier family 22, member 16 NM O21977 solute carrier family 22 member 3 NM OO6672 solute carrier family 22 member 7 isoform a NM OO4727 solute carrier family 24 NM 153646 solute carrier family 24 member 4 isoform 1 NM O14251 solute carrier family 25, member 13 (citrin) NM O14252 solute carrier family 25 (mitochondrial carrier; NM 024103 solute carrier family 25 (mitochondrial carrier; NM 0010.06641 solute carrier family 25, member 25 isoform b NM 213612 solute carrier family 25 member 3 isoform c NM OOO112 solute carrier family 26 member 2 NM 000441 pendrin NM 052961 solute carrier family 26, member 8 isoform a NM 198580 solute carrier family 27 (fatty acid NM 005094 solute carrier family 27 (fatty acid NM OO6931 Solute carrier family 2 (facilitated glucose NM OO3O39 solute carrier family 2 (facilitated NM OO3459 solute carrier family 30 (zinc transporter), NM 173851 solute carrier family 30 member 8 NM OO6345 solute carrier family 30 (zinc transporter), NM OO1859 Solute carrier family 31 (copper transporters), NM OO1860 Solute carrier family 31 (copper transporters), NM 080670 solute carrier family 35, member A4 NM O17945 solute carrier family 35, member A5 NM OO5827 solute carrier family 35, member B1 NM 032826 solute carrier family 35, member B4 NM 007001 solute carrier family 35, member D2 NM O24881 solute carrier family 35, member E1 NM 001029858 solute carrier family 35, member F1 NM O25181 solute carrier family 35, member F5 NM O78483 solute carrier family 36 member 1 NM 198277 solute carrier family 37 (glycerol-3-phosphate NM 018976 solute carrier family 38, member 2 NM OO6841 solute carrier family 38, member 3 NM O2O342 solute carrier family 39 (zinc transporter), US 2009/0232893 A1 Sep. 17, 2009 43

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description SLC39A11 NM 139177 solute carrier family 39 (metalion SLC39A3 NM 213568 solute carrier family 39 (zinc transporter), SLC41A1 NM 173854 solute carrier family 41 member 1 SLC45A3 NM 033102 prostein SLCSA6 NM 021095 solute carrier family 5 (sodium-dependent SLCSA8 NM 145913 solute carrier family 5 (iodide transporter), SLC6A1 NM 003042 solute carrier family 6 (neurotransmitter SLC6A2O NM 020208 solute carrier family 6, member 20 isoform 1 SLC6A6 NM 003043 solute carrier family 6 (neurotransmitter SLC6A7 NM O14228 solute carrier family 6, member 7 SLC7AS NM 0034.86 Solute carrier family 7 (cationic amino acid SLC7A6 NM OO3983 Solute carrier family 7 (cationic amino acid SLC8A2 NM O15063 solute carrier family 8 member 2 SLC8A3 NM 033262 solute carrier family 8 member 3 isoform A SLC9A1 NM 003047 solute carrier family 9, isoform A1 SLC9AS NM OO4594 Solute carrier family 9 (sodium hydrogen SLC9A.8 NM O15266 Na+ H+ exchanger isoform 8 SLCO2A1 NM OO5630 Solute carrier organic anion transporter family, SLCO2B1 NM 007256 Solute carrier organic anion transporter family, SLFN13 NM 144682 schlafen family member 13 SLFNS NM 144975 schlafen family member 5 SLFNL1 NM 144990 hypothetical protein LOC200172 SLITRK3 NM O14926 slit and trk like 3 protein SMA4 NM 021652 SMA4 SMAD2 NM 001003652 Sma- and Mad-related protein 2 SMAD3 NM OO5902 MAD, mothers against decapentaplegic homolog 3 SMARCB1 NM OO1007468 SWISNF related, matrix associated, actin SMARCD2 NMOO3.077 SWISNF-related matrix-associated SMC1L1 NM OO6306 SMC1 structural maintenance of SMC2L1 NM O06444 structural maintenance of chromosomes 2-like 1 SMCR7 NM 1391.62 Smith-Magenis Syndrome chromosome region, SMG7 NM O14837 SMG-7 homolog isoform 3 SMNDC1 NM OO5871 Survival motor neuron domain containing 1 SMO NM OO5631 Smoothened SMPD3 NM 018667 sphingomyelin phosphodiesterase 3, neutral SMURF1 NM 020429 Smad ubiquitination regulatory factor 1 isoform SMYD4 NM 052928 SET and MYND domain containing 4 SNF1LK2 NM O15191 SNF1-like kinase 2 SNIP NM O25248 SNAP25-interacting protein SNPH NM 014723 Syntaphilin SNRPN NM 003097 Small nuclear ribonucleoprotein polypeptide N SNTB2 NM 130845 basic beta 2 syntrophin isoform b SNURF NM OO5678 SNRPN upstream reading frame protein SNX11 NM 013323 Sorting nexin 11 SNX13 NM O15132 Sorting nexin 13 SNX27 NM 030918 Sorting nexin family member 27 SOHLH2 NM 017826 hypothetical protein LOC54937 SON NM 003103 SON DNA-binding protein isoform G SORBS1 NM O15385 Sorbin and SH3 domain containing 1 isoform 2 SORCS1 NM 00101.3031 SORCS receptor 1 isoform b SORCS2 NM O2O777 VPS10 domain receptor protein SORCS 2 SOST NM O25237 Sclerostin precursor SOX NM OO5986 SRY (sex determining region Y)-box 1 SOX13 NM 005686 SRY-box 13 SOX8 NM 014587 SRY (sex determining region Y)-box 8 SP1 NM 138473 Sp1 transcription factor SP4 NM 003112 Sp4 transcription factor SP6 NM 199262 Sp6 transcription factor SP7 NM 152860 osterix SPACA4 NM 133498 sperm acrosomal membrane protein 14 SPAG16 NM 001025436 sperm associated antigen 16 isoform 2 SPANXA1 NM 013453 sperm protein associated with the nucleus, X SPANXA2 NM 145662 sperm protein associated with the nucleus, X SPANXC NM 022661 sperm protein associated with the nucleus, X SPANXD NM 032417 sperm protein associated with the nucleus, X SPANXE NM 145665 sperm protein associated with the nucleus, X SPATA12 NM 181727 spermatogenesis associated 12 SPATA18 NM 145263 spermatogenesis associated 18 homolog SPATA2 NM OO6038 spermatogenesis associated 2 SPECC1 NM OO1033554 spectrin domain with coiled-coils 1 NSP5a3a SPG21 NM 016630 acid cluster protein 33 US 2009/0232893 A1 Sep. 17, 2009 44

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description PIB NM OO3121 Spi-B transcription factor (Spi-1/PU.1 related) PINLW1 NM O2O398 serine peptidase inhibitor-like, with Kunitz and PIRE1 NM O2O148 pire homolog 1 PN NM OO1030288 ialophorin POCK1 NM 004598 parcosteonectin, cwcv and kazal-like domains POCK2 NM 014767 parcosteonectin, cwcv and kazal-like domains PRN NM 001012508 hadow of prion protein PRY3 NM 005840 prouty homolog 3 PRYD3 NM 032840 hypothetical protein LOC84926 PTB NM 001024858 spectrin beta isoform a PTBN2 NM OO6946 spectrin, beta, non-erythrocytic 2 PTLC2 NM 004.863 serine palmitoyltransferase, long chain base PTY2D1 NM 194285 hypothetical protein LOC144108 RDSA1 NM OO1047 steroid-5-alpha-reductase 1 RDSA2L2 NM 001010874 steroid 5 alpha-reductase 2-like 2 RGAP2 NM O15326 SLIT-ROBO Rho GTPase activating protein 2 RM NM OO3132 spermidine synthase S RP72 NM OO6947 signal recognition particle 72 kDa SS18L1 NM O15558 SS18-like protein 1 SSBP3 NM 001009955 single stranded DNA binding protein 3 isoform c SSH2 NM 03.3389 slingshot 2 SSR3 NM 007107 signal sequence receptor gamma Subunit SSTR1 NM 001049 Somatostatin receptor 1 SSX1 NM OO5635 synovial sarcoma, X breakpoint 1 SSX8 NM 174961 synovial sarcoma, X breakpoint 8 ST6GAL1 NM OO3O32 sialyltransferase 1 isoform a ST6GALNAC4 NM 175040 sialyltransferase 7D isoform b ST7L NMO17744 Suppression of tumorigenicity 7-like isoform 1 ST8SLA2 NM OO6011 ST8 alpha-N-acetyl-neuraminide ST8SIA4 NM OO5668 ST8 alpha-N-acetyl-neuraminide STAB2 NM 017564 stabilin 2 precursor STAC NM OO3149 SH3 and cysteine rich domain STAR NM OOO349 steroidogenic acute regulator isoform 1 STARD13 NM 052851 START domain containing 13 isoform gamma STARD4 NM 1391.64 START domain containing 4, Sterol regulated STARDS NM O30574 StAR-related lipid transfer protein 5 isoform 2 STATSA NM OO3152 signal transducer and activator of transcription STAU2 NM O14393 Staufen homolog 2 STCH NM OO6948 stress 70 protein chaperone, STEAP3 NM 001008410 dudulin 2 isoform b STIP1 NM OO6819 stress-induced-phosphoprotein 1 STK10 NM OO5990 serine threonine kinase 10 STK16 NM OO10O8910 serine threonine kinase 16 STK32B NM 018401 serine threonine kinase 32B STK35 NM 08.0836 serine threonine kinase 35 STK4 NM OO6282 serine threonine kinase 4 STMN3 NM O15894 SCG10-like-protein STON1 NM OO6873 stonin 1 STOX2 NM 020225 storkhead box 2 STRN NM OO3162 striatin, calmodulin binding protein STRN3 NM 014574 nuclear autoantigen STS NM 000351 steryl-sulfatase precursor STX17 NM O17919 Syntaxin 17 STXBP1 NM OO1032221 Syntaxin binding protein 1 isoform b STXBP5 NM 139244 tomosyn SUFU NM 016169 Suppressor of fused SUHW1 NM 080740 Suppressor of hairy wing homolog 1 SULT1A3 NM 001017387 Sulfotransferase family, cytosolic, 1A, SULT1A4 NM 001017389 Sulfotransferase family, cytosolic, 1A, SULT1E1 NM 005420 Sulfotransferase, estrogen-preferring SULT2A1 NM OO3167 Sulfotransferase family, cytosolic, 2A, SUMO3 NM OO6936 Small ubiquitin-like modifier protein 3 SURB7 NM 004264 SRB7 Suppressor of RNA polymerase B homolog SURF4 NM 03.3161 Surfeit 4 SURFS NM 133640 Surfeit 5 isoform b SUSD2 NM 0196O1 Sushi domain containing 2 SUSD4. NM O17982 Sushi domain containing 4 isoform a SUV42OH1 NM 016028 Suppressor of variegation 4-20 homolog 1 isoform SV2A NM 014849 synaptic vesicle glycoprotein 2 SV2B NM 014848 synaptic vesicle protein 2B homolog SVOP NM 018711 SV2 related protein US 2009/0232893 A1 Sep. 17, 2009 45

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description SWAP70 NM O15055 SWAP-70 protein SYBL1 NM OO5638 synaptobrevin-like 1 SYN2 NM OO3178 synapsin II isoform IIb SYN3 NM 133632 synapsin III isoform IIIb SYNGR1 NM 004711 synaptogyrin 1 isoform 1 a SYNJ2 NM OO3898 synaptoanin 2 SYN2BP NM 018373 synaptoanin 2 binding protein SYT10 NM 198992 synaptotagmin 10 SYT11 NM 152280 synaptotagmin 12 SYT3 NM 032298 synaptotagmin 3 SYT6 NM 205848 synaptotagmin VI SYT7 NM 004200 synaptotagmin VII SYT9 NM 175733 synaptotagmin DX TACC1 NM OO6283 transforming, acidic coiled-coil containing TACSTD2 NM 002353 tumor-associated calcium signal transducer 2 TADA3L NM 133480 transcriptional adaptor 3-like isoform b TAF12 NM 005644 TAF12 RNA polymerase II, TATA box binding TAF1L, NM 1538.09 TBP-associated factor RNA polymerase 1-like TAOK2 NM OO4783 TAOkinase 2 isoform 1 TAPBP NM OO3190 apasin isoform 1 precursor TARDBP NM OO7375 CAR DNA binding protein TATDN2 NM 014760 atD DNase domain containing 2 TAZ NM 181314 afazzin isoform 5 TBC1D1 NM O15173 CBC1 (tre-2/USP6, BUB2, ccdc16) domain family, TBC1D10B NM O15527 TBC1 domain family, member 10B TBC1D14 NM O2O773 TBC1 domain family, member 14 TBC1D2O NM 144628 TBC1 domain family, member 20 TBC1D22A NMO14346 CBC1 domain family, member 22A TBC1D22B NM O17772 TBC1 domain family, member 22B TBC1D2B NM O15079 TBC1 domain family, member 2B TBL1X NM 005647 transducin beta-like 1X TBX21 NM 013351 T-box 21 TBX3 NM OO5996 T-box 3 protein isoform 1 TC A. 7 NM 152278 hypothetical protein LOC56849 TC NM 004609 basic helix-loop-helix transcription factor 15 TC NM OO5650 transcription factor 20 isoform 1 TC NM 198392 transcription factor 21 TC NM OO32O2 transcription factor 7 (T-cell specific, C H H L 1 NM OO1008536 trichohyalin-like 1 NM 032300 Erichoplein NM OOO355 transcobalamin II precursor NM 004610 -complex 10 NM 022171 T-cell leukemia translocation altered gene NM 021961 TEA domain family member 1 NM OO3214 TEA domain family member 3 NM 198253 elomerase reverse transcriptase isoform 3 NM 018469 estis expressed sequence 2 NM 144582 estis expressed sequence 261 NM OO3221 transcription factor AP-2 beta (activating NM OO3226 trefoil factor 3 precursor NM O21809 TGFB-induced factor 2 NM 004613 2 isoform a NM 198554 hyroid adenoma associated isoform 2 NM 144721 THAP domain containing 6 NM 003246 hrombospondin 1 precursor NM 018324 hioesterase domain containing 1 isoform 1 NM O53055 hioesterase Superfamily member 4 isoform a NM 182578 hioesterase Superfamily member 5 NM OO6288 Thy-1 cell Surface antigen NM O22037 TIA1 protein isoform 1 NM 032862 igger transposable element derived 5 NM O06335 of inner mitochondrial membrane 17 NM 004614 hymidine kinase 2, mitochondrial NM 012253 transketolase-like 1 NM 032136 transketolase-like 2 NM OO6852 Ousled-like kinase 2 NM O15059 alin 2 NM 001017388 ol-like receptor 10 precursor NM O16170 T-cell leukemia, homeobox2 NM 001024380 TM2 domain containing 2 isoform b NM O15993 plasmolipin US 2009/0232893 A1 Sep. 17, 2009 46

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description TM4SF2O NM O24795 transmembrane 4 L six family member 20 TM7SF4 NM 030788 dendritic cell-specific transmembrane protein TMBIM1 NM 022152 transmembrane BAX inhibitor motif containing 1 TMC5 NM O24780 transmembrane channel-like 5 TMCC3 NM 020698 transmembrane and coiled-coil domains 3 TMED2 NM OO6815 coated vesicle membrane protein TM NM 001001723 transmembrane protein 1 isoform b TM NM 178520 hypothetical protein LOC284186 TM NM 145041 hypothetical protein LOC113277 TME NM O25222 hypothetical protein PRO2730 TM NM 138341 hypothetical protein LOC89894 TM NM 181724 hypothetical protein LOC338773 TM NM 152311 transmembrane protein 12 TM NM O25268 hole protein TM NM O17849 hypothetical protein LOC55654 TM NM 133448 hypothetical protein LOC121256 TM NM O25124 hypothetical protein LOC80194 TM NM 018295 hypothetical protein LOC55281 TM NM 153238 hypothetical protein LOC197196 TM NM O2O373 transmembrane protein 16B TM NM 001025356 transmembrane protein 16F TM NM 001001891 transmembrane protein 16G isoform NGEP long TME NM 018279 transmembrane protein 19 TM NM 014138 hypothetical protein LOC29057 TM NM 001017970 transmembrane protein 3OB TM NM 018126 transmembrane protein 33 TM NM 018306 transmembrane protein 40 TM NMO15O12 transmembrane protein 41B TM NM 024334 transmembrane protein 43 TM NM O24587 transmembrane protein 53 TM NM 1524.87 transmembrane protein 56 TM NM 198149 transmembrane protein 58 TM NM 032936 transmembrane protein 60 TM NM 014698 transmembrane protein 63A TM NM 016486 transmembrane protein 69 TM NM 174940 hypothetical protein LOC283232 TM NM 014573 hypothetical protein MAC30 TM NM 018196 trimethyllysine hydroxylase, epsilon TMOD2 NM 014548 2 (neuronal) TMPRSS11B NM 1825O2 transmembrane protease, serine 11B TMPRSS3 NM 024022 transmembrane protease, serine 3 isoform 1 TMPRSS4 NM 019894 transmembrane protease, serine 4 isoform 1 TNFAIP1 NM 021137 tumor necrosis factor, alpha-induced protein 1 TNFAIP8L1 NM 152362 tumor necrosis factor, alpha-induced protein TNFAIP8L3 NM 207381 tumor necrosis factor, alpha-induced protein TNFRSF10B NM OO3842 tumor necrosis factor receptor Superfamily, TNFRSF10C NM 003841 tumor necrosis factor receptor Superfamily, TNFRSF1OD NM OO3840 tumor necrosis factor receptor Superfamily, TNFRSF19 NM 148957 tumor necrosis factor receptor Superfamily, TNFRSF8 NM 001243 tumor necrosis factor receptor Superfamily, TNFSF10 NM OO3810 tumor necrosis factor (ligand) Superfamily, TNFSF4 NM OO3326 tumor necrosis factor (ligand) Superfamily, TNFSF9 NM OO3811 tumor necrosis factor (ligand) Superfamily, TNIP3 NM O24873 hypothetical protein LOC79931 TNNI1 NM OO3281 I, skeletal, slow TNP1 NM 003284 transition protein 1 (during histone to TNPO2 NM 013433 transportin 2 (importin 3, karyopherin beta 2b) TNRC15 NM O15575 Erinucleotide repeat containing 15 TNRC6B NM 001024843 Erinucleotide repeat containing 6B isoform 2 TNS3 NM O22748 ensin-like SH2 domain containing 1 TOB2 NM O16272 transducer of ERBB2, 2 TOLLIP NM O19009 oll interacting protein TOM1L2 NM OO1033551 arget of myb1-like 2 isoform 1 TOMM4OL NM 032174 translocase of outer mitochondrial membrane 40 TOP2A NM OO1067 DNA topoisomerase II, alpha isozyme TOR2A NM 130459 orsin family 2, member A TOR3A NM 022371 orsin family 3, member A TP53 NM 000546 tumor protein p53 TP53INP1 NM 033285 tumor protein p53 inducible nuclear protein 1 TP53RK NM 033550 p53-related protein kinase TPD52L3 NM 033516 protein kinase NYD-SP25 isoform 1 US 2009/0232893 A1 Sep. 17, 2009 47

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description TPM3 NM 153649 3 isoform 2 TPM4 NM OO3290 tropomyosin 4 TPP1 NM OOO391 tripeptidyl-peptidase I precursor TRAF7 NM 032271 ring finger and WD repeat domain 1 isoform 1 TRAIP NM OO5879 TRAF interacting protein TRAM2 NM 012288 translocation-associated membrane protein 2 TRAPPC3 NM O14408 BET3 homolog TRIAD3 NM 207111 TRIAD3 protein isoform a TRIB3 NM 021158 ribbles 3 TRIM10 NM OO6778 tripartite motif-containing 10 isoform 1 TRIM14 NM 033220 tripartite motif protein TRIM14 isoform alpha TRIM22 NM OO6074 tripartite motif-containing 22 TRIM24 NM OO3852 transcriptional intermediary factor 1 alpha TRIM2S NM 005082 tripartite motif-containing 25 TRIM26 NM 003449 tripartite motif-containing 26 TRIM29 NM 012101 tripartite motif protein TRIM29 isoform alpha TRIM3S NM O15066 tripartite motif-containing 35 isoform 1 TRIM37 NM O15294 tripartite motif-containing 37 protein TRIM44 NM 017583 DIPB protein TRIMS NM 033034 tripartite motif protein TRIM5 isoform alpha TRIMS2 NM 032765 hypothetical protein LOC84851 TRIM55 NM 033058 ring finger protein 29 isoform 2 TRIMS6 NM 030961 tripartite motif-containing 56 TRIMS8 NM O15431 tripartite motif-containing 58 TRIM62 NM 0182O7 tripartite motif-containing 62 TRIM6S NM 173547 tripartite motif containing 65 TRIM67 NM 001004342 hypothetical protein LOC440730 TRIM73 NM198924 hypothetical protein LOC375593 TRIM74 NM 198853 hypothetical protein LOC378108 TRIM9 NM 052978 tripartite motif protein 9 isoform 2 TRIO NM 007118 triple functional domain (PTPRF interacting) TRIT1 NM O17646 RNA isopentenyltransferase 1 TRMT5 NM 020810 RNA-(N1G37) methyltransferase TRPC5 NM 012471 transient receptor potential cation channel, TRPM1 NM 002420 transient receptor potential cation channel, TRPM2 NM 001001188 transient receptor potential cation channel, TRPS1 NM 014112 Zinc finger transcription factor TRPS1 TRPVS NM 019841 transient receptor potential cation channel, TRPV6 NM 018646 transient receptor potential cation channel, TRUB2 NM O15679 TruB pseudouridine (psi) synthase homolog 2 TSC1 NM OOO368 tuberous sclerosis 1 protein isoform 1 TSC22D3 NM 001015881 TSC22 domain family, member 3 isoform 3 TSN NM 004622 translin TSNAX NM OO5999 translin-associated factor X TSPAN13 NM O14399 etraspan NET-6 TSPAN15 NM 012339 transmembrane 4 superfamily member 15 TSPAN2 NM OO5725 etraspan 2 TSPAN9 NM OO6675 etraspanin 9 TSPYL5 NM 033512 TSPY-like S TTBK1 NM 032538 autubulin kinase 1 TTBK2 NM 173500 autubulin kinase 2 TTC12 NM O17868 etratricopeptide repeat domain 12 TTC19 NM 017775 etratricopeptide repeat domain 19 TTC21B NM O24753 etratricopeptide repeat domain 21B TTF2 NM 003594 transcription termination factor, RNA polymerase TTL NM 153712 tubulin tyrosine ligase TTLL2 NM 031949 tubulin tyrosine ligase-like family, member 2 TTLL3 NM 001025930 tubulin tyrosine ligase-like family, member 3 TTLL6 NM 173623 hypothetical protein LOC284076 TTLL9 NM OO10084.09 tubulin tyrosine ligase-like family, member 9 TTYH2 NM 032.646 weety 2 isoform 1 TTYH3 NM O25250 weety 3 TUB NM OO3320 tubby isoform a TUBB NM 178O14 tubulin, beta polypeptide TUBB1 NM 030773 beta tubulin 1, class VI TUBB4 NM OO6087 tubulin, beta 4 TUBG1 NM 001070 tubulin, gamma 1 TUBG2 NM 016437 tubulin, gamma 2 TUBGCP6 NM OO10O8658 tubulin, gamma complex associated protein 6 TUFT1 NM O2O127 tuftelin 1 TULP3 NM OO3324 tubby like protein 3 US 2009/0232893 A1 Sep. 17, 2009 48

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description TUSC5 NM 172367 LOST TXLNA NM 175852 taxilin TXLNB NM 153235 muscle-derived protein 77 TXNDC13 NM 021156 thioredoxin domain containing 13 TXNDC4 NM O15051 thioredoxin domain containing 4 (endoplasmic TXNL4B NM O17853 thioredoxin-like 4B TXNRD1 NM OO3330 thioredoxin reductase 1 TYSND1 NM 173555 trypsin domain containing 1 isoform a UACA NM 0010O8224 uveal autoantigen with coiled-coil domains and UAP1L1 NM 207309 UDP-N-acteylglucosamine pyrophosphorylase 1-like UBE2E NM OO3341 ubiquitin-conjugating enzyme E2E 1 isoform 1 UBE2E NM O06357 ubiquitin-conjugating enzyme E2E 3 UBE2G1 NM OO3342 ubiquitin-conjugating enzyme E2G 1 isoform 1 UBE2 NM OO3345 ubiquitin-conjugating enzyme E2I UBE21 NM 016021 ubiquitin-conjugating enzyme E2, J1 UBE2O1 NM 017582 ubiquitin-conjugating enzyme E2O UBE2R2 NM 017811 ubiquitin-conjugating enzyme UBC3B UBE3B NM 183414 ubiquitin protein ligase E3B isoform b UBE3C NM 014671 ubiquitin protein ligase E3C UBL3 NM 007106 ubiquitin-like 3 UBL7 NM 032907 ubiquitin-like 7 (bone marrow stromal UBN NM 016936 ubinuclein 1 UBOXS NM O14948 U-box domain containing 5 isoform a UBXD2 NM 014607 UBX domain containing 2 UBXD8 NM 014613 UBX domain containing 8 UGDH NM OO3359 UDP-glucose dehydrogenase UGT1A1 NM 000463 UDP-glycosyltransferase 1 family, polypeptide A1 UGT1A10 NM O19075 UDP-glycosyltransferase 1 family, polypeptide UGT1A3 NM O19093 UDP-glycosyltransferase 1 family, polypeptide A3 UGT1A4 NM 007120 UDP-glycosyltransferase 1 family, polypeptide A4 UGT1AS NM O19078 UDP-glycosyltransferase 1 family, polypeptide A5 UGT1A6 NM 001072 UDP-glycosyltransferase 1 family, polypeptide A6 UGT1A7 NM O1907 7 UDP-glycosyltransferase 1 family, polypeptide A7 UGT1A8 NM O19076 UDP-glycosyltransferase 1 family, polypeptide A8 UGT1A9 NM 021027 UDP-glycosyltransferase 1 family, polypeptide A9 ULBP1 NM O25218 UL16 binding protein 1 UMOD NM OO10O8389 uromodulin precursor UNC13D NM 199242 unc-13 homolog D UNC4SB NM OO1033576 cardiomyopathy associated 4 isoform 2 UNCSA NM 133369 netrin receptor Unc5h1 UNCSD NM 080872 netrin receptor Unc5h4 UNC93A NM 018974 unc-93 homolog A UPF1 NM OO2911 regulator of nonsense transcripts 1 UPF2 NM O15542 UPF2 regulator of nonsense transcripts homolog USF1 NM 007122 upstream stimulatory factor 1 isoform 1 USP18 NM 017414 ubiquitin specific protease 18 USP2 NM OO4205 ubiquitin specific protease 2 isoform a USP37 NM 020935 ubiquitin specific protease 37 USP46 NM O22832 ubiquitin specific protease 46 USP47 NM O17944 ubiquitin specific protease 47 USP49 NM 018561 ubiquitin specific protease 49 UTP14C NM 021645 UTP14, U3 small nucleolar ribonucleoprotein, UTS2D NM 198152 urotensin 2 domain containing UVRAG NM 003369 UV radiation resistance associated gene WANGL2 NM 020335 vang-like 2 (van gogh, Drosophila) WAPB NM 004.738 VAMP-associated protein B/C WASH1 NM O14909 vasohibin 1 WAT1 NM OO6373 vesicle amine transport protein 1 WAX1 NM 1991.31 ventral anterior homeobox 1 VBP1 NM OO3372 von Hippel-Lindau binding protein 1 VCPIP1 NM O25054 valosin containing protein (p97), p.47 complex WDAC1 NM OO3374 voltage-dependent anion channel 1 VEGF NM 001025366 vascular endothelial growth factor isoform a WGLL3 NM O16206 colon carcinoma related protein VHL NM 000551 von Hippel-Lindau tumor suppressor isoform 1 VIPR1 NM 004624 vasoactive intestinal peptide receptor 1 VISA NM 020746 virus-induced signaling adapter WMD2L3 NM 152439 vitelliform macular dystrophy 2-like 3 VPREB1 NM 007128 immunoglobulin iota chain preproprotein VPS13A NM 001018037 vacuolar protein sorting 13A isoform C VPS13D NM O15378 vacuolar protein sorting 13D isoform 1 US 2009/0232893 A1 Sep. 17, 2009 49

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq, ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description VPS16 NM O22575 vacuolar protein sorting 16 isoform 1 VPS26A NM 004.896 vacuolar protein sorting 26 homolog A isoform 1 VPS37A NM 152415 hepatocellular carcinoma related protein 1 VPS4SA NM 007259 vacuolar protein sorting 45A VPS4B NM 004.869 vacuolar protein sorting factor 4B VPS52 NM O22553 Suppressor of actin mutations 2-like VPS72 NM OO5997 transcription factor-like 1 WSIG4 NM OO7268 V-set and immunoglobulin domain containing 4 WSIG9 NM 173799 hypothetical protein LOC201633 VTCN1 NM O24626 V-set domain containing T cell activation WASF3 NM OO6646 WAS protein family, member 3 WASPIP NM OO3387 WASP-interacting protein WBP2 NM 012478 WW domain binding protein 2 WBPS NM OO1 OO6612 WW domain binding protein 5 WBSCR17 NM O22479 UDP-GalNAc:polypeptide WDFY3 NM 014991 WD repeat and FYVE domain containing 3 isoform WDR17 NM 170710 WD repeat domain 17 isoform 1 WDR22 NM OO3861 Breakpoint cluster region protein, uterine WDR23 NM O25230 WD repeat domain 23 isoform 1 WDR33 NM 018383 WD repeat domain 33 isoform 1 WDR36 NM 139281 WD repeat domain 36 WDR42B NM 001017930 WD repeat domain 42B WDR48 NM 020839 WD repeat domain 48 WDR50 NM 016001 WD repeat domain 50 WDR6 NM 018031 WD repeat domain 6 protein WDR64 NM 144625 hypothetical protein LOC128025 WDR68 NM OO5828 WD-repeat protein WDR7 NM O15285 rabconnectin-3 beta isoform 1 WDR81 NM 152348 alpha-2-plasmin inhibitor WDTC1 NM O15023 WD and tetratricopeptide repeats 1 WFDC1 NM 021197 WAP four-disulfide core domain 1 precursor WFS1 NM OO6005 wolframin WHSC1 NM O14919 Wolf-Hirschhorn syndrome candidate 1 protein WIG1 NM O22470 p53 target Zinc finger protein isoform 1 WIRE NM 133264 WIRE protein WNK4 NM 032387 WNK lysine deficient protein kinase 4 WNT2 NM OO3391 wingless-type MMTV integration site family WNTSB NM 030775 wingless-type MMTV integration site family, WSB1 NM O15626 WD repeat and SOCS box-containing 1 isoform 1 WWC3 NM O15691 hypothetical protein LOC55841 WWP2 NM 007014 WW domain containing E3 ubiquitin protein ligase XK NM 021083 McLeod syndrome-associated, Kell blood group XKRS NM 207411 XK-related protein 5a XLKD1 NM OO6691 extracellular link domain containing 1 XPO4 NM O224.59 exportin 4 XPOS NM 020750 exportin 5 XRCC2 NM 005431 X-ray repair cross complementing protein 2 XRN1 NM O19001 5'-3' exoribonuclease 1 XYLB NM 005108 xylulokinase homolog YAF2 NM 001012424 YY1-associated factor 2 isoform b YARS NM OO368O tyrosyl-tRNA synthetase YEATS2 NM 018023 YEATS domain containing 2 YIF1B NM 033557 Yip 1 interacting factor homolog B isoform 2 YPEL1 NM 013313 yippee-like 1 YPEL2 NM 0010054.04 yippee-like 2 YPEL5 NM 016061 yippee-like 5 YTHDC2 NM 022828 YTH domain containing 2 YWHAB NM 003404 tyrosine 3-monooxygenase/tryptophan ZADH1 NM 152444 Zinc binding alcohol dehydrogenase, domain ZADH2 NM 175907 Zinc binding alcohol dehydrogenase, domain ZAK NM 016653 MLK-related kinase isoform 1 ZBTB40 NM O14870 Zinc finger and BTB domain containing 40 ZBTB41 NM 194314 Zinc finger and BTB domain containing 41 ZBTBS NM O14872 Zinc finger and BTB domain containing 5 ZBTB6 NM OO6626 Zinc finger protein 482 US 2009/0232893 A1 Sep. 17, 2009 50

TABLE 3-continued Predicted target genes of hsa-miR-143 for RefSeq, ID reference - Pruitt et al., 2005. Gene RefSeq, Symbol Transcript ID Description NM O25079 Zinc finger CCCH-type containing 12A NM 015144 Zinc finger, CCHC domain containing 14 DHHC11 NM O24786 Zinc finger, DHHC domain containing 11 DHHC2 NM 016353 (C. DHHC23 NM 173570 Zinc finger, DHHC domain containing 23 DHHC4 NM 018106 Zinc finger, DHHC domain containing 4 DHHC9 NM OO10O8222 Zinc finger, DHHC domain containing 9 FAND2B NM 138802 Zinc finger, AN1-type domain 2B FP30 NM O14898 Zinc finger protein 30 homolog FP36L1 NM 004926 butyrate response factor 1 FP41 NM 173832 Zinc finger protein 41 homolog FP91 NM 053023 Zinc finger protein 91 isoform 1 FP95 NM 014569 Zinc finger protein 95 homolog FYVE16 NM 014733 endosome-associated FYVE-domain protein FYVE27 NM OO10O2.261 Zinc finger, FYVE domain containing 27 isoform FYVE28 NM 020972 Zinc finger, FYVE domain containing 28 GPAT NM 181484 Zinc finger, CCCH-type with G patch domain HX3 NM O15035 Zinc fingers and homeoboxes 3 NM 003412 Zinc finger protein of the cerebellum 1 NM OO3413 Zinc finger protein of the cerebellum 3 NM 032153 Zinc finger protein of the cerebellum 4 M3 NM 052882 Zinc finger, imprinted 3 KSCAN 1 NM OO3439 Zinc finger protein 36 ZMYM3 NM 005096 Zinc finger protein 261 ZMYM4 NM 005095 Zinc finger protein 262 ZMYND11 NMOO6624 Zinc finger, MYND domain containing 11 isoform ZMYND19 NM 138462 Zinc finger, MYND domain containing 19 F132 NM 003433 Zinc finger protein 132 (clone pHZ-12) F136 NM OO3437 Zinc finger protein 136 (clone pHZ-20) F137 NM OO3438 Zinc finger protein 137 (clone pHZ-30) F157 NM 003446 Zinc finger protein 157 F160 NM 033288 Zinc finger protein 160 F167 NM 018651 Zinc finger protein ZFP isoform 1 F17 NM OO6959 Zinc finger protein 17 F182 NM OO1007088 Zinc finger protein 21 isoform 2 F187 NM 001023560 Zinc finger protein 187 F192 NM OO6298 Zinc finger protein 192 F200 NM OO3454 Zinc finger protein 200 isoform 1 F2O2 NM OO3455 Zinc finger protein 202 F217 NM OO6526 Zinc finger protein 217 F226 NM OO1032374 Zinc finger protein 226 isoform b F236 NM OO7345 Zinc finger protein 236 F264 NM OO3417 Zinc finger protein 264 F265 NM 005455 Zinc finger protein 265 isoform 2 F272 NM OO6635 Zinc finger protein 272 F276 NM 152287 Zinc finger protein 276 homolog F294 NM O15565 Zinc finger protein 294 F300 NM 052860 Zinc finger protein 300 F31 NM 145238 Zinc finger protein 31 F313 NM 018683 Zinc finger protein 313 F317 NM 020933 Zinc finger protein 317 F318 NM O14345 Zinc finger protein 318 F32O NM 207333 Zinc finger protein 320 F322A NM 024639 Zinc finger protein 322A F322B NM 199005 Zinc finger protein 322B F329 NM O24620 Zinc finger protein 329 F333 NM 032433 Zinc finger protein 333 F33A NM OO6974 Zinc finger protein 33A F33B NM OO6955 Zinc finger protein 33B F346 NM 012279 Zinc finger protein 346 F365 NM 1994.51 Zinc finger protein 365 isoform C F37A NM OO1007094 Zinc finger protein 37a F384 NM 133476 nuclear matrix transcription factor 4 isoform a F385 NM O15481 Zinc finger protein 385 F394 NM 032164 Zinc finger protein 99 US 2009/0232893 A1 Sep. 17, 2009 51

TABLE 3-continued

Predicted target genes of hsa-miR-143 for RefSeq, ID reference - Pruitt et al., 2005.

Gene RefSeq, Symbol Transcript ID Description

ZNF397 NM 032347 Zinc finger protein 397 ZNF41 NM 007130 Zinc finger protein 41 ZNF425 NM 001001661 Zinc finger protein 425 ZNF426 NM 024106 Zinc finger protein 426 ZNF43 NM OO3423 Zinc finger protein 43 (HTF6) ZNF430 NM O251.89 Zinc finger protein 430 ZNF445 NM 181489 Zinc finger protein 445 ZNF471 NM 020813 Zinc finger protein 471 ZNF48O NM 144684 Zinc finger protein 480 ZNF483 NM OO1007169 Zinc finger protein 483 isoform b ZNF485 NM 145312 Zinc finger protein 485 ZNF490 NM 020714 Zinc finger protein 490 ZNF493 NM 175910 Zinc finger protein 493 ZNF497 NM 198458 Zinc finger protein 497 ZNF498 NM 145115 Zinc finger protein 498 ZNFSOO NM 021646 Zinc finger protein 500 ZNFS14 NM 032788 Zinc finger protein 514 ZNF526 NM 133444 Zinc finger protein 526 ZNF529 NM 020951 Zinc finger protein 529 ZNFS43 NM 213598 Zinc finger protein 543 ZNF545 NM 133466 Zinc finger protein 545 ZNF547 NM 173631 Zinc finger protein 547 ZNFS62 NM O17656 Zinc finger protein 562 ZNF565 NM 152477 Zinc finger protein 565 ZNF570 NM 144694 Zinc finger protein 570 ZNF571 NM O16536 Zinc finger protein 571 ZNF577 NM 032679 Zinc finger protein 577 ZNF581 NM O16535 Zinc finger protein 581 ZNF583 NM 152478 Zinc finger protein 583 ZNF592 NM 014630 Zinc finger protein 592 ZNF599 NM OO1007247 Zinc finger protein 599 isoform b ZNF600 NM 198457 Zinc finger protein 600 ZNF605 NM 183238 Zinc finger protein 605 ZNF607 NM 032689 Zinc finger protein 607 ZNF621 NM 198484 Zinc finger protein 621 ZNF622 NM 033414 Zinc finger protein 622 ZNF623 NM 014789 Zinc finger protein 623 ZNF650 NM 172070 Zinc finger protein 650 ZNF651 NM 145166 Zinc finger protein 651 ZNF652 NM O14897 Zinc finger protein 652 ZNF660 NM 173658 Zinc finger protein 660 ZNF662 NM 2074.04 Zinc finger protein 662 ZNF677 NM 182609 Zinc finger protein 677 ZNF694 NM 001012.981 Zinc finger protein 694 ZNF696 NM O3O895 Zinc finger protein 696 ZNF702 NM 024924 Zinc finger protein 702 ZNF705A NM OO1004328 hypothetical protein LOC440077 ZNF708 NM 021269 Zinc finger protein 15-like 1 (KOX8) ZNF81 NM 007137 Zinc finger protein 81 (HFZ20) ZNF93 NM 001004126 Zinc finger protein 93 isoform b ZNRF2 NM 147128 Zinc finger/RING finger 2 ZSCAN2 NM 181877 Zinc finger protein 29 isoform 1 ZSWIM4 NM 023072 Zinc finger, SWIM domain containing 4 ZWILCH NM O17975 Zwilch ZWINT NM 001005414 ZW10 interactor isoform c ZYG11A NM OO1004339 hypothetical protein LOC440590 ZYG11B NM O24646 hypothetical protein LOC79699 US 2009/0232893 A1 Sep. 17, 2009 52

53, 54, 55, 56, 57, 58, 59, 60, 61, 100, 150, 200 or more TABLE 4 probes, recombinant nucleic acid, or synthetic nucleic acid molecules related to the markers to be assessed oran miRNA hsa-miR-143 targets that exhibited altered mRNA expression levels or miRNA inhibitor to be expressed or modulated, and may in human cancer cells after transfection with pre-miRhsa-miR-143. include any range or combination derivable therein. Kits may for RefSeq ID reference - Pruitt et al., 2005. comprise components, which may be individually packaged or placed in a container, Such as a tube, bottle, vial, Syringe, or Gene RefSeq, other Suitable container means. Individual components may Symbol Transcript ID Description also be provided in a in concentrated amounts; in some ATP6V1A NM OO1690 ATPase, H+ transporting, lysosomal embodiments, a component is provided individually in the 70 kD, V1 same concentration as it would be in a solution with other ATXN1 NM OOO332 ataxin 1 components. Concentrations of components may be provided CCND1 NM 053056 cyclin D1 CLIC4 NM O13943 chloride intracellular channel 4 as 1x, 2x, 5x, 10x, or 20x or more. Kits for using probes, DDAH1 NM 012137 dimethylarginine synthetic nucleic acids, recombinant nucleic acids, or non dimethylaminohydrolase 1 synthetic nucleic acids of the invention for therapeutic, prog GALC NM OOO153 galactosylceramidase nostic, or diagnostic applications are included as part of the isoform a precursor invention. Specifically contemplated are any such molecules GATM NM 001482 glycine amidinotransferase corresponding to any miRNA reported to influence biological (L-arginine:glycine activity or expression of one or more marker gene or gene GOLPH2 NM O16548 golgi phosphoprotein 2 pathway described herein. In certain aspects, negative and/or IGFBP3 NM 000598 insulin-like growth factor binding protein 3 positive controls are included in some kit embodiments. The LMO4 NM OO6769 LIM domain only 4 control molecules can be used to verify transfection effi MCL1 NM O21960 myeloid cell leukemia sequence ciency and/or control for transfection-induced changes in 1 isoform 1 cells. PROSC NM 007198 proline synthetase co-transcribed 0056 Certain embodiments are directed to a kit for assess homolog ment of a pathological condition or the risk of developing a RAB11 FIP1 NM 001002814 Rab coupling protein isoform 3 pathological condition in a patient by nucleic acid profiling of RBL1 NM 002895 retinoblastoma-like protein 1 isoform a a sample comprising, in Suitable container means, two or RHOBTB1 NM 001.032380 Rho-related BTB domain containing 1 more nucleic acid hybridization or amplification reagents. SERPINE1 NM OOO602 plasminogen activator inhibitor-1 The kit can comprise reagents for labeling nucleic acids in a SLC3SB1 NM OO5827 solute carrier family 35, member B1 sample and/or nucleic acid hybridization reagents. The WASPIP NM OO3387 WASP-interacting protein hybridization reagents typically comprise hybridization WDR50 NMO16001 WD repeat domain 50 probes. Amplification reagents include, but are not limited to amplification primers, reagents, and . 0053. The predicted gene targets of hsa-miR-143 whose 0057. In some embodiments of the invention, an expres mRNA expression levels are affected by hsa-miR-143 repre sion profile is generated by steps that include: (a) labeling sent particularly useful candidates for cancer therapy and nucleic acid in the sample; (b) hybridizing the nucleic acid to a number of probes, or amplifying a number of nucleic acids, therapy of other diseases through manipulation of their and (c) determining and/or quantitating nucleic acid hybrid expression levels. ization to the probes or detecting and quantitating amplifica 0054 Certain embodiments of the invention include deter tion products, wherein an expression profile is generated. See mining expression of one or more marker, gene, or nucleic U.S. Provisional Patent Application 60/575,743 and the U.S. acid segment representative of one or more genes, by using an Provisional Patent Application 60/649.584, and U.S. patent amplification assay, a hybridization assay, or protein assay, a application Ser. No. 1 1/141,707 and U.S. patent application variety of which are well known to one of ordinary skill in the Ser. No. 1 1/273,640, all of which are hereby incorporated by art. In certain aspects, an amplification assay can be a quan reference. titative amplification assay, such as quantitative RT-PCR or 0.058 Methods of the invention involve diagnosing and/or the like. In still further aspects, a hybridization assay can assessing the prognosis of a patient based on a miRNA and/or a marker nucleic acid expression profile. In certain embodi include array hybridization assays or Solution hybridization ments, the elevation or reduction in the level of expression of assays. The nucleic acids from a sample may be labeled from a particular gene or genetic pathway or set of nucleic acids in the sample and/or hybridizing the labeled nucleic acid to one a cell is correlated with a disease State or pathological condi or more nucleic acid probes. Nucleic acids, mRNA, and/or tion compared to the expression level of the same in a normal nucleic acid probes may be coupled to a Support. Such Sup or non-pathologic cell or tissue sample. This correlation ports are well known to those of ordinary skill in the art and allows for diagnostic and/or prognostic methods to be carried include, but are not limited to glass, plastic, metal, or latex. In out when the expression level of one or more nucleic acid is particular aspects of the invention, the Support can be planar measured in a biological sample being assessed and then compared to the expression level of a normal or non-patho or in the form of a bead or other geometric shapes or configu logic cell or tissue sample. It is specifically contemplated that rations known in the art. Proteins are typically assayed by expression profiles for patients, particularly those Suspected immunoblotting, chromatography, or mass spectrometry or of having or having a propensity for a particular disease or other methods known to those of ordinary skill in the art. condition Such as cancer, can be generated by evaluating any 0055. The present invention also concerns kits containing oforsets of the miRNAs and/or nucleic acids discussed in this compositions of the invention or compositions to implement application. The expression profile that is generated from the methods of the invention. In some embodiments, kits can be patient will be one that provides information regarding the used to evaluate one or more marker molecules, and/or particular disease or condition. In many embodiments, the express one or more miRNA or miRNA inhibitor. In certain profile is generated using nucleic acid hybridization or ampli embodiments, a kit contains, contains at least or contains at fication, (e.g., array hybridization or RT-PCR). In certain most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, aspects, an expression profile can be used in conjunction with 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, other diagnostic and/or prognostic tests, such as histology, 36, 37,38, 39, 40, 41,42, 43,44, 45,46, 47,48, 49, 50, 51, 52, protein profiles in the serum and/or cytogenetic assessment. US 2009/0232893 A1 Sep. 17, 2009 53

TABLE 5 Tumor associated mRNAS altered by hsa-miR-143 having prognostic or therapeutic value for the treatment of various malignancies. Gene Cellular Symbol Gene Title Process Cancer Type Reference AKAP12 Akap-12. signal CRC, PC, LC, GC, AML, CML (Xia et al., 2001;Wikman et al., 2002; Boultwood SSeCKS, transduction et al., 2004; Choi et al., 2004: Mori et al., 2006) Gravin BCL2L1 BCL-XL Apoptosis NSCLC, SCLC, CRC, BC, BldC, RCC, HL, NHL, (Manion and Hockenbery, 2003) AML, ALL, HCC, OC, MB, G., ODG, My, OepC CCND1 cyclin D1 cell cycle MCL, BC, SCCHN, OepC, HCC, CRC, BldC, EC, (Donnellan and Chetty, 1998) OC, M, AC, GB, GC, PaC CCNG1 cyclin G1 cell cycle OS, BC, PC (Skotzko et al., 1995; Reimer et al., 1999) IGFBP3 IGFBP-3 signal BC, PC, LC, CRC (Firth and Baxter, 2002) transduction IL8 IL-8 signal BC, CRC, PaC, NSCLC, PC, HCC (Akiba et al., 2001; Sparmann and Bar-Sagi, 2004) transduction LMO4 Lmo-4 transcription BC, SCCHN, SCLC (Visvader et al., 2001; Mizunuma et al., 2003; Taniwaki et al., 2006) MCL1 McI-1 apoptosis HCC, MM, TT, CLL, ALCL, BCL, PC (Krajewska et al., 1996; Kitada et al., 1998; Cho Vega et al., 2004: Rust et al., 2005; Sano et al., 2005; Wuilleme-Toumi et al., 2005; Fleischer et al., 2006: Sieghart et al., 2006) PDCD4 Polcd-4 apoptosis G, HCC, L, RCC (Chen et al., 2003; Jansen et al., 2004; Zhang et al., 2006; Gao et al., 2007) RBL1 p107 cell cycle BCL, PC, CRC, TC (Takimoto et al., 1998; Claudio et al., 2002; Wu et al., 2002: Ito et al., 2003) TGFBR2 TGFbeta signal BC, CRC (Markowitz, 2000; Lucke et al., 2001: Biswas et receptor type transduction al., 2004) II TXN thioredoxin thioredoxin LC, PaC, CeC, HCC (Marks, 2006) (trx) redox System WEE1 Wee-1 kinase cell cycle NSCLC (Yoshida et al., 2004)

Abbreviations: AC, astrocytoma; ALCL, anaplastic large cell lymphoma; ALL, acute lymphoblastic leukemia; A.ML, acute myelogenous leukemia; C, breast carcinoma; CL, B-cell lymphoma; dC, bladder carcinoma; CeC, cervical carcinoma; LL, chronic lymphoblastic leukemia; RC, colorectal carcinoma; C, endometrial carcinoma; , glioma: B, glioblastoma; C, gastric carcinoma; CC, hepatocellular carcinoma; L., Hodgkin lymphoma; L. leukemia; LC, lung carcinoma; M, melanoma; MB, medulloblastoma: MCL, mantle cell lymphoma; MM, multiple myeloma; My, myeloma; NHL, non-Hodgkin lymphoma; NSCLC, non-Small cell lung carcinoma; OC, ovarian carcinoma; ODG, oligodendroglioma: OepC, oesophageal carcinoma; OS, Osteosarcoma; PaC, pancreatic carcinoma; PC, prostate carcinoma; RCC, renal cell carcinoma; SCCHN, Squamous cell carcinoma of the head and neck; SCLC, Small cell lung carcinoma; TC, thyroid carcinoma; TT, testicular tumor. US 2009/0232893 A1 Sep. 17, 2009 54

0059. The methods can further comprise one or more of 0.066 Throughout this application, the term “about is the steps including: (a) obtaining a sample from the patient, used to indicate that a value includes the standard deviation of (b) isolating nucleic acids from the sample, (c) labeling the error for the device or method being employed to determine nucleic acids isolated from the sample, and (d) hybridizing the value. the labeled nucleic acids to one or more probes. Nucleic acids 0067. The use of the term “or' in the claims is used to of the invention include one or more nucleic acid comprising mean “and/or unless explicitly indicated to refer to alterna at least one segment having a sequence or complementary tives only or the alternatives are mutually exclusive, although sequence of to a nucleic acid representative of one or more of the disclosure supports a definition that refers to only alter genes or markers in Table 1, 3, 4, and/or 5. natives and “and/or.” 0068. As used in this specification and claim(s), the words 0060. It is contemplated that any method or composition “comprising (and any form of comprising, such as "com described herein can be implemented with respect to any prise' and "comprises”), “having (and any form of having, other method or composition described herein and that dif such as “have and “has'), “including' (and any form of ferent embodiments may be combined. It is specifically con including, such as “includes and “include’) or “containing templated that any methods and compositions discussed (and any form of containing, such as “contains and “con herein with respect to miRNA molecules, miRNA, genes, and tain’) are inclusive or open-ended and do not exclude addi nucleic acids representative of genes may be implemented tional, unrecited elements or method steps. with respect to synthetic nucleic acids. In some embodiments 0069. Other objects, features and advantages of the the synthetic nucleic acid is exposed to the proper conditions present invention will become apparent from the following to allow it to become a processed or mature nucleic acid, Such detailed description. It should be understood, however, that as a miRNA under physiological circumstances. The claims the detailed description and the specific examples, while indi originally filed are contemplated to cover claims that are cating specific embodiments of the invention, are given by multiply dependent on any filed claim or combination of filed way of illustration only, since various changes and modifica claims. tions within the spirit and scope of the invention will become 0061 Also, any embodiment of the invention involving apparent to those skilled in the art from this detailed descrip specific genes (including representative fragments there of), tion. mRNA, or miRNAs by name is contemplated also to cover embodiments involving miRNAS whose sequences are at DESCRIPTION OF THE DRAWING least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,90,91, 92,93, 94, 0070 The following drawing forms part of the present 95, 96, 97,98, 99% identical to the mature sequence of the specification and is included to further demonstrate certain specified miRNA. aspects of the present invention. The invention may be better 0062. It will be further understood that shorthand nota understood by reference to this drawing in combination with tions are employed Such that a generic description of a gene or the detailed description of specific embodiments presented marker thereof, or of an miRNA refers to any of its gene herein. family members (distinguished by a number) or representa 0071 FIG. 1. Average tumor volumes in mice harboring xenografts of A549 lung cancer cells treated with hsa-miR tive fragments thereof, unless otherwise indicated. It is under 143 (white squares; n=5) or treated with a negative control stood by those of skill in the art that a “gene family’ refers to miRNA (black diamonds; n=5). Standard deviations are a group of genes having the same coding sequence or miRNA shown in the graph. Data points with p values less than 0.05 coding sequence. Typically, miRNA members of a gene fam are indicated by an asterisk. Abbreviation: miR-143, hsa ily are identified by a number following the initial designa miR-143; NC, negative control miRNA. tion. For example, miR-16-1 and miR-16-2 are members of the miR-16 gene family and “mir-7 refers to miR-7-1, miR DETAILED DESCRIPTION OF THE INVENTION 7-2 and miR-7-3. Moreover, unless otherwise indicated, a shorthand notation refers to related miRNAs (distinguished 0072 The present invention is directed to compositions by a letter). Exceptions to these shorthand notations will be and methods relating to the identification and characteriza otherwise identified. tion of genes and biological pathways related to these genes as represented by the expression of the identified genes, as 0063. Other embodiments of the invention are discussed well as use of miRNAs related to such, for therapeutic, prog throughout this application. Any embodiment discussed with nostic, and diagnostic applications, particularly those meth respect to one aspect of the invention applies to other aspects ods and compositions related to assessing and/or identifying of the invention as well and vice versa. The embodiments in pathological conditions directly or indirectly related to miR the Example and Detailed Description section are understood 143 expression or the aberrant expression thereof. to be embodiments of the invention that are applicable to all 0073. In certain aspects, the invention is directed to meth aspects of the invention. ods for the assessment, analysis, and/or therapy of a cell or 0064. The terms “inhibiting.” “reducing,” or “prevention.” Subject where certain genes have a reduced or increased or any variation of these terms, when used in the claims and/or expression (relative to normal) as a result of an increased or the specification includes any measurable decrease or com decreased expression of any one or a combination of miR-143 plete inhibition to achieve a desired result. family members (including, but not limited to lla-mir-143 0065. The use of the word “a” or “an when used in con M10002552; Xtr-mir-143 MI0004937; dre-mir-143-2 junction with the term “comprising in the claims and/or the MI0002008: rno-mir-143 MI0000916; ptr-mir-143 specification may mean “one.” but it is also consistent with MI0002549; ppy-mir-143 MI0002551; go-mir-143 the meaning of “one or more.”s “at leastone.”s and “one or more MI0002550; dre-mir-143-1 MI0002007; hsa-mir-143 than one.” MI0000459: ppa-mir-143 MI0002553; mdo-mir-143 US 2009/0232893 A1 Sep. 17, 2009

MI0005302; and mmu-mir-143 MI0000257) and/or genes miRNA and miRNA inhibitors of the invention are collec with an increased expression (relative to normal) as a result of tively referred to as “synthetic nucleic acids.” decreased expression thereof. The expression profile and/or 0077. In some embodiments, there is a miRNA or a syn response to miR-143 expression or lack of expression may be thetic miRNA having a length of between 17 and 130 resi indicative of an individual with a pathological condition, e.g., dues. The present invention concerns miRNA or synthetic CaCC. miRNA molecules that are, are at least, or are at most 15, 16, 0074 Prognostic assays featuring any one or combination 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, of the miRNAs listed or the markers listed (including nucleic 34, 35,36, 37,38, 39, 40, 41,42, 43,44, 45,46, 47, 48,49, 50, acids representative thereof) could be used in assessment of a 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 65,66, 67, patient to determine what if any treatment regimen is justi 68, 69,70, 71,72, 73,74, 75,76, 77,78, 79,80, 81, 82, 83, 84, fied. As with the diagnostic assays mentioned above, the 85, 86, 87, 88, 89,90,91, 92,93, 94, 95, 96, 97,98, 99, 100, absolute values that define low expression will depend on the 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, platform used to measure the miRNA(s). The same methods 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, described for the diagnostic assays could be used for prog 125, 126, 127, 128, 129, 130, 140, 145, 150, 160, 170, 180, nostic assays. 190, 200 or more residues in length, including any integer or any range there between. II. THERAPEUTIC METHODS 0078. In certain embodiments, synthetic miRNA have (a) a “miRNA region' whose sequence or binding region from 5' 0075 Embodiments of the invention concern nucleic to 3' is identical or complementary to all or a segment of a acids that perform the activities of or inhibit endogenous mature miRNA sequence, and (b) a “complementary region' miRNAs when introduced into cells. In certain aspects, whose sequence from 5' to 3' is between 60% and 100% nucleic acids are synthetic or non-synthetic miRNA. complementary to the miRNA sequence in (a). In certain Sequence-specific miRNA inhibitors can be used to inhibit embodiments, these synthetic miRNA are also isolated, as sequentially or in combination the activities of one or more defined above. The term “miRNA region” refers to a region endogenous miRNAS in cells, as well those genes and asso on the synthetic miRNA that is at least 75, 80, 85,90, 95, or ciated pathways modulated by the endogenous miRNA. 100% identical, including all integers there between, to the 0076. The present invention concerns, in some embodi entire sequence of a mature, naturally occurring miRNA ments, short nucleic acid molecules that function as miRNAS sequence or a complement thereof. In certain embodiments, or as inhibitors of miRNA in a cell. The term "short” refers to the miRNA region is or is at least 90,91, 92,93, 94.95, 96.97, a length of a single polynucleotide that is 15, 16, 17, 18, 19. 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or 20, 21, 22, 23, 24, 25, 50, 100, or 150 nucleotides or fewer, 100% identical to the sequence of a naturally-occurring including all integers or ranges derivable there between. The miRNA or complement thereof. nucleic acid molecules are typically synthetic. The term "syn 007.9 The term “complementary region' or “comple thetic' refers to a nucleic acid molecule that is not produced ment” refers to a region of a nucleic acid or mimetic that is or naturally in a cell. In certain aspects the chemical structure is at least 60% complementary to the mature, naturally occur deviates from a naturally-occurring nucleic acid molecule, ring miRNA sequence. The complementary region is or is at such as an endogenous precursor miRNA or miRNA mol least 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, ecule or complement thereof. While in some embodiments, 75, 76, 77,78, 79,80, 81,82, 83, 84,85, 86,87, 88, 89,90,91, nucleic acids of the invention do not have an entire sequence 92,93,94, 95, 96, 97,98,99,99.1,99.2, 99.3,99.4,99.5, 99.6, that is identical or complementary to a sequence of a natu 99.7. 99.8, 99.9 or 100% complementary, or any range deriv rally-occurring nucleic acid, Such molecules may encompass able therein. With single polynucleotide sequences, there all or part of a naturally-occurring sequence or a complement may be a hairpin loop structure as a result of chemical bond thereof. It is contemplated, however, that a synthetic nucleic ing between the miRNA region and the complementary acid administered to a cell may Subsequently be modified or region. In other embodiments, the complementary region is altered in the cell Such that its structure or sequence is the on a different nucleic acid molecule than the miRNA region, same as non-synthetic or naturally occurring nucleic acid, in which case the complementary region is on the comple Such as a mature miRNA sequence. For example, a synthetic mentary Strand and the miRNA region is on the active strand. nucleic acid may have a sequence that differs from the 0080. In other embodiments of the invention, there are sequence of a precursor miRNA, but that sequence may be synthetic nucleic acids that are miRNA inhibitors. A miRNA altered once in a cell to be the same as an endogenous, inhibitor is between about 17 to 25 nucleotides in length and processed miRNA or an inhibitor thereof. The term "isolated comprises a 5' to 3' sequence that is at least 90% complemen means that the nucleic acid molecules of the invention are tary to the 5' to 3' sequence of a mature miRNA. In certain initially separated from different (in terms of sequence or embodiments, a miRNA inhibitor molecule is 17, 18, 19, 20, structure) and unwanted nucleic acid molecules Such that a 21, 22, 23, 24, or 25 nucleotides in length, or any range population of isolated nucleic acids is at least about 90% derivable therein. Moreover, an miRNA inhibitor may have a homogenous, and may be at least about 95, 96, 97,98, 99, or sequence (from 5' to 3') that is or is at least 70, 75, 80, 85,90, 100% homogenous with respect to other polynucleotide mol 91, 92,93, 94, 95, 96, 97,98, 99,99.1, 99.2, 99.3, 99.4, 99.5, ecules. In many embodiments of the invention, a nucleic acid 99.6, 99.7, 99.8, 99.9 or 100% complementary, or any range is isolated by virtue of it having been synthesized in vitro derivable therein, to the 5' to 3' sequence of a mature miRNA, separate from endogenous nucleic acids in a cell. It will be particularly a mature, naturally occurring miRNA. One of understood, however, that isolated nucleic acids may be Sub skill in the art could use a portion of the miRNA sequence that sequently mixed or pooled together. In certain aspects, Syn is complementary to the sequence of a mature miRNA as the thetic miRNA of the invention are RNA or RNA analogs. sequence for a miRNA inhibitor. Moreover, that portion of the miRNA inhibitors may be DNA or RNA, or analogs thereof. nucleic acid sequence can be altered so that it is still com US 2009/0232893 A1 Sep. 17, 2009 56 prises the appropriate percentage of complementarity to the I0086. The miRNA region and the complementary region sequence of a mature miRNA. may be on the same or separate polynucleotides. In cases in 0081. In some embodiments, of the invention, a synthetic which they are contained on or in the same polynucleotide, miRNA or inhibitor contains one or more design element(s). the miRNA molecule will be considered a single polynucle These design elements include, but are not limited to: (i) a otide. In embodiments in which the different regions are on replacement group for the phosphate or hydroxyl of the nucle separate polynucleotides, the synthetic miRNA will be con otide at the 5' terminus of the complementary region; (ii) one sidered to be comprised of two polynucleotides. or more Sugar modifications in the first or last 1 to 6 residues I0087. When the RNA molecule is a single polynucleotide, of the complementary region; or, (iii) noncomplementarity there can be a linker region between the miRNA region and between one or more nucleotides in the last 1 to 5 residues at the complementary region. In some embodiments, the single the 3' end of the complementary region and the corresponding polynucleotide is capable of forming a hairpin loop structure nucleotides of the miRNA region. A variety of design modi as a result of bonding between the miRNA region and the fications are known in the art, see below. complementary region. The linker constitutes the hairpin 0082 In certain embodiments, a synthetic miRNA has a loop. It is contemplated that in Some embodiments, the linker nucleotide at its 5' end of the complementary region in which region is, is at least, or is at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, the phosphate and/or hydroxyl group has been replaced with 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, another chemical group (referred to as the “replacement 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 residues in design). In some cases, the phosphate group is replaced, length, or any range derivable therein. In certain embodi while in others, the hydroxyl group has been replaced. In ments, the linker is between 3 and 30 residues (inclusive) in particular embodiments, the replacement group is biotin, an length. amine group, a lower alkylamine group, an aminohexyl phos I0088. In addition to having a miRNA or inhibitor region phate group, an acetyl group, 2"O-Me (2'oxygen-methyl), and a complementary region, there may be flanking DMTO (4,4'-dimethoxytrity1 with oxygen), fluorescein, a sequences as well at either the 5' or 3' end of the region. In thiol, or acridine, though other replacement groups are well some embodiments, there is or is at least 1, 2, 3, 4, 5, 6, 7, 8, known to those of skill in the art and can be used as well. This 9, 10 nucleotides or more, or any range derivable therein, design element can also be used with a miRNA inhibitor. flanking one or both sides of these regions. 0083. Additional embodiments concern a synthetic I0089 Methods of the invention include reducing or elimi miRNA having one or more Sugar modifications in the first or nating activity of one or more miRNAS in a cell comprising last 1 to 6 residues of the complementary region (referred to introducing into a cell a miRNA inhibitor (which may be as the 'Sugar replacement design). In certain cases, there is described generally hereinas an miRNA, so that a description one or more Sugar modifications in the first 1, 2, 3, 4, 5, 6 or of miRNA, where appropriate, also will refer to a miRNA more residues of the complementary region, or any range inhibitor); or Supplying or enhancing the activity of one or derivable therein. In additional cases, there are one or more more miRNAs in a cell. The present invention also concerns Sugar modifications in the last 1, 2, 3, 4, 5, 6 or more residues inducing certain cellular characteristics by providing to a cell of the complementary region, or any range derivable therein, a particular nucleic acid, such as a specific synthetic miRNA have a sugar modification. It will be understood that the terms molecule or a synthetic miRNA inhibitor molecule. However, “first and “last’ are with respect to the order of residues from in methods of the invention, the miRNA molecule or miRNA the 5' end to the 3' end of the region. In particular embodi inhibitor need not be synthetic. They may have a sequence ments, the sugar modification is a 2"O-Me modification, a 2F that is identical to a naturally occurring miRNA or they may modification, a 2H modification, a 2'amino modification, a not have any design modifications. In certain embodiments, 4'thioribose modification or a phosphorothioate modification the miRNA molecule and/or the miRNA inhibitor are syn on the carboxy group linked to the carbon at position 6'. In thetic, as discussed above. further embodiments, there are one or more Sugar modifica 0090 The particular nucleic acid molecule provided to the tions in the first or last 2 to 4 residues of the complementary cell is understood to correspond to a particular miRNA in the region or the first or last 4 to 6 residues of the complementary cell, and thus, the miRNA in the cell is referred to as the region. This design element can also be used with a miRNA “corresponding miRNA. In situations in which a named inhibitor. Thus, a miRNA inhibitor can have this design ele miRNA molecule is introduced into a cell, the corresponding ment and/or a replacement group on the nucleotide at the 5' miRNA will be understood to be the induced or inhibited terminus, as discussed above. miRNA or induced or inhibited miRNA function. It is con 0084. In other embodiments of the invention, there is a templated, however, that the miRNA molecule introduced synthetic miRNA or inhibitor in which one or more nucle into a cell is not a mature miRNA but is capable of becoming otides in the last 1 to 5 residues at the 3' end of the comple or functioning as a mature miRNA under the appropriate mentary region are not complementary to the corresponding physiological conditions. In cases in which a particular cor nucleotides of the miRNA region (“noncomplementarity”) responding miRNA is being inhibited by a miRNA inhibitor, (referred to as the “noncomplementarity design). The non the particular miRNA will be referred to as the “targeted complementarity may be in the last 1,2,3,4, and/or 5 residues miRNA. It is contemplated that multiple corresponding of the complementary miRNA. In certain embodiments, there miRNAs may be involved. In particular embodiments, more is noncomplementarity with at least 2 nucleotides in the than one miRNA molecule is introduced into a cell. More complementary region. over, in other embodiments, more than one miRNA inhibitor I0085. It is contemplated that synthetic miRNA of the is introduced into a cell. Furthermore, a combination of invention have one or more of the replacement, Sugar modi miRNA molecule(s) and miRNA inhibitor(s) may be intro fication, or noncomplementarity designs. In certain cases, duced into a cell. The inventors contemplate that a combina synthetic RNA molecules have two of them, while in others tion of miRNA may act at one or more points in cellular these molecules have all three designs in place. pathways of cells with aberrant phenotypes and that Such US 2009/0232893 A1 Sep. 17, 2009 57 combination may have increased efficacy on the target cell miRNA once it is accessible to miRNA processing machin while not adversely effecting normal cells. Thus, a combina ery. The term “nonsynthetic' in the context of miRNA means tion of miRNA may have a minimal adverse effect on a that the miRNA is not “synthetic.' as defined herein. Further Subject or patient while Supplying a Sufficient therapeutic more, it is contemplated that in embodiments of the invention effect, Such as amelioration of a condition, growth inhibition that concern the use of synthetic miRNAs, the use of corre of a cell, death of a targeted cell, alteration of cell phenotype sponding nonsynthetic miRNAS is also considered an aspect or physiology, slowing of cellular growth, sensitization to a of the invention, and vice versa. It will be understand that the second therapy, sensitization to a particular therapy, and the term “providing an agent is used to include “administering like. the agent to a patient. 0091 Methods include identifying a cell or patient in need of inducing those cellular characteristics. Also, it will be 0.095. In certain embodiments, methods also include tar understood that an amount of a synthetic nucleic acid that is geting a miRNA to modulate in a cell or organism. The term provided to a cellor organism is an “effective amount,” which “targeting a miRNA to modulate” means a nucleic acid of the refers to an amount needed (or a sufficient amount) to achieve invention will be employed so as to modulate the selected a desired goal. Such as inducing a particular cellular charac miRNA. In some embodiments the modulation is achieved teristic(s). Certain embodiments of the methods include pro with a synthetic or non-synthetic miRNA that corresponds to viding or introducing to a cell a nucleic acid molecule corre the targeted miRNA, which effectively provides the targeted sponding to a mature miRNA in the cell in an amount miRNA to the cellor organism (positive modulation). In other effective to achieve a desired physiological result. embodiments, the modulation is achieved with a miRNA 0092. Moreover, methods can involve providing synthetic inhibitor, which effectively inhibits the targeted miRNA in or nonsynthetic miRNA molecules. It is contemplated that in the cell or organism (negative modulation). these embodiments, that the methods may or may not be 0096. In some embodiments, the miRNA targeted to be limited to providing only one or more synthetic miRNA mol modulated is a miRNA that affects a disease, condition, or ecules or only one or more nonsynthetic miRNA molecules. pathway. In certain embodiments, the miRNA is targeted Thus, in certain embodiments, methods may involve provid because a treatment can be provided by negative modulation ing both synthetic and nonsynthetic miRNA molecules. In of the targeted miRNA. In other embodiments, the miRNA is this situation, a cell or cells are most likely provided a syn targeted because a treatment can be provided by positive thetic miRNA molecule corresponding to a particular miRNA modulation of the targeted miRNA or its targets. and a nonsynthetic miRNA molecule corresponding to a dif 0097. In certain methods of the invention, there is a further ferent miRNA. Furthermore, any method articulated using a step of administering the selected miRNA modulator to a cell, list of miRNAS using Markush group language may be articu tissue, organ, or organism (collectively “biological matter”) lated without the Markush group language and a disjunctive in need of treatment related to modulation of the targeted article (i.e., or) instead, and vice versa. miRNA or in need of the physiological or biological results 0093. Typically, an endogenous gene, miRNA or mRNA is discussed herein (such as with respect to a particular cellular modulated in the cell. In particular embodiments, the nucleic pathway or result like decrease in cell viability). Conse acid sequence comprises at least one segment that is at least quently, in some methods of the invention there is a step of 70, 75, 80, 85, 90, 95, or 100% identical in nucleic acid identifying a patient in need of treatment that can be provided sequence to one or more miRNA or gene sequence. Modula by the miRNA modulator(s). It is contemplated that an effec tion of the expression or processing of an endogenous gene, tive amount of a miRNA modulator can be administered in miRNA, or mRNA can be through modulation of the process Some embodiments. In particular embodiments, there is a ing of a mRNA, such processing including transcription, therapeutic benefit conferred on the biological matter, where transportation and/or translation with in a cell. Modulation a “therapeutic benefit” refers to an improvement in the one or may also be effected by the inhibition or enhancement of more conditions or symptoms associated with a disease or miRNA activity with a cell, tissue, or organ. Such processing condition or an improvement in the prognosis, duration, or may affect the expression of an encoded product or the sta status with respect to the disease. It is contemplated that a bility of the mRNA. In still other embodiments, a nucleic acid therapeutic benefit includes, but is not limited to, a decrease in sequence can comprise a modified nucleic acid sequence. In pain, a decrease in morbidity, a decrease in a symptom. For certain aspects, one or more miRNA sequence may include or example, with respect to cancer, it is contemplated that a comprise a modified nucleobase or nucleic acid sequence. therapeutic benefit can be inhibition of tumor growth, preven 0094. It will be understood in methods of the invention tion of metastasis, reduction in number of metastases, inhi that a cell or other biological matter Such as an organism bition of cancer cell proliferation, induction of cell death in (including patients) can be provided a miRNA or miRNA cancer cells, inhibition of angiogenesis near cancer cells, molecule corresponding to a particular miRNA by adminis induction of apoptosis of cancer cells, reduction in pain, tering to the cell or organism a nucleic acid molecule that reduction in risk of recurrence, induction of chemo- or radi functions as the corresponding miRNA once inside the cell. osensitivity in cancer cells, prolongation of life, and/or delay The form of the molecule provided to the cell may not be the of death directly or indirectly related to cancer. form that acts a miRNA once inside the cell. Thus, it is (0098. Furthermore, it is contemplated that the miRNA contemplated that in some embodiments, a synthetic miRNA compositions may be provided as part of a therapy to a or a nonsynthetic miRNA is provided such that it becomes patient, in conjunction with traditional therapies or preventa processed into a mature and active miRNA once it has access tive agents. Moreover, it is contemplated that any method to the cell's miRNA processing machinery. In certain discussed in the context of therapy may be applied preventa embodiments, it is specifically contemplated that the miRNA tively, particularly in a patient identified to be potentially in molecule provided is not a mature miRNA molecule but a need of the therapy or at risk of the condition or disease for nucleic acid molecule that can be processed into the mature which a therapy is needed. US 2009/0232893 A1 Sep. 17, 2009

0099. In addition, methods of the invention concern construct encoding the same. An "effective amount of the employing one or more nucleic acids corresponding to a pharmaceutical composition, generally, is defined as that miRNA and a therapeutic drug. The nucleic acid can enhance amount sufficient to detectably and repeatedly to achieve the the effect or efficacy of the drug, reduce any side effects or stated desired result, for example, to ameliorate, reduce, toxicity, modify its bioavailability, and/or decrease the dos minimize or limit the extent of the disease or its symptoms. age or frequency needed. In certain embodiments, the thera Other more rigorous definitions may apply, including elimi peutic drug is a cancer therapeutic. Consequently, in some nation, eradication or cure of disease. embodiments, there is a method of treating cancer in a patient comprising administering to the patient the cancer therapeu 0102 B. Administration tic and an effective amount of at least one miRNA molecule (0103. In certain embodiments, it is desired to kill cells, that improves the efficacy of the cancertherapeutic or protects inhibit cell growth, inhibit metastasis, decrease tumor or tis non-cancer cells. Cancer therapies also include a variety of Sue size, and/or reverse or reduce the malignant or disease combination therapies with both chemical and radiation phenotype of cells. The routes of administration will vary, based treatments. Combination chemotherapies include but naturally, with the location and nature of the lesion or site to are not limited to, for example, 5-fluorouracil, alemtuzumab, be targeted, and include, e.g., intradermal, Subcutaneous, amrubicin, bevacizumab, bleomycin, bortezomib, buSulfan, regional, parenteral, intravenous, intramuscular, intranasal, camptothecin, capecitabine, carboplatin, cetuximab, systemic, and oral administration and formulation. Direct chlorambucil, cisplatin (CDDP), COX-2 inhibitors (e.g., injection, intratumoral injection, or injection into tumor vas celecoxib), cyclophosphamide, cytarabine, dactinomycin, culature is specifically contemplated for discrete, Solid, dasatinib, daunorubicin, dexamethasone, docetaxel, doxoru accessible tumors, or other accessible target areas. Local, bicin (adriamycin), EGFR inhibitors (gefitinib and cetux regional, or systemic administration also may be appropriate. imab), erlotinib, estrogen receptor binding agents, etoposide For tumors of>4 cm, the volume to be administered will be (VP16), everolimus, farnesyl-protein transferase inhibitors, about 4-10 ml (preferably 10 ml), while for tumors of <4 cm, gefitinib, gemcitabine, gemtuzumab, ibritumomab, ifosfa a volume of about 1-3 ml will be used (preferably 3 ml). mide, imatinib mesylate, larotaxel, lapatinib, lonafarnib, mechlorethamine, melphalan, methotrexate, mitomycin, 0104 Multiple injections delivered as a single dose com navelbine, nitroSurea, nocodazole, Oxaliplatin, paclitaxel, pli prise about 0.1 to about 0.5 ml volumes. Compositions of the comycin, procarbazine, raloxifene, rituximab, sirolimus, Sor invention may be administered in multiple injections to a afenib, Sunitinib, tamoxifen, taxol, taxotere, temsirolimus, tumor or a targeted site. In certain aspects, injections may be tipifamib, toSitumomab, transplatinum, trastuzumab, Vin spaced at approximately 1 cm intervals. blastin, Vincristin, or vinorelbine or any analog or derivative 0105. In the case of Surgical intervention, the present variant of the foregoing. invention may be used preoperatively, to render an inoperable 0100 Generally, inhibitors of miRNAs can be given to tumor Subject to resection. Alternatively, the present inven decrease the activity of an endogenous miRNA. For example, tion may be used at the time of Surgery, and/or thereafter, to inhibitors of miRNA molecules that increase cell prolifera treat residual or metastatic disease. For example, a resected tion can be provided to cells to decrease cell proliferation. The tumor bed may be injected or perfused with a formulation present invention contemplates these embodiments in the comprising a miRNA or combinations thereof. Administra context of the different physiological effects observed with tion may be continued post-resection, for example, by leaving the different miRNA molecules and miRNA inhibitors dis a catheter implanted at the site of the surgery. Periodic post closed herein. These include, but are not limited to, the fol Surgical treatment also is envisioned. Continuous perfusion lowing physiological effects: increase and decreasing cell of an expression construct or a viral construct also is contem proliferation, increasing or decreasing apoptosis, increasing plated. transformation, increasing or decreasing cell viability, acti Vating or inhibiting a kinase (e.g., Erk), activating/inducing or 0106 Continuous administration also may be applied inhibiting hTert, inhibit stimulation of growth promoting where appropriate, for example, where a tumor or other pathway (e.g., Stat3 signaling), reduce or increase viable cell undesired affected area is excised and the tumor bed or tar number, and increase or decrease number of cells at a particu geted site is treated to eliminate residual, microscopic dis lar phase of the cell cycle. Methods of the invention are ease. Delivery via Syringe or catherization is contemplated. generally contemplated to include providing or introducing Such continuous perfusion may take place for a period from about 1-2 hours, to about 2-6 hours, to about 6-12 hours, to one or more different nucleic acid molecules corresponding about 12-24 hours, to about 1-2 days, to about 1-2 wk or to one or more different miRNA molecules. It is contemplated longer following the initiation of treatment. Generally, the that the following, at least the following, or at most the fol dose of the therapeutic composition via continuous perfusion lowing number of different nucleic acid or miRNA molecules will be equivalent to that given by a single or multiple injec may be provided or introduced: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, tions, adjusted over a period of time during which the perfu 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, sion occurs. 29, 30, 31, 32,33,34, 35,36, 37,38, 39, 40, 41,42, 43,44, 45, 0107 Treatment regimens may vary as well and often 46,47, 48,49, 50, 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62, depend on tumor type, tumor location, immune condition, 63,64, 65,66, 67,68, 69,70, 71,72, 73,74, 75,76, 77,78,79, target site, disease progression, and health and age of the 80, 81, 82, 83, 84,85, 86, 87, 88, 89,90,91, 92,93, 94, 95, 96, patient. Certain tumor types will require more aggressive 97, 98, 99, 100, or any range derivable therein. This also treatment. The clinician will be best Suited to make such applies to the number of different miRNA molecules that can decisions based on the known efficacy and toxicity (if any) of be provided or introduced into a cell. the therapeutic formulations. III. PHARMACEUTICAL FORMULATIONS AND 0108. In certain embodiments, the tumor or affected area DELIVERY being treated may not, at least initially, be resectable. Treat 0101 Methods of the present invention include the deliv ments with compositions of the invention may increase the ery of an effective amount of a miRNA or an expression resectability of the tumor due to shrinkage at the margins or US 2009/0232893 A1 Sep. 17, 2009 59 by elimination of certain particularly invasive portions. Fol all cases the form must be sterile and must be fluid to the lowing treatments, resection may be possible. Additional extent that easy Syringability exists. It must be stable under treatments Subsequent to resection may serve to eliminate the conditions of manufacture and storage and must be pre microscopic residual disease at the tumor or targeted site. served against the contaminating action of microorganisms, 0109 Treatments may include various “unit doses. A unit Such as bacteria and fungi. The carrier can be a solvent or dose is defined as containing a predetermined quantity of a dispersion medium containing, for example, water, ethanol, therapeutic composition(s). The quantity to be administered, polyol (e.g., glycerol, propylene glycol, and liquid polyeth and the particular route and formulation, are within the skill ylene glycol, and the like), Suitable mixtures thereof, and/or of those in the clinical arts. A unit dose need not be adminis vegetable oils. Proper fluidity may be maintained, for tered as a single injection but may comprise continuous infu example, by the use of a coating, such as lecithin, by the sion over a set period of time. With respect to a viral compo maintenance of the required particle size in the case of dis nent of the present invention, a unit dose may conveniently be persion and by the use of surfactants. The prevention of the described in terms of ug or mg of miRNA or miRNA mimetic. action of microorganisms can be brought about by various Alternatively, the amount specified may be the amount antibacterial and antifungal agents, for example, parabens, administered as the average daily, average weekly, or average chlorobutanol, phenol, Sorbic acid, thimerosal, and the like. monthly dose. In many cases, it will be preferable to include isotonic agents, 0110 miRNA can be administered to the patient in a dose for example, Sugars or Sodium chloride. Prolonged absorp or doses of about or of at least about 0.5, 1, 5, 10, 15, 20, 25, tion of the injectable compositions can be brought about by 30, 35, 40, 45,50, 60, 70, 80,90, 100, 110, 120, 130, 140, 150, the use in the compositions of agents delaying absorption, for 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, example, aluminum monostearate and gelatin. 280, 290, 300, 310,320, 330,340,350, 360, 370, 380,390, 0.115. In certain formulations, a water-based formulation 400, 410, 420, 430, 440, 450, 460, 470, 480,490, 500, 510, is employed while in others, it may be lipid-based. In particu 520, 530, 540, 550,560, 570,580,590, 600, 610, 620, 630, lar embodiments of the invention, a composition comprising 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, a tumor Suppressor protein or a nucleic acid encoding the 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, same is in a water-based formulation. In other embodiments, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, the formulation is lipid based. 1000 ug or mg, or more, or any range derivable therein. 0116 For parenteral administration in an aqueous solu Alternatively, the amount specified may be the amount tion, for example, the solution should be suitably buffered if administered as the average daily, average weekly, or average necessary and the liquid diluent first rendered isotonic with monthly dose, or it may be expressed in terms of mg/kg, Sufficient Saline or glucose. These particular aqueous solu where kg refers to the weight of the patient and the mg is tions are especially suitable for intravenous, intramuscular, specified above. In other embodiments, the amount specified Subcutaneous, intratumoral, intralesional, and intraperitoneal is any number discussed above but expressed as mg/m (with administration. In this connection, sterile aqueous media respect to tumor size or patient Surface area). which can be employed will be known to those of skill in the 0111 C. Injectable Compositions and Formulations artin light of the present disclosure. For example, one dosage 0112. In some embodiments, the method for the delivery may be dissolved in 1 ml of isotonic NaCl solution and either of a miRNA or an expression construct encoding Such or added to 1000 ml of hypodermoclysis fluid or injected at the combinations thereof is via systemic administration. How proposed site of infusion, (see for example, "Remington's ever, the pharmaceutical compositions disclosed herein may Pharmaceutical Sciences' 15th Edition, pages 1035-1038 also be administered parenterally, Subcutaneously, directly, and 1570-1580). Some variation in dosage will necessarily intratracheally, intravenously, intradermally, intramuscu occur depending on the condition of the Subject being treated. larly, or even intraperitoneally as described in U.S. Pat. Nos. The person responsible for administration will, in any event, 5,543,158; 5,641,515 and 5,399,363 (each specifically incor determine the appropriate dose for the individual subject. porated herein by reference in its entirety). Moreover, for human administration, preparations should 0113. Injection of nucleic acids may be delivered by meet Sterility, pyrogenicity, general safety and purity stan Syringe or any other method used for injection of a solution, dards as required by FDA Office of Biologics standards. as long as the nucleic acid and any associated components can 0117. As used herein, a “carrier includes any and all pass through the particular gauge of needle required for injec Solvents, dispersion media, vehicles, coatings, diluents, anti tion. A syringe system has also been described for use in gene bacterial and antifungal agents, isotonic and absorption therapy that permits multiple injections of predetermined delaying agents, buffers, carrier Solutions, Suspensions, col quantities of a solution precisely at any depth (U.S. Pat. No. loids, and the like. The use of Such media and agents for 5,846,225). pharmaceutical active Substances is well known in the art. 0114 Solutions of the active compounds as free base or Except insofar as any conventional media or agent is incom pharmacologically acceptable salts may be prepared in water patible with the active ingredient, its use in the therapeutic Suitably mixed with a surfactant, Such as hydroxypropylcel compositions is contemplated. Supplementary active ingre lulose. Dispersions may also be prepared in glycerol, liquid dients can also be incorporated into the compositions. polyethylene glycols, mixtures thereof, and in oils. Under 0118. The phrase “pharmaceutically acceptable' refers to ordinary conditions of storage and use, these preparations molecular entities and compositions that do not produce an contain a preservative to prevent the growth of microorgan allergic or similar untoward reaction when administered to a isms. The pharmaceutical forms suitable for injectable use human. include sterile aqueous solutions or dispersions and sterile 0119 The nucleic acid(s) are administered in a manner powders for the extemporaneous preparation of sterile inject compatible with the dosage formulation, and in Such amount able solutions or dispersions (U.S. Pat. No. 5,466,468, spe as will be therapeutically effective. The quantity to be admin cifically incorporated herein by reference in its entirety). In istered depends on the Subject to be treated, including, e.g., US 2009/0232893 A1 Sep. 17, 2009 60 the aggressiveness of the disease or cancer, the size of any extend the time period for treatment significantly, however, tumor(s) or lesions, the previous or other courses of treat where several days (2, 3, 4, 5, 6 or 7) to several weeks (1,2,3, ment. Precise amounts of active ingredient required to be 4, 5, 6, 7 or 8) lapse between the respective administrations. administered depend on the judgment of the practitioner. 0.124. In certain embodiments, a course of treatment will Suitable regimes for initial administration and Subsequent last 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, administration are also variable, but are typified by an initial 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, 36, administration followed by other administrations. Such 37,38,39, 40, 41, 42, 43,44, 45,46, 47, 48,49, 50, 51, 52,53, administration may be systemic, as a single dose, continuous 54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 65,66, 67,68, 69,70, over a period of time spanning 10, 20, 30, 40, 50, 60 minutes, 71, 72,73,74, 75,76, 77,78, 79,80, 81, 82,83, 84,85, 86, 87, and/or 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 88, 89,90 days or more. It is contemplated that one agent may 19, 20, 21, 22, 23, 24 or more hours, and/or 1, 2, 3, 4, 5, 6, 7, be given on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, days or more. Moreover, administration may be through a 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, time release or Sustained release mechanism, implemented by 33,34,35,36, 37,38, 39, 40, 41, 42, 43,44, 45,46, 47, 48,49, formulation and/or mode of administration. 50, 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 65,66, 0120 Various methods for nucleic acid delivery are 67,68, 69,70, 71,72, 73,74, 75,76, 77,78, 79,80, 81, 82,83, described, for example in Sambrook et al., 1989 and Ausubel 84, 85,86, 87, 88,89, and/or 90, any combination thereof, and et al., 1994. Such nucleic acid delivery systems comprise the another agent is given on day 1, 2, 3, 4, 5, 6,7,8,9, 10, 11, 12. desired nucleic acid, by way of example and not by limitation, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, in either “naked’ form as a “naked nucleic acid, or formu 30, 31, 32,33, 34,35, 36, 37,38, 39, 40, 41,42, 43,44, 45,46, lated in a vehicle suitable for delivery, such as in a complex 47, 48,49, 50, 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, with a cationic molecule or a liposome forming lipid, or as a 64, 65,66, 67,68, 69,70,71, 72,73,74, 75,76, 77,78, 79,80, component of a vector, or a component of a pharmaceutical 81, 82, 83, 84, 85, 86, 87, 88, 89, and/or 90, or any combina composition. The nucleic acid delivery system can be pro tion thereof. Within a single day (24-hour period), the patient vided to the cell either directly, such as by contacting it with may be given one or multiple administrations of the agent(s). the cell, or indirectly, such as through the action of any bio Moreover, after a course of treatment, it is contemplated that logical process. By way of example, and not by limitation, the there is a period of time at which no treatment is administered. nucleic acid delivery system can be provided to the cell by This time period may last 1, 2, 3, 4, 5, 6, 7 days, and/or 1, 2, endocytosis; receptor targeting; coupling with native or Syn 3, 4, 5 weeks, and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months thetic cell membrane fragments; physical means such as elec or more, depending on the condition of the patient, such as troporation; combining the nucleic acid delivery system with their prognosis, strength, health, etc. a polymeric carrier, Such as a controlled release film or nano 0.125 Various combinations may be employed, for particle or microparticle or biocompatible molecules or bio example miRNA therapy is “A” and a second therapy is “B”: degradable molecules; with vector. The nucleic acid delivery system can be injected into a tissue or fluid Surrounding the cell, or administered by diffusion of the nucleic acid delivery ABA B.A.B B.B.A. AAB AB,B BAA system across the cell membrane, or by any active or passive AB.B.B. B.A.B.B. B.B.B.A. B.B.A.B AABAB AFB, AFB transport mechanism across the cell membrane. Additionally, ABBA BBiAA BABA BAAB AAAB BAAA the nucleic acid delivery system can be provided to the cell ABAA AABA using techniques such as -related targeting and anti body-mediated immobilization of a viral vector. 0.126 Administration of any compound or therapy of the 0121 D. Combination Treatments present invention to a patient will follow general protocols for 0122. In certain embodiments, the compositions and the administration of Such compounds, taking into account methods of the present invention involve a miRNA, or expres the toxicity, if any, of the vector or any protein or other agent. sion construct encoding such. These miRNA composition can Therefore, in Some embodiments there is a step of monitoring be used in combination with a second therapy to enhance the toxicity that is attributable to combination therapy. It is effect of the miRNA therapy, or increase the therapeutic effect expected that the treatment cycles would be repeated as nec of another therapy being employed. These compositions essary. It also is contemplated that various standard therapies, would be provided in a combined amount effective to achieve as well as Surgical intervention, may be applied in combina the desired effect, such as the killing of a cancer cell and/or tion with the described therapy. the inhibition of cellular hyperproliferation. This process may I0127. In specific aspects, it is contemplated that a second involve contacting the cells with the miRNA or second therapy, such as chemotherapy, radiotherapy, immuno therapy at the same or different time. This may beachieved by therapy, Surgical therapy or other genetherapy, is employed in contacting the cell with one or more compositions or phar combination with the miRNA therapy, as described herein. macological formulation that includes or more of the agents, I0128 2. Chemotherapy or by contacting the cell with two or more distinct composi I0129. A wide variety of chemotherapeutic agents may be tions or formulations, wherein one composition provides (1) used in accordance with the present invention. The term “che miRNA; and/or (2) a second therapy. A second composition motherapy” refers to the use of drugs to treat cancer. A “che or method may be administered that includes a chemotherapy, motherapeutic agent' is used to connote a compound or com radiotherapy, Surgical therapy, immunotherapy or gene position that is administered in the treatment of cancer. These therapy. agents or drugs are categorized by their mode of activity 0123. It is contemplated that one may provide a patient within a cell, for example, whether and at what stage they with the miRNA therapy and the second therapy within about affect the cell cycle. Alternatively, an agent may be charac 12-24 h of each other and, more preferably, within about 6-12 terized based on its ability to directly cross-link DNA, to h of each other. In some situations, it may be desirable to intercalate into DNA, or to induce chromosomal and mitotic US 2009/0232893 A1 Sep. 17, 2009 aberrations by affecting nucleic acid synthesis. Most chemo 0141 3. Radiotherapy therapeutic agents fall into the following categories: alkylat 0.142 Radiotherapy, also called radiation therapy, is the ing agents, antimetabolites, antitumor antibiotics, mitotic treatment of cancer and other diseases with ionizing radia inhibitors, and nitrosoureas. tion. Ionizing radiation deposits energy that injures or 0130 b. Alkylating Agents destroys cells in the area being treated by damaging their 0131 Alkylating agents are drugs that directly interact genetic material, making it impossible for these cells to con with genomic DNA to prevent the cancer cell from prolifer tinue to grow. Although radiation damages both cancer cells ating. This category of chemotherapeutic drugs represents and normal cells, the latter are able to repair themselves and agents that affect all phases of the cell cycle, that is, they are function properly. Radiotherapy may be used to treat local not phase-specific. Alkylating agents can be implemented to ized solid tumors, such as cancers of the skin, tongue, larynx, treat chronic leukemia, non-Hodgkin’s lymphoma, brain, breast, or cervix. It can also be used to treat leukemia Hodgkin's disease, multiple myeloma, and particular cancers and lymphoma (cancers of the blood-forming cells and lym of the breast, lung, and ovary. They include: buSulfan, phatic system, respectively). chlorambucil, cisplatin, cyclophosphamide (cytoxan), dacar 0.143 Radiation therapy used according to the present bazine, ifosfamide, mechlorethamine (mustargen), and mel invention may include, but is not limited to, the use of Y-rays, phalan. Troglitazaone can be used to treat cancer in combi X-rays, and/or the directed delivery of radioisotopes to tumor nation with any one or more of these alkylating agents. cells. Other forms of DNA damaging factors are also contem 0132 c. Antimetabolites plated such as microwaves, proton beam irradiation (U.S. Pat. 0.133 Antimetabolites disrupt DNA and RNA synthesis. Nos. 5,760,395 and 4,870,287) and UV-irradiation. It is most Unlike alkylating agents, they specifically influence the cell likely that all of these factors effect a broad range of damage cycle during S phase. They have been used to combat chronic on DNA, on the precursors of DNA, on the replication and leukemias in addition to tumors of breast, ovary and the repair of DNA, and on the assembly and maintenance of . Antimetabolites include 5-fluorouracil chromosomes. Dosage ranges for X-rays range from daily (5-FU), cytarabine (Ara-C), fludarabine, gemcitabine, and doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage methotrexate. ranges for radioisotopes vary widely, and depend on the half 0134) 5-Fluorouracil (5-FU) has the chemical name of 5-fluoro-2,4(1H.3H)-pyrimidinedione. Its mechanism of life of the isotope, the strength and type of radiation emitted, action is thought to be by blocking the methylation reaction of and the uptake by the neoplastic cells. Radiotherapy may deoxyuridylic acid to thymidylic acid. Thus, 5-FU interferes comprise the use of radiolabeled to deliver doses with the synthesis of deoxyribonucleic acid (DNA) and to a of radiation directly to the cancer site (radioimmunotherapy). lesser extent inhibits the formation of ribonucleic acid Once injected into the body, the antibodies actively seek out (RNA). Since DNA and RNA are essential for cell division the cancer cells, which are destroyed by the cell-killing (cyto and proliferation, it is thought that the effect of 5-FU is to toxic) action of the radiation. This approach can minimize the create a deficiency leading to cell death. Thus, the risk of radiation damage to healthy cells. 0144 Stereotactic radio-surgery (gamma knife) for brain effect of 5-FU is found in cells that rapidly divide, a charac and other tumors does not use a knife, but very precisely teristic of metastatic cancers. targeted beams of gamma radiotherapy from hundreds of 0135 d. Antitumor Antibiotics different angles. Only one session of radiotherapy, taking 0136 Antitumor antibiotics have both antimicrobial and about four to five hours, is needed. For this treatment a spe cytotoxic activity. These drugs also interfere with DNA by cially made metal frame is attached to the head. Then, several chemically inhibiting enzymes and mitosis or altering cellu scans and X-rays are carried out to find the precise area where lar membranes. These agents are not phase specific So they the treatment is needed. During the radiotherapy for brain work in all phases of the cell cycle. Thus, they are widely used tumors, the patient lies with their head in a large helmet, for a variety of cancers. Examples of antitumor antibiotics which has hundreds of holes in it to allow the radiotherapy include bleomycin, dactinomycin, daunorubicin, doxorubi beams through. Related approaches permit positioning for cin (Adriamycin), and idarubicin, Some of which are dis the treatment of tumors in other areas of the body. cussed in more detail below. Widely used in clinical setting for the treatment of neoplasms, these compounds are admin 0145 4. Immunotherapy istered through bolus injections intravenously at doses rang 0146 In the context of cancer treatment, immunothera ing from 25-75 mg/m at 21 day intervals for adriamycin, to peutics, generally, rely on the use of immune effector cells 35-100 mg/m for etoposide intravenously or orally. and molecules to target and destroy cancer cells. Trastuzumab (HerceptinTM) is such an example. The immune effector may 0.137 e. Mitotic Inhibitors be, for example, an antibody specific for Some marker on the 0138 Mitotic inhibitors include alkaloids and other Surface of a tumor cell. The antibody alone may serve as an natural agents that can inhibit either protein synthesis effector of therapy or it may recruit other cells to actually required for cell division or mitosis. They operate during a affect cell killing. The antibody also may be conjugated to a specific phase during the cell cycle. Mitotic inhibitors com drug or toxin (chemotherapeutic, radionuclide, ricin. A chain, prise docetaxel, etoposide (VP16), paclitaxel, taxol, taxotere, cholera toxin, pertussis toxin, etc.) and serve merely as a vinblastine, Vincristine, and vinorelbine. targeting agent. Alternatively, the effector may be a lympho 0139 f. Nitrosureas cyte carrying a surface molecule that interacts, either directly 0140 Nitrosureas, like alkylating agents, inhibit DNA or indirectly, with a tumor cell target. Various effector cells repair proteins. They are used to treat non-Hodgkin’s lym include cytotoxic T cells and NK cells. The combination of phomas, multiple myeloma, malignant melanoma, in addi therapeutic modalities, i.e., direct cytotoxic activity and inhi tion to brain tumors. Examples include carmustine and bition or reduction of ErbB2 would provide therapeutic ben lomustine. efit in the treatment of ErbB2 overexpressing cancers. US 2009/0232893 A1 Sep. 17, 2009 62

0147 In one aspect of immunotherapy, the tumor or dis ease cell must bear Some marker that is amenable to targeting, TABLE 6-continued i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in Generic Name Target the context of the present invention. Common tumor markers mAb 8H9 8H9 antigen include carcinoembryonic antigen, prostate specific antigen, M195 CD33 urinary tumor associated antigen, fetal antigen, tyrosinase pilimumab CTLA4 HuLuc63 CS1 (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, Alemtuzumab CD53 Much3, PLAP, estrogen receptor, receptor, erb Band Epratuzumab CD22 p155. An alternative aspect of immunotherapy is to combine BC8 CD45 anticancer effects with immune stimulatory effects. Immune HuJS91 Prostate specific membrane antigen stimulating molecules also exist including: cytokines such as Lexatumumab TRAIL receptor-2 IL-2, IL-4, IL-12, GM-CSF, gamma-IFN. chemokines such Pertuzumab HER-2 receptor as MIP-1, MCP-1, IL-8 and growth factors such as FLT3 Mik-beta-1 IL-2R ligand. Combining immune stimulating molecules, either as RAV12 RAAG12 SGN-30 CD30 proteins or using gene delivery in combination with a tumor AME-133w CD2O Suppressor Such as MDA-7 has been shown to enhance anti HeFi-1 CD30 tumor effects (Ju et al., 2000). Moreover, antibodies against BMS-663S13 CD137 any of these compounds can be used to target the anti-cancer Volociximab anti-C531 integrin GC1008 TGFB agents discussed herein. HCD122 CD40 0148 Examples of immunotherapies currently under Siplizumab CD2 investigation or in use are immune adjuvants e.g., Mycobac MORAb-003 Folate receptor alpha CNTO 328 IL-6 terium bovis, Plasmodium falciparum, dinitrochlorobenzene MDX-060 CD30 and aromatic compounds (U.S. Pat. Nos. 5,801,005 and Ofatumumab CD2O 5,739,169: Hui and Hashimoto, 1998; Christodoulides et al., SGN-33 CD33 1998), cytokine therapy e.g., C, B and Y: IL-1, GM-CSF and TNF (Bukowski et al., 1998; Davidson et al., 1998: Hellstrand et al., 1998) gene therapy e.g., TNF, IL-1, (O150 5. Gene Therapy IL-2, p53 (Qinet al., 1998; Austin-Ward and Villaseca, 1998: 0151. In yet another embodiment, a combination treat U.S. Pat. Nos. 5,830,880 and 5,846,945) and monoclonal ment involves genetherapy in which atherapeutic polynucle antibodies e.g., anti-ganglioside GM2, anti-HER-2, anti otide is administered before, after, or at the same time as one p185; Pietras et al., 1998: Hanibuchietal., 1998: U.S. Pat. No. or more therapeutic miRNA. Delivery of a therapeutic 5,824.311). Herceptin (trastuzumab) is a chimeric (mouse polypeptide or encoding nucleic acid in conjunction with a human) monoclonal antibody that blocks the HER2-neu miRNA may have a combined therapeutic effect on target receptor. It possesses anti-tumor activity and has been tissues. A variety of proteins are encompassed within the approved for use in the treatment of malignant tumors invention, some of which are described below. Various genes (Dillman, 1999). Table 6 is a non-limiting list of several that may be targeted for gene therapy of some form in com known anti-cancer immunotherapeutic agents and their tar bination with the present invention include, but are not lim gets. It is contemplated that one or more of these therapies ited to inducers of cellular proliferation, inhibitors of cellular may be employed with the miRNA therapies described proliferation, regulators of programmed cell death, cytokines herein. and other therapeutic nucleic acids or nucleic acid that encode 0149. A number of different approaches for passive immu therapeutic proteins. notherapy of cancer exist. They may be broadly categorized 0152 The tumor suppressor oncogenes function to inhibit into the following: injection of antibodies alone; injection of excessive cellular proliferation. The inactivation of these antibodies coupled to toxins or chemotherapeutic agents; genes destroys their inhibitory activity, resulting in unregu injection of antibodies coupled to radioactive isotopes; injec lated proliferation. The tumor Suppressors (e.g., therapeutic tion of anti-idiotype antibodies; and finally, purging of tumor polypeptides) p53, FHIT, p16 and C-CAM can be employed. cells in bone marrow. 0153. In addition to p53, another inhibitor of cellular pro liferation is p16. The major transitions of the eukaryotic cell cycle are triggered by cyclin-dependent kinases, or CDKs. TABLE 6 One CDK, cyclin-dependent kinase 4 (CDK4), regulates pro Generic Name Target gression through the G1. The activity of this enzyme may be to phosphorylate Rb at late G1. The activity of CDK4 is Cetuximab EGFR Panitumumab EGFR controlled by an activating Subunit, D-type cyclin, and by an Trastuzumab erbB2 receptor inhibitory subunit, the p161NK4 has been biochemically Bevacizumab VEGF characterized as a protein that specifically binds to and inhib Alemtuzumab CD52 its CDK4, and thus may regulate Rb phosphorylation (Ser Gemtuzumab ozogamicin CD33 Rituximab CD2O rano et al., 1993: Serrano et al., 1995). Since the p161NK4 Tositumomab CD2O protein is a CDK4 inhibitor (Serrano, 1993), deletion of this Matuzumab EGFR gene may increase the activity of CDK4, resulting in hyper Ibritumomab tiuxetan CD2O phosphorylation of the Rb protein. p16 also is known to Tositumomab CD2O HuPAM4 MUC1 regulate the function of CDK6. MORAb-009 Mesothelin 0154 p161NK4 belongs to a newly described class of G2SO carbonic anhydrase IX CDK-inhibitory proteins that also includes p16B, p 19, p21 WAF1, and p27KIP1. The p161NK4 gene maps to 9p21, a US 2009/0232893 A1 Sep. 17, 2009 chromosome region frequently deleted in many tumor types. potentiate the apoptotic inducing abilities of the present Homozygous deletions and mutations of the p161NK4 gene invention by establishment of an autocrine or paracrine effect are frequent in human tumor cell lines. This evidence Sug on hyperproliferative cells. Increases intercellular signaling gests that the p161NK4 gene is a tumor suppressor gene. This by elevating the number of GAPjunctions would increase the interpretation has been challenged, however, by the observa anti-hyperproliferative effects on the neighboring hyperpro tion that the frequency of the p161NK4 gene alterations is liferative cell population. In other embodiments, cytostatic or much lower in primary uncultured tumors than in cultured differentiation agents can be used in combination with the cell lines (Caldas et al., 1994; Cheng et al., 1994; Hussussian present invention to improve the anti-hyperproliferative effi et al., 1994; Kamb et al., 1994; Mori et al., 1994: Okamoto et cacy of the treatments. Inhibitors of cell adhesion are con al., 1994: Nobori et al., 1995: Orlow et al., 1994; Arap et al., templated to improve the efficacy of the present invention. 1995). Restoration of wild-type p161NK4 function by trans Examples of cell adhesion inhibitors are focal adhesion fection with a plasmid expression vector reduced colony for kinase (FAKs) inhibitors and Lovastatin. It is further contem mation by some human cancer cell lines (Okamoto, 1994: plated that other agents that increase the sensitivity of a hyper Arap, 1995). proliferative cell to apoptosis, such as the antibody c225, 0155. Other genes that may be employed according to the could be used in combination with the present invention to present invention include Rb, APC, DCC, NF-1, NF-2, WT-1, improve the treatment efficacy. MEN-1, MEN-II, Zac1, p73, VHL, MMAC1/PTEN, 0162 Apo2 ligand (Apo2L, also called TRAIL) is a mem DBCCR-1, FCC, rsk-3, p27, p27/p16 fusions, p21/p27 ber of the tumor necrosis factor (TNF) cytokine family. fusions, anti-thrombotic genes (e.g., COX-1, TFPI), PGS, TRAIL activates rapid apoptosis in many types of cancer Dp, E2F, ras, myc, neu, raf, erb, fms, trk, ret, gsp, hist, abl. cells, yet is not toxic to normal cells. TRAIL mRNA occurs in E1A, p300, genes involved in angiogenesis (e.g., VEGF, FGF, a wide variety of tissues. Most normal cells appear to be thrombospondin, BAI-1. GDAIF, or their receptors) and resistant to TRAIL's cytotoxic action, Suggesting the exist MCC. ence of mechanisms that can protect againstapoptosis induc 0156 6. Surgery tion by TRAIL. The first receptor described for TRAIL, 0157 Approximately 60% of persons with cancer will called (DR4), contains a cytoplasmic “death undergo Surgery of some type, which includes preventative, domain': DR4 transmits the apoptosis signal carried by diagnostic or staging, curative and palliative Surgery. Cura TRAIL. Additional receptors have been identified that bind to tive Surgery is a cancer treatment that may be used in con TRAIL. One receptor, called DR5, contains a cytoplasmic junction with other therapies, such as the treatment of the death domain and signals apoptosis much like DR4. The DR4 present invention, chemotherapy, radiotherapy, hormonal and DR5 mRNAs are expressed in many normal tissues and therapy, gene therapy, immunotherapy and/or alternative tumor cell lines. Recently, decoy receptors such as DcR1 and therapies. DcR2 have been identified that prevent TRAIL from inducing 0158 Curative surgery includes resection in which all or apoptosis through DR4 and DR5. These decoy receptors thus part of cancerous tissue is physically removed, excised, and/ represent a novel mechanism for regulating sensitivity to a or destroyed. Tumor resection refers to physical removal of at pro-apoptotic cytokine directly at the cell's surface. The pref least part of a tumor. In addition to tumor resection, treatment erential expression of these inhibitory receptors in normal by Surgery includes laser Surgery, cryoSurgery, electroSur tissues suggests that TRAIL may be useful as an anticancer gery, and microscopically controlled Surgery (Mohs Sur agent that induces apoptosis in cancer cells while sparing gery). It is further contemplated that the present invention normal cells. (Marsters et al., 1999). may be used in conjunction with removal of Superficial can 0163 There have been many advances in the therapy of cers, precancers, or incidental amounts of normal tissue. cancer following the introduction of cytotoxic chemothera 0159. Upon excision of part of all of cancerous cells, tis peutic drugs. However, one of the consequences of chemo Sue, or tumor, a cavity may be formed in the body. Treatment therapy is the development/acquisition of drug-resistant phe may be accomplished by perfusion, direct injection or local notypes and the development of multiple drug resistance. The application of the area with an additional anti-cancer therapy. development of drug resistance remains a major obstacle in Such treatment may be repeated, for example, every 1, 2, 3, 4, the treatment of such tumors and therefore, there is an obvi 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, ous need for alternative approaches Such as gene therapy. 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may 0164. Another form of therapy for use in conjunction with be of varying dosages as well. chemotherapy, radiation therapy or biological therapy (0160 7. Other Agents includes hyperthermia, which is a procedure in which a 0161 It is contemplated that other agents may be used in patient's tissue is exposed to high temperatures (up to 106° combination with the present invention to improve the thera F.). External or internal heating devices may be involved in peutic efficacy of treatment. These additional agents include the application of local, regional, or whole-body hyperther immunomodulatory agents, agents that affect the upregula mia. Local hyperthermia involves the application of heat to a tion of cell Surface receptors and GAP junctions, cytostatic Small area, such as a tumor. Heat may be generated externally and differentiation agents, inhibitors of cell adhesion, agents with high-frequency waves targeting a tumor from a device that increase the sensitivity of the hyperproliferative cells to outside the body. Internal heat may involve a sterile probe, apoptotic inducers, or other biological agents. Immunomodu including thin, heated wires or hollow tubes filled with warm latory agents include tumor necrosis factor, interferon alpha, water, implanted microwave antennae, or radiofrequency beta, and gamma; IL-2 and other cytokines; F42K and other electrodes. cytokine analogs; or MIP-1, MIP-1beta, MCP-1, RANTES, 0.165. A patient's organ or a limb is heated for regional and other chemokines. It is further contemplated that the therapy, which is accomplished using devices that produce upregulation of cell Surface receptors or their ligands such as high energy, Such as magnets. Alternatively, some of the Fas/, DR4 or DR5/TRAIL (Apo-2 ligand) would patient's blood may be removed and heated before being US 2009/0232893 A1 Sep. 17, 2009 64 perfused into an area that will be internally heated. Whole 1000 per square centimeter. Microarrays typically use coated body heating may also be implemented in cases where cancer glass as the Solid Support, in contrast to the nitrocellulose has spread throughout the body. Warm-water blankets, hot based material offilter arrays. By having an ordered array of wax, inductive coils, and thermal chambers may be used for marker RNA and/or miRNA-complementing nucleic acid this purpose. samples, the position of each sample can be tracked and 0166 Hormonal therapy may also be used in conjunction linked to the original sample. with the present invention or in combination with any other 0172 A variety of different array devices in which a plu cancer therapy previously described. The use of hormones rality of distinct nucleic acid probes are stably associated with may be employed in the treatment of certain cancers such as the surface of a solid support are known to those of skill in the breast, prostate, ovarian, or cervical cancer to lower the level art. Useful Substrates for arrays include nylon, glass, metal, or block the effects of certain hormones such as testosterone plastic, latex, and silicon. Such arrays may vary in a number or estrogen. This treatment is often used in combination with of different ways, including average probe length, sequence at least one other cancer therapy as a treatment option or to or types of probes, nature of bond between the probe and the reduce the risk of metastases. array Surface, e.g. covalent or non-covalent, and the like. The 0167. This application incorporates U.S. application Ser. labeling and screening methods of the present invention and No. 1 1/349,727 filed on Feb. 8, 2006 claiming priority to U.S. the arrays are not limited in its utility with respect to any Provisional Application Ser. No. 60/650,807 filed Feb. 8, parameter except that the probes detect miRNA, or genes or 2005 herein by references in its entirety. nucleic acid representative of genes; consequently, methods and compositions may be used with a variety of different IV. miRNAMOLECULES types of nucleic acid arrays. (0168 MicroRNA molecules (“miRNAs) are generally 0173 Representative methods and apparatus for preparing 21 to 22 nucleotides in length, though lengths of 19 and up to a microarray have been described, for example, in U.S. Pat. 23 nucleotides have been reported. The miRNAs are each Nos. 5,143,854:5,202,231:5,242,974:5,288,644; 5,324,633; processed from alongerprecursor RNA molecule (“precursor 5,384,261; 5,405,783; 5,412,087; 5,424, 186; 5,429,807; miRNA). Precursor miRNAs are transcribed from non-pro 5,432,049; 5,436,327: 5,445,934; 5,468,613; 5,470,710; tein-encoding genes. The precursor miRNAS have two 5,472,672; 5,492,806; 5,525,464; 5,503,980; 5,510,270; regions of complementarity that enables them to form a stem 5,525,464; 5,527,681: 5,529,756; 5,532,128; 5,545,531; loop- or fold-back-like structure, which is cleaved in animals 5,547,839; 5,554,501; 5,556,752; 5,561,071; 5,571,639; by a ribonuclease III-like nuclease enzyme called Dicer. The 5,580,726; 5,580,732: 5,593,839; 5,599,695; 5,599,672: processed miRNA is typically a portion of the stem. 5,610,287: 5,624,711; 5,631,134, 5,639,603; 5,654,413; 0169. The processed miRNA (also referred to as “mature 5,658,734; 5,661,028; 5.665,547; 5,667,972; 5,695,940; miRNA) becomes part of a large complex to down-regulate 5,700,637; 5,744,305; 5,800,992; 5,807,522; 5,830,645; a particular target gene or its gene product. Examples of 5,837, 196; 5,871,928; 5,847.219; 5,876,932; 5,919,626; animal miRNAs include those that imperfectly basepair with 6,004,755; 6,087,102; 6,368,799; 6,383,749; 6,617,112: the target, which halts translation (Olsen et al., 1999; Segger 6,638,717; 6,720,138, as well as WO 93/17126; WO son et al., 2002). siRNA molecules also are processed by 95/11995; WO95/21265; WO95/21944; WO95/35505; WO Dicer, but from a long, double-stranded RNA molecule. siR 96/31622; WO 97/10365; WO 97/27317; WO99/35505; WO NAs are not naturally found in animal cells, but they can 09923256; WO 09936760; WO0138580; WO 0168255; WO direct the sequence-specific cleavage of an mRNA target 03020898; WO 03040410; WO 03053586: WO 03087297; through a RNA-induced silencing complex (RISC) (Denliet WO 03091426; WO03100012: WO 04020085; WO al, 2003). 04027093: EP 373 203; EP 785 280; EP 799 897 and UK 8 (0170 B. Array Preparation 803 000; the disclosures of which are all herein incorporated 0171 Certain embodiments of the present invention con by reference. cerns the preparation and use of mRNA or nucleic acid arrays, 0.174. It is contemplated that the arrays can be high density miRNA or nucleic acid arrays, and/or miRNA or nucleic acid arrays, such that they contain 2, 20, 25, 50, 80, 100 or more probe arrays, which are macroarrays or microarrays of different probes. It is contemplated that they may contain nucleic acid molecules (probes) that are fully or nearly 1000, 16,000, 65,000, 250,000 or 1,000,000 or more different complementary (over the length of the prove) or identical probes. The probes can be directed to mRNA and/or miRNA (over the length of the prove) to a plurality of nucleic acid, targets in one or more different organisms or cell types. The mRNA or miRNA molecules, precursor miRNA molecules, oligonucleotide probes range from 5 to 50, 5 to 45, 10 to 40, or nucleic acids derived from the various genes and gene 9 to 34, or 15 to 40 nucleotides in length in some embodi pathways modulated by miR-143 miRNAs and that are posi ments. In certain embodiments, the oligonucleotide probes tioned on a Support or Support material in a spatially separated are 5, 10, 15, 20 to 20, 25, 30, 35, 40 nucleotides in length organization. Macroarrays are typically sheets of nitrocellu including all integers and ranges there between. lose or nylon upon which probes have been spotted. Microar 0.175. The location and sequence of each different probe rays position the nucleic acid probes more densely such that sequence in the array are generally known. Moreover, the up to 10,000 nucleic acid molecules can be fit into a region large number of different probes can occupy a relatively small typically 1 to 4 square centimeters. Microarrays can be fab area providing a high density array having a probe density of ricated by spotting nucleic acid molecules, e.g., genes, oligo generally greater than about 60, 100, 600, 1000, 5,000, nucleotides, etc., onto Substrates or fabricating oligonucle 10,000, 40,000, 100,000, or 400,000 different oligonucle otide sequences in situ on a Substrate. Spotted or fabricated otide probes per cm. The surface area of the array can be nucleic acid molecules can be applied in a high density matrix about or less than about 1, 1.6,2,3,4,5,6,7,8,9, or 10 cm. pattern of up to about 30 non-identical nucleic acid molecules 0176 Moreover, a person of ordinary skill in the art could per square centimeter or higher, e.g. up to about 100 or even readily analyze data generated using an array. Such protocols US 2009/0232893 A1 Sep. 17, 2009

are disclosed above, and include information found in WO that disease or condition. A sample that is not normal is one 9743450; WO 03023058: WO 03022421; WO 03029485; exhibiting phenotypic or genotypic trait(s) of a disease or WO 03067217; WO 03066906; WO 03076928: WO condition, or one believed to be not normal with respect to 03093810; WO 03100448A1, all of which are specifically that disease or condition. It may be compared to a cell that is incorporated by reference. normal with respect to that disease or condition. Phenotypic (0177) C. Sample Preparation traits include symptoms of, or Susceptibility to, a disease or (0178. It is contemplated that the RNA and/or miRNA of a condition of which a component is or may or may not be wide variety of samples can be analyzed using the arrays, genetic, or caused by a hyperproliferative or neoplastic cellor index of probes, or array technology of the invention. While cells. endogenous miRNA is contemplated for use with composi 0185. An array comprises a solid support with nucleic acid tions and methods of the invention, recombinant miRNA probes attached to the Support. Arrays typically comprise a including nucleic acids that are complementary oridentical to plurality of different nucleic acid probes that are coupled to a endogenous miRNA or precursor miRNA can also be surface of a substrate in different, known locations. These handled and analyzed as described herein. Samples may be arrays, also described as “microarrays' or colloquially biological samples, in which case, they can be from biopsy, “chips' have been generally described in the art, for example, fine needle aspirates, exfoliates, blood, tissue, organs, semen, U.S. Pat. Nos. 5,143,854, 5,445,934, 5,744,305, 5,677, 195, saliva, tears, other bodily fluid, hair follicles, skin, or any 6,040,193, 5,424,186 and Fodoret al., (1991), each of which sample containing or constituting biological cells, particu is incorporated by reference in its entirety for all purposes. larly cancer or hyperproliferative cells. In certain embodi Techniques for the synthesis of these arrays using mechanical ments, samples may be, but are not limited to, biopsy, or cells synthesis methods are described in, e.g., U.S. Pat. No. 5,384, purified or enriched to some extent from a biopsy or other 261, incorporated herein by reference in its entirety for all bodily fluids or tissues. Alternatively, the sample may not be purposes. Although a planar array Surface is used in certain a biological sample, but be a chemical mixture. Such as a aspects, the array may be fabricated on a Surface of virtually cell-free reaction mixture (which may contain one or more any shape or even a multiplicity of Surfaces. Arrays may be biological enzymes). nucleic acids on beads, gels, polymeric Surfaces, fibers such 0179 D. Hybridization as fiber optics, glass or any other appropriate Substrate, see 0180. After an array or a set of probes is prepared and/or U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 the nucleic acid in the sample or probe is labeled, the popu and 5,800,992, which are hereby incorporated in their entirety lation of target nucleic acids is contacted with the array or for all purposes. Arrays may be packaged in such a manner as probes under hybridization conditions, where such condi to allow for diagnostics or other manipulation of an all inclu tions can be adjusted, as desired, to provide for an optimum sive device, see for example, U.S. Pat. Nos. 5.856,174 and level of specificity in view of the particular assay being per 5,922.591 incorporated in their entirety by reference for all formed. Suitable hybridization conditions are well known to purposes. See also U.S. patent application Ser. No. 09/545, those of skill in the art and reviewed in Sambrook et al. (2001) 207, filed Apr. 7, 2000 for additional information concerning and WO95/21944. Of particular interest in many embodi arrays, their manufacture, and their characteristics, which is ments is the use of stringent conditions during hybridization. incorporated by reference in its entirety for all purposes. Stringent conditions are known to those of skill in the art. 0186 Particularly, arrays can be used to evaluate samples 0181. It is specifically contemplated that a single array or with respect to pathological condition such as cancer and set of probes may be contacted with multiple samples. The related conditions. It is specifically contemplated that the samples may be labeled with different labels to distinguish invention can be used to evaluate differences between stages the samples. For example, a single array can be contacted or Sub-classifications of disease, such as between benign, with a tumor tissue sample labeled with Cy3, and normal cancerous, and metastatic tissues or tumors. tissue sample labeled with Cy5. Differences between the 0187 Phenotypic traits to be assessed include character samples for particular miRNAS corresponding to probes on istics Such as longevity, morbidity, expected Survival, Suscep the array can be readily ascertained and quantified. tibility or receptivity to particular drugs or therapeutic treat 0182. The small surface area of the array permits uniform ments (drug efficacy), and risk of drug toxicity. Samples that hybridization conditions, such as temperature regulation and differ in these phenotypic traits may also be evaluated using salt content. Moreover, because of the small area occupied by the compositions and methods described. the high density arrays, hybridization may be carried out in 0188 In certain embodiments, miRNA and/or expression extremely small fluid volumes (e.g., about 250 ul or less, profiles may be generated to evaluate and correlate those including volumes of about or less than about 5, 10, 25, 50. profiles with pharmacokinetics or therapies. For example, 60, 70, 80,90, 100 ul, or any range derivable therein). In small these profiles may be created and evaluated for patient tumor Volumes, hybridization may proceed very rapidly. and blood samples prior to the patient's being treated or 0183 E. Differential Expression Analyses during treatment to determine if there are miRNA or genes 0184 Arrays of the invention can be used to detect differ whose expression correlates with the outcome of the patient’s ences between two samples. Specifically contemplated appli treatment. Identification of differential miRNAs or genes can cations include identifying and/or quantifying differences lead to a diagnostic assay for evaluation of tumor and/or blood between miRNA or gene expression from a sample that is samples to determine what drug regimen the patient should be normal and from a sample that is not normal, between a provided. In addition, it can be used to identify or select disease or condition and a cell not exhibiting Such a disease or patients suitable for a particular clinical trial. If an expression condition, or between two differently treated samples. Also, profile is determined to be correlated with drug efficacy or miRNA or gene expression may be compared between a drug toxicity that profile is relevant to whether that patient is sample believed to be susceptible to a particular disease or an appropriate patient for receiving a drug, for receiving a condition and one believed to be not susceptible or resistant to combination of drugs, or for a particular dosage of the drug. US 2009/0232893 A1 Sep. 17, 2009 66

0189 In addition to the above prognostic assay, samples 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, from patients with a variety of diseases can be evaluated to 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, determine if different diseases can be identified based on 240, 250, 260, 270, 280, 290, 300, 310,320, 330, 340, 350, miRNA and/or related gene expression levels. A diagnostic 360, 370, 380,390, 400, 410, 420, 430, 440, 450, 460, 470, assay can be created based on the profiles that doctors can use 480,490,500, 510,520, 530, 540, 550,560,570,580,590, to identify individuals with a disease or who are at risk to 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, develop a disease. Alternatively, treatments can be designed 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, based on miRNA profiling. Examples of such methods and compositions are described in the U.S. Provisional Patent 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, Application entitled “Methods and Compositions Involving 960, 970, 980, 990, or 1000 nucleotides, or any range deriv miRNA and miRNA Inhibitor Molecules' filed on May 23, able therein, in length. Such lengths cover the lengths of 2005, which is hereby incorporated by reference in its processed miRNA, miRNA probes, precursor miRNA, entirety. miRNA containing vectors, mRNA, mRNA probes, control (0190. F. Other Assays nucleic acids, and other probes and primers. 0191 In addition to the use of arrays and microarrays, it is 0.195. In many embodiments, miRNA are 19-24 nucle contemplated that a number of different assays could be otides in length, while miRNA probes are 19-35 nucleotides employed to analyze miRNAs or related genes, their activi in length, depending on the length of the processed miRNA ties, and their effects. Such assays include, but are not limited and any flanking regions added. miRNA precursors are gen to, nucleic acid amplification, polymerase chain reaction, erally between 62 and 110 nucleotides in humans. quantitative PCR, RT-PCR, in situ hybridization, Northern 0196. Nucleic acids of the invention may have regions of hybridization, hybridization protection assay (HPA)(Gen identity or complementarity to another nucleic acid. It is Probe), branched DNA (bDNA) assay (Chiron), rolling circle contemplated that the region of complementarity or identity amplification (RCA), single molecule hybridization detec can be at least 5 contiguous residues, though it is specifically tion (US Genomics), Invader assay (ThirdWave Technolo gies), and/or Bridge Litigation Assay (Genaco). contemplated that the region is, is at least, or is at most 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, V. NUCLEICACIDS 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, 0.192 The present invention concerns nucleic acids, modi 60, 61, 62,63, 64, 65, 66, 67,68, 69,70, 71,72, 73,74, 75,76, fied or mimetic nucleic acids, miRNAs, mRNAs, genes, and 77,78, 79,80, 81, 82, 83, 84,85, 86, 87, 88,89,90,91, 92,93, representative fragments thereof that can be labeled, used in array analysis, or employed in diagnostic, therapeutic, or 94, 95, 96, 97,98, 99, 100, 110, 120, 130, 140, 150, 160, 170, prognostic applications, particularly those related to patho 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, logical conditions such as cancer. The molecules may have 300, 310,320, 330, 340, 350, 360, 370, 380,390, 400, 410, been endogenously produced by a cell, or been synthesized or 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510,520, produced chemically or recombinantly. They may be isolated 530, 540, 550,560,570,580,590, 600, 610, 620, 630, 640, and/or purified. Each of the miRNAs described herein and 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, include the corresponding SEQ ID NO and accession num 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, bers for these miRNA sequences. The name of a miRNA is 890,900,910,920,930,940,950,960,970,980,990, or 1000 often abbreviated and referred to without a “hsa- prefix and contiguous nucleotides. It is further understood that the will be understood as such, depending on the context. Unless length of complementarity within a precursor miRNA or otherwise indicated, miRNAs referred to in the application other nucleic acid or between a miRNA probe and a miRNA are human sequences identified as miR-X or let-X, where X is or a miRNA gene are such lengths. Moreover, the comple a number and/or letter. mentarity may be expressed as a percentage, meaning that the 0193 In certain aspects, a miRNA probe designated by a complementarity between a probe and its target is 90% or Suffix '5P or “3P can be used. “5P indicates that the greater over the length of the probe. In some embodiments, mature miRNA derives from the 5' end of the precursor and a complementarity is or is at least 90%. 95% or 100%. In corresponding “3P indicates that it derives from the 3' end of particular, Such lengths may be applied to any nucleic acid the precursor, as described on the world wide web at sanger. comprising a nucleic acid sequence identified in any of SEQ ac.uk. Moreover, in some embodiments, a miRNA probe is ID NO: 1-13, accession number, or any other sequence dis used that does not correspond to a known human miRNA. It closed herein. Typically, the commonly used name of the is contemplated that these non-human miRNA probes may be miRNA is given (with its identifying source in the prefix, for used in embodiments of the invention or that there may exist example, "hsa' for human sequences) and the processed a human miRNA that is homologous to the non-human miRNA sequence. Unless otherwise indicated, a miRNA miRNA. In other embodiments, any mammaliancell, biologi without a prefix will be understood to refer to a human cal sample, or preparation thereof may be employed. miRNA. Moreover, a lowercase letter in a miRNA name may 0194 In some embodiments of the invention, methods and or may not be lowercase; for example, hsa-mir-130b can also compositions involving miRNA may concern miRNA, mark be referred to as miR-130B. The term “miRNA probe' refers ers (mRNAs), and/or other nucleic acids. Nucleic acids may to a nucleic acid probe that can identify a particular miRNA or be, beat least, or beat most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, structurally related miRNAs. 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 0197) It is understood that some nucleic acids are derived 31, 32,33, 34,35,36, 37,38, 39, 40, 41, 42,43, 44, 45, 46,47, from genomic sequences or a gene. In this respect, the term 48,49, 50, 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 'gene' is used for simplicity to refer to the genomic sequence 65, 66,67,68, 69,70, 71,72, 73,74, 75,76, 77,78, 79,80, 81, encoding the precursor nucleic acid or miRNA for a given 82, 83, 84,85, 86, 87, 88, 89,90,91, 92,93,94, 95, 96, 97,98, miRNA or gene. However, embodiments of the invention may US 2009/0232893 A1 Sep. 17, 2009 67 involve genomic sequences of a miRNA that are involved in naturally occurring miRNA molecule. In other embodiments, its expression, such as a promoter or other regulatory a synthetic miRNA molecule may have the sequence of a Sequences. naturally occurring miRNA molecule, but the chemical struc 0198 The term “recombinant may be used and this gen ture of the molecule, particularly in the part unrelated specifi erally refers to a molecule that has been manipulated in vitro cally to the precise sequence (non-sequence chemical struc or that is a replicated or expressed product of such a molecule. ture) differs from chemical structure of the naturally (0199 The term “nucleic acid is well known in the art. A occurring miRNA molecule with that sequence. In some “nucleic acid as used herein will generally refer to a mol cases, the synthetic miRNA has both a sequence and non ecule (one or more strands) of DNA, RNA or a derivative or sequence chemical structure that are not found in a naturally analog thereof, comprising a nucleobase. A nucleobase occurring miRNA. Moreover, the sequence of the synthetic includes, for example, a naturally occurring purine or pyri molecules will identify which miRNA is effectively being midine base found in DNA (e.g., an adenine “A” a guanine provided or inhibited; the endogenous miRNA will be “G” a “Tora cytosine“C”) or RNA (e.g., an A, a G, referred to as the “corresponding miRNA. Corresponding an “U” or a C). The term “nucleic acid encompasses miRNA sequences that can be used in the context of the the terms "oligonucleotide' and “polynucleotide.” each as a invention include, but are not limited to, all or a portion of subgenus of the term “nucleic acid.” those sequences in the SEQ IDs provided herein, as well as 0200. The term “miRNA generally refers to a single any other miRNA sequence, miRNA precursor sequence, or Stranded molecule, but in specific embodiments, molecules any sequence complementary thereof. In some embodiments, implemented in the invention will also encompass a region or the sequence is or is derived from or contains all or part of a an additional strand that is partially (between 10 and 50% sequence identified herein to target a particular miRNA (or complementary across length of strand), Substantially set of miRNAs) that can be used with that sequence. (greater than 50% but less than 100% complementary across (0204 As used herein, “hybridization”, “hybridizes” or length of strand) or fully complementary to another region of “capable of hybridizing is understood to mean the forming the same single-stranded molecule or to another nucleic acid. of a double or triple stranded molecule or a molecule with Thus, miRNA may encompass a molecule that comprises one partial double or triple stranded nature. The term “anneal as or more complementary or self-complementary Strand(s) or used herein is synonymous with “hybridize.” The term “complement(s) of a particular sequence. For example, pre “hybridization”, “hybridize(s) or “capable of hybridizing” cursor miRNA may have a self-complementary region, which encompasses the terms "stringent condition(s) or “high is up to 100% complementary. miRNA probes or nucleic stringency” and the terms “low stringency” or “low strin acids of the invention can include, can be or can be at least 60, gency condition(s). 65, 70, 75, 80, 85,90, 95, 96, 97, 98, 99 or 100% comple 0205 As used herein “stringent condition(s) or “high mentary to their target. stringency” are those conditions that allow hybridization 0201 It is understood that a “synthetic nucleic acid of the between or within one or more nucleic acid strand(s) contain invention means that the nucleic acid does not have all or part ing complementary sequence(s), but preclude hybridization of a chemical structure or sequence of a naturally occurring of random sequences. Stringent conditions tolerate little, if nucleic acid. Consequently, it will be understood that the term any, mismatch between a nucleic acid and a target Strand. “synthetic miRNA refers to a “synthetic nucleic acid' that Such conditions are well known to those of ordinary skill in functions in a cell or under physiological conditions as a the art, and are preferred for applications requiring high selec naturally occurring miRNA. tivity. Non-limiting applications include isolating a nucleic 0202 While embodiments of the invention may involve acid, such as a gene or a nucleic acid segment thereof, or synthetic miRNAS or synthetic nucleic acids, in some detecting at least one specific mRNA transcript or a nucleic embodiments of the invention, the nucleic acid molecule(s) acid segment thereof, and the like. need not be “synthetic.” In certain embodiments, a non-syn 0206 Stringent conditions may comprise low salt and/or thetic nucleic acid or miRNA employed in methods and com high temperature conditions, such as provided by about 0.02 positions of the invention may have the entire sequence and M to about 0.5 M NaCl at temperatures of about 42° C. to structure of a naturally occurring mRNA or miRNA precursor about 70° C. It is understood that the temperature and ionic or the mature mRNA or miRNA. For example, non-synthetic strength of a desired stringency are determined in part by the miRNAs used in methods and compositions of the invention length of the particular nucleic acid(s), the length and nucleo may not have one or more modified nucleotides or nucleotide base content of the target sequence(s), the charge composi analogs. In these embodiments, the non-synthetic miRNA tion of the nucleic acid(s), and to the presence or concentra may or may not be recombinantly produced. In particular tion of formamide, tetramethylammonium chloride or other embodiments, the nucleic acid in methods and/or composi solvent(s) in a hybridization mixture. tions of the invention is specifically a synthetic miRNA and 0207. It is also understood that these ranges, compositions not a non-synthetic miRNA (that is, not an miRNA that quali and conditions for hybridization are mentioned by way of fies as “synthetic'); though in other embodiments, the inven non-limiting examples only, and that the desired stringency tion specifically involves a non-synthetic miRNA and not a for a particular hybridization reaction is often determined synthetic miRNA. Any embodiments discussed with respect empirically by comparison to one or more positive or negative to the use of synthetic miRNAs can be applied with respect to controls. Depending on the application envisioned it is pre non-synthetic miRNAs, and vice versa. ferred to employ varying conditions of hybridization to 0203. It will be understood that the term “naturally occur achieve varying degrees of selectivity of a nucleic acid ring refers to something found in an organism without any towards a target sequence. In a non-limiting example, identi intervention by a person; it could refer to a naturally-occur fication of a related target nucleic acid that does not hybridize ring wildtype or mutant molecule. In some embodiments a to a nucleic acid under Stringent conditions may be achieved synthetic miRNA molecule does not have the sequence of a by hybridization at low temperature and/or high ionic US 2009/0232893 A1 Sep. 17, 2009 strength. Such conditions are termed “low stringency” or nucleotide comprises derivatives or analogs of a naturally “low stringency conditions.” and non-limiting examples of occurring 5-carbon Sugar or phosphorus moiety. low stringency include hybridization performed at about 0.15 0213. A nucleic acid may comprise, or be composed M to about 0.9 MNaCl at a temperature range of about 20°C. entirely of a derivative or analog of a nucleobase, a nucleo to about 50° C. Of course, it is within the skill of one in the art base linker moiety and/or backbone moiety that may be to further modify the low or high Stringency conditions to present in a naturally occurring nucleic acid. RNA with Suite a particular application. nucleic acid analogs may also be labeled according to meth 0208 B. Nucleobase, Nucleoside, Nucleotide, and Modi ods of the invention. As used herein a "derivative' refers to a fied Nucleotides chemically modified or altered form of a naturally occurring molecule, while the terms “mimic' or “analog refer to a 0209. As used herein a “nucleobase' refers to a heterocy molecule that may or may not structurally resemble a natu clic base. Such as for example a naturally occurring nucleo rally occurring molecule or moiety, but possesses similar base (i.e., an A. T. G., C or U) found in at least one naturally functions. As used herein, a "moiety” generally refers to a occurring nucleic acid (i.e., DNA and RNA), and naturally or Smaller chemical or molecular component of a larger chemi non-naturally occurring derivative(s) and analogs of Such a cal or molecular structure. Nucleobase, nucleoside and nucle nucleobase. A nucleobase generally can form one or more otide analogs or derivatives are well known in the art, and hydrogen bonds (“anneal or “hybridize') with at least one have been described (see for example, Scheit, 1980, incorpo naturally occurring nucleobase in a manner that may substi rated herein by reference). tute for naturally occurring nucleobase pairing (e.g., the 0214. Additional non-limiting examples of nucleosides, hydrogen bonding between A and T. G and C, and A and U). nucleotides or nucleic acids include those in: U.S. Pat. Nos. 0210) “Purine” and/or “pyrimidine' nucleobase(s) 5,681,947, 5,652,099 and 5,763,167, 5,614,617, 5,670.663, encompass naturally occurring purine and/or pyrimidine 5,872,232, 5,859,221, 5,446,137, 5,886,165, 5,714,606, nucleobases and also derivative(s) and analog(s) thereof, 5,672,697, 5,466,786, 5,792,847, 5,223,618, 5,470,967, including but not limited to, those a purine or pyrimidine 5,378,825, 5,777,092, 5,623,070, 5,610,289, 5,602,240, Substituted by one or more of an alkyl, caboxyalkyl, amino, 5,858,988, 5,214,136, 5,700,922, 5,708,154, 5,728,525, hydroxyl, halogen (i.e., fluoro, chloro, bromo, or iodo), thiol 5,637,683, 6,251,666, 5,480,980, and 5,728,525, each of or alkylthiol moiety. Preferred alkyl (e.g., alkyl, caboxyalkyl, which is incorporated herein by reference in its entirety. etc.) moieties comprise of from about 1, about 2, about 3, 0215 Labeling methods and kits of the invention specifi about 4, about 5, to about 6 carbonatoms. Other non-limiting cally contemplate the use of nucleotides that are both modi examples of a purine or pyrimidine include a deazapurine, a fied for attachment of a label and can be incorporated into a 2,6-diaminopurine, a 5-fluorouracil, a Xanthine, a hypoxan miRNA molecule. Such nucleotides include those that can be thine, a 8-bromoguanine, a 8-chloroguanine, a bromothym labeled with a dye, including a fluorescent dye, or with a ine, a 8-aminoguanine, a 8-hydroxyguanine, a 8-methylgua molecule such as biotin. Labeled nucleotides are readily nine, a 8-thioguanine, an azaguanine, a 2-aminopurine, a available; they can be acquired commercially or they can be 5-ethylcytosine, a 5-methylcyosine, a 5-bromouracil, a synthesized by reactions known to those of skill in the art. 5-ethyluracil, a 5-iodouracil, a 5-chlorouracil, a 5-propylu 0216 Modified nucleotides for use in the invention are not racil, a thiouracil, a 2-methyladenine, a methylthioadenine, a naturally occurring nucleotides, but instead, refer to prepared N,N-diemethyladenine, anazaadenines, a 8-bromoadenine, a nucleotides that have a reactive moiety on them. Specific 8-hydroxyadenine, a 6-hydroxyaminopurine, a 6-thiopurine, reactive functionalities of interest include: amino, sulfhydryl, a 4-(6-aminohexyl/cytosine), and the like. Other examples Sulfoxyl, aminosulfhydryl, azido, epoxide, isothiocyanate, are well known to those of skill in the art. isocyanate, anhydride, monochlorotriazine, dichlorotriazine, 0211. As used herein, a “nucleoside” refers to an indi mono- or dihalogen Substituted pyridine, mono- or disubsti vidual chemical unit comprising a nucleobase covalently tuted diazine, maleimide, epoxide, aziridine, Sulfonylhalide, attached to a nucleobase linker moiety. A non-limiting acid halide, alkyl halide, aryl halide, alkylsulfonate, N-hy example of a “nucleobase linker moiety' is a Sugar compris droxysuccinimide ester, imido ester, hydrazine, azidonitro ing 5-carbon atoms (i.e., a 5-carbon Sugar), including but phenyl, azide, 3-(2-pyridyl dithio)-propionamide, glyoxal, not limited to a deoxyribose, a ribose, an arabinose, or a aldehyde, iodoacetyl, cyanomethyl ester, p-nitrophenyl ester, derivative or an analog of a 5-carbon Sugar. Non-limiting o-nitrophenyl ester, hydroxypyridine ester, carbonyl imida examples of a derivative or an analog of a 5-carbon Sugar Zole, and the other Such chemical groups. In some embodi include a 2'-fluoro-2'-deoxyribose or a carbocyclic Sugar ments, the reactive functionality may be bonded directly to a where a carbon is Substituted for an oxygen atom in the Sugar nucleotide, or it may be bonded to the nucleotide through a ring. Different types of covalent attachment(s) of a nucleo linking group. The functional moiety and any linker cannot base to a nucleobase linker moiety are known in the art substantially impair the ability of the nucleotide to be added (Kornberg and Baker, 1992). to the miRNA or to be labeled. Representative linking groups 0212. As used herein, a “nucleotide' refers to a nucleoside include carbon containing linking groups, typically ranging further comprising a “backbone moiety'. A backbone moiety from about 2 to 18, usually from about 2 to 8 carbon atoms, generally covalently attaches a nucleotide to another mol where the carbon containing linking groups may or may not ecule comprising a nucleotide, or to another nucleotide to include one or more heteroatoms, e.g. S. O. Netc., and may or form a nucleic acid. The “backbone moiety” in naturally may not include one or more sites of unsaturation. Of particu occurring nucleotides typically comprises a phosphorus moi lar interest in many embodiments are alkyl linking groups, ety, which is covalently attached to a 5-carbon Sugar. The typically lower alkyl linking groups of 1 to 16, usually 1 to 4 attachment of the backbone moiety typically occurs at either carbon atoms, where the linking groups may include one or the 3'- or 5'-position of the 5-carbon sugar. However, other more sites of unsaturation. The functionalized nucleotides (or types of attachments are known in the art, particularly when a primers) used in the above methods of functionalized target US 2009/0232893 A1 Sep. 17, 2009 69 generation may be fabricated using known protocols or pur 571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, chased from commercial vendors, e.g., Sigma, Roche, 5,574,146, 5,602.244, each of which is incorporated herein Ambion, Biosearch Technologies and NEN. Functional by reference. groups may be prepared according to ways known to those of 0222. A non-limiting example of an enzymatically pro skill in the art, including the representative information found duced nucleic acid include one produced by enzymes in in U.S. Pat. Nos. 4,404,289; 4,405,711; 4,337,063 and 5,268, amplification reactions such as PCRTM (see for example, U.S. 486, and U.K. Patent 1,529.202, which are all incorporated by Pat. Nos. 4,683.202 and 4,682,195, each incorporated herein reference. by reference), or the synthesis of an oligonucleotide described in U.S. Pat. No. 5,645,897, incorporated herein by 0217 Amine-modified nucleotides are used in several reference. See also Sambrook et al., 2001, incorporated embodiments of the invention. The amine-modified nucle herein by reference). otide is a nucleotide that has a reactive amine group for 0223 Oligonucleotide synthesis is well known to those of attachment of the label. It is contemplated that any ribonucle skill in the art. Various different mechanisms of oligonucle otide (G, A, U, or C) or deoxyribonucleotide (G, A, T, or C) otide synthesis have been disclosed in for example, U.S. Pat. can be modified for labeling. Examples include, but are not Nos. 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, limited to, the following modified ribo- and deoxyribo-nucle 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is otides: 5-(3-aminoallyl)-UTP; 8-(4-amino)butyl-amino incorporated herein by reference. ATP and 8-(6-amino)butyl-amino-ATP: N6-(4-amino)bu 0224 Recombinant methods for producing nucleic acids tyl-ATP N6-(6-amino)butyl-ATP, N4-2.2-oxy-bis in a cell are well known to those of skill in the art. These (ethylamine)-CTP; N6-(6-Amino)hexyl-ATP; 8-(6- include the use of vectors (viral and non-viral), plasmids, Amino)hexyl-amino-ATP: 5-propargylamino-CTP, cosmids, and other vehicles for delivering a nucleic acid to a 5-propargylamino-UTP; 5-(3-aminoallyl)-dUTP; 8-(4- cell, which may be the target cell (e.g., a cancer cell) or simply amino)butyl-amino-dATP and 8-(6-amino)butyl-amino a host cell (to produce large quantities of the desired RNA dATP; N6-(4-amino)butyl-dATP, N6-(6-amino)butyl-dATP, molecule). Alternatively, such vehicles can be used in the N4-2.2-oxy-bis-(ethylamine)-dCTP; N6-(6-Amino)hexyl context of a cell free system so long as the reagents for dATP; 8-(6-Amino)hexyl-amino-dATP; 5-propargy generating the RNA molecule are present. Such methods lamino-dCTP, and 5-propargylamino-dUTP. Such nucle include those described in Sambrook, 2003, Sambrook, 2001 otides can be prepared according to methods known to those and Sambrook, 1989, which are hereby incorporated by ref of skill in the art. Moreover, a person of ordinary skill in the CCC. art could prepare other nucleotide entities with the same 0225. D. Isolation of Nucleic Acids amine-modification, such as a 5-(3-aminoallyl)-CTP, GTP. 0226 Nucleic acids may be isolated using techniques well ATP, dCTP, dGTP, dTTP, ord UTP in place of a 5-(3-aminoal known to those of skill in the art, though in particular embodi lyl)-UTP. ments, methods for isolating Small nucleic acid molecules, and/or isolating RNA molecules can be employed. Chroma 0218 C. Preparation of Nucleic Acids tography is a process often used to separate or isolate nucleic 0219. A nucleic acid may be made by any technique acids from protein or from other nucleic acids. Such methods known to one of ordinary skill in the art, such as for example, can involve electrophoresis with a gel matrix, filter columns, chemical synthesis, enzymatic production, or biological pro alcohol precipitation, and/or other chromatography. If duction. It is specifically contemplated that miRNA probes of miRNA from cells is to be used or evaluated, methods gen the invention are chemically synthesized. erally involve lysing the cells with a chaotropic (e.g., guani 0220. In some embodiments of the invention, miRNAs are dinium isothiocyanate) and/or detergent (e.g., N-lauroylsar recovered or isolated from a biological sample. The miRNA cosine) prior to implementing processes for isolating may be recombinant or it may be natural or endogenous to the particular populations of RNA. cell (produced from the cell's genome). It is contemplated 0227. In particular methods for separating miRNA from that a biological sample may be treated in a way so as to other nucleic acids, a gel matrix is prepared using polyacry enhance the recovery of small RNA molecules such as lamide, though agarose can also be used. The gels may be miRNA. U.S. patent application Ser. No. 10/667,126 graded by concentration or they may be uniform. Plates or describes Such methods and it is specifically incorporated by tubing can be used to hold the gel matrix for electrophoresis. reference herein. Generally, methods involve lysing cells Usually one-dimensional electrophoresis is employed for the with a solution having guanidinium and a detergent. separation of nucleic acids. Plates are used to prepare a slab 0221 Alternatively, nucleic acid synthesis is performed gel, while the tubing (glass or rubber, typically) can be used to according to standard methods. See, for example, Itakura and preparea tube gel. The phrase “tube electrophoresis” refers to Riggs (1980) and U.S. Pat. Nos. 4,704,362, 5,221,619, and the use of a tube or tubing, instead of plates, to form the gel. 5,583,013, each of which is incorporated herein by reference. Materials for implementing tube electrophoresis can be Non-limiting examples of a synthetic nucleic acid (e.g., a readily prepared by a person of skill in the art or purchased, synthetic oligonucleotide), include a nucleic acid made by in such as from C.B.S. Scientific Co., Inc. or Scie-Plas. vitro chemically synthesis using phosphotriester, phosphite, 0228 Methods may involve the use of organic solvents or phosphoramidite chemistry and Solid phase techniques and/or alcohol to isolate nucleic acids, particularly miRNA such as described in EP 266.032, incorporated herein by used in methods and compositions of the invention. Some reference, or via deoxynucleoside H-phosphonate intermedi embodiments are described in U.S. patent application Ser. ates as described by Froehler et al., 1986 and U.S. Pat. No. No. 10/667,126, which is hereby incorporated by reference. 5,705,629, each incorporated herein by reference. Various Generally, this disclosure provides methods for efficiently different mechanisms of oligonucleotide synthesis have been isolating Small RNA molecules from cells comprising: add disclosed in for example, U.S. Pat. Nos. 4,659.774, 4,816, ing an alcohol solution to a cell lysate and applying the US 2009/0232893 A1 Sep. 17, 2009 70 alcohol/lysate mixture to a solid support before eluting the terminus of a nucleic acid. Polynucleotide phosphorylase can RNA molecules from the solid support. In some embodi polymerize nucleotide diphosphates without the need for a ments, the amount of alcohol added to a cell lysate achieves primer. an alcohol concentration of about 55% to 60%. While differ 0235 C. Labels ent alcohols can be employed, ethanol works well. A solid Support may be any structure, and it includes beads, filters, 0236 Labels on miRNA or miRNA probes may be colo and columns, which may include a mineral or polymer Sup rimetric (includes visible and UV spectrum, including fluo port with electronegative groups. A glass fiber filter or column rescent), luminescent, enzymatic, or positron emitting (in has worked particularly well for such isolation procedures. cluding radioactive). The label may be detected directly or 0229. In specific embodiments, miRNA isolation pro indirectly. Radioactive labels include ''I, P. P. and S. cesses include: a) lysing cells in the sample with a lysing Examples of enzymatic labels include alkaline phosphatase, Solution comprising guanidinium, wherein a lysate with a luciferase, horseradish peroxidase, and B-galactosidase. concentration of at least about 1 M guanidinium is produced; Labels can also be proteins with luminescent properties, e.g., b) extracting miRNA molecules from the lysate with an green fluorescent protein and phycoerythrin. extraction solution comprising phenol; c) adding to the lysate 0237. The colorimetric and fluorescent labels contem an alcohol solution for forming a lysatefalcohol mixture, plated for use as conjugates include, but are not limited to, wherein the concentration of alcohol in the mixture is Alexa Fluor dyes, BODIPY dyes, such as BODIPY FL: Cas between about 35% to about 70%; d) applying the lysate/ cade Blue; Cascade Yellow; coumarin and its derivatives, alcohol mixture to a solid support; e) eluting the miRNA Such as 7-amino-4-methylcoumarin, aminocoumarin and molecules from the Solid Support with an ionic solution; and, hydroxycoumarin; cyanine dyes, such as Cy3 and Cy5; eosins f) capturing the miRNA molecules. Typically the sample is and erythrosins; fluorescein and its derivatives, such as fluo dried and resuspended in a liquid and Volume appropriate for rescein isothiocyanate; macrocyclic chelates of lanthanide Subsequent manipulation. ions, such as Quantum DyeTM: Marina Blue: Oregon Green; rhodamine dyes, such as rhodamine red, tetramethyl VI. LABELS AND LABELING TECHNIQUES rhodamine and rhodamine 6G, Texas Red; fluorescent energy transfer dyes. Such as thiazole orange-ethidium heterodimer; 0230. In some embodiments, the present invention con and, TOTAB. cerns miRNA that are labeled. It is contemplated that miRNA may first be isolated and/or purified prior to labeling. This 0238 Specific examples of dyes include, but are not lim may achieve a reaction that more efficiently labels the ited to, those identified above and miRNA, as opposed to other RNA in a sample in which the 0239 the following: Alexa Fluor 350, Alexa Fluor 405, miRNA is not isolated or purified prior to labeling. In many Alexa Fluor 430, Alexa Fluor 488, Alexa Fluor 500. Alexa embodiments of the invention, the label is non-radioactive. Fluor 514, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor Generally, nucleic acids may be labeled by adding labeled 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 610, nucleotides (one-step process) or adding nucleotides and Alexa Fluor 633, Alexa Fluor 647, Alexa Fluor 660, Alexa labeling the added nucleotides (two-step process). Fluor 680, Alexa Fluor 700, and, Alexa Fluor 750; amine 0231 B. Labeling Techniques reactive BODIPY dyes, such as BODIPY 493/503, BODIPY 0232. In some embodiments, nucleic acids are labeled by 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY catalytically adding to the nucleic acid an already labeled 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY nucleotide or nucleotides. One or more labeled nucleotides 650/655, BODIPY FL, BODIPY R6G, BODIPY TMR, and, can be added to miRNA molecules. See U.S. Pat. No. 6,723, BODIPY-TR: Cy3, Cy5, 6-FAM, Fluorescein Isothiocyanate, 509, which is hereby incorporated by reference. HEX, 6-JOE, Oregon Green 488, Oregon Green 500, Oregon 0233. In other embodiments, an unlabeled nucleotide or Green 514, Pacific Blue, REG, Rhodamine Green, nucleotides is catalytically added to a miRNA, and the unla Rhodamine Red, Renographin, ROX, SYPRO, TAMRA, beled nucleotide is modified with a chemical moiety that 2',4',5'7"-Tetrabromosulfonefluorescein, and TET. enables it to be subsequently labeled. In embodiments of the 0240 Specific examples of fluorescently labeled ribo invention, the chemical moiety is a reactive amine Such that nucleotides are available from Molecular Probes, and these the nucleotide is an amine-modified nucleotide. Examples of include, Alexa Fluor 488-5-UTP. Fluorescein-12-UTP, amine-modified nucleotides are well known to those of skill BODIPY FL-14-UTP, BODIPYTMR-14-UTP. Tetramethyl in the art, many being commercially available Such as from rhodamine-6-UTP, Alexa Fluor 546-14-UTP, Texas Red-5- Ambion, Sigma, Jena BioScience, and TriLink. UTP and BODIPY TR-14-UTP. Other fluorescentribonucle 0234. In contrast to labeling of cDNA during its synthesis, otides are available from Amersham Biosciences, such as the issue for labeling miRNA is how to label the already Cy3-UTP and Cy5-UTP. existing molecule. The present invention concerns the use of 0241 Examples of fluorescently labeled deoxyribonucle an enzyme capable of using a di- or tri-phosphate ribonucle otides include Dinitrophenyl (DNP)-1-dUTP, Cascade Blue otide or deoxyribonucleotide as a substrate for its addition to 7-dUTP, Alexa Fluor 488-5-dUTP, Fluorescein-12-dUTP, a miRNA. Moreover, in specific embodiments, it involves Oregon Green 488-5-dUTP BODIPY FL-14-dUTP, using a modified di- or tri-phosphate ribonucleotide, which is Rhodamine Green-5-dUTP, Alexa Fluor 532-5-dUTP, added to the 3' end of a miRNA. Enzymes capable of adding BODIPY TMR-14-dUTP. Tetramethylrhodamine-6-dUTP. Such nucleotides include, but are not limited to, poly(A)poly Alexa Fluor 546-14-dUTP, Alexa Fluor 568-5-dUTP, Texas merase, terminal transferase, and polynucleotide phosphory Red-12-dUTP, Texas Red-5-dUTP BODIPY TR-14-dUTP, lase. In specific embodiments of the invention, a ligase is Alexa Fluor 594-5-dUTP BODIPY 630/650-14-dUTP, contemplated as not being the enzyme used to add the label, BODIPY 650/665-14-dUTP; Alexa Fluor 488-7-OBEA and instead, a non-ligase enzyme is employed. Terminal dCTP, Alexa Fluor 546-16-OBEA-dCTP, Alexa Fluor 594-7- transferase catalyzes the addition of nucleotides to the 3' OBEA-dCTP, Alexa Fluor 647-12-OBEA-dCTP. US 2009/0232893 A1 Sep. 17, 2009

0242. It is contemplated that nucleic acids may be labeled otides (G. A. T. C., and/or U); (3) a modified nucleotide with two different labels. Furthermore, fluorescence reso (labeled or unlabeled); (4) poly(A) polymerase buffer; and, nance energy transfer (FRET) may be employed in methods (5) at least one microfilter; (6) label that can be attached to a of the invention (e.g., Klostermeier et al., 2002; Emptage, nucleotide; (7) at least one miRNA probe; (8) reaction buffer; 2001; Didenko, 2001, each incorporated by reference). (9) a miRNA array or components for making such an array; 0243 Alternatively, the label may not be detectable perse, (10) acetic acid; (11) alcohol; (12) Solutions for preparing, but indirectly detectable or allowing for the isolation or sepa isolating, enriching, and purifying miRNAS or miRNA ration of the targeted nucleic acid. For example, the label probes or arrays. Other reagents include those generally used could be biotin, digoxigenin, polyvalent cations, chelator groups and the other ligands, include ligands for an antibody. for manipulating RNA, such as formamide, loading dye, ribo 0244 D. Visualization Techniques nuclease inhibitors, and DNase. 0245. A number of techniques for visualizing or detecting 0249. In specific embodiments, kits of the invention labeled nucleic acids are readily available. Such techniques include an array containing miRNA probes, as described in include, microscopy, arrays, Fluorometry, Light cyclers or the application. An array may have probes corresponding to other real time PCR machines, FACS analysis, scintillation all known miRNAS of an organism or a particular tissue or counters, Phosphoimagers, Geiger counters, MRI. CAT, anti organ in particular conditions, or to a Subset of Such probes. body-based detection methods (Westerns, immunofluores The subset of probes on arrays of the invention may be or cence, immunohistochemistry), histochemical techniques, include those identified as relevant to a particular diagnostic, HPLC (Griffey et al., 1997), spectroscopy, capillary gel elec therapeutic, or prognostic application. For example, the array trophoresis (Cummins et al., 1996), spectroscopy; mass spec may contain one or more probes that is indicative or Sugges troscopy; radiological techniques; and mass balance tech tive of (1) a disease or condition (acute myeloid leukemia), niques. (2) Susceptibility or resistance to a particular drug or treat 0246 When two or more differentially colored labels are ment; (3) Susceptibility to toxicity from a drug or Substance; employed, fluorescent resonance energy transfer (FRET) (4) the stage of development or severity of a disease or con techniques may be employed to characterize association of dition (prognosis); and (5) genetic predisposition to a disease one or more nucleic acid. Furthermore, a person of ordinary skill in the art is well aware of ways of visualizing, identify or condition. ing, and characterizing labeled nucleic acids, and accord 0250 For any kit embodiment, including an array, there ingly, such protocols may be used as part of the invention. can be nucleic acid molecules that contain or can be used to Examples of tools that may be used also include fluorescent amplify a sequence that is a variant of identical to or comple microscopy, a BioAnalyzer, a plate reader, Storm (Molecular mentary to all or part of any of SEQIDs described herein. In Dynamics), Array Scanner, FACS (fluorescent activated cell certain embodiments, a kit or array of the invention can con Sorter), or any instrument that has the ability to excite and tain one or more probes for the miRNAs identified by the SEQ detect a fluorescent molecule. IDs described herein. Any nucleic acid discussed above may be implemented as part of a kit. VII. KITS 0251. The components of the kits may be packaged either 0247 Any of the compositions described herein may be in aqueous media or in lyophilized form. The container means comprised in a kit. In a non-limiting example, reagents for of the kits will generally include at least one vial, test tube, isolating miRNA, labeling miRNA, and/or evaluating a flask, bottle, Syringe or other container means, into which a miRNA population using an array, nucleic acid amplification, component may be placed, and preferably, Suitably aliquoted. and/or hybridization can be included in a kit, as well reagents Where there is more than one component in the kit (labeling for preparation of samples from blood samples. The kit may reagent and label may be packaged together), the kit also will further include reagents for creating or synthesizing miRNA generally contain a second, third or other additional container probes. The kits will thus comprise, in suitable container into which the additional components may be separately means, an enzyme for labeling the miRNA by incorporating placed. However, various combinations of components may labeled nucleotide or unlabeled nucleotides that are subse be comprised in a vial. The kits of the present invention also quently labeled. In certain aspects, the kit can include ampli will typically include a means for containing the nucleic fication reagents. In other aspects, the kit may include various acids, and any other reagent containers in close confinement Supports, such as glass, nylon, polymeric beads, and the like, for commercial sale. Such containers may include injection or and/or reagents for coupling any probes and/or target nucleic blow molded plastic containers into which the desired vials acids. It may also include one or more buffers, such as reac are retained. tion buffer, labeling buffer, washing buffer, or a hybridization 0252. When the components of the kit are provided in one buffer, compounds for preparing the miRNA probes, and and/or more liquid Solutions, the liquid Solution is an aqueous components for isolating miRNA. Other kits of the invention Solution, with a sterile aqueous solution being particularly may include components for making a nucleic acid array preferred. comprising miRNA, and thus, may include, for example, a 0253) However, the components of the kit may be pro Solid Support. vided as dried powder(s). When reagents and/or components 0248 Kits for implementing methods of the invention are provided as a dry powder, the powder can be reconstituted described herein are specifically contemplated. In some by the addition of a suitable solvent. It is envisioned that the embodiments, there are kits for preparing miRNA for multi Solvent may also be provided in another container means. In labeling and kits for preparing miRNA probes and/or miRNA Some embodiments, labeling dyes are provided as a dried arrays. In these embodiments, kit comprise, in Suitable con power. It is contemplated that 10, 20, 30, 40, 50, 60, 70, 80, tainer means, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more of the 90, 100, 120, 120, 130, 140, 150, 160, 170, 180, 190, 200, following: (1) poly(A) polymerase; (2) unmodified nucle 300, 400, 500, 600, 700, 800, 900, 1000 ug or at least or at US 2009/0232893 A1 Sep. 17, 2009 72 most those amounts of dried dye are provided in kits of the and 72 h post transfection. Total RNA was extracted using invention. The dye may then be resuspended in any Suitable RNAqueous-4PCR (Ambion) according to the manufactur solvent, such as DMSO. er's recommended protocol. 0254. Such kits may also include components that facili 0261 mRNA array analyses were performed by Asuragen tate isolation of the labeled miRNA. It may also include components that preserve or maintain the miRNA or that Services (Austin,Tex.), according to the company's standard protect against its degradation. Such components may be operating procedures. Using the MessageAmpTMII-96 aRNA RNAse-free or protect against RNAses. Such kits generally Amplification Kit (Ambion, cat #1819) 2 ug of total RNA will comprise, in Suitable means, distinct containers for each were used for target preparation and labeling with biotin. individual reagent or solution. cRNA yields were quantified using an Agilent Bioanalyzer 0255. A kit will also include instructions for employing 2100 capillary electrophoresis protocol. Labeled target was the kit components as well the use of any other reagent not hybridized to Affymetrix mRNA arrays (Human HG-U133A included in the kit. Instructions may include variations that 2.0 arrays) using the manufacturer's recommendations and can be implemented. the following parameters. Hybridizations were carried out at 0256 Kits of the invention may also include one or more 45° C. for 16 hr in an Affymetrix Model 640 hybridization of the following: Control RNA; nuclease-free water; RNase oven. Arrays were washed and stained on an Affymetrix free containers, such as 1.5 ml tubes; RNase-free elution FS450 Fluidics station, running the wash script Midi tubes; PEG or dextran; ethanol; acetic acid; sodium acetate; euk2v3 450. The arrays were scanned on a Affymetrix ammonium acetate; guanidinium; detergent; nucleic acid size GeneChip Scanner 3000. Summaries of the image signal marker; RNase-free tube tips; and RNase or DNase inhibi data, group mean values, p-values with significance flags, log tOrS. ratios and gene annotations for every gene on the array were 0257. It is contemplated that such reagents are embodi generated using the Affymetrix Statistical Algorithm MAS ments of kits of the invention. Such kits, however, are not 5.0 (GCOS v 1.3). Data were reported in a file (cabinet) con limited to the particular items identified above and may taining the Affymetrix data and result files and in files (cel) include any reagent used for the manipulation or character containing the primary image and processed cell intensities of ization of miRNA. the arrays. Data were normalized for the effect observed by the average of two negative control microRNA sequences and VIII. EXAMPLES then were averaged together for presentation. A list of genes 0258. The following examples are included to demon whose expression levels varied by at least 0.7 log from the strate preferred embodiments of the invention. It should be average negative control was assembled. Results of the appreciated by those of skill in the art that the techniques microarray gene expression analysis are shown in Table 1 disclosed in the examples which follow represent techniques above. discovered by the inventor to function well in the practice of 0262 Manipulation of the expression levels of the genes the invention, and thus can be considered to constitute pre ferred modes for its practice. However, those of skill in the art listed in Table 1 represents a potentially useful therapy for should, in light of the present disclosure, appreciate that many cancer and other diseases in which increased or reduced changes can be made in the specific embodiments which are expression of hsa-miR-143 has a role in the disease. disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention. Example 2 Example 1 Cellular Pathways Affected by HSA-miR-143 Gene Expression Analysis Following Transfection with HSA-miR-143 0263. The mis-regulation of gene expression by hsa-miR 143 (Table 1) affects many cellular pathways that represent 0259 miRNAs are believed to regulate gene expression by potential therapeutic targets for the control of cancer and binding to target mRNA transcripts and (1) initiating tran other diseases and disorders. The inventors determined the Script degradation or (2) altering protein translation from the identity and nature of the cellular genetic pathways affected transcript. Translational regulation leading to an up or down by the regulatory cascade induced by hsa-miR-143 expres change in protein expression may lead to changes in activity Sion. Cellular pathway analyses were performed using Inge and expression of downstream gene products and genes that are in turn regulated by those proteins. These numerous regu nuity Pathways Analysis (Version 4.0, Ingenuity(R) Systems, latory effects may be revealed as changes in the global mRNA Redwood City, Calif.). Alteration of a given pathway was expression profile. Microarray gene expression analyses were determined by Fisher's Exact test (Fisher, 1922). The most performed to identify genes that are mis-regulated by hsa significantly affected pathways following over-expression of miR-143 expression. hsa-miR-143 in A549 cells are shown in Table 2. 0260 Synthetic Pre-miR-143 (Ambion) or two negative 0264. These data demonstrate that hsa-miR-143 directly control miRNAs (pre-miR-NC1, Ambion cat. no. AM17110 or indirectly affects the expression of several, cellular prolif and pre-miR-NC2, Ambion, cat. no. AM17111) were reverse eration-, development-, and cell growth-related genes and transfected into quadruplicate samples of A549 cells for each thus primarily affects functional pathways related to cellular of three time points. Cells were transfected using siPORT growth, cellular development, and cell proliferation. Those NeoFX (Ambion) according to the manufacturer's recom cellular processes have integral roles in the development and mendations using the following parameters: 200,000 cells per progression of various cancers. Manipulation of the expres well in a 6 well plate, 5.0 ul of NeoFX, 30 nM final concen sion levels of genes in the cellular pathways shown in Table 2 tration of miRNA in 2.5 ml. Cells were harvested at 4h, 24h, represents a potentially useful therapy for cancer and other US 2009/0232893 A1 Sep. 17, 2009

diseases in which increased or reduced expression of hsa McGowan and Russell, 1993). Lack of Weel expression in miR-143 has a role in the disease. lung cancer is correlated with a higher proliferation index, a higher relapse rate and poor prognosis (Yoshida et al., 2004). Example 3 Anotherhsa-miR-143 target is LMO-4 (LIM domain only 4), a Zinc fingerprotein regulating transcription. LMO-4 is inher Predicted Gene Targets of HSA-miR-143 ently oncogenic and inactivates the BRCA-1 tumor Suppres 0265 Gene targets for binding of and regulation by hsa sor protein (breast cancer 1) (Sum et al., 2002; Sum et al., miR-143 were predicted using the proprietary algorithm 2005). LMO-4 is frequently overexpressed in multiple cancer miRNATargetTM (Asuragen), which is an implementation of types and predicts poor outcome in breast cancer (Visvader et the method proposed by Krek et al. (2005). Predicted target al., 2001; Mizunuma et al., 2003; Sum et al., 2005; Taniwaki genes are shown in Table 3. et al., 2006). Accordingly, RNAi directed against LMO-4 0266 The predicted gene targets that exhibited altered leads to reduced breast cancer cell growth and migration mRNA expression levels in human cancer cells, following (Sum et al., 2005). Our data indicate that hsa-miR-143 dimin transfection with pre-miRhsa-miR-143, are shown in Table ishes LMO-4 transcripts and therefore may intercept with the 4. oncogenic properties of LMO-4. 0267. The predicted gene targets of hsa-miR-143 whose 0270. Hsa-miR-143 also governs the expression of mRNA expression levels are affected by hsa-miR-143 repre PDCD4, BCL2L1 and MCL1, all of which are functionally sent particularly useful candidates for cancer therapy and linked to the apoptotic pathway. Pdcd-4 (programmed cell therapy of other diseases through manipulation of their death 4) is a tumor Suppressor that is induced in response to expression levels. apoptosis in normal cells. The growth inhibitory properties of Pdcd-4 are due to Pdcd-4 mediated inhibition of the c-Jun Example 4 proto-oncoprotein, inhibition of cap-dependent mRNA trans lation and activation of the p21 Waf1/Cip1 CDK inhibitor Cancer Related Gene Expression Altered by HSA (Yang et al., 2003; Bitomsky et al., 2004: Goke et al., 2004). miR-143 Pdcd-4 frequently shows reduced or lost expression in vari 0268 Cell proliferation, survival, and growth pathways ous human malignancies, such as gliomas, hepatocellular are commonly altered in tumors (Hanahan and Weinberg, carcinomas, lung and renal cell carcinomas (Jansen et al., 2000). The inventors have shown that hsa-miR-143 directly 2004; Zhang et al., 2006; Gao et al., 2007). Expression of or indirectly regulates the transcripts of proteins that are Pdcd-4 interferes with skin carcinogenesis in a mouse model critical in the regulation of these pathways. Many of these and Suppresses growth of human colon carcinoma cells (Jan targets have inherent oncogenic or tumor Suppressor activity. sen et al., 2005; Yang et al., 2006). Loss of Pdcd-4 also Hsa-miR-143 targets that have prognostic and/or therapeutic correlates with lung tumor progression (Chen et al., 2003). value for the treatment of various malignancies are shown in Since hsa-miR-143 positively regulates Pdcd-4 expression, a Table 5. hsa-miR-143 based therapy may reconstitute Pdcd-4 func 0269. Hsa-miR-143 targeted cancer genes are regulators tion. BCL2L1 and MCL1 are members of the anti-apoptotic of the cell cycle, transcription, intracellular signaling, apop BCL-2 (B cell lymphoma 2) gene family that give rise to two tosis and the thioredoxin redox pathway. Hsa-miR-143 regu alternatively spliced gene products with opposing functions lates cell cycle progression by altering the expression of (Boise et al., 1993; Bae et al., 2000). The predominantly Weel, the retinoblastoma-like 1 protein (RBL1) as well as the expressed protein encoded by BCL2L1 is Bcl-XL which— cyclins D1 and G1. RBL1, also known as p107, is a member next to BCL-2 is a major inhibitor of programmed cell of the retinoblastoma tumor Suppressor protein family that death. Overexpression of Bcl-XL is detected in numerous includes the pocket proteins p107, p130 and pRb. Similar to cancer types and correlates with tumor progression as well as the pRb prototype, RBL1 interacts with the E2F family of poor survival (Manion and Hockenbery, 2003). Increased transcription factors and blocks cell cycle progression and levels of Bcl-XL are also associated with resistance to chemo DNA replication (Sherr and McCormick, 2002). A subset of and radiotherapy (Fesik, 2005). Transient transfection of hsa cancers show deregulated expression of RBL 1 (Takimoto et miR-143 leads to a reduction of Bcl-XL transcripts and there al., 1998; Claudio et al., 2002; Wu et al., 2002: Ito et al., fore might provide a therapeutic benefit to oncogenic cells 2003). Transient transfection of hsa-miR-143 leads to a with increased expression of Bcl-XL. Mcl-1 (myeloid leuke decrease in RBL1 mRNA levels which may suggest a prolif mia 1) is overexpressed in hepatocellular carcinoma, prostate erative function for hsa-miR-143. In contrast, negative regu cancer, testicular tumor, multiple myeloma and various leu lation of cyclin D1 and positive regulation of cyclin G1 are kemias see refs in Table 5. Similar to Bcl-XL, high levels of indicators of a growth-inhibitory role for hsa-miR-143. Mcl-1 is correlated with poor prognosis of patients with ova Cyclins are co-factors of cyclin-dependent kinases (CDKs) rian carcinoma and is indicative for leukemic relapse (Kauf and function in the progression of the cell cycle. Cyclin D1 is mann et al., 1998; Shigemasa et al., 2002). RNA interference required for the transition from G1 into S phase and is over against Mcl-1 induces a therapeutic response in gastric and expressed in numerous cancer types (Donnellan and Chetty, hepatocellular carcinoma cells (Schulze-Bergkamen et al., 1998). (Donnellan and Chetty, 1998). Hsa-miR-143 nega 2006; Zangemeister-Wittke and Huwiler, 2006). tively regulates cyclin D1 expression and therefore might 0271 Molecules regulated by hsa-miR-143 that function interfere with abnormal cell growth that depends on high in intracellular signal transduction include the inflammatory levels of cyclin D1. In accordance, cyclin G1 has growth interleukin 8 (IL-8), transforming growth factor beta (TGF-B) inhibitory activity and is upregulated by hsa-miR-143 (Zhao receptor 2 (TGFBR2) and A-kinase anchor protein 12 et al., 2003). Weel is a tyrosine kinase that functions as a (AKAP12). IL-8 is frequently upregulated in various cancers mitotic inhibitor by phosphorylating the CDK1(cdc2)/cy and correlates with tumor vascularization, metastasis and clinB1 complex (Parker and Piwnica-Worms, 1992: poor prognosis (Rosenkilde and Schwartz, 2004; Sparmann US 2009/0232893 A1 Sep. 17, 2009 74 and Bar-Sagi, 2004). TGFBR-2 forms a functional complex USA; cat. no. 356237) in a 1:1 ratio and injected subcutane with TGFBR-1 and is the primary receptor for TGF-B (Mas ously into the flank of female NOD/SCID mice (Charles sague et al., 2000). Central role of TGF-B is inhibition of River Laboratories, Inc.; Wilmington, Mass., USA). As a cellular growth of numerous cell types, such as epithelial, negative control, A549 cells were electroporated with nega endothelial, hematopoietic neural and mesenchymal cells. tive control miRNA (NC: Pre-miRTM microRNA Precursor Many mammary and colorectal carcinomas with microsatel Molecule-Negative Control #2: Ambion cat. no. AM17111) lite instability harbor inactivating mutations of TGFBR-2, as described above. To assess the anti-oncogenic activity of and therefore escape the growth-inhibitory function of TGF-B miR-143, a group of five animals was injected with A549 (Markowitz et al., 1995; Lucke et al., 2001). AKAP12, also cells. NC-treated cells were injected into the opposite flank of referred to as gravin or SSeCKS (Src suppressed C kinase the same animal to control for animal-to-animal variability. Substrate), functions as a kinase scaffold protein that tethers Once tumors reached a measurable size (9 days post injec the enzyme-substrate interaction (Nauertet al., 1997). Expres tion), the length and width of tumors were determined every sion of AKAP12 interferes with oncogenic cell transforma day until day 13 after Xenograft implantation. Tumor Volumes tion induced by the Src or Jun. oncoproteins invitro and is lost were calculated using the formula, Volume=(length X width or reduced in numerous cancers, such as leukemia and carci X width)/2, in which the length is greater than the width. nomas of the rectum, lung and stomach (Lin and Gelman, Tumor volumes derived from NC-treated cells and miR-143 1997; Cohen et al., 2001; Xia et al., 2001: Wikman et al., treated cells were averaged and plotted over time (FIG. 1). 2002; Boultwood et al., 2004; Choi et al., 2004; Mori et al., Data points with p values less than 0.05 are indicated in the 2006). An apparent anti-oncogenic activity of AKAP12 in graph. prostate and gastric cancers marks this protein as a putative 0275 Administration of miR-143 into the A549 lung can tumor suppressor (Xia et al., 2001; Choi et al., 2004). cer cells inhibited tumor growth in vivo (FIG. 1). Cancer cells 0272 Based on the functions for most of these targets and that received negative control miRNA developed more rap how they are regulated by hsa-miR-143, hsa-miR-143 idly than cells treated with hsa-miR-143. These data suggest appears to have tumor Suppressor potential. This view is that hsa-miR-143 represents a particularly useful candidate in Supported by our observation that most cancers show reduced the treatment of lung cancer and potentially other diseases. expression of miR-143. However, hsa-miR-143 also regu lates gene expression in a manner that suggests a role for REFERENCES hsa-miR-143 in the development or progression of disease. 0276. 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SEQUENCE LISTING

<16 Oc NUMBER OF SEO ID NOS : 13

<210 SEQ ID NO 1 <211 LENGTH: 22 &212> TYPE RNA <213> ORGANISM: Homo sapiens

<4 OO SEQUENCE: 1

ugagalugaag cacuguagcu. Ca 22

<210 SEQ ID NO 2 <211 LENGTH: 106 &212> TYPE RNA <213> ORGANISM: Homo sapiens <4 OO SEQUENCE: 2

gcgcagcgcc clugucuccca gC Cugagglug cagugclugca lucucuggluca gulugggaguc 60

ugagalugaag cacuguagcu. Caggalagaga galaguuguuc lugcagc 106

<210 SEQ ID NO 3 <211 LENGTH: 83 &212> TYPE RNA <213> ORGANISM: Homo sapiens

<4 OO SEQUENCE: 3

lugu Cucccag cc caaggugc agugclugcau cucugglucag uugugaglucu gagalugaagc 60

aculgulag Cuc gigaaggggg aall 83

US 2009/0232893 A1 Sep. 17, 2009 79

- Continued <213> ORGANISM: Homo sapiens <4 OO SEQUENCE: 10 gcgcagcgcc clugu Cuccca gcclugagglug Caglugclugca ulcucuggluca guugggaguc 6 O ulgagaugaag cacuguagcu. Caggaagaga gaaguuguuc lugcagc 106

<210 SEQ ID NO 11 <211 LENGTH: 106 &212> TYPE : RNA <213> ORGANISM: Homo sapiens <4 OO SEQUENCE: 11 gcgcagcgcc clugu Cuccca gcclugagglug Caglugclugca ulcucuggluca guugggaguc 6 O ulgagaugaag cacuguagcu. Caggaagaga gaaguuuuuc lugcagc 106

<210 SEQ ID NO 12 <211 LENGTH: 63 &212> TYPE : RNA <213> ORGANISM: Homo sapiens <4 OO SEQUENCE: 12 cc.cgagglugc agugclugcau cucugglucag lulugugaglucu gagaugaagc acuguagculc 6 O

999 63

<210 SEQ ID NO 13 <211 LENGTH: 63 &212> TYPE : RNA <213> ORGANISM: Homo sapiens

<4 OO SEQUENCE: 13 cCugagglugc agugclugcau cucugglucag lulugggaglucu gagaugaagc acuguagculc 6 O agg 63

1. A method of modulating gene expression in a cell com the head and neck, Small cell lung carcinoma, thyroid carci prising administering to the cell an amount of an isolated noma, or testicular tumor, wherein the modulation of one or nucleic acid comprising a miR-143 nucleic acid sequence in more gene is Sufficient for a therapeutic response. an amount Sufficient to modulate the expression of one or 5. The method of claim 4, wherein the cancerous condition more genes identified in Table 1, 3, 4, or 5. is lung carcinoma. 2. The method of claim 1, wherein the cell is in a subject 6. The method of claim 5, wherein lung carcinoma is having, Suspected of having, or at risk of developing a meta adenocarcinoma, squamous cell carcinoma, large cell carci bolic, an immunologic, an infectious, a cardiovascular, a noma or bronchioalveolar carcinoma. digestive, an endocrine, an ocular, a genitourinary, a blood, a 7. The method of claim 1, wherein the expression of a gene musculoskeletal, a nervous system, a congenital, a respira is up-regulated. tory, a skin, or a cancerous disease or condition. 8. The method of claim 1, wherein the expression of a gene 3. (canceled) is down-regulated. 4. The method of claim 2, wherein the cancerous condition 9. The method of claim 1, wherein the cell is an endothelial, is astrocytoma, anaplastic large cell lymphoma, acute lym a mesothelial, an epithelial, a stromal, or a mucosal cell. phoblastic leukemia, acute myelogenous leukemia, breast 10. The method of claim 1, wherein the cell is a brain, a carcinoma, B-cell lymphoma, bladder carcinoma, cervical neuronal, a blood, an esophageal, a lung, a cardiovascular, a carcinoma, chronic lymphoblastic leukemia, colorectal car liver, a breast, a bone, a thyroid, a glandular, an adrenal, a cinoma, endometrial carcinoma, glioma, glioblastoma, gas pancreatic, a stomach, an intestinal, a kidney, a bladder, a tric carcinoma, hepatocellular carcinoma, Hodgkin lym prostate, a cervical, a uterine, an ovarian, a testicular, a phoma, leukemia, lung carcinoma, melanoma, splenic, a skin, a Smooth muscle, a cardiac muscle, or a medulloblastoma, mantle cell lymphoma, multiple myeloma, striated muscle cell. myeloma, non-Hodgkin lymphoma, non-Small cell lung car 11. The method of claim 1, wherein the cell is a cancer cell. cinoma, ovarian carcinoma, oligodendroglioma, oesophageal 12. The method of claim 11, wherein the cancer cell is a carcinoma, osteosarcoma, pancreatic carcinoma, prostate neuronal, glial, lung, liver, brain, breast, bladder, blood, leu carcinoma, renal cell carcinoma, squamous cell carcinoma of kemic, colon, endometrial, stomach, skin, ovarian, fat, bone, US 2009/0232893 A1 Sep. 17, 2009 cervical, esophageal, pancreatic, prostate, kidney, testicular, 45. A method of treating a patient diagnosed with or Sus intestinal, lymphoid, colorectal, or thyroid cell. pected of having or Suspected of developing a pathological condition or disease related to a gene modulated by a miRNA 13. The method of claim 1, wherein the isolated miR-143 comprising the steps of nucleic acid is a recombinant nucleic acid. (a) administering to the patient an amount of an isolated 14-18. (canceled) nucleic acid comprising a miR-143 nucleic acid 19. The method of claim 1, wherein the miR-143 nucleic sequence in an amount Sufficient to modulate a cellular acid is a synthetic nucleic acid. pathway or a physiologic pathway; and 20. (canceled) (b) administering a second therapy, wherein the modula 21. The method of claim 1, wherein the miR-143 is a tion of the cellular pathway or physiologic pathway hsa-miR-143. sensitizes the patient to the second therapy. 46. (canceled) 22-24. (canceled) 47. A method of selecting a miRNA to be administered to 25. The method of claim 1, wherein the nucleic acid is a Subject with, Suspected of having, or having a propensity for comprised in a pharmaceutical formulation. developing a pathological condition or disease comprising: 26. The method of claim 25, wherein the pharmaceutical (a) determining an expression profile of one or more genes formulation is a lipid composition. selected from Table 1, 3, 4, or 5: 27. The method of claim 25 wherein the pharmaceutical (b) assessing the sensitivity of the subject to miRNA formulation is a nanoparticle composition. therapy based on the expression profile; and (c) selecting one or more miRNA based on the assessed 28. The method of claim 25 wherein the pharmaceutical sensitivity. formulation consists of biocompatible and biodegradable molecules. 48-52. (canceled) 29-44. (canceled)