US 20090227533A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0227533 A1 Bader et al. (43) Pub. Date: Sep. 10, 2009

(54) MIR-34 REGULATED AND Related U.S. Application Data PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION (60) Provisional application No. 60/942.971, filed on Jun. 8, 2007. (76) Inventors: Andreas G. Bader, Austin, TX Publication Classification (US); Lubna Patrawala, Austin, TX (US); Jason F. Wiggins, Austin, (51) Int. Cl. TX (US); Mike W. Byrom, Austin, A 6LX 3L/705 (2006.01) TX (US); Charles D. Johnson, CI2N 5/06 (2006.01) Austin, TX (US); David Brown, GOIN 33/50 (2006.01) Austin, TX (US) CI2O I/68 (2006.01) A6IP35/00 (2006.01) Correspondence Address: (52) U.S. Cl...... 514/44; 435/375; 436/94; 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.: 12/134,932 34, using miR-34 to modulate a or gene pathway, using this profile in assessing the condition of a patient and/or (22) Filed: Jun. 6, 2008 treating the patient with an appropriate miRNA.

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MR-34 REGULATED GENES AND cells (22Rv1), lung cancer cells (A549), basal cell carcinoma PATHWAYS AS TARGETS FOR cells (TE354T), cervical cancer cells (HeLa), and leukemic T THERAPEUTIC INTERVENTION cells (Jurkat), but miR-34a had no anti-proliferative effect on normal human T cells. Upon transformation, miR-34a increased (Jurkat) or decreased (HeLa) programmed cell 0001. This application claims priority to U.S. Provisional death (apoptosis) in cells. Uncontrolled cell proliferation is a Application Ser. No. 60/942,971 filed Jun. 8, 2007, which is hallmark of cancer. Apoptosis is a natural cellular process that incorporated herein by reference in its entirety. helps control cancer by inducing death in cells with onco genic potential. Many oncogenes function by altering induc BACKGROUND OF THE INVENTION tion of apoptosis. More recently, others have observed miR 0002 I. Field of the Invention 34a to be over-expressed in cancerous liver cells (Meng et al., 0003. The present invention relates to the fields of molecu 2006). lar biology and medicine. More specifically, the invention 0009 Bioinformatics analyses suggest that any given relates to methods and compositions for the treatment of miRNA may bind to and alter the expression of up to several diseases or conditions that are affected by miR-34 microR hundred different genes. In addition, a single gene may be NAS, microRNA expression, and genes and cellular pathways regulated by several miRNAs. Thus, each miRNA may regu directly and indirectly modulated by such. late a complex interaction among genes, gene pathways, and 0004 II. Background gene networks. Mis-regulation or alteration of these regula 0005. In 2001, several groups used a cloning method to tory pathways and networks, involving miRNAS, are likely to isolate and identify a large group of “microRNAs (miRNAs) contribute to the development of disorders and diseases such from C. elegans, Drosophila, and humans (Lagos-Quintana et as cancer. Although bioinformatics tools are helpful in pre al., 2001; Lau et al., 2001; Lee and Ambros, 2001). Several dicting miRNA binding targets, all have limitations. Because hundreds of miRNAs have been identified in plants and ani of the imperfect complementarity with their target binding mals—including humans—which do not appear to have sites, it is difficult to accurately predict the mRNA targets of endogenous siRNAs. Thus, while similar to siRNAs, miR miRNAs with bioinformatics tools alone. Furthermore, the NAS are distinct. complicated interactive regulatory networks among miRNAS 0006 miRNAs thus far observed have been approximately and target genes make it difficult to accurately predict which 21-22 nucleotides in length, and they arise from longer pre genes will actually be mis-regulated in response to a given cursors, which are transcribed from non--encoding miRNA. genes. See review of Carrington and Ambros (2003). The 0010 Correcting errors by manipulating precursors form structures that fold back on themselves in miRNA expression or by repairing miRNA mis-regulation self-complementary regions; they are then processed by the represent promising methods to repair genetic disorders and nuclease Dicer (in animals) or DCL1 (in plants) to generate cure diseases like cancer. A current, disabling limitation of the short double-stranded miRNA. One of the miRNA strands this approach is that, as mentioned above, the details of the is incorporated into a complex of and miRNA called regulatory pathways and networks that are affected by any the RNA-induced silencing complex. The miRNA guides the given miRNA, including miR-34, remain largely unknown. RISC complex to a target mRNA, which is then cleaved or This represents a significant limitation for treatment of can translationally silenced, depending on the degree of sequence cers in which miR-34 may play a role. A need exists to complementarity of the miRNA to its target mRNA. Cur identify the genes, genetic pathways, and genetic networks rently, it is believed that perfect or nearly perfect complemen that are regulated by or that may regulate hsa-miR-34 expres tarity leads to mRNA degradation, as is most commonly S1O. observed in plants. In contrast, imperfect base pairing, as is primarily found in animals, leads to translational silencing. SUMMARY OF THE INVENTION However, recent data Suggest additional complexity (Bagga 0011. The present invention provides additional composi et al., 2005; Lim et al., 2005), and mechanisms of gene tions and methods by identifying genes that are direct targets silencing by miRNAS remain under intense study. for miR-34 regulation or that are indirect or downstream 0007 Recent studies have shown that changes in the targets of regulation following the miR-34-mediated modifi expression levels of numerous miRNAs are associated with cation of another gene(s) expression. Furthermore, the inven various cancers (reviewed in Esquela-Kerscher and Slack, tion describes gene, disease, and/or physiologic pathways 2006; Calin and Croce, 2006). miRNAs have also been impli and networks that are influenced by miR-34 and its family cated in regulating cell growth and cell and tissue differen members. In certain aspects, compositions of the invention tiation—cellular processes that are associated with the devel are administered to a Subject having, Suspected of having, or opment of cancer. at risk of developing a metabolic, an immunologic, an infec 0008. The inventors previously demonstrated that hsa tious, a cardiovascular, a digestive, an endocrine, an ocular, a miR-34 is involved with the regulation of numerous cell genitourinary, a blood, a musculoskeletal, a nervous system, activities that represent intervention points for cancer therapy a congenital, a respiratory, a skin, or a cancerous disease or and for therapy of other diseases and disorders (U.S. patent condition. application Ser. No. 1 1/141,707 filed May 31, 2005 and Ser. 0012. In particular aspects, a subject or patient may be No. 1 1/273,640 filed Nov. 14, 2005, each of which is incor selected for treatment based on expression and/or aberrant porated herein by reference in its entirety). In a survey of 24 expression of one or more miRNA or mRNA. In a further different humantissues, the inventors observed that miR-34 is aspect, a subject or patient may be selected for treatment preferentially or exclusively expressed in human lymph node based on aberrations in one or more biologic or physiologic tissues. When transformed into various cancer cell lines from pathway(s), including aberrant expression of one or more humans, miR-34a inhibits the proliferation of prostate cancer gene associated with a pathway, or the aberrant expression of US 2009/0227533 A1 Sep. 10, 2009

one or more protein encoded by one or more gene associated cervical, a uterine, a brain, a neuronal, a blood, a cervical, an with a pathway. In still a further aspect, a Subject or patient esophageal, a lung, a cardiovascular, a liver, a breast, a bone, may be selected based on aberrations in miRNA expression, a thyroid, a glandular, an adrenal, a pancreatic, a stomach, a or biologic and/or physiologic pathway(s). A subject may be intestinal, a kidney, a bladder, a prostate, a uterus, an ovarian, assessed for sensitivity, resistance, and/or efficacy of a a testicular, a splenic, a skin, a smooth muscle, a cardiac therapy or treatment regime based on the evaluation and/or muscle, or a striated muscle cell. In certain aspects, the cell, analysis of miRNA or mRNA expression or lack thereof. A tissue, or target may not be defective in miRNA expression subject may be evaluated for amenability to certain therapy yet may still respond therapeutically to expression or over prior to, during, or after administration of one or therapy to a expression of a miRNA. miR-34 could be used as a therapeu Subject or patient. Typically, evaluation or assessment may be tic target for any of these diseases. In certain embodiments done by analysis of miRNA and/or mRNA, as well as com miR-34 can be used to modulate the activity of miR-34 in a bination of other assessment methods that include but are not Subject, organ, tissue, or cell. limited to histology, immunohistochemistry, blood work, etc. 0015. A cell, tissue, or subject may be a cancer cell, a 0013. In some embodiments, an infectious disease or con cancerous tissue, harbor cancerous tissue, or be a Subject or dition includes a bacterial, viral, parasite, or fungal infection. patient diagnosed or at risk of developing a disease or condi Many of these genes and pathways are associated with vari tion. In certain aspects a cancer cell is a neuronal, glial, lung, ous cancers and other diseases. Cancerous conditions liver, brain, breast, bladder, blood, leukemic, colon, colorec include, but are not limited to astrocytoma, anaplastic large tal, endometrial, stomach, skin, ovarian, fat, bone, cervical, cell lymphoma, acute lymphoblastic leukemia, acute myeloid esophageal, pancreatic, prostate, kidney, epithelial, intestinal, leukemia, angiosarcoma, breast carcinoma, B-cell lym lymphoid, muscle, adrenal, salivary gland, testicular, orthy phoma, bladder carcinoma, cervical carcinoma, carcinoma of roid cell. In still a further aspect cancer includes, but is not the head and neck, chronic lymphocytic leukemia, chronic limited to astrocytoma, anaplastic large cell lymphoma, acute myeloid leukemia, colorectal carcinoma, endometrial carci lymphoblastic leukemia, acute myeloid leukemia, angiosar noma, glioma, glioblastoma, gastric carcinoma, gastrinoma, coma, breast carcinoma, B-cell lymphoma, bladder carci hepatoblastoma, hepatocellular carcinoma, Hodgkin lym noma, cervical carcinoma, carcinoma of the head and neck, phoma, Kaposi's sarcoma, leukemia, lung carcinoma, lei chronic lymphocytic leukemia, chronic myeloid leukemia, omyosarcoma, laryngeal squamous cell carcinoma, mela colorectal carcinoma, endometrial carcinoma, glioma, glio noma, mucosa-associatedlymphoid tissue B-cell lymphoma, blastoma, gastric carcinoma, gastrinoma, hepatoblastoma, medulloblastoma, mantle cell lymphoma, meningioma, hepatocellular carcinoma, Hodgkin lymphoma, Kaposi's sar myeloid leukemia, multiple myeloma, high-risk myelodys coma, leukemia, lung carcinoma, leiomyosarcoma, laryngeal plastic syndrome, mesothelioma, neurofibroma, non squamous cell carcinoma, melanoma, mucosa-associated Hodgkin lymphoma, non-small cell lung carcinoma, ovarian lymphoid tissue B-cell lymphoma, medulloblastoma, mantle carcinoma, esophageal carcinoma, oropharyngeal carci cell lymphoma, meningioma, myeloid leukemia, multiple noma, osteosarcoma, pancreatic carcinoma, papillary carci myeloma, high-risk myelodysplastic syndrome, mesothe noma, prostate carcinoma, pheochromocytoma, rhabdomyo lioma, neurofibroma, non-Hodgkin lymphoma, non-Small sarcoma, squamous cell carcinoma of the head and neck, cell lung carcinoma, ovarian carcinoma, esophageal carci Schwannoma, Small cell lung cancer, Salivary gland tumor, noma, oropharyngeal carcinoma, osteosarcoma, pancreatic sporadic papillary renal carcinoma, thyroid carcinoma, tes carcinoma, papillary carcinoma, prostate carcinoma, pheo ticular tumor, urothelial carcinoma wherein the modulation chromocytoma, rhabdomyosarcoma, squamous cell carci of one or more gene is Sufficient for a therapeutic response. noma of the head and neck, Schwannoma, Small cell lung Typically a cancerous condition is an aberrant hyperprolif cancer, salivary gland tumor, sporadic papillary renal carci erative condition associated with the uncontrolled growth or noma, thyroid carcinoma, testicular tumor, urothelial carci inability to undergo cell death, including apoptosis. noma. In certain aspects the cancerous condition is lung car 0014. The present invention provides methods and com cinoma. In a further aspect the lung carcinoma is a non-Small positions for identifying genes that are direct targets for miR cell carcinoma. In yet a further aspect the non-Small cell 34 regulation or that are downstream targets of regulation carcinoma is an adenocarcinoma, a squamous cell carcinoma, following the miR-34-mediated modification of upstream a large cell carcinoma, an adenosquamous cell carcinoma, or gene expression. Furthermore, the invention describes gene a bronchioalveolar carcinoma. In certain aspects the cancer pathways and networks that are influenced by miR-34 expres ous condition is prostate carcinoma. In a further aspect the Sionin biological samples. Many of these genes and pathways prostate carcinoma can be PSA positive or negative and/or are associated with various cancers and other diseases. The androgen dependent or independent. altered expression or function of miR-34 in cells would lead 0016 Embodiments of the invention include methods of to changes in the expression of these key genes and contribute modulating gene expression, or biologic or physiologic path to the development of disease or other conditions. Introduc ways in a cell, a tissue, or a subject comprising administering ing miR-34 (for diseases where the miRNA is down-regu to the cell, tissue, or Subject an amount of an isolated nucleic lated) or a miR-34 inhibitor (for diseases where the miRNA is acid or mimetic thereof comprising a miR-34 nucleic acid, up-regulated) into disease cells or tissues or Subjects would mimetic, or inhibitor sequence in an amount Sufficient to result in a therapeutic response. The identities of key genes modulate the expression of a gene positively or negatively that are regulated directly or indirectly by miR-34 and the modulated by a miR-34 miRNA. A “miR-34 nucleic acid disease with which they are associated are provided herein. In sequence' or “miR-34 inhibitor includes the full length pre certain aspects a cell may be an endothelial, a mesothelial, an cursor of miR-34, or complement thereof or processed (i.e., epithelial, a stromal, or a mucosal cell. In certain aspects the mature) sequence of miR-34 and related sequences set forth cell is a glial, a leukemic, a colorectal, an endometrial, a fat, herein, as well as 5,6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, a meninges, a lymphoid, a connective tissue, a retinal, a 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or more nucleotides US 2009/0227533 A1 Sep. 10, 2009

of a precursor miRNA or its processed sequence, or comple GCAGUGUUGUUAGCUGAUUG (MIMAT0003346; SEQ ment thereof, including all ranges and integers there between. ID NO:31): rno-miR-34c AGGCAGUGUAGUUAGCUGA In certain embodiments, the miR-34 nucleic acid sequence or UUGC (MIMAT0000814; SEQ ID NO:32); mne-miR-34a miR-34 inhibitor contains the full-length processed miRNA UGGCAGUGUCUUAGCUGGUUGU (MIMAT0002502; sequence or complement thereof and is referred to as the SEQ ID NO:33): ptr-miR-34a UGGCAGUGUCU UAGCUGGUUGU (MIMAT0002498; SEQID NO:34) or a “miR-34 full-length processed nucleic acid sequence' or complement thereof. In certain aspects, a Subset of these “miR-34 full-length processed inhibitor sequence.” In still miRNAs will be used that include somebut not all of the listed further aspects, the miR-34 nucleic acid comprises at least 5, miR-34 family members. In one aspect, miR-34 sequences 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, have a consensus sequence of SEQID NO:72. In one embodi 24, 25, 50 nucleotide (including all ranges and integers there ment only sequences comprising the consensus sequence of between) segment or complementary segment of a miR-34 WGGCAGUGUVIRUUAGGUGRUUG (wherein the that is at least 75, 80, 85,90, 95, 98, 99 or 100% identical to bracketed nucleotide is optional) (SEQ ID NO:73) will be SEQ ID NO:1 to SEQID NO:73. The general term miR-34 included with all other miRNAs excluded. The term miR-34 includes all members of the miR-34 family that share at least includes all members of the miR-34 family unless specifically part of a mature miR-34 sequence. Mature miR-34 sequences identified. In certain aspects, a subset of these miRNAs will include hsa-miR-34a UGGCAGUGUCUUAGCUGGUU be used that include some but not all of the listed miR-34 GUU (MIMAT0000255; SEQID NO:1); hsa-miR-34b UAG family members. For instance, in one embodiment only GCAGUGUCAUUAGCUGAUUG (MIMAT0000685; SEQ sequences comprising the consensus sequence of SEQ ID ID NO:2); hsa-miR-34c AGGCAGUGUAGUUAGCUGA NO: 73 will be included with all other miRNAs excluded. UUGC (MIMAT0000686; SEQ ID NO:3); chr-miR-34 0017. In a further aspect, a “miR-34 nucleic acid AGGCAGUGUGGUUAGCUGGUUG (MIMAT0000466; sequence' includes all or a segment of the full length precur SEQ ID NO:4); mo-miR-34b UAGGCAGUGUAA sor of miR-34 family members. Stem-loop sequences of miR UUAGCUGAUUG (MIMAT0000813; SEQID NO:5); dps 34 family members include hsa-mir-34a GGCCAGCU miR-34 UGGCAGUGUGGUUAGCUGGUUG (MI GUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUU MAT0001223; SEQ ID NO:6): cel-miR-34 GUUGUGAGCAAUA GUAAGGAAGCAAUCAG AGGCAGUGUGGUUAGCUGGUUG (MIMAT0000005; CAAGUAUACUGCCCUAGAAGUGCUG SEQ ID NO:7); mml-miR-34a UGGCAGUGUCU CACGUUGUGGGGC cc (MI0000268: SEQ ID NO:35); UAGCUGGUUGU (MIMAT0002499; SEQ ID NO:8); hSa-mir-34b GUGCUCGG UUUGUAGGCAGUGUCA immu-miR-34b UAGGCAGUGUAAUUAGCUGAUUG. UUAGCUGAUUGUACUGUGGUGGUUA (MIMAT0000382: SEQ ID NO:9); sla-miR-34a CAAUCACUAACUC CACUGCCAUCAAAACAAG UGGCAGUGUCUUAGCUGGUUGU (MIMAT0002500; GCAC (MI0000742: SEQ ID NO:36); hsa-mir-34c SEQ ID NO:10): ppy-miR-34a UGGCAGUGUCU AGUCUAGUUACUAGGCAGUGUAG UAGCUGGUUGU (MIMAT0002497; SEQID NO:11):bta UUAGCUGAUUGCUAAUAGUACCAAUCACUAA miR-34c AGGCAGUGUAGUUAGCUGAUUG (MI CCACACGGCCAGGUAAAAAGAUU (MI0000743: SEQ MAT0003854; SEQ ID NO:12); dre-miR-34c ID NO:37); gga-mir-34c AGCCUGGUUACCAGGCAGU AGGCAGUGCAGUUAGUUGAUUAC (MIMAT0003759; GUAGUUAGCUGAUUGCCACCAGGACCAA UCAC SEQ ID NO:13): immu-miR-34a UGGCAGUGUCU UAACCACACAGCCAGGUAAAAAG (MI0001261; SEQ UAGCUGGUUGUU (MIMAT0000542: SEQ ID NO:14); ID NO:38): xtr-mir-34b-4 UUCAGGCAGUGUAG rno-miR-34a UGGCAGUGUCUUAGCUGGUUGUU (MI UUAGCUGAUUGUGUUAUAUCAAAUUUGCAAU MAT0000815; SEQID NO:15); bta-miR-34b AGGCAGU CACUAGCUAAACUACCAUAAAA (MI0004818: SEQID GUAAUUAGCUGAUUG (MIMAT0003549; SEQ ID NO:39); age-mir-34a GGCCAGCUGUGAGUGUUUCU NO:16); dme-miR-34 UGGCAGUGUGGUUAGCUGG UUGGCAGUGUCUUAGCUGGUUGUUGU UUG (MIMAT0000350; SEQ ID NO:17); go-miR-34a GUGCAAUA GUGAAGGAAGCAAUCAG UGGCAGUGUCUUAGCUGGUUGU (MIMAT0002494; CAAGUAUACUGCCCUAGAAGUGCUGCACGUUGUG SEQ ID NO:18): mdo-miR-34a UGGCAGUGUCU GGG CCC (MI0002797; SEQID NO:40): ptr-mir-34a GGC UAGCUGGUUGUU (MIMAT0004096; SEQ ID NO:19); CAGCUGUGAGUGUUUCUUUGGCAGUGU gga-miR-34a UGGCAGUGUCUUAGCUGGUUGUU (MI CUUAGCUGGUUGUUGUGAGCAAUA GUAAGGAAG MAT0001173; SEQ ID NO:20); age-miR-34a UGGCAGU CAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGC GUCUUAGCUGGUUGU (MIMAT0002495; SEQ ID ACGUUGUG GGGC CC (MI0002800; SEQ ID NO:41); NO:21); gga-miR-34b CAGGCAGUGUAGUUAGCUGA bta-mir-34b GUGCUCGGUUUGUAGGCAGUGUAA UUG (MIMAT0001179; SEQ ID NO:22): lla-miR-34a UUAGCUGAUUGUACUCUCAUGCUUACAAUC UGGCAGUGUCUUAGCUGGUUGU (MIMAT0002501; ACUAGUUCCACUGCCAUCAAAACAAGGCAC SEQ ID NO:23): gga-miR-34c AGGCAGUGUAG (MI0004763; SEQID NO:42); mne-mir-34a GGCCAGCU UUAGCUGAUUGC (MIMAT0001180: SEQ ID NO:24); GUGAGUGUUUCUUUGG CAGUGUCUUAGCUGGUU Xtr-miR-34b CAGGCAGUGUAGUUAGCUGAUUG (MI GUUGUGAGCAAUAGUAAGGAAGCAAU MAT0003579; SEQID NO:25); ppa-miR-34a UGGCAGU CAGCAAGUAUA GUCUUAGCUGGUUGU (MIMAT0002496; SEQ ID CUGCCCUAGAAGUGCUACACAUUGUGGGGCCU NO:26); mmu-miR-34c AGGCAGUGUAGUUAGCUGA (MI0002804; SEQ ID NO:43); gga-mir-34b GUGCUUG UUGC (MIMAT0000381; SEQ ID NO:27); dre-miR-34 GUUUGCAGGCAGUGUAGUUAGCUG AUUGUAC UGGCAGUGUCUUAGCUGGUUGU (MIMAT00012.69; CCAGCGCCCCACAAUCACUAAAUU SEQ ID NO:28): xtr-miR-34a UGGCAGUGUCU CACUGCCAUCAAAACAAGGCAC (MI0001260: SEQID UAGCUGGUUGUU (MIMAT0003578; SEQ ID NO:29); NO:44): rno-mir-34c AGUCUAGUUACUAGG CAGU bmo-miR-34 UGGCAGUGUGGUUAGCUGGUUG (MI GUAGUUAGCUGAUUGCUAAUAGUAC MAT0004197; SEQ ID NO:30); dre-miR-34b UAG CAAUCACUAACCACACAGCCAGGUA AAAAGACU

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inhibitors. miRNAs or their complements can be adminis Such as mRNA or encoded protein, is down-regulated or tered concurrently, in sequence, or in an ordered progression. up-regulated. In a particular aspect the gene modulated com In certain aspects, a miR-34 or miR-34 inhibitor can be prises or is selected from (and may even exclude) 1, 2, 3, 4, 5, administered in combination with one or more of a let-7, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, let-7b, let-7c, let-7g, miR-15, miR-16, miR-20, miR-21. 24, 25, 26.27, 28, or all of the genes identified in Tables 1, 3, miR-26a, miR-124a, miR-126, miR-143, miR-147, miR-188, 4, and/or 5, or any combinations thereof. In certain embodi miR-200, miR-215, miR-216, miR-292-3p, and/or miR-331 ments a gene modulated or selected to be modulated is from nucleic acid. All or combinations of miRNAs or inhibitors Table 1. In further embodiments a gene modulated or selected thereof may be administered in a single formulation. Admin to be modulated is from Table 3. In still further embodiments istration may be before, during or after a second therapy. a gene modulated or selected to be modulated is from Table 4. miR-34 nucleic acids or complements thereof may also In yet further embodiments a gene modulated or selected to be include various heterologous nucleic acid sequence, i.e., modulated is from Table 5. Embodiments of the invention those sequences not typically found operatively coupled with may also include obtaining or assessing a gene expression miR-34 in nature, Such as promoters, enhancers, and the like. profile or miRNA profile of a target cell prior to selecting the The miR-34 nucleic acid is a recombinant nucleic acid, and mode of treatment, e.g., administration of a miR-34 nucleic can be a ribonucleic acid or a deoxyribonucleic acid. The acid, inhibitor of miR-34, or mimetics thereof . . . . The recombinant nucleic acid may comprise a miR-34 or miR-34 database content related to all nucleic acids and genes desig inhibitor expression cassette, i.e., a nucleic acid segment that nated by an accession number or a database Submission are expresses a nucleic acid when introduce into an environment incorporated herein by reference as of the filing date of this containing components for nucleic acid synthesis. In a further application. In certain aspects of the invention one or more aspect, the expression cassette is comprised in a viral vector, miRNA or miRNA inhibitor may modulate a single gene. In or plasmid DNA vector or other therapeutic nucleic acid a further aspect, one or more genes in one or more genetic, vector or delivery vehicle, including liposomes and the like. cellular, or physiologic pathways can be modulated by one or In certain aspects a nucleic acid is a RNA and/or a synthetic more miRNAs or complements thereof, including miR-34 nucleic acid. In a particular aspect, the miR-34 nucleic acid is nucleic acids and miR-34 inhibitors in combination with a synthetic nucleic acid. Moreover, nucleic acids of the inven other miRNAs. tion may be fully or partially synthetic. In certain aspects, 0023 miR-34 nucleic acids may also include various het viral vectors can be administered at 1x10, 1x10, 1x10' erologous nucleic acid sequence, i.e., those sequences not 1x10, 1x10, 1x107, 1x10, 1x10, 1x10, 1x10'', 1x10", typically found operatively coupled with miR-34 in nature, 1x10", 1x10 pfu or viral particle (vp). Such as promoters, enhancers, and the like. The miR-34 0020. In a particular aspect, the miR-34 nucleic acid or nucleic acid is a recombinant nucleic acid, and can be a miR-34 inhibitor is a synthetic nucleic acid. Moreover, ribonucleic acid or a deoxyribonucleic acid. The recombinant nucleic acids of the invention may be fully or partially syn nucleic acid may comprise a miR-34 expression cassette. In a thetic. In still further aspects, a DNA encoding such a nucleic further aspect, the expression cassette is comprised in a viral, acid of the invention can be administered at 0.001, 0.01, 0.1, or plasmid DNA vector or other therapeutic nucleic acid 1, 10, 20, 30, 40, 50, 100, 200, 400, 600, 800, 1000, 2000, to vector or delivery vehicle, including liposomes and the like. 4000 ug or mg, including all values and ranges there between. In a particular aspect, the miR-34 nucleic acid is a synthetic In yet a further aspect, nucleic acids of the invention, includ nucleic acid. Moreover, nucleic acids of the invention may be ing synthetic nucleic acid, can be administered at 0.001, 0.01, fully or partially synthetic. 0.1. 1, 10, 20, 30, 40, 50, 100, to 200 ug or mg per kilogram 0024. A further embodiment of the invention is directed to (kg) of body weight. Each of the amounts described herein methods of modulating a cellular pathway comprising admin may be administered over a period of time, including 0.5, 1,2, istering to the cell an amount of an isolated nucleic acid 3, 4, 5, 6, 7, 8, 9, 10, minutes, hours, days, weeks, months or comprising a miR-34 nucleic acid sequence in an amount years, including all values and ranges there between. Sufficient to modulate the expression, function, status, or state 0021. In certain embodiments, administration of the com of a cellular pathway, in particular those pathways described position(s) can be enteral or parenteral. In certain aspects, in Table 2 or the pathways known to include one or more enteral administration is oral. In further aspects, parenteral genes from Table 1, 3, 4, and/or 5. Modulation of a cellular administration is intralesional, intravascular, intracranial, pathway includes, but is not limited to modulating the expres intrapleural, intratumoral, intraperitoneal, intramuscular, sion of one or more gene. Modulation of a gene can include intralymphatic, intraglandular, Subcutaneous, topical, intra inhibiting the function of an endogenous miRNA or provid bronchial, intratracheal, intranasal, inhaled, or instilled. ing a functional miRNA to a cell, tissue, or subject. Modula Compositions of the invention may be administered region tion refers to the expression levels or activities of a gene or its ally or locally and not necessarily directly into a lesion. related gene product or protein, e.g., the mRNA levels may be 0022. In certain aspects, the gene or genes modulated modulated or the translation of an mRNA may be modulated, comprises 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, 15, 20, 25, etc. Modulation may increase or up regulate a gene or gene 30, 35, 40, 45, 50, 100, 150, 200 or more genes or combina product or it may decrease or down regulate a gene or gene tions of genes identified in Tables 1, 3, 4, and/or 5. In still product. further aspects, the gene or genes modulated may exclude 1. 0025 Still a further embodiment includes methods of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, treating a patient with a pathological condition comprising 45, 50, 100, 150, 175 or more genes or combinations of genes one or more of step (a) administering to the patient an amount identified in Tables 1, 3, 4, and/or 5. Modulation includes of an isolated nucleic acid comprising a miR-34 nucleic acid modulating transcription, mRNA levels, mRNA translation, sequence in an amount Sufficient to modulate the expression and/or protein levels in a cell, tissue, or organ. In certain of a cellular pathway; and (b) administering a second therapy, aspects the expression of a gene or level of a gene product, wherein the modulation of the cellular pathway sensitizes the US 2009/0227533 A1 Sep. 10, 2009

patient to the second therapy. A cellular pathway may include, 0030 Certain embodiments of the invention are directed but is not limited to one or more pathway described in Table to compositions and methods for assessing, prognosing, or 2 below or a pathway that is know to include one or more treatingapathological condition in a patient comprising mea genes of Tables 1, 3, 4, and/or 5. A second therapy can include Suring or determining an expression profile of one or more administration of a second miRNA or therapeutic nucleic marker(s) in a sample from the patient, wherein a difference acid, or may include various standard therapies, such as che in the expression profile in the sample from the patient and an motherapy, radiation therapy, drug therapy, immunotherapy, expression profile of a normal sample or reference expression and the like. Embodiments of the invention may also include profile is indicative of pathological condition and particularly the determination or assessment of a gene expression profile cancer (e.g., In certain aspects of the invention, the cellular for the selection of an appropriate therapy. pathway, gene, or genetic marker is or is representative of one 0026. Embodiments of the invention include methods of or more pathway or marker described in Table 1, 3, 4, and/or treating a Subject with a pathological condition comprising 5, including any combination thereof. 0031 Aspects of the invention include diagnosing, assess one or more of the steps of (a) determining an expression ing, or treating a pathologic condition or preventing a patho profile of one or more genes selected from Table 1,3,4, and/or logic condition from manifesting. For example, the methods 5; (b) assessing the sensitivity of the subject to therapy based can be used to screen for a pathological condition; assess on the expression profile; (c) selecting a therapy based on the prognosis of a pathological condition; stage a pathological assessed sensitivity; and (d) treating the Subject using condition; assess response of a pathological condition to selected therapy. Typically, the pathological condition will therapy, or to modulate the expression of a gene, genes, or have as a component, indicator, or result the mis-regulation of related pathway as a first therapy or to render a Subject sen one or more gene of Table 1, 3, 4, and/or 5. sitive or more responsive to a second therapy. In particular 0027. Further embodiments include the identification and aspects, assessing the pathological condition of the patient assessment of an expression profile indicative of miR-34 can be assessing prognosis of the patient. Prognosis may status in a cell or tissue comprising expression assessment of include, but is not limited to an estimation of the time or one or more gene from Table 1, 3, 4, and/or 5, or any combi expected time of Survival, assessment of response to a nation thereof. therapy, and the like. In certain aspects, the altered expression 0028. The term “miRNA is used according to its ordinary of one or more gene or marker is prognostic for a patient and plain meaning and refers to a microRNA molecule found having a pathologic condition, wherein the marker is one or in eukaryotes that is involved in RNA-based gene regulation. more of Table 1, 3, 4, and/or 5, including any combination See, e.g., Carrington et al., 2003, which is hereby incorpo thereof. rated by reference. The term can be used to refer to the single-stranded RNA molecule processed from a precursor or TABLE 1 in certain instances the precursor itself. Genes with increased (positive values) or decreased (negative 0029. In some embodiments, it may be useful to know values) expression following transfection of human cancer cells whether a cell expresses a particular miRNA endogenously or with pre-miRhsa-miR-34a. whether such expression is affected under particular condi tions or when it is in a particular disease state. Thus, in some RefSeq, Transcript ID embodiments of the invention, methods include assaying a Gene Symbol (Pruitt et al., 2005) A log2 cell or a sample containing a cell for the presence of one or 1SE1.2 NM 176818 -0.855883 AADAC NM 001086 4245 more marker gene or mRNA or other analyte indicative of the ABAT NM OOO663, NM 020686 2.09337 expression level of a gene of interest. Consequently, in some ABCA1 NM OO55O2 74-697 embodiments, methods include a step of generating an RNA ABCB6/ ATG9A NM 005689, NM 024085 -158.186 profile for a sample. The term “RNA profile' or “gene expres ABHD3 NM 138340 0.867787 sion profile' refers to a set of data regarding the expression ABLIM3 NM O14945 3482 ADARB1 NM OO1033049, NM 001112, O.842409 pattern for one or more gene or genetic marker in the sample NM O15833, NM O15834 (e.g., a plurality of nucleic acid probes that identify one or ADM NM OO1124 O2O6 more markers from Tables 1,3,4, and/or 5); it is contemplated ADRB2 NM 000024 O.98.7993 AER61 NM 173654 O6132 that the nucleic acid profile can be obtained using a set of AGR2 NM OO6408 -O.735648 RNAS, using for example nucleic acid amplification or AIP NM OO3977 -0.81314 hybridization techniques well know to one of ordinary skill in AKAP12 NM 005100, NM 144497 O6844 the art. The difference in the expression profile in the sample AKAP2 NM OO1004065, NM 0072O3, 41369 from the patient and a reference expression profile, Such as an PALM2-AKAP2 NM 147150 AMBP NM OO1633 8111 expression profile from a normal or non-pathologic sample, is ANG, RNASE4 NM OO1145, NM OO2937. -106683 indicative of a pathologic, disease, or cancerous condition. A NM 194430. NM 194431 nucleic acid or probe set comprising or identifying a segment ANK3 NM OO1149, NM 020987 -1.95944 of a corresponding mRNA can include all or part of 1, 2, 3, 4, ANKRD46 NM 1984.01 2.27544 ANXA10 NM 007193 47535 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, ANXA6 NM 001155, NM OO4033 O4941 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, 36, 37,38, 39, AOX NM OO1159 0.985.795 40, 41,42, 43,44, 45,46,47, 48,49, 50, 51, 52,53,54, 55,56, APBA2BP NM 031231, NM 031232 38542 57, 58, 59, 60, 61, 62, 100, 200, 500, or more nucleotides, APBB2 NM 173075 O1175 APOEH NM 000042 -1.01185 including any integer or range derivable there between, of a APOL1 NM OO3661, NM 145343, 41657 gene, genetic marker, a nucleic acid, mRNA or a probe rep NM 145344 resentative thereof that is listed in Tables 1, 3, 4, and/or 5 or APOL2 NM O3O882, NM 145637 32603 identified by the methods described herein.

US 2009/0227533 A1 Sep. 10, 2009

0033. A further embodiment of the invention is directed to as a component, indicator, or resulting mis-regulation of one methods of modulating a cellular pathway comprising admin or more gene of Table 1, 3, 4, and/or 5. istering to the cell an amount of an isolated nucleic acid 0037. In certain aspects, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more comprising a nucleic acid sequence in an amount Sufficient to miRNA may be used in sequence or in combination; for modulate the expression, function, status, or state of a cellular instance, any combination of miR-34 or a miR-34 inhibitor pathway, in particular those pathways described in Table 2 or with another miRNA. Further embodiments include the iden the pathways known to include one or more genes from Table tification and assessment of an expression profile indicative 1, 3, 4, and/or 5. Modulation of a cellular pathway includes, of miR-34 status in a cell or tissue comprising expression but is not limited to modulating the expression of one or more assessment of one or more gene from Table 1, 3, 4, and/or 5. gene(s). Modulation of a gene can include inhibiting the or any combination thereof. function of an endogenous miRNA or providing a functional 0038. The term “miRNA is used according to its ordinary miRNA to a cell, tissue, or subject. Modulation refers to the and plain meaning and refers to a microRNA molecule found expression levels or activities of a gene or its related gene in eukaryotes that is involved in RNA-based gene regulation. product (e.g., mRNA) or protein, e.g., the mRNA levels may See, e.g., Carrington and Ambros, 2003, which is hereby be modulated or the translation of an mRNA may be modu incorporated by reference. The term can be used to refer to the lated. Modulation may increase or up regulate a gene or gene single-stranded RNA molecule processed from a precursor or product or it may decrease or down regulate a gene or gene in certain instances the precursor itself. product (e.g., protein levels or activity). 0039. In some embodiments, it may be useful to know 0034 Still a further embodiment includes methods of whether a cell expresses a particular miRNA endogenously or administering an miRNA or mimic thereof, and/or treating a whether such expression is affected under particular condi Subject or patient having, Suspected of having, or at risk of tions or when it is in a particular disease state. Thus, in some developing a pathological condition comprising one or more embodiments of the invention, methods include assaying a of step (a) administering to a patient or Subject an amount of cell or a sample containing a cell for the presence of one or an isolated nucleic acid comprising a miR-34 nucleic acid more marker gene or mRNA or other analyte indicative of the sequence or a miR-34 inhibitor in an amount Sufficient to expression level of a gene of interest. Consequently, in some modulate expression of a cellular pathway; and (b) adminis embodiments, methods include a step of generating an RNA tering a second therapy, wherein the modulation of the cellu profile for a sample. The term “RNA profile' or “gene expres lar pathway sensitizes the patient or subject, or increases the sion profile' refers to a set of data regarding the expression efficacy of a second therapy. An increase in efficacy can pattern for one or more gene or genetic marker or miRNA in include a reduction in toxicity, a reduced dosage or duration the sample (e.g., a plurality of nucleic acid probes that iden of the second therapy, or an additive or synergistic effect. A tify one or more markers from Tables 1, 3, 4, and/or 5); it is cellular pathway may include, but is not limited to one or contemplated that the nucleic acid profile can be obtained more pathway described in Table 2 below or a pathway that is using a set of RNAS, using for example nucleic acid amplifi know to include one or more genes of Tables 1, 3, 4, and/or 5. cation or hybridization techniques well know to one of ordi The second therapy may be administered before, during, and/ nary skill in the art. The difference in the expression profile in or after the isolated nucleic acid or miRNA or inhibitor is the sample from the patient and a reference expression pro administered file. Such as an expression profile of one or more genes or 0035. A second therapy can include administration of a miRNAs, are indicative of which miRNAs to be adminis second miRNA ortherapeutic nucleic acid such as a siRNA or tered. antisense oligonucleotide, or may include various standard 0040. In certain aspects, miR-34 or miR-34 inhibitor and therapies, such as pharmaceuticals, chemotherapy, radiation let-7 can be administered to patients with breast carcinoma, therapy, drug therapy, immunotherapy, and the like. Embodi cervical carcinoma, chronic lymphoblastic leukemia, col ments of the invention may also include the determination or orectal carcinoma, glioma, glioblastoma, gastric carcinoma, assessment of gene expression or gene expression profile for hepatocellular carcinoma, leukemia, lung carcinoma, mul the selection of an appropriate therapy. In a particular aspect, tiple myeloma, non-small cell lung carcinoma, ovarian car a second therapy is a chemotherapy. A chemotherapy can cinoma, oesophageal carcinoma, pancreatic carcinoma, pros include, but is not limited to paclitaxel, cisplatin, carboplatin, tate carcinoma, squamous cell carcinoma of the head and doxorubicin, oxaliplatin, larotaxel, taxol, lapatinib, doc neck, thyroid carcinoma. etaxel, methotrexate, capecitabine, Vinorelbine, cyclophos 0041 Further aspects include administering miR-34 or phamide, gemcitabine, amrubicin, cytarabine, etoposide, miR-34 inhibitor and miR-15 to patients with breast carci camptothecin, dexamethasone, dasatinib, tipifamib, bevaci noma, B-cell lymphoma, cervical carcinoma, colorectal car Zumab, sirolimus, temsirolimus, everolimus, lonafarnib, cinoma, glioma, glioblastoma, gastric carcinoma, hepatocel cetuximab, erlotinib, gefitinib, imatinib mesylate, rituximab, lular carcinoma, lung carcinoma, multiple myeloma, non trastuzumab, nocodazole, Sorafenib, Sunitinib, bortezomib, Small cell lung carcinoma, ovarian carcinoma, oesophageal alemtuzumab, gemtuzumab, to situmomab or ibritumomab. carcinoma, pancreatic carcinoma, prostate carcinoma, rhab 0.036 Embodiments of the invention include methods of domyosarcoma, squamous cell carcinoma of the head and treating a Subject with a disease or condition comprising one neck, thyroid carcinoma. or more of the steps of (a) determining an expression profile 0042. In still further aspects, miR-34 or miR-34 inhibitor of one or more genes selected from Table 1, 3, 4, and/or 5; (b) and miR-16 are administered to patients with breast carci assessing the sensitivity of the Subject to therapy based on the noma, B-cell lymphoma, colorectal carcinoma, glioblastoma, expression profile; (c) selecting a therapy based on the gastric carcinoma, hepatocellular carcinoma, multiple assessed sensitivity; and (d) treating the Subject using a myeloma, non-small cell lung carcinoma, ovarian carcinoma, selected therapy. Typically, the disease or condition will have oesophageal carcinoma, pancreatic carcinoma, prostate car US 2009/0227533 A1 Sep. 10, 2009 cinoma, rhabdomyosarcoma, squamous cell carcinoma of the cinoma, esophageal carcinoma, pancreatic carcinoma, pros head and neck, thyroid carcinoma. tate carcinoma, squamous cell carcinoma of the head and 0043. In certain aspects, miR-34 or miR-34 inhibitor and neck, thyroid carcinoma, testicular tumor. miR-20 are administered to patients with breast carcinoma, 0050. In yet a further aspect, miR-34 or miR-34 inhibitor cervical carcinoma, colorectal carcinoma, glioma, glioblas and miR-200 are administered to patients with anaplastic toma, gastric carcinoma, hepatocellular carcinoma, leuke large cell lymphoma, breast carcinoma, B-cell lymphoma, mia, lipoma, multiple myeloma, non-Small cell lung carci cervical carcinoma, chronic lymphoblastic leukemia, col noma, ovarian carcinoma, oesophageal carcinoma, orectal carcinoma, glioma, glioblastoma, gastric carcinoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, hepatocellular carcinoma, leukemia, lung carcinoma, mul squamous cell carcinoma of the head and neck, thyroid car tiple myeloma, mesothelioma, non-Small cell lung carci cinoma. noma, ovarian carcinoma, oesophageal carcinoma, osteosar 0044 Aspects of the invention include methods where coma, pancreatic carcinoma, prostate carcinoma, miR-34 or miR-34 inhibitor and miR-21 are administered to rhabdomyosarcoma, squamous cell carcinoma of the head patients with breast carcinoma, colorectal carcinoma, glioma, and neck, thyroid carcinoma, testicular tumor. glioblastoma, gastric carcinoma, hepatocellular carcinoma, 0051. In other aspects, miR-34 or miR-34 inhibitor and non-Small cell lung carcinoma, ovarian carcinoma, oesoph miR-215 are administered to patients with anaplastic large ageal carcinoma, pancreatic carcinoma, prostate carcinoma, cell lymphoma, breast carcinoma, B-cell lymphoma, cervical rhabdomyosarcoma, squamous cell carcinoma of the head carcinoma, chronic lymphoblastic leukemia, colorectal car and neck. cinoma, glioma, glioblastoma, gastric carcinoma, hepatocel 0045. In still further aspects, miR-34 or miR-34 inhibitor lular carcinoma, leukemia, lung carcinoma, lipoma, multiple and miR-26a are administered to patients with anaplastic myeloma, mesothelioma, non-Small cell lung carcinoma, large cell lymphoma, breast carcinoma, B-cell lymphoma, ovarian carcinoma, oesophageal carcinoma, osteosarcoma, cervical carcinoma, chronic lymphoblastic leukemia, col pancreatic carcinoma, prostate carcinoma, rhabdomyosar orectal carcinoma, glioma, glioblastoma, gastric carcinoma, coma, squamous cell carcinoma of the head and neck, thyroid hepatocellular carcinoma, leukemia, lung carcinoma, mul carcinoma, testicular tumor. tiple myeloma, non-Small cell lung carcinoma, ovarian car 0052. In certain aspects, miR-34 or miR-34 inhibitor and cinoma, oesophageal carcinoma, osteosarcoma, pancreatic miR-216 are administered to patients with breast carcinoma, carcinoma, prostate carcinoma, rhabdomyosarcoma, testicu cervical carcinoma, colorectal carcinoma, glioma, glioblas lar tumor. toma, gastric carcinoma, hepatocellular carcinoma, leuke 0046. In yet further aspects, miR-34 or miR-34 inhibitor mia, lung carcinoma, non-small cell lung carcinoma, ovarian and miR-126 are administered to patients with breast carci carcinoma, oesophageal carcinoma, osteosarcoma, prostate noma, cervical carcinoma, colorectal carcinoma, glioma, carcinoma, squamous cell carcinoma of the head and neck, glioblastoma, gastric carcinoma, hepatocellular carcinoma, testicular tumor. leukemia, lung carcinoma, mesothelioma, non-Small cell 0053. In a further aspect, miR-34 or miR-34 inhibitor and lung carcinoma, ovarian carcinoma, oesophageal carcinoma, miR-292-3p are administered to patients with anaplastic large osteosarcoma, pancreatic carcinoma, prostate carcinoma, cell lymphoma, breast carcinoma, B-cell lymphoma, cervical rhabdomyosarcoma, squamous cell carcinoma of the head carcinoma, colorectal carcinoma, glioma, glioblastoma, gas and neck, thyroid carcinoma. tric carcinoma, hepatocellular carcinoma, leukemia, lung car 0047. In a further aspect, miR-34 or miR-34 inhibitor and cinoma, lipoma, multiple myeloma, non-Small cell lung car miR-143 are administered to patients with anaplastic large cinoma, ovarian carcinoma, oesophageal carcinoma, cell lymphoma, breast carcinoma, B-cell lymphoma, cervical osteosarcoma, pancreatic carcinoma, prostate carcinoma, carcinoma, chronic lymphoblastic leukemia, colorectal car rhabdomyosarcoma, squamous cell carcinoma of the head cinoma, glioma, glioblastoma, gastric carcinoma, hepatocel and neck, thyroid carcinoma, testicular tumor. lular carcinoma, leukemia, lung carcinoma, multiple 0054. In still a further aspect, miR-34 or miR-34 inhibitor myeloma, non-small cell lung carcinoma, ovarian carcinoma, and miR-331 are administered to patients with anaplastic oesophageal carcinoma, osteosarcoma, pancreatic carci large cell lymphoma, breast carcinoma, B-cell lymphoma, noma, prostate carcinoma, squamous cell carcinoma of the cervical carcinoma, chronic lymphoblastic leukemia, col head and neck, thyroid carcinoma, testicular tumor. orectal carcinoma, glioma, glioblastoma, gastric carcinoma, 0048. In still a further aspect, miR-34 or miR-34 inhibitor hepatocellular carcinoma, leukemia, lung carcinoma, mul and miR-147 are administered to patients with breast carci tiple myeloma, ovarian carcinoma, oesophageal carcinoma, noma, cervical carcinoma, colorectal carcinoma, glioma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, glioblastoma, gastric carcinoma, hepatocellular carcinoma, rhabdomyosarcoma, squamous cell carcinoma of the head leukemia, lipoma, multiple myeloma, non-Small cell lung and neck, thyroid carcinoma, testicular tumor. carcinoma, ovarian carcinoma, oesophageal carcinoma, 0055. It is contemplated that when miR-34 or a miR-34 osteosarcoma, pancreatic carcinoma, prostate carcinoma, inhibitor is given in combination with one or more other squamous cell carcinoma of the head and neck, thyroid car miRNA molecules, the two different miRNAs or inhibitors cinoma. may be given at the same time or sequentially. In some 0049. In yet another aspect, miR-34 or miR-34 inhibitor embodiments, therapy proceeds with one miRNA or inhibitor and miR-188 are administered to patients with anaplastic and that therapy is followed up with therapy with the other large cell lymphoma, breast carcinoma, B-cell lymphoma, miRNA or inhibitor 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, cervical carcinoma, chronic lymphoblastic leukemia, col 35, 40, 45, 50, 55 minutes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, orectal carcinoma, glioma, glioblastoma, gastric carcinoma, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 hours, 1, 2, 3, 4, hepatocellular carcinoma, leukemia, lung carcinoma, mul 5, 6, 7 days, 1, 2, 3, 4, 5 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. tiple myeloma, non-Small cell lung carcinoma, ovarian car 11, or 12 months or any such combination later. US 2009/0227533 A1 Sep. 10, 2009

0056 Further embodiments include the identification and logic condition from manifesting. For example, the methods assessment of an expression profile indicative of miR-34 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 0057 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 and Ambros, 2003, which is hereby can be assessing prognosis of the patient. Prognosis may incorporated 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 0058. 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 TABLE 2 more miRNA marker gene or mRNA or other analyte indica Significantly affected functional cellular pathways tive of the expression level of a gene of interest. Conse following hsa-miR-34a over-expression in human cancer cells. quently, in some embodiments, methods include a step of generating an RNA profile for a sample. The term “RNA Number profile' or “gene expression profile' refers to a set of data Of regarding the expression pattern for one or more gene or Genes Pathway Functions genetic marker in the sample (e.g., a plurality of nucleic acid 35 Cellular Growth and Proliferation, Cellular Movement, Cell Death probes that identify one or more markers or genes from Tables 35 Gene Expression, Cellular Growth and Proliferation, Cell Death 1, 3, 4, and/or 5); it is contemplated that the nucleic acid 25 Gene Expression, DNA Replication, Recombination, and Repair, profile can be obtained using a set of RNAs, using for Cell Cycle example nucleic acid amplification or hybridization tech 23 DNA Replication, Recombination, and Repair, Cell Cycle, Cellular Development niques well know to one of ordinary skill in the art. The Cardiovascular Disease, Hematological Disease, Organismal difference in the expression profile in the sample from a Injury and Abnormalities patient and a reference expression profile, Such as an expres Cancer, Cell Cycle, Hepatic System Disease sion profile from a normal or non-pathologic sample, or a Immune Response, Cell Signaling, Molecular Transport Cancer, Cellular Growth and Proliferation, Neurological Disease digitized reference, is indicative of a pathologic, disease, or Immune Response, Cellular Movement, Hematological System cancerous condition. In certain aspects the expression profile Development and Function is an indicator of a propensity to or probability of (i.e., risk 7 Lipid Metabolism, Molecular Transport, Small Molecule factor for a disease or condition) developing Such a condition Biochemistry 7 Cell Cycle, Cancer, Cellular Growth and Proliferation (s). Such a risk or propensity may indicate a treatment, 6 Cell-To-Cell Signaling and Interaction, Cellular Movement, increased monitoring, prophylactic measures, and the like. A Hematological System Development and Function nucleic acid or probe set may comprise or identify a segment 6 Cellular Movement, Cellular Development, Cardiovascular of a corresponding mRNA and may include all or part of 1, 2, System Development and Function 5 Organ Development, Gene Expression, Developmental Disorder 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 5 Cell Death, Cancer, Cellular Growth and Proliferation 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33,34, 35,36, 37,38, 5 Carbohydrate Metabolism, Small Molecule Biochemistry, 39, 40, 41,42, 43,44, 45,46, 47, 48,49, 50, 51, 52,53,54, 55, Lipid Metabolism 56, 57, 58, 59, 60, 61, 62, 100, 200, 500, or more segments, 5 Cellular Assembly and Organization, Cell Cycle, Connective Tissue Development and Function including any integer or range derivable there between, of a 5 DNA Replication, Recombination, and Repair, Gene Expression, gene or genetic marker, or a nucleic acid, mRNA or a probe Cancer representative thereofthat is listed in Tables 1, 3, 4, and/or 5 4 Hematological System Development and Function, Immune or identified by the methods described herein. Response, Immune and Lymphatic System Development and Function 0059 Certain embodiments of the invention are directed 4 Protein Synthesis, Cell Signaling, Nucleic Acid Metabolism to compositions and methods for assessing, prognosing, or 7 Cell Death, Neurological Disease, Cellular Development treating a pathological condition in a patient comprising mea 1 Cellular Assembly and Organization, Cell Morphology, Cellular Compromise Suring or determining an expression profile of one or more 1 Cell Cycle, Cellular Assembly and Organization, miRNA or marker(s) in a sample from the patient, wherein a DNA Replication, Recombination, and Repair difference in the expression profile in the sample from the 1 Cancer, Cell Death, Reproductive System Disease patient and an expression profile of a normal sample or ref 1 Amino Acid Metabolism, Molecular Transport, Small erence expression profile is indicative of pathological condi Molecule Biochemistry 1 Cell Cycle, Cancer, Cell Death tion and particularly cancer (e.g., In certain aspects of the 1 Cell Death invention, the miRNAS, cellular pathway, gene, or genetic 1 Cellular Compromise, Auditory and Vestibular marker is or is representative of one or more pathway or System Development and Function, Protein Trafficking 1 Cell Morphology, Cellular Assembly and Organization, marker described in Table 1, 2, 3, 4, and/or 5, including any Cellular Compromise combination thereof. 1 Cellular Assembly and Organization, Cell Morphology, 0060 Aspects of the invention include diagnosing, assess Molecular Transport ing, or treating a pathologic condition or preventing a patho US 2009/0227533 A1 Sep. 10, 2009 15

TABLE 2-continued TABLE 2-continued

Significantly affected functional cellular pathways Significantly affected functional cellular pathways following hsa-miR-34a over-expression in human cancer cells. following hsa-miR-34a over-expression in human cancer cells. Number Number Of Of Genes Pathway Functions Genes Pathway Functions 1 Cellular Assembly and Organization, Cell Morphology, Cellular Function and Maintenance 1 Cardiovascular System Development and Function, Organ 1 Cell Signaling, Molecular Transport, Neurological Disease Morphology, Neurological Disease

TABLE 3 Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description A1BG NM 130786 alpha 1 B-glycoprotein AADACL1 NM 020792 arylacetamide deacetylase-like 1 AASDHPPT NM O15423 aminoadipate-semialdehyde BCA1 NM OO55O2 ATP-binding cassette, sub-family A member 1 BCC1 NM 004996 ATP-binding cassette, sub-family C, member 1 BCC12 NM 033226 ATP-binding cassette protein C12 BCC13 NM 172024 ATP-binding cassette protein C13 isoform b BCC4 NM 005845 ATP-binding cassette, sub-family C, member 4 BCC5 NM 005688 ATP-binding cassette, sub-family C, member 5 BCD1 NM OOOO33 ATP-binding cassette, sub-family D (ALD), member BCE NM OO2940 ATP-binding cassette, Sub-family E, member 1 BCF2 NM 007189 ATP-binding cassette, sub-family F, member 2 BCF3 NM 018358 ATP-binding cassette, sub-family F (GCN20), BCG4 NM 0221.69 ATP-binding cassette, sub-family G, member 4 BHD12 NM O15600 abhydrolase domain containing 12 BHD4 NM O22060 abhydrolase domain containing 4 BI3 NM 016428 NESH protein BL NM OO5157 V-abl Abelson murine leukemia viral oncogene BLIM1 NM 001003407 -binding LIM protein 1 isoform b BLIM3 NM O14945 actin binding LIM protein family, member 3 BR NM 001092 active breakpoint cluster region-related CACA NM 198834 acetyl-Coenzyme A carboxylase alpha isoform 1 CAD11 NM 0321.69 putative acyl-CoA dehydrogenase CAD8 NM 014384 acyl-Coenzyme A dehydrogenase family, member 8 CADL NM OO1608 acyl-Coenzyme A dehydrogenase, long chain ACADS NM OOOO17 acyl-Coenzyme A dehydrogenase, C-2 to C-3 short ACADSB NM OO1609 acyl-Coenzyme A dehydrogenase, short branched ACADVL NM 000018 acyl-Coenzyme A dehydrogenase, very long chain ACBD3 NM O22735 acyl-Coenzyme Abinding domain containing 3 ACCN1 NM 001094 amiloride-sensitive cation channel 1, neuronal ACE NM 152831 angiotensin I converting enzyme isoform 3 ACOT11 NM 147161 thioesterase, adipose associated isoform BFIT2 ACP5 NM OO1611 tartrate resistant acid phosphatase 5 precursor ACPP NM 001099 prostatic acid phosphatase precursor ACPT NM 080789 testicular acid phosphatase isoform b precursor ACSL1 NM OO1995 acyl-CoA synthetase long-chain family member I ACSL3 NM OO4457 acyl-CoA synthetase long-chain family member 3 ACSL4 NM 004.458 acyl-CoA synthetase long-chain family member 4 ACSS2 NM 018677 acyl-CoA synthetase short-chain family member 2 ACTBL1 NM 001004053 protein expressed in prostate, ovary, testis, ACTL6A NM 004301 actin-like 6A isoform 1 ACTL8 NM O3O812 actin like protein ACTN2 NM 001103 , alpha 2 ACTN4 NM 004924 actinin, alpha 4 ACTR1A NM OO5736 ARP1 actin-related protein 1 homologA, ACTRS NM O24855 ARP5 actin-related protein 5 homolog ACTR8 NM 022899 actin-related protein 8 ACVR1B NM 004302 activin A type IB isoform a precursor ADAM10 NM 001110 ADAM metallopeptidase domain 10 ADAM11 NM 002390 ADAM metallopeptidase domain 11 preproprotein ADAM12 NM OO3474 ADAM metallopeptidase domain 12 isoform 1 ADAM19 NM 033274 ADAM metallopeptidase domain 19 isoform 2 ADAMTS1 NM OO6988 ADAM metallopeptidase with thrombospondin type 1 US 2009/0227533 A1 Sep. 10, 2009 16

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description DAMTS10 NM 030957 ADAM metallopeptidase with thrombospondin type 1 DAMTS4 NM 005099 ADAM metallopeptidase with thrombospondin type 1 DAMTSL1 NM 139264 ADAMTS-like 1 isoform 3 DAMTSL4 NM O19032 thrombospondin repeat containing 1 isoform 1 DAT1 NM 012091 adenosine deaminase, tRNA-specific 1 DCY1 NM 021116 brain adenylate cyclase 1 DCY2 NM 020546 enylate cyclase 2 DCY7 NM 001114 enylate cyclase 7 DD2 NM OO1617 ducin 2 isoform a DIPOQ NM OO4797 iponectin precursor DIPOR2 NM O24551 iponectin receptor 2 DK NM OO1123 enosine kinase isoform a DM2 NM O24866 renomedulin 2 precusor DNP NM O15339 activity-dependent neuroprotector DORA2A NM OOO675 adenosine A2a receptor DPN NM O25225 adiponutrin DPRH NM OO1125 ADP-ribosylarginine hydrolase DRA1A NM 0333O2 alpha-1A-adrenergic receptor isoform 3 DRA1D NM OOO678 alpha-1D-adrenergic receptor DRA2A NM OOO681 alpha-2A-adrenergic receptor DRA2B NM OOO682 alpha-2B-adrenergic receptor DRBK2 NM OO5160 beta adrenergic receptor kinase 2 FAP NM 021638 actin filament associated protein FF2 NM 002025 fragile X mental retardation 2 FF3 NM 0010251.08 AF4/FMR2 family, member 3 isoform 2 FF4 NM O14423 ALL1 fused gene from 5q31 FG3L1 NM OO 1031805 AFG3 ATPase family gene 3-like 1 isoform 2 GTR1 NM OOO685 angiotensin II receptor, type 1 GTRAP NM O2O350 angiotensin II receptor-associated protein HNAK NM OO1620 AHNAKnucleoprotein isoform 1 PL1 NM OO1033054 aryl hydrocarbon receptor interacting AP1 NM 018836 transmembrane protein SHREW1 NM 013411 adenylate kinase 2 isoform b NM 016282 adenylate kinase 3 KA NM 139275 A-kinase anchor protein 1 isoform 2 precursor KAP13 NM OO6738 A-kinase anchor protein 13 isoform 1 KA NM OO4274 A-kinase anchor protein 6 KA NM 004.842 A-kinase anchor protein 7 isoform alpha KR NM OO1.007536 aldo-keto reductase family 1, member C-like 1 NM OOOO31 delta-aminolevulinic acid dehydratase isoform b NM OO1627 activated leukocyte cell adhesion molecule NM OO3888 aldehyde dehydrogenase 1A2 isoform 1 NM OOO693 aldehyde dehydrogenase 1A3 NM OOO695 aldehyde dehydrogenase 3B2 NM 001080 aldehyde dehydrogenase 5A1 precursor, isoform 2 NM OO5589 aldehyde dehydrogenase 6A1 precursor NM OOOO34 aldolase A NM 1721.96 TFIIA-alphabeta-like factor isoform 2 NM 019109 beta-1,4-mannosyltransferase NM O24105 asparagine-linked glycosylation 12 NM OOO698 arachidonate 5-lipoxygenase NM 147129 ALS2 C-terminal like isoform 1 NM 173511 amyotrophic lateral sclerosis 2 (juvenile) NM 138468 Icaé9-related protein NM OO6492 aristaless-like 3 NM O14324 alpha-methylacyl-CoA racemase isoform 1 NM OO1033059 S-adenosylmethionine decarboxylase 1 isoform 2 NM 032797 apoptosis-inducing factor (AIF)-like NM 001025580 AMMECR1 protein isoform 2 NM 016201 angiomotin like 2 NM 004037 adenosine monophosphate deaminase 2 (isoform L) NM 000480 erythrocyte adenosine monophosphate deaminase NM 133463 archaemetzincin-1 NM O15305 angelhomolog 1 NM 021146 angiopoietin-like 7 NM 001148 2 isoform 1 NM 001149 ankyrin 3 isoform 2 NM 016376 ankyrin repeat and FYVE domain containing 1 NM 014.391 cardiac ankyrin repeat protein NM O17664 ankyrin repeat domain 10 US 2009/0227533 A1 Sep. 10, 2009 17

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description ANKRD12 NM O15208 ankyrin repeat domain 12 ANKRD13 NM 033121 ankyrin repeat domain 13 ANKRD17 NM 032217 ankyrin repeat domain protein 17 isoform a ANKRD23 NM 144994 diabetes related ankyrin repeat protein ANKRD25 NM O15493 ankyrin repeat domain 25 ANKS1A NM O15245 ankyrin repeat and sterile alp ha motif domain ANKS1B NM 181670 cajalin 2 isoform b ANKS6 NM 173551 sterile alpha motif domain containing 6 ANP32A NM OO6305 acidic (leuci ne-rich) nuclear phosphoprotein 32 ANP32B NM OO6401 acidic (leuci ne-rich) nuclear phosphoprotein 32 ANTXR1 NM 032208 tumor endo helial marker 8 isoform 1 precursor ANXA11 NM OO1157 annexin A11 ANXAS NM 001154 annexin 5 P1B1 NM OO1127 adap or-related protein comp ex 1 beta 1 subunit P1 G1 NM OO1030007 adap or-related protein comp eX 1, gamma 1 P1GBP1 NM OO7247 AP gamma Subunit binding protein 1 isoform 1 P1S2 NM OO3916 adap or-related protein comp ex 1 sigma 2 P2S1 NM 004.069 adap or-related protein comp eX 2, Sigma 1 P3M1 NM 012095 adap or-related protein comp ex3, mu 1 subunit P3M2 NM OO6803 adap or-related protein comp ex3, mu 2 subunit P3S2 NM OO5829 adap or-related protein comp ex3, Sigma 2 P4S1 NM 007077 or-related protein comp ex4, Sigma 1 PBA1 NM 001163 amyloid beta A4 precursor protein-binding, PBB3 NM 133175 amyloid beta precursor protein-binding, family PH1A NM 016022 anterior pharynx defective 1 homolog A PITD1 NM 199294 apoptosis-inducing, TAF9-like domain 1 isoform PLP2 NMOO1642 amyloid beta (A4) precursor-like protein 2 POB NM OOO384 ipoprotein B precursor POLD1 NM O3O817 apolipoprotein L. domain containing 1 PPBP2 NM OO6380 amyloid beta precursor protein-binding protein NM 198098 aquaporin 1 P10 NM 08.0429 aquaporin 10 P3 NM 004925 aquaporin 3 NM 001169 aquaporin 8 EG NM OO1657 amphiregulin preproprotein F3 NM OO1659 DP-ribosylation factor 3 FGAP3 NM 014570 DP-ribosylation factor GTPase activating FGEF2 NM OO6420 DP-ribosylation factor guanine G 2 NM 001172 ginase, type II precursor GAP1 NM 004308 ho GTPase activating protein 1 HGAP19 NM 032900 ho GTPase activating protein 19 HGAP26 NM O15071 TPase regulator associated with the focal HGAP29 NM 004.815 TPL1-associated RhoGAP 1 HGAP30 NM 001025598 ho GTPase activating protein 30 isoform 1 HGDIB NM 001175 ho GDP dissociation inhibitor (GDI) beta GEF1OL NM 001011722 hoguanine nucleotide exchange factor (GEF) HGEF12 NM O15313 hoguanine nucleotide exchange factor (GEF) 12 HGEF2 NM OO4723 horac guanine nucleotide exchange factor 2 HGEF3 NM O19555 hoguanine nucleotide exchange factor 3 HGEF4 NM 032995 hoguanine nucleotide exchange factor 4 isoform HGEF5 NM OO10O2861 rho guanine nucleotide exchange factor 5 isoform HGEF6 NM 004840 RaciCdc42 guanine nucleotide exchange factor 6 HGEF7 NM OO3899 Rho guanine nucleotide exchange factor 7 isoform HGEF9 NM O1518.5 Cdc42 guanine exchange factor 9 D2 NM 152641 AT rich interactive domain 2 (ARID, RFX-like) NM OO6465 AT rich interactive domain 3B (BRIGHT-like) NM 002892 retinoblastoma-binding protein 1 isoform I NM 016374 AT rich interactive domain 4B isoform 1 NM OO6673 AT rich interactive domain 5A isoform 2 NM OO6321 ariadne homolog 2 LAC NM 005.737 ADP-ribosylation factor-like 4C NM 178815 ADP-ribosylation factor-like 8 NM OO10O2252 SRp25 nuclear protein isoform 4 NM 138795 ADP-ribosylation factor-like 10B NM 018184. ADP-ribosylation factor-like 10C NM O24742 armadillo repeat containing 5 NM 033415 armadillo repeat containing 6 NM O24585 armadillo repeat containing 7 NM O15396 armadillo repeat containing 8 isoform 2 NM 152583 hypothetical protein LOC158947 US 2009/0227533 A1 Sep. 10, 2009 18

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description ARPCS NM OO5717 actin related protein 2/3 complex subunit 5 ARPP-19 NM OO6628 cyclic AMP phosphoprotein, 19 kD ARPP-21 NM 001025068 cyclic AMP-regulated phosphoprotein, 21 kD ARRDC3 NM 020801 arrestin domain containing 3 ARSB NM 000046 arylsulfatase B isoform 1 precursor ARS NM O24590 arylsulfatase J ARTS-1 NM 016442 type 1 tumor necrosis factor receptor shedding ARVP612S NM OO1030078 hypothetical protein LOC442092 ARX NM 139058 aristaless related homeobox AS3MT NM O2O682 arsenic (+3 oxidation state) methyltransferase NM 016114 ankyrin repeat and SOCS box-containing protein NM O24701 ankyrin repeat and SOCS box-containing protein NM 080874 ankyrin repeat and SOCS box-containing protein NM O17873 ankyrin repeat and SOCS box-containing 6 isoform NM O15251 ATM ATR-Substrate Chk2-Interacting Zn2+-finger NM 004316 achaete-scute complex homolog-like 1 NM 004674 ash2 (absent, Small, or homeotic)-like NM 004319 astrotactin isoform 1 NM O15338 ditional sex combs like 1 NM 018263 ditional sex combs like 2 NM 013325 PG4 autophagy 4 homolog B isoform a NM 004849 PG5 autophagy 5-like NM 024085 PG9 autophagy 9-like 1 NM 000051 axiatelangiectasia mutated protein isoform 1 NM 020410 TPase type 13A1 NM 000702 Na+K+-ATPase alpha 2 subunit proprotein NM OO1679 Na+K+-ATPase beta 3 subunit NM OO5173 sarco/endoplasmic reticulum Ca2+-ATPase isoform NM 001001485 calcium-transporting ATPase 2C1 isoform 1c NM 000704 ATPase, H+/K+ exchanging, alpha polypeptide NM OO1 OO1975 ATP synthase, H+ transporting, mitochondrial F1 NM OO10O3805 ATP synthase, H+ transporting, mitochondrial FO NM 012463 ATPase, H+ transporting, lysosomal VO subunita NM 004691 ATPase, H+ transporting, lysosomal, VO subunit NM OO1007254 ATPase, H+ transporting, lysosomal 42kDa, V1 NM OO1696 vacuolar H--ATPase E1 isoform a NM 000053 ATPase, Cu++ transporting, beta polypeptide NM O24837 ATPase class I type 8B member 4 NM OO6045 ATPase, Class II, type 9A NM 080650 ATP binding domain 4 NM 178191 ATPase inhibitory factor 1 isoform 3 precursor NM OOO332 ataxin 1 NM OO7245 ataxin 2 related protein isoform A NM 153340 ataxin 7-like 2 NM 000707 arginine vasopressin receptor 1B NM 004655 axin 2 NM OO1699 AXL receptor tyrosine kinase isoform 2 AYTL2 NM O24830 hypothetical protein FLJ12443 B3GALNT1 NM 003781 UDP-Gal:betaGlcNAc beta B3GALTS NM OO6057 UDP-Gal:betaGlcNAc beta B3GAT1 NM 018644 beta-1,3-glucuronyltransferase 1 B3GAT3 NM 012200 beta-1,3-glucuronyltransferase 3 B3GNT3 NM O14256 UDP-GlcNAc:beta,Gal B4GALT1 NM OO1497 UDP-Gal:betaGlcNAc beta 14 B4GALT2 NM 001005417 UDP-Gal:betaGlcNAc beta 14 BAALC NM 001024372 brain and acute leukemia, cytoplasmic isoform 2 BAAT NM OO1701 bile acid Coenzyme A:amino acid BACE1 NM 012104 beta-site APP-cleaving enzyme 1 isoform A BACH2 NM 021813 BTB and CNC homology 1, basic BAD NM 004322 BCL2-antagonist of cell death protein BAI2 NM OO1703 brain-specific angiogenesis inhibitor 2 BAK1 NM 00118.8 BCL2-antagonist/killer 1 BAT1 NM 004640 HLA-B associated transcript 1 BATF2 NM 138456 basic leucine Zipper , BAX NM 004324 BCL2-associated X protein isoform beta BAZ2A NM 013449 bromodomain adjacent to domain, 2A BBS1 NM O24649 Bardet-Biedl syndrome 1 BBS10 NM O24685 hypothetical protein LOC79738 BCAN NM 021948 brevican isoform 1 BCAP29 NM OO10O8407 B-cell receptor-associated protein BAP29 isoform US 2009/0227533 A1 Sep. 10, 2009 19

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description BCAS3 NM O17679 breast carcinoma amplified sequence 3 BCCIP NM O78469 BRCA2 and CDKN1A-interacting protein isoform C BCKDK NM OO5881 branched chain ketoacid dehydrogenase kinase BCL10 NM OO3921 B-cell CLL/lymphoma 10 BCL11B NMO 22898 B-cell CLL/lymphoma 11B isoform 2 BCL2 NM 000633 B-cell lymphoma protein 2 alpha isoform BCL6 NM OO1706 B-cell lymphoma 6 protein BCL7A NM 001024808 B-cell CLL/lymphoma 7A isoform b BCL9L. NM 182557 B-cell CLL/lymphoma 9-like BCORL1 NM 021946 BCL6 co-repressor-like 1 BDKRB2 NM 000623 bradykinin receptor B2 BET1L. NM O16526 blocked early in transport 1 homolog (S. BFAR NM O16561 apoptosis regulator BHLHBS NM 152414 basic helix-loop-helix domain containing, class BICD1 NM 001003398 bicaudal Dhomolog 1 isoform 2 BIK NM OO1197 BCL2-interacting killer BIRC1 NM OO4536 baculoviral IAP repeat-containing 1 BIRCS NM 00101.2270 baculoviral IAP repeat-containing protein 5 BM88 NM O16564 BM88 antigen BMF NM OO10O3940 Bcl2 modifying factor isoform bmf-1 BMP1 NM OO6129 bone morphogenetic protein 1 isoform 3, BMP6 NM OO1718 bone morphogenetic protein 6 precursor BMP7 NM OO1719 bone morphogenetic protein 7 precursor BMP8B NM OO1720 bone morphogenetic protein 8B preproprotein BMPR2 NM 001204 bone morphogenetic protein receptor type II BNC2 NM O17637 basonuclin 2 BOLA2 NM OO 1031833 BolA-like protein 2 isoform b BRCA1 NM OO7306 breast cancer 1, early onset isoform BRD4. NM O14299 bromodomain-containing protein 4 isoform short BRE NM OO4899 brain and reproductive organ-expressed (TNFRSF1A BRPF1 NM 001003694 bromodomain and PHD finger-containing protein 1 BRPF3 NM O15695 bromodomain and PHD finger containing, 3 BRRN1 NM O15341 8t BRUNOL6 NM 052840 bruno-like 6, RNA binding protein BRWD1 NM 03.3656 bromodomain and WD repeat domain containing 1 BSDC1 NM 018045 BSD domain containing 1 BSN NM OO3458 bassoon protein BSPRY NM O17688 B-box and SPRY domain containing BTBD11 NM 001017523 BTB (POZ) domain containing 11 isoform 2 BTBD12 NM 032444 BTB (POZ) domain containing 12 BTBD2 NM O17797 BTB (POZ) domain containing 2 BTBD3 NM O14962 BTBPOZ domain containing protein 3 isoform a BTBD4 NM O25224 BTB (POZ) domain containing 4 BTBD7 NM OO10O2860 BTB (POZ) domain containing 7 isoform I BTG2 NM OO6763 B-cell translocation gene 2 BTG4 NM 017589 B-cell translocation gene 4 BTN1A1 NM OO1732 butyrophilin, subfamily 1, member Al BTN3A2 NM 007047 butyrophilin, subfamily 3, member A2 precursor BTNL9 NM 152547 butyrophilin-like 9 BTRC beta-transducin repeat containing protein Oorf10 asting induced gene Oorf13 hypothetical protein LOG143282 0orf22 hypothetical protein LOC84890 0orf26 hypothetical protein LOC54838 0orf28 growth inhibition and differentiation related 0orf32 hypothetical protein MGC27171 Oorf38 hypothetical protein LOC221061 Oorf24 FRA10AC1 protein isoform FRA10AC1-1 Oorf242 hypothetical protein LOC90550 Oorf249 hypothetical protein LOC221044 Oorf53 hypothetical protein LOC282966 Oorf54 hypothetical protein LOC64115 Oorf SS hypothetical protein LOC414236 Oorf56 hypothetical protein LOC219654 Oorf57 hypothetical protein LOC80195 Oorf58 hypothetical protein LOC84293 Oorf63 enkurin OOrf6S NM 138413 hypothetical protein LOC112817 Oorf72 NM OO1031746 hypothetical protein LOC196740 isoform 1 Oorf76 NM 024541 hypothetical protein LOC79591 US 2009/0227533 A1 Sep. 10, 2009 20

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description 77 NM O24789 hypo hetical protein LOC79847 3 NM 178832 hypo hetical protein LOC118812 9 NM 153336 hypo hetical protein LOC118672 91 NM 173541 hypo hetical protein LOC170393 95 NM 024886 hypo hetical protein LOC79946 NM O22761 hypo hetical protein LOC64776 1 NM O06133 neural stem cell-derived dendrite regulator 7 NM 020642 11 open reading frame 17 30 NM O2O193 EMSY protein 38 NM 212555 hypo hetical protein LOC399967 A4 NM 173580 hypo hetical protein LOC283171 A5 NM 145013 hypo hetical protein LOC219833 A9 NM 001003676 hypo hetical protein LOC79096 isoform 1 57 NM 018195 hypo hetical protein LOC55216 68 NM 031450 basophilic leukemia expressed protein BLES03 9 NM 013279 hypo hetical protein LOC745 29 NM 0010098.94 hypo hetical protein LOC91298 31 NM 032338 hypo hetical protein LOC84298 32 NM 031465 hypo hetical protein LOC83695 A3 NM 022895 hypo hetical protein LOC64897 S4 NM 152319 hypo hetical protein LOC121273 57 NM 138425 C10 protein 59 NM 153022 hypo hetical protein LOC120939 61 NM 175895 hypo hetical protein LOC283416 NM 020456 hypo hetical protein LOC57213 23 NM O25138 hypo hetical protein LOC80209 21 NM 138360 hypo hetical protein LOC90668 32 NM 020215 hypo hetical protein LOC56967 40 NM O24643 hypo hetical protein LOC79696 51 NM 032714 hypo hetical protein LOC84800 53 NM 032374 hypo hetical protein LOC84334 73 NM OO1031714 hypo hetical protein LOC64423 isoform 1 28 NM 001017923 hetical protein LOC 22525 32 MAPK-interacting and spindle-stabilizing A. chromosome 14 open rea ing frame 4 A3 hypo hetical protein LOC91748 58 hypo hetical protein LOC55640 68 chromosome 14 open rea ing frame 68 79 hetical protein LOC 22616 92 rmal Langerhans cel protein LCP1 2O helicase homolog PIF1 37 hetical protein LOC283.687 38 hetical protein LOC348110 25 hetical protein LOC 24093 isoform 2 3 hetical protein LOC750 34 chromosome 16 open rea ing frame 34 5 cell eath inducing protein SO chromosome 16 open rea ing frame 50 S4 NM 75900 hypo hetical protein LOC283897 57 NM O24598 hypo hetical protein LOC79.650 58 NM 022744 hypo hetical protein LOC64755 7 NM OO4913 chromosome 16 open rea ing frame 7 27 NM 020914 open rea ing frame 27 28 NM 030630 hypo hetical protein LOC283987 32 NM 52464 hypo hetical protein LOC 47007 53 hypo hetical protein LOC78995 55 hypo hetical protein LOC284.185 65 hypo hetical protein LOC3392.01 74 hypo hetical protein LOC201243 hypo hetical protein LOC753 isoform gamma 1 hypo hetical protein LOC125228 chromosome 18 open reading frame 25 isoform b hypo hetical protein LOC92126 chromosome 18 open reading frame 43 hypo hetical protein LOC162681 hypo hetical protein LOC126353 hypo hetical protein LOC148223 hypo hetical protein LOC126321 hypo hetical protein LOC404664 hypo hetical protein LOC126299 US 2009/0227533 A1 Sep. 10, 2009 21

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description C19Corfa. NM 012109 brain-specific membrane-anchored protein C19Crf6 NM 001033026 membralin isoform 1 C1orf106 NM 018265 hypothetical protein LOC55765 C1orf107 NM 014388 hypothetical protein LOC27042 C1orf109 NM O17850 hypothetical protein LOC54955 C1orf115 NM O24709 hypothetical protein LOC79762 C1orf116 NM O23938 specifically androgen-regulated protein C1orf119 NM 020141 hypothetical protein LOC56900 C1orf126 NM 182534 hypothetical protein LOC200197 C1orf128 NM O2O362 hioredoxin family Trp26 C1orf144 NM O15609 putative MAPK activating protein PM20, PM21 C1orf145 NM 001025495 hypothetical protein LOC574407 C1orf147 NM 001025592 hypothetical protein LOC574431 C1orf151 NM 001.032363 chromosome 1 open reading frame 151 protein C1orf159 NM O17891 hypothetical protein LOC54991 C1orf162 NM 174896 hypothetical protein LOC128346 C1orf163 NM O23.077 hypothetical protein LOC65260 C1orf183 NM O19099 hypothetical protein LOC55924 isoform 1 C1orf19 NM 052965 hypothetical protein LOC116461 C1orf21 NM 030806 chromosome 1 open reading frame 21 C1orf24 NM 052966 niban protein isoform 2 C1orf26 NM O17673 hypothetical protein LOC54823 C1orf58 NM 004848 -induced gene isoform 1 C1orf249 NM 03.2126 hypothetical protein LOC84.066 C1orf62 NM 152763 hypothetical protein LOC25.4268 C1orf69 NM 001010867 hypothetical protein LOC200205 C1orf71 NM 152609 hypothetical protein LOC163882 C1orf74 NM 152485 hypothetical protein LOC148304 C1orf&2 NM 024.813 hypothetical protein LOC79871 C1orf&4 NM 1825.18 RP11-506B15.1 protein isoform 3 C1orf NM O14283 chromosome 1 open reading frame 9 protein C1orf1 NM 019118 hypothetical protein LOC56063 C1orf3 NM 152371 hypothetical protein LOC127281 C1orf5 NM 001003665 hypothetical protein LOC375057 C1orf6 NM 145257 hypothetical protein LOC126731 C1QG NM 172369 complement component 1, Subcomponent, gamma C1QDC1 NM 001002259 C1q domain containing 1 isoform 1 C1QL1 NM OO6688 complement component 1, q. Subcomponent-like 1 C1OTNF1 NM 030968 C1q and tumor necrosis factor related protein 1 C1QTNF7 NM 03.1911 C1q and tumor necrosis factor related protein 7 C1OTNF8 NM 207419 hypothetical protein LOC390664 C2 NM OOOO63 complement component 2 precursor C20orf100 NM 032883 chromosome 20 open reading frame 100 C20orf102 NM 080607 hypothetical protein LOC128434 C20orf11 NM O17896 chromosome 20 open reading frame 11 C20orf112 NM 080616 hypothetical protein LOC140688 C20orf117 NM 080627 hypothetical protein LOC140710 isoform 1 C20orf118 NM 080628 hypothetical protein LOC140711 C20orf134 NM 001024675 hypothetical protein LOC170487 C20orf173 NM 080828 hypothetical protein LOC140873 C20orf2O NM 018270 MRG-binding protein C20orf59 NM O24893 hypothetical protein LOC79953 C20orf242 NM O17671 chromosome 20 open reading frame 42 C20orf243 NM 016407 hypothetical protein LOC51507 C20orf77 NM 021215 hypothetical protein LOC58490 C20orf3 NM O24958 hypothetical protein LOC80023 C21orf124 NM 032920 hypothetical protein LOC85006 C21orf128 NM 152507 hypothetical protein LOC150147 C21orf129 NM 152506 hypothetical protein LOC15O135 C21orf25 NM 199050 hypothetical protein LOC25966 C21orf58 NM 199071 hypothetical protein LOC54058 isoform 2 C21orf6 NM 016940 hypothetical protein LOC10069 C21orf69 NM 0581.89 open reading frame 69 C21orf7 NM O2O152 chromosome 21 open reading frame 7 C21orf70 NM 058190 hypothetical protein LOC85395 C21orf3 NM 145179 hypothetical protein LOC246704 C22Orf15 NM 182520 hypothetical protein LOC150248 C22Orf23 NM 032561 hypothetical protein LOC84645 C22Orf25 NM 152906 hypothetical protein LOC128989 C22Orfs NM 012264 open reading frame 5 US 2009/0227533 A1 Sep. 10, 2009 22

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 00100988O hypothetical protein LOC23313 isoform b NM 1447O6 hypothetical protein LOC150590 NM 032266 hypothetical protein LOC84226 NM O17877 hypothetical protein LOCS4978 NM 001025072 hypothetical protein LOC25871 isoform b NM 016210 hypothetical protein LOCS1161 NM 153215 hypothetical protein LOC132228 NM 173552 hypothetical protein LOC20S428 hypothetical protein LOC37S341 retinoblastoma-associated protein 140 FBI4 protein hypothetical protein LOC84068 isoform b hypothetical protein LOC285613 hypothetical protein LOC79614 hypothetical protein LOC134SS3 chromosome 6 open reading frame 106 isoform b hypothetical protein LOC112609 hypothetical protein LOC387263 chromosome 6 open reading frame 122 hypothetical protein LOC79969 isoform 2 hypothetical protein LOC221749 hypothetical protein LOCS27128

hypothetical protein LOC88745 NM 145025 hypothetical protein LOC221264 NM 018452 hypothetical protein LOCSS836 NM021184 NM 013397 over-expressed breas tumor protein NM 203395 chromosome 6 open reading frame 71 NM 152734 hypothetical protein LOC221477 NM 152743 hypothetical protein LOC221927 NM 178829 hypothetical protein LOC135927 NM 004337 hypothetical protein LOC734 NM 053279 hypothetical protein LOC83648 NM 016458 brain protein 16 NM O23O80 hypothetical protein LOC6526S NM 177965 hypothetical protein LOC157657 hypothetical protein LOCS6260 hypothetical protein LOC2S4778 hypothetical protein LOC606SS3 hypothetical protein LOC78998 mesenchymal stem cell protein DSCD75 hypothetical protein LOCS41565 hypothetical protein LOC15.7376 hypothetical protein LOC414318 hypothetical protein LOC158293 chromosome 9 open reading frame 111 hypothetical protein LOCS1490 hypothetical protein LOC843O2 hypothetical protein LOC89958 hypothetical protein LOC4O1546 hypothetical protein LOC138716 hypothetical protein LOC2O3259 hypothetical protein LOC89853 isoform 2 NM 138333 hypothetical protein LOC116224 NM 030814 hypothetical protein LOC81571 NM 001001938 hypothetical protein LOC286223 NM OO10O2260 chromosome 9 open reading frame 58 isoform 2 NM 017586 hypothetical protein LOC11094 NM 173691 hypothetical protein LOC286262 NM O24718 hypothetical protein LOCSS684 NM 139246 hypothetical protein LOC158427 NM O2O178 carbonic anhydrase X NM OO1218 carbonic anhydrase XII isoform 1 precursor NM 001014435 carbonic anhydrase VII isoform 2 NM 001216 carbonic anhydrase IX precursor NM 03.1215 CdkS and Ab1 enzyme substrate 2 NM OO1033677 calcium binding protein 1 isoform 3 NM 020925 cache domain containing 1 NM 000721 calcium channel, Voltage-dependent, alpha 1E US 2009/0227533 A1 Sep. 10, 2009 23

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description CACNA1I NM OO10O3406 voltage-dependent T-type calcium channel CACNA2D2 NM 001005.505 calcium channel, Voltage-dependent, alpha CACNA2D4 NM 001005.737 voltage-gated calcium channel alpha(2) delta-4 CACNB1 NM 000723 calcium channel, Voltage-dependent, beta 1 CACNB3 NM 000725 calcium channel, Voltage-dependent, beta 3 CACNG4 NM O14405 voltage-dependent calcium channel gamma-4 CADPS NM 003716 Ca2+-dependent secretion activator isoform 1 CALB1 NM 004929 cabindin 1 CALCA NM OO 1033953 calcitonin isoform CGRP preproprotein CALCB NM 000728 calcitonin-related polypeptide, beta CALCOCO2 NM OO5831 calcium binding and coiled-coil domain 2 CALCR NM OO1742 calcitonin receptor CALM3 NM 005184 calmodulin 3 CALML3 NM 005185 calmodulin-like 3 CALMLS NM O17422 calmodulin-like skin protein CALN1 NM 001017440 calneuron 1 CAMK2B NM OO1220 calcium calmodulin-dependent protein kinase IIB CAMKK1 NM 032294 calcium calmodulin-dependent protein kinase 1 CAMKK2 NM 172214 calcium calmodulin-dependent protein kinase CAMLG NM OO1745 calcium modulating ligand CAMSAP1 NM 015447 calmodulin regulated -associated protein CAMTA1 NM O15215 calmodulin-binding transcription activator 1 CAMTA2 NM O15099 calmodulin binding transcription activator 2 CAP1 NM OO6367 adenylyl cyclase-associated protein CAPN3 NM 212467 calpain 3 isoformh CAPNS NM 004.055 calpain 5 CAPN6 NMO14289 calpain 6 CAPN9 NM 016452 calpain 9 isoform 2 CAPNS1 NM OO10O3962 calpain, Small subunit 1 CARD4 NM OO6092 caspase recruitment domain family, member 4 CARD9 NM 052813 caspase recruitment domain protein 9 CARKL NM 013276 carbohydrate kinase-like CARM1 NM 199141 coactivator-associated arginine CASKIN1 NM 020764 CASK interacting protein 1 CASKIN2 NM 020753 cask-interacting protein 2 CASP2 NM 032982 caspase 2 isoform 1 preproprotein CASP4 NM 033307 caspase 4 isoform delta CASP6 NM 001226 caspase 6 isoform alpha preproprotein CASP7 NM OO1227 caspase 7 isoform alpha precursor CASR NM 000388 calcium-sensing receptor CAST1 NM O15576 cytomatrix protein p110 CASZ1 NM O17766 castor homolog 1, Zinc finger CAV NM OO1753 caveolin 1 CAV2 NM OO1233 caveolin 2 isoform a and b CAV3 NM 001234 caveolin 3 CB NM OO1032999 core-binding factor, runt domain, alpha Subunit CB NM 005187 myeloid translocation gene-related protein 2 CB NM OO1755 core-binding factor, beta Subunit isoform 2 CB NM 012116 Cas-Br-M (murine) ecotropic retroviral CB NM 004352 cerebellin 1 precursor CB NM 080617 cerebellin 4 precursor CBS NM OOOO71 cystathionine-beta-synthase NM 005189 chromobox homolog 2 isoform 1 NM OO7276 chromobox homolog 3 NM O14292 chromobox homolog 6 CC NM OO4059 cytoplasmic cysteine conjugate-beta lyase CC NM 024296 coiled-coil domain containing 28B CC NM 031455 coiled-coil domain containing 3 CC NM 1827.91 hypothetical protein LOC80125 CC NM 144609 hypothetical protein LOC1248.08 CC NM O24768 hypothetical protein LOC79825 CC NM O17748 hypothetical protein LOC54883 CC NM 174908 Ymer protein short isoform CC NM 144718 coiled-coil domain containing 52 CC NM 005436 coiled-coil domain containing 6 CC NM O25214 CTCL tumor antigen se57-1 CC NM O15621 hypothetical protein LOC26112 CC NM 024098 coiled-coil domain containing 86 CC NM 052848 hypothetical protein LOC90324 CC NM OO2990 Small inducible cytokine A22 precursor US 2009/0227533 A1 Sep. 10, 2009 24

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description CCND1 NM 053056 cyclin D1 CCND2 NM OO1759 cyclin D2 CCND3 NM OO1760 cyclin D3 CCNE2 NM 057735 cyclin E2 isoform 2 CCNF NM OO1761 cyclin F CCNG1 NM 004060 cyclin G1 CCNJ NM O19084 cyclin J CCR1 NM 001295 chemokine (C-C motif) receptor 1 CCRL1 NM O16557 chemokine (C-C motif) receptor-like 1 D109 NM 133493 D109 D14 NM 000591 D14 antigen precursor D151 NM 004357 D151 antigen D160 NM 007053 D160 antigen D164L2 NM 207397 D164 sialomucin-like 2 D18O NM OO5582 D180 antigen D2OO NM 0010041.96 D200 antigen isoform b D247 NM OOO734 cell receptor Zeta chain isoform 2 precursor D276 NM 001024736 D276 antigen isoform a D28 NM OO6139 D28 antigen NM OOO733 D3E antigen, epsilon polypeptide (TIT3 NM OOOO74 D40 ligand NM 000610 D44 antigen isoform 1 precursor D46 NM 002389 D46 antigen, complement regulatory protein D47 NM 001025079 D47 molecule isoform 3 precursor NM 000611 D59 antigen p18-20 NM OO3874 D84 antigen (leukocyte antigen) NMOO6889 D86 antigen isoform 2 precursor NM OO1768 D8 antigen alpha polypeptide isoform 1 D97 NM 001025160 D97 antigen isoform 3 precursor D99L2 NM 031462 D99 antigen-like 2 isoform E3'-E4'-E3-E4 DA NM OO1785 cytidine deaminase DADC1 NM 030911 cytidine and dCMP deaminase domain containing 1 DAN1 NM 138477 codanin 1 DC23 NM 004661 cell division cycle protein 23 DC25A NM OO1789 cell division cycle 25A isoform a DC2L6 NM O15076 cyclin-dependent kinase (CDC2-like) 11 DC37 NM 007065 CDC37 homolog DC4O NM O15891 cell division cycle 40 homolog DC42BPB NM OO6035 CDC42-bindin protein kinase beta DC42EP1 NM 007061 CDC42 effector protein 1 isoform b DC42EP4 NM 012121 Cdc42 effector protein 4 DC42SE1 NM O2O239 CDC42 Small effector 1 DCAS NM 080668 cell division cycle associated 5 DCA8 NM 018101 cell division cycle associated 8 DGAP NM 020754 Cdc42 GTPase-activating protein DH13 NM OO1257 cadherin 13 preproprotein DH16 NM 004.062 cadherin 16 precursor DH17 NM 004O63 cadherin 17 precursor DH6 NM OO4932 cadherin 6, type 2 preproprotein DH9 NM O16279 cadherin 9, type 2 preproprotein DK10 NM 052988 cyclin-dependent kinase 10 isoform 3 DK2AP1 NM 004642 CDK2-associated protein 1 DKSR2 NM OO3936 cyclin-dependent kinase 5, regulatory subunit 2 DK6 NM OO1259 cyclin-dependent kinase 6 DKN1B NM 004.064 cyclin-dependent kinase inhibitor 1B DON NM 016952 Surface glycoprotein, Ig Superfamily member DRT4 NM 173622 hypothetical protein LOC284040 EACAM1 NM 001024912 carcinoembryonic antigen-related cell adhesion EACAM21 NM 033.543 carcinoembryonic antigen-related cell adhesion EACAM7 NM OO6890 carcinoembryonic antigen-related cell adhesion EACAM8 NM 001816 carcinoembryonic antigen-related cell adhesion EECAM1 NM O16174 cerebral endothelial cell adhesion molecule 1 ELSR1 NM O14246 cadherin EGF LAG seven-pass G-type receptor 1 ELSR2 NM OO1408 cadherin EGF LAG seven-pass G-type receptor 2 ELSR3 NM OO1407 cadherin EGF LAG seven-pass G-type receptor 3 ENPB NM OO1810 centromere protein B ENTG1 NM 014770 centaurin, gamma 1 EP192 NM 018069 hypothetical protein LOC55125 isoform 2 EP250 NM 007186 centrosomal protein 2 isoform 1 EP55 NM 018131 centrosomal protein 55 kDa US 2009/0227533 A1 Sep. 10, 2009 25

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description EP72 NM 018140 centrosomal protein 72 kDa ERK NM O22766 ceramide kinase isoform a FD NM OO1928 complement factor D preproprotein FTR NM 000492 cystic fibrosis transmembrane conductance GA. NM OOO735 glycoprotein hormones, alpha polypeptide GGBP1 NM OO10O8390 CGG triplet repeat binding protein 1 GNL1 NM 032866 cingulin-like 1 HCHDS NM 032309 coiled-coil-helix-coiled-coil-helix domain HCHD7 NM 001011667 coiled-coil-helix-coiled-coil-helix domain HD1 NM OO1270 hromodomain helicase DNA binding protein 1 HD2 NM OO1271 hromodomain helicase DNA binding protein 2 HD3 NM 001005271 hromodomain helicase DNA binding protein 3 HDS NM O15557 hromodomain helicase DNA binding protein 5 HERP NM OO6387 alcium homeostasis endoplasmic reticulum HES1 NM 005197 heckpoint Suppressor 1 HKB NM 152253 holine ethanolamine kinase isoform b HMP4A NM 014169 hromatin modifying protein 4A HMP7 NM 152272 CHMP family, member 7 HR415SYT NM 001014372 hr415 synaptotagmin HRAC1 NM 017444 hromatin accessibility complex 1 HRD NM 177978 hordin isoform b HRFAM7A NM 1393.20 CHRNA7-FAM7A fusion isoform 1 HRNA7 NM OOO746 holinergic receptor, nicotinic, alpha 7 HRNE NM 000080 icotinic acetylcholine receptor epsilon HST1 NM OO3654 arbohydrate (keratan sulfate Gal-6) HST10 NM 004854 HNK-1 sulfotransferase HST12 NMO18641 arbohydrate (chondroitin 4) sulfotransferase HST13 NM 152889 arbohydrate (chondroitin 4) sulfotransferase HST3 NM OO4273 arbohydrate (chondroitin 6) sulfotransferase 3 B2 NM OO6383 DNA-dependent protein kinase catalytic RBP NM 001280 old inducible RNA binding protein TED2 NM OO6079 Cbp/p300-interacting transactivator, with TED4 NM 133467 Cbp/p300-interacting transactivator, with KAP NM 001281 associated protein 1 KAP4 NM OO6825 cytoskeleton-associated protein 4 LASP1 NM O15282 CLIP-associating protein 1 LDN NM 021101 audin 1 LDN NM 012129 audin 12 LDN NM O14343 audin 15 isoform 1 LDN NM OO1002026 audin 18 isoform 2 LDN NM 148960 audin 19 LDN2 NM O2O384 audin 2 LDN6 NM 021195 audin 6 LDN9 NM 020982 audin 9 LDND1 NM 019895 audin domain containing 1 protein isoform a LEC2A NM 207375 C-type lectin domain family 2, member A LICS NM 016929 C hloride intracellular channel 5 LIC6 NM 053277 C hloride intracellular channel 6 NM O15526 CLIP-170-related protein NM 001025233 hypothetical protein LOC574028 NM O17882 CLN6 protein NM 004898 ock NM 030813 Suppressor of potassium transport defect 3 NM 0221.31 alsyntenin 2 NM 030629 -Maf-inducing protein Tc-mip isoform NM 181521 hemokine-like factor Superfamily 4 isoform 2 NM 194293 ardiomyopathy associated 1 NM 032488 ornifelin NM OO5140 cyclic nucleotide gated channel alpha 2 NM 001298 cyclic nucleotide gated channel alpha 3 NM 001297 cyclic nucleotide gated channel beta 1 NM 173515 CNKSR family member 3 NM O17623 cyclin M3 isoform 1 NM 020184 cyclin M4 NM OO10O8225 CCR4-NOT transcription complex, subunit 4 NM O15455 CCR4-NOT transcription complex, subunit 6 NM 054026 CCR4-NOT transcription complex, subunit 7 NM 033133 2',3'-cyclic nucleotide 3' phosphodiesterase NM 000614 ciliary neurotrophic factor NM 005076 contactin 2 precursor US 2009/0227533 A1 Sep. 10, 2009 26

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description CNTN3 NM 020872 contactin 3 CNTN4 NM 1756O7 contactin 4 isoform a precursor CNTNAP1 NM 003632 contactin associated protein 1 CNTNAP2 NM 014141 cell recognition molecule Caspir2 precursor CNTNAP4 NM 033401 cell recognition protein CASPR4 isoform 1 CNTNAP5 NM 130773 contactin associated protein-like 5 isoform 1 COBRA1 NM O15456 cofactor of BRCA1 COG3 NM 031431 component of golgi transport complex 3 COG6 NM 020751 component of oligomeric golgi complex 6 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 COL20A1 NM 020882 collagen-like protein COL22A1 NM 152888 collagen, type XXII, alpha 1 COL23A1 NM 173465 collagen, type XXIII, alpha 1 COL25A1 NM 032518 collagen, type XXV, alpha 1 isoform 2 COL2A1 NM OO1844 alpha 1 type II collagen isoform 1 COL4A2 NM 001846 alpha 2 type IV collagen preproprotein COL4A4 NM 000092 alpha 4 type IV collagen precursor COLSA1 NM 000093 alpha 1 preproprotein COL6A2 NM 058175 alpha 2 type VI collagen isoform 2C2a precursor COMMD3 NM 012071 COMM domain containing 3 COMMD4 NM 017828 COMM domain containing 4 COMMDS NM 014066 hypertension-related calcium-regulated gene COMMD9 NM 014186 COMM domain containing 9 COPS7B NM O22730 COP9 constitutive photomorphogenic homolog COPZ1 NM O16057 coatomer protein complex, subunit Zeta 1 COQ9 NM 020312 hypothetical protein LOC57017 CORIN NM OO6587 corin CORO1B NM 001018070 coronin, actin binding protein, 1B CORO1C NM O14325 coronin, actin binding protein, 1C CORO2B NM OO6091 coronin, actin binding protein, 2B CORO6 NM 032854 coronin 6 COVA1 NM OO6375 cytosolic ovarian carcinoma antigen 1 isoform a COX10 NM OO1303 heme A:farnesyltransferase COX7A2 NM OO1865 cytochrome c oxidase subunit Vila polypeptide 2 PA4 NM 016352 carboxypeptidase A4 preproprotein PA6 NM O2O361 carboxypeptidase B precursor PD NM OO1304 carboxypeptidase D precursor PEB2 NM 182485 cytoplasmic polyadenylation element binding PEB3 NM O14912 cytoplasmic polyadenylation element binding PLX2 NM OO10O8220 complexin 2 NM 0010055O2 carboxypeptidase M precursor NM 020939 copine V NM OO6693 cleavage and polyadenylation specific factor 4, NM 007007 cleavage and polyadenylation specific factor 6, NM OO1 OO6658 complement component (3d Epstein Barr virus) NM OO1878 cellular retinoic acid binding protein 2 NM 020825 Crm, cramped-like NM 201253 crumbs homolog 1 precursor NM 173689 crumbs homolog 2 NM 139161 crumbs 3 isoform a precursor NM 052854 cAMP responsive element binding protein 3-like NM 194071 cAMP responsive element binding protein 3-like NM 0326O7 cAMP responsive element binding protein 3-like NM 001011666 cAMP responsive element binding protein 5 NM OO3851 cellular repressor of E1A-stimulated genes 2 NM 153836 cellular repressor of E1A-stimulated genes 2 H R 1 NM 004382 corticotropin releasing 1 NM O14335 CREBBP, EP300 inhibitor 1 2 NM 001312 cysteine-rich protein 2 SPLD2 NM 031476 cysteine-rich Secretory protein LCCL domain NM OO52O6 v-crk sarcoma virus CT10 oncogene homolog RMP1 NM 001014809 collapsin response mediator protein 1 isoform 1 RNKL1 NM 016652 crooked neck-like 1 protein NM OOO567 C-reactive protein, pentraxin-related RSP7 NM 004831 cofactor required for Sp1 transcriptional RSP8 NM 004269 cofactor required for Sp1 transcriptional RTAP NM OO6371 cartilage associated protein precursor RTC1 NM O15321 mucoepidermoid carcinoma translocated 1 isoform US 2009/0227533 A1 Sep. 10, 2009 27

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description CRTC3 NM O22769 transducer of regulated CREB protein 3 CRY2 NM 021117 cryptochrome 2 (photolyase-like) CRYZL.1 NM 145858 crystallin, Zeta-like 1 CSDC2 NM O14460 RNA-binding protein pippin CSF1R NM OO5211 colony stimulating factor 1 receptor precursor CSMD1 NM 033225 CUB and Sushi multiple domains 1 CSNK1A1 NM OO O25105 casein kinase 1, alpha 1 isoform 1 CSNK1 G1 NM OO O11664 casein kinase 1, gamma 1 isoform L. CSNK1G3 NM OO O31812 casein kinase 1, gamma 3 isoform 2 CSRP1 NM 004.078 cysteine and glycine-rich protein 1 CST.9 O08693 cystatin 9 CTCF NM OO6565 CCCTC-binding factor CTCFL NM 080618 CCCTC-binding factor-like protein CTDSP1 198 CTD (carboxy-terminal domain, RNA polymerase II, CTDSP2 NM OO5730 nuclear LIM interactor-interacting factor 2 CTDSPL NM OO O08392 Small CTD phosphatase 3 isoform 1 CTF1 NM OO 330 cardiotrophin 1 CTNNBIP1 NM OO O12329 , beta interacting protein 1 CTNND1 NM OO 331 catenin (cadherin-associated protein), delta 1 CTNND2 NM OO 332 catenin (cadherin-associated protein), delta 2 CTPS NM OO 905 CTP synthase CTPS2 NM 019857 cytidine triphosphate synthase II CTSB 908 cathepsin B preproprotein CTSC NM 148170 cathepsin C isoform b precursor CTSW NM OO 335 cathepsin W preproprotein CTTNBP2NL NM 018704 hypothetical protein LOC55917 CUEDC1 NMO17949 CUE domain-containing 1 CUGBP2 NM OO O25076 CUG triplet repeat, RNA binding protein 2 CUL5 NM OO3478 Vasopressin-activated calcium-mobilizing CUTL2 NM O15267 cut-like 2 CX3CR1 NM OO 337 chemokine (C-X3-C motif) receptor 1 CXCL1 NM OO 511 chemokine (C-X-C motif) ligand 1 CXCL10 NM OO 565 Small inducible cytokine B10 precursor CXCL11 NM OO5409 Small inducible cytokine B11 precursor CXCL12 NM OOO609 chemokine (C-X-C motif) ligand 12 (stromal CXCL14 NM OO4887 Small inducible cytokine B14 precursor CXCL16 NM O22059 chemokine (C-X-C motif) ligand 16 CXCL2 NM O02089 chemokine (C-X-C motif) ligand 2 CXCLS NM OO2994 chemokine (C-X-C motif) ligand 5 precursor CXCR3 NM OO1504 chemokine (C-X-C motif) receptor 3 CXorf12 NM OO3492 chromosome X open reading frame 12 CXorf15 NM 018360 gamma-taxilin CXorf NM 018990 SH3 protein expressed in lymphocytes CYB561D2 NM 007022 cytochrome b-561 domain containing 2 CYB5B NM O30579 cytochrome b5 outer mitochondrial membrane CYB5R2 NM OO1 OO1336 cytochrome b5 reductase b5R.2 isoform 2 CYBASC3 NM 153611 cytochrome b, ascorbate dependent 3 CYBRD1 NM 024843 cytochrome b reductase 1 CYCS NM 018947 cytochromec CYP11B1 NM 000497 cytochrome P450, family 11, subfamily B, CYP19A1 NM OOO103 cytochrome P450, family 19 CYP2OA1 NM O2O674 cytochrome P450, family 20, subfamily A, CYP27B1 NM OOO785 cytochrome P450, family 27, subfamily B, CYP4F3 NM OOO896 cytochrome P450, family 4, Subfamily F, CYP4F8 NM 007253 cytochrome P450, family 4, Subfamily F, CYR61 NM OO1554 cysteine-rich, angiogenic inducer, 61 CYYR1 NM 052954 cysteine and tyrosine-rich 1 protein precursor D1 SWS75e NM O15704 hypothetical protein LOC27351 D2HGDH NM 152783 D-2-hydroxyglutarate dehydrogenase D4ST1 NM 130468 dermatan 4 Sulfotransferase 1 DAAM1 NM 014992 dishevelled-associated activator of DAAM2 NM O15345 dishevelled associated activator of DAB2IP NM 032552 DAB2 interacting protein isoform 1 DAG1 NM 004393 1 precursor DAK NM O15533 dihydroxyacetone kinase 2 DAO NM OO1917 D-amino-acid oxidase DAPK2 NM O14326 death-associated protein kinase 2 DARC NM 002036 Duffy blood group DBC1 NM 014618 deleted in bladder cancer 1 DBF4B NM 145663 DBF4 homolog B isoform 1 US 2009/0227533 A1 Sep. 10, 2009 28

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description DBNDD1 NM 024043 dysbindin (dystrobrevin binding protein 1) DBNDD2 NM 033542 SCF apoptosis response protein 1 isoform 2 DBNL NM 001014436 drebrin-like isoform b DCBLD1 NM 173674 discoidin, CUB and LCCL domain containing 1 DCLRE1B NM 022836 DNA cross-link repair 1B (PSO2 homolog, S. DCST2 NM 144622 hypothetical protein LOC127579 DCTNS NM 032486 dynactin 4 DCUN1D3 NM 173475 hypothetical protein LOC123879 DCX NM 000555 doublecortin isoform a DB NM OO1923 damage-specific DNA binding protein 1 DEF1 NM 018482 development and differentiation enhancing factor DEF2 NM 003887 development-and differentiation-enhancing DN NM O15086 dendrin DX NM 004398 EAD (Asp-Glu-Ala-Asp) box polypeptide 10 DX NM 004399 EAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 DX NM OO6386 EAD box polypeptide 17 isoform p82 DX19A NM 018332 DX19-like protein DX19B NM 001014449 EAD (Asp-Glu-Ala-As) box polypeptide 19 isoform DX19-DDX19L. NM 001015047 DX19-DDX19L protein DX21 NM OO4728 EAD (Asp-Glu-Ala-Asp) box polypeptide 21 NM 182540 hypothetical protein LOC203522 DX41 NM 016222 DEAD-box protein abstrakt DX58 NM 014314 DEAD H (Asp-Glu-Ala-Asp/His) box polypeptide NM 031306 DEAD (Asp-Glu-Ala-Asp) box polypeptide 59 EADC1 NM 182503 deaminase domain containing 1 EDD2 NM 133328 death effector domain-containing DNA binding ENND1A NM020946 hypothetical protein LOC57706 isoform 1 ENND2D NM 024901 DENN/MADD domain containing 2D EPDC5 NM 014662 DEP domain containing 5 isoform 1 EPDC6 NM O22783 DEP domain containing 6 ERL3 NM OO10O2862 erlin-3 protein isoform b FFA NM 004401 DNA fragmentation factor, 45 kDa, alpha DFNB31 NM 015404 CASK-interacting protein C1P98 DGAT1 NM 012079 iacylglycerol O-acyltransferase 1 DGAT2 NM 032564 iacylglycerol O-acyltransferase homolog 2 DGAT2L6 NM 198512 iacylglycerol O-acyltransferase 2 like 6 DGCR13 NM 001024733 DiGeorge syndrome gene H DGCR2 NM OO5137 integral membrane protein DGCR2 DGCR6 NM OO5675 DiGeorge syndrome critical region protein 6 NM 033257 DiGeorge syndrome critical region gene 6 like DGKB NM 145695 iacylglycerol kinase, beta isoform 2 DGKI NM 004717 iacylglycerol kinase, iota NM 003646 iacylglycerol kinase, Zeta 104 kDa isoform 2 HCR 24 NM 014762 24-dehydrocholesterol reductase precursor HCR7 NM OO1360 7-dehydrocholesterol reductase HTKDI NM 0187O6 ehydrogenase E1 and transketolase domain NM 194428 DEAH (Asp-Glu-Ala-His) box polypeptide 34 NM O24612 DEAH (Asp-Glu-Ala-His) box polypeptide 40 ABLO NM 019887 iablo isoform 1 precursor CER1 NM 030621 icer DO1 NM 022105 eath inducer-obliterator 1 isoform a NM O15124 eath-inducing-protein NM O14974 hypothetical protein LOC22982 RAS1 NM 145173 Small GTP-binding tumor suppressor 1 SC1 NM 001012957 isrupted in schizophrenia 1 isoform LV SP2 NM 033510 ispatched B NM 033425 DIX domain containing 1 isoform b NM 194295 hypothetical protein LOC196968 NM 001003.399 hypothetical protein LOC400169 NM 0321.21 implantation-associated protein NM 0010099.13 hypothetical protein LOC374383 NM 173463 hypothetical protein LOC91050 NM 031297 hypothetical protein LOC83459 NM 001010903 hypothetical protein LOC38.9384 NM 012242 dickkopfhomolog 1 precursor LAT NM OO1931 dihydrolipoamide S-acetyltransferase (E2 LEC1 NM OO7335 deleted in lung and esophageal cancer 1 isoform LGS NM 004747 discs large homolog 5 LGAP2 NM 004745 discs large-associated protein 2 LL1 NM OO5618 delta-like 1 US 2009/0227533 A1 Sep. 10, 2009 29

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description DLL4 NM O19074 delta-like 4 protein precursor DLX NM 178120 distal-less homeobox 1 isoform 1 NM OO5220 distal-less homeobox 3 NM 033053 DMRT-like family C1 NM 004943 dystrophia myotonica-containing WD repeat motif NM 207437 , axonemal, heavy polypeptide 10 NM OO6145 DnaJ (Hsp40) homolog, subfamily B, member 1 NM 001002762 DnaJ (Hsp40) homolog, subfamily B, member 12 NM OO6736 DnaJ (Hsp40) homolog, subfamily B, member 2 NM 018981 DnaJ (Hsp40) homolog, subfamily C, member 10 NM 018198 DnaJ (Hsp40) homolog, subfamily C, member 11 NM 032364 opamine receptor interacting protein NM 1526.86 DnaJ (Hsp40) homolog, subfamily C, member 18 DNAL4 NM OO5740 ynein light chain 4, axonemal DNALI1 NM 003462 axonemal dynein light chain DNASE1L2 NM OO1374 eoxyribonuclease I-like 2 DNMIL NM OO5690 ynamin 1-like protein isoform 3 DNM3 NM O15569 ynamin 3 DNMT3A NM 175630 DNA cytosine methyltransferase 3alpha isoform DOCK3 NM OO4947 edicator of cytokinesis 3 DOCK8 NM 203447 edicator of cytokinesis 8 DOCK9 NM O15296 edicator of cytokinesis 9 DOK4 NM 018110 ownstream of tyrosine kinase 4 DOKS NM 018431 DOK5 protein isoform a DOLPP1 NM 020438 olichyl pyrophosphate phosphatase 1 DPF2 NM OO6268 D4, zinc and double PHD fingers family 2 DPF3 NMO12074 D4, zinc and double PHD fingers, family 3 DPH NM OO1383 iptheria toxin resistance protein required for DPP3 NM 005700 ipeptidyl peptidase III DPP4 NM OO1935 ipeptidylpeptidase IV DPY19L3 NM 207325 py-19-like 3 DPYD NM 000110 ihydropyrimidine dehydrogenase DPYSL3 NM OO1387 ihydropyrimidinase-like 3 DPYSL4 NM OO6426 ihydropyrimidinase-like 4 DR1 NM OO1938 own-regulator of transcription 1 DRD2 NM 000795 opamine receptor D2 isoform long DSC3 NM OO1941 esmocollin 3 isoform Dsc3a preproprotein DSCR1 NM 004414 calcipressin 1 isoform a DSCR3 NM OO6052 Down syndrome critical region protein 3 DTNA NM 001390 ystrobrevin alpha isoform 1 DTX3L NM 138287 eltex 3-like DULLARD NM O15343 ullard homolog DUOX NM O17434 ual oxidase 1 precursor DUOX2 NM O14080 ual oxidase 2 precursor DUSP13 NM 001007271 muscle-restricted dual specificity phosphatase DUSP22 NM O20185 ual specificity phosphatase 22 DUSP3 NM 004O90 ual specificity phosphatase 3 DUSPS NM 004419 ual specificity phosphatase 5 DYNC1LI1 NM 016141 ynein light chain-A DYRK2 NM 003583 ual-specificity tyrosine-(Y)-phosphorylation NM 004.091 transcription factor 2 NM OO1949 E2F transcription factor 3 NM OO1951 E2F transcription factor 5 EAF NM 033083 ELL associated factor 1 EARS2 NM 133451 hypothetical protein LOC1244.54 ECEL1 NM 004826 endothelin converting enzyme-like 1 ECHDC3 NM O24693 enoyl Coenzyme A hydratase domain containing 3 ECOP NM 030796 EGFR-coamplified and overexpressed protein EDAR NM 022336 ectodysplasin A receptor EDARADD NM 080738 EDAR-associated death domain isoform B EDEM3 NM O25.191 ER degradation enhancer, mannosidase alpha-like EDG3 NM OO5226 endothelial differentiation, sphingolipid EDG4 NM 004.720 endothelial differentiation, lysophosphatidic EDN2 NM OO1956 endothelin 2 EDNRA NM OO1957 endothelin receptor type A EDNRB NM 000115 endothelin receptor type B isoform 1 EEF2K NM 013302 elongation factor-2 kinase EEFSEC NM O21937 elongation factor for selenoprotein translation EFCAB1 NM O24593 EF-hand calcium binding domain 1 EFEHD1 NM O252O2 EF hand domain family, member D1 US 2009/0227533 A1 Sep. 10, 2009 30

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM O24329 EF hand domain family, member D2 NM OO4952 ephrin A3 NM 004.429 ephrin-B1 precursor NM 001406 ephrin-B3 precursor NM O22073 egl nine homolog 3 E NM OOO399 early growth response 2 protein E NM 014601 EH-domain containing 2 EHD4 NM 139265 EH-domain containing 4 EI24 NM 001007277 etoposide induced 2.4 isoform 2 EIF2AK1 NM O14413 heme-regulated initiation factor 2-alpha kinase EIF2B5 NM OO3907 eukaryotic translation initiation factor 2B, EIF2C1 NM 012199 eukaryotic translation initiation factor 2C, 1 EIF2C4 NM O17629 eukaryotic translation initiation factor 2C. 4 EIF2S2 NM OO3908 eukaryotic translation initiation factor 2 beta EIF4EBP2 NM 004.096 eukaryotic translation initiation factor 4E EIF4G1 NM OO4953 eukaryotic translation initiation factor 4 R NM OO6874 E74-like factor 2 (ets domain transcription NM 001422 E74-like factor SESE-2b NM OO6532 elongation factor RNA polymerase II NM 152793 hypothetical protein LOC222166 NM O14800 engulfment and cell motility 1 isoform 1 NM 018712 ELMO domain containing 1 NM 018091 elongation protein 3 homolog NM 022142 epididymal sperm binding protein 1 NM OOO117 emerin NM 152463 essential meiotic endonuclease 1 homolog 1 NM 183387 echinoderm associated protein like NM 001423 epithelial membrane protein 1 NM 013447 egf-like module-containing, mucin-like, hormone NM 152939 egf-like module-containing mucin-like receptor 3 NM OO1427 homolog 2 NM 031889 enamelin NM OO6208 ectonucleotide pyrophosphatase/phosphodiesterase NM 207043 endosulfine alpha isoform 2 NM OO1248 ectonucleoside triphosphate diphosphohydrolase NM OO4437 erythrocyte membrane protein band 4.1 NM 004438 ephrin receptor EphA4 NM 004442 ephrin receptor EphB2 isoform 2 precursor NM O14964 epsin 2 isoform b NM O17957 epsin 3 EPS15L1 NM 021235 epidermal growth factor receptor pathway EPSTI1 NM 033255 epithelial stromal interaction 1 isoform 2 ERBB2 NM 001005862 erbB-2 isoform b ERGIC1 NM 001031711 endoplasmic reticulum-golgi intermediate ERMAP NM 001017922 erythroblast membrane-associated protein ESPN NM 031475 ESRRA NM 004.451 estrogen-related receptor alpha ESRRG NM 001438 estrogen-related receptor gamma isoform 1 ETS1 NM OO5238 v-ets erythroblastosis virus E26 Oncogene ETV6 NM OO1987 ets variant gene 6 EVA1 NM 144765 epithelial V-like antigen 1 precursor EVC NM 153717 Ellis van Creveld syndrome protein EVISL NM 145245 hypothetical protein LOC115704 EXOSC6 NM 058219 homolog of yeast mRNA transport regulator 3 F11R NM 016946 F11 receptor isoform a precursor F2RL2 NM 004101 coagulation factor II (thrombin) receptor-like 2 F8 NM OOO132 coagulation factor VIII isoform a precursor FABP3 NM 004102 atty acid binding protein 3 FAIM2 NM 012306 Fas apoptotic inhibitory molecule 2 FAM1 OOB NM 182565 hypothetical protein LOC283991 FAM101A NM 181709 hypothetical protein LOC144347 FAM101B NM 182705 hypothetical protein LOC359845 FAM102A NM 203305 early estrogen-induced gene 1 protein isoform b FAM104A NM 032837 hypothetical protein LOC84923 FAM1 OSB NM 138348 hypothetical protein LOC90268 FAM107A NM 007177 downregulated in renal cell carcinoma FAM109A NM 144671 hypothetical protein LOC144717 FAM109B NM 001002034 hypothetical protein LOC150368 FAM111B NM 198947 hypothetical protein LOC374393 FAM112A NM 001.008901 hypothetical protein LOC149699 isoform 2 US 2009/0227533 A1 Sep. 10, 2009 31

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description FAM11A NM 032508 amily with sequence similarity 11, member A FAM26C NM 001001412 hypothetical protein LOC255022 FAM36A NM 198076 amily with sequence similarity 36, member A FAM38A NM 014745 amily with sequence similarity 38, member A FAM3A NM O21806 amily 3, member A protein FAM3C NM O14888 amily with sequence similarity 3, member C FAM3D NM 138805 amily with sequence similarity 3, member D FAM49B NM 016623 hypothetical protein LOC51571 FAM51A1 NM O17856 amily with sequence similarity 51, member Al FAMS3A NM 001013622 dorsal neural-tube nuclear protein FAMS3B NM 014661 hypothetical protein LOC9679 FAMS3C NM 016605 amily 53, member C protein FAMSSC NM 145037 ical protein LOC91775 FAM60A NM 021238 sequence similarity 60, member A FAM62C NM 03.1913 sequence similarity 62 (C2 domain FAM64A NM O19013 protein LOC54.478 FAM7OA NM O17938 ny O l e protein LOC55026 FAM71A NM 153606 protein LOC149647 FAM73B NM 032809 protein LOC84895 FAM76A NM 152660 sequence similarity 76, member A FAM77C NM O24522 hypothetical protein LOC79570 FAM78A NM 03.3387 hypothetical protein LOC286336 FAM81A NM 152450 hypothetical protein LOC145773 FAM83A NM 032899 hypothetical protein LOC84985 isoform a FAM84A NM 1451.75 FAM86A NM 201400 hypothetical protein LOC196483 isoform 1 FAM86B1 NMO32916 hypothetical protein LOC85002 FAM86C NM 018172 hypothetical protein LOC55199 isoform 1 FAM89B NM 152832 Mouse Mammary Turmor Virus Receptor homolog 1 FAM8A1 NM O16255 Autosomal Highly Conserved Protein FAM92B NM 198491 hypothetical protein LOC339145 FAM9C NM 174901 amily with sequence similarity 9, member C FANCA NM 000135 Fanconi anemia, complementation group A isoform EANCC NM OOO136 Fanconi anemia, complementation group C EANCE NM O21922 Fanconi anemia, complementation group E EANCM NM 020937 Fanconi anemia, complementation group M FARP2 NM 014808 FERM, RhoGEF and pleckstrin domain protein 2 FARSLB NM 005687 phenylalanine-tRNA synthetase-like, beta FAS NM OOOO43 tumor necrosis factor receptor Superfamily, FASN NM 004104 atty acid synthase FAT2 NM OO1447 FAT tumor Suppressor 2 precursor FATE1 NM 033085 etal and adult testis expressed transcript FBLN1 NM OO6485 fibulin 1 isoform B precursor FBXL17 NM 022824 F-box and leucine-rich repeat protein 17 FBXL19 NM O19085 F-box and leucine-rich repeat protein 19 FBXL8 NM 018378 F-box and leucine-rich repeat protein 8 FBXO16 NM 172366 F-box only protein 16 FBXO17 NM 024907 F-box protein FBG4 isoform 2 FBXO25 NM 012173 F-box only protein 25 isoform 3 FBXO3O NM 032145 F-box only protein 30 FBXO34 NM O17943 -box only protein 34 FBXO39 NM 153230 -box protein 39 FBXO40 NM O16298 -box protein 40 FBXO44 NM 001014765 -box protein 44 isoform 1 FBXW4 NM O22039 -box and WD-40 domain protein 4 FBXW9 NM 032301 -box and WD-40 domain protein 9 FCER1G NM 004106 Fc fragment of IgE, high affinity 1, receptor FCGR2B NM OO10O2273 Fc fragment of IgG, low affinity IIb, receptor FCHO2 NM 138782 FCH domain only 2 FCHSD2 NM O14824 FCH and double SH3 domains 2 FCMD NM OO6731 ukutin FCRLS NM 031281 Fc receptor-like 5 FDFT1 NM 004.462 airnesyl-diphosphate farnesyltransferase 1 FEM1A NM 018708 em-1 homologa (C. elegans) FEM1C NM O2O177 eminization 1 homolog a FES NM OO2005 V-FES feline sarcoma viral/V-FPS fujinami avian FETUB NM O14375 etuin B FGD2 NM 173558 FYVE, RhoGEF and PH domain containing 2 FGD3 NM 033086 FYVE, RhoGEF and PH domain containing 3 FGD6 NM 018351 FYVE, RhoGEF and PH domain containing 6 US 2009/0227533 A1 Sep. 10, 2009 32

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description FGF13 NM 004114 fibroblast growth factor 13 isoform 1A FGF2 NM OO2006 fibroblast growth factor 2 FGF23 NM 020638 fibroblast growth factor 23 precursor FGF7 NM OO2009 fibroblast growth factor 7 precursor FGFR1 NM 000604 fibroblast growth factor receptor 1 isoform 1 FGFR2 NM 000141 fibroblast growth factor receptor 2 isoform 1 FGFRL1 NM 001004356 fibroblast growth factor receptor-like 1 FIGN NM 018086 idgetin FKBP1A NM 054014 FK506-binding protein 1A FKBP1B NM 004116 FK506-binding protein 1B isoform a FKBP8 NM 012181 FK506-binding protein 8 FKBP9 NM OO7270 FK506 binding protein 9 FKBP9L. NM 182827 FK506 binding protein 9-like FKSG24 NM 032683 hypothetical protein LOC84769 FLJ10081 NM O17991 hypothetical protein LOC55683 FLJ101.59 NM 018013 hypothetical protein LOC55084 FLJ10241 NM 018035 hypothetical protein LOC55101 FLJ10324 NM 018059 hypothetical protein LOC55698 FLJ104.04 NM O19057 hypothetical protein LOC54540 FLJ10769 NM 018210 hypothetical protein LOC55739 FLJ108O3 NM 018224 hypothetical protein LOC55744 FLJ10815 NM 018231 amino acid transporter FLJ10945 NM 01828O hypothetical protein LOC55267 FLJ11292 NM 018382 hypothetical protein LOC55338 FLJ11506 NM 024666 hypothetical protein LOC79719 FLJ12331 NM 024986 hypothetical protein LOC80052 FLJ12505 NMO24749 hypothetical protein LOC798.05 FLJ12529 NM 024811 pre-mRNA cleavage factor I, 59 kDa subunit FLJ12700 NM 024910 hypothetical protein LOC79970 FLJ12949 NM 023008 hypothetical protein LOC65095 isoform 1 FLJ13197 NM O24614 hypothetical protein LOC79667 FLJ14001 NM O24677 hypothetical protein LOC79730 FLJ14154 NM 024845 hypothetical protein LOC79903 FLJ14768 NM 032836 hypothetical protein FLJ14768 FLJ14816 NM 032845 hypothetical protein LOC84931 FLJ14834 NM 032849 hypothetical protein LOC84935 FLJ1616S NM 001004318 hypothetical protein LOC390928 FLJ16171 NM 001004348 hypothetical protein LOC441116 FLJ16323 NM 001004352 hypothetical protein LOC441390 FLJ2O152 NM O19000 hypothetical protein LOC54463 isoform 2 FLJ2O232 NM O19008 hypothetical protein LOC54471 FLJ2O297 NM O17751 hypothetical protein LOC55627 isoform 1 FLU20489 NM O17842 hypothetical protein LOC55652 FLU20699 NM O17931 hypothetical protein LOC55020 FLU20701 NM O17933 hypothetical protein LOC55022 FLJ20758 NM O17952 hypothetical protein LOC55037 FLJ20850 NM O17967 hypothetical protein LOC55049 FLJ2O859 NM 001029992 FLJ20859 protein isoform 3 FL21742 NM 0322O7 hypothetical protein LOC84167 FL21820 NM O21925 hypothetical protein LOC60526 FL21945 NM O25203 hypothetical protein LOC80304 FLJ22795 NM O25084 hypothetical protein LOC80154 FLU23322 NM O24955 hypothetical protein LOC80020 FLU23447 NM O24825 hypothetical protein LOC79883 FLJ251.02 NM 182626 hypothetical protein LOC348738 FLJ2S222 NM 1991.63 hypothetical protein LOC374666 FLJ253.71 NM 152543 hypothetical protein LOC152940 FLJ25996 NM 001001699 hypothetical protein LOC4O1109 FLJ26850 NM 001001687 hypothetical protein LOC400710 FLJ3OOS8 NM 144967 hypothetical protein LOC158763 FLJ30707 NM 145019 hypothetical protein LOC220108 FLJ3O834 NM 152399 hypothetical protein LOC132332 FLJ31132 NM 001004355 hypothetical protein LOC441522 FLJ31568 NM 152509 hypothetical protein LOC150244 FLJ31951 NM 144726 hypothetical protein LOC153830 FLJ32O11 NM 182516 hypothetical protein LOC148930 FLJ322O6 NM 152497 hypothetical protein LOC149421 FLJ33534 NM 182586 hypothetical protein LOC285150 FLJ33641 NM 152687 hypothetical protein LOC202309 FLJ33708 NM 173675 hypothetical protein LOC285780 US 2009/0227533 A1 Sep. 10, 2009 33

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 173510 hypothetical protein LOC150275 NM 207481 hypothetical protein LOC4O1013 NM OO1029883 hypothetical protein LOC388939 NM 173661 hypothetical protein LOC285.492 NM OO10O3807 hypothetical protein LOC285830 NM 207444 hypothetical protein LOC4OO359 NM 152544 hypothetical protein LOC152992 isoform 2 NM 182574 hypothetical protein LOC284358 NM 207511 hypothetical protein LOC4O1563 NM 173815 hypothetical protein LOC283848 NM 178557 hypothetical protein LOC339983 NM 173667 hypothetical protein LOC285668 NM 173805 hypothetical protein FLJ38723 NM 153689 hypothetical protein LOC205327 NM 182798 hypothetical protein LOC133584 isoform 2 NM 178314 hypothetical protein LOC3S3116 NM 207445 hypothetical protein LOC4OO360 NM 1738O3 Mpv17-like protein type 2 NM 152424 hypothetical protein LOC13928S NM 173649 hypothetical protein LOC28SOS1 NM 173677 hypothetical protein LOC28S962 NM 1984.76 hypothetical protein LOC284.325 NM 001001679 hypothetical protein LOC399886 NM 001001669 hypothetical protein LOC38.9337 NM 207473 hypothetical protein LOC40O870 NM 001001694 hypothetical protein LOC4OO935 NM 207503 hypothetical protein LOC4O1388 NM 207367 hypothetical protein LOC346S47 NM 207488 hypothetical protein LOC4O1105 NM 207436 hypothetical protein LOC4OOO77 NM 207380 hypothetical protein LOC38.8115 NM 207497 hypothetical protein LOC4O12S3 NM 201628 hypothetical protein LOC399563 NM 0010016.86 hypothetical protein LOC4OO686 NM 001001696 hypothetical protein LOC4OO997 NM 207486 hypothetical protein LOC4O1080 NM 207478 hypothetical protein LOC4OO934 NM 207422 hypothetical protein LOC392490 NM 001001691 hypothetical protein LOC40O8SO NM 207454 hypothetical protein LOC4OOS91 NM 207500 hypothetical protein LOC4O1278 NM 207451 hypothetical protein LOC4OOSS6 NM 207510 hypothetical protein LOC4O1562 NM 207443 hypothetical protein LOC4OO242 NM 207465 hypothetical protein LOC4007S4 NM 001004349 hypothetical protein LOC441140 NM 207386 hypothetical protein LOC388336 NM 001001709 hypothetical protein LOC4O1535 NM 207462 hypothetical protein LOC4OO666 NM 001001684 hypothetical protein LOC400576 NM 207395 hypothetical protein LOC38.8569 NM 207458 hypothetical protein LOC4OO627 NM 1984.62 FLJ46154 protein NM 207463 hypothetical protein LOC4OO679 NM 207430 hypothetical protein LOC399949 NM 001001677 hypothetical protein LOC3998.27 NM 207509 hypothetical protein LOC4O1554 NM 207475 hypothetical protein LOC4OO926 NM 004475 lotill in 2 NM 013281 fibronectin leucine rich transmembrane protein 3 NM 032296 FLYWCH-type zinc finger 1 isoform a NM 052905 ormin-like 2 NM 175736 ormin-like 3 isoform 1 NM 001460 flavin containing monooxygenase 2 NM 001461 flavin containing monooxygenase 5 NM 001024948 ormin binding protein 1-like isoform 1 NM O22763 fibronectin type III domain containing 3B NM 153756 fibronectin type III domain containing 5 NM 017559 hypothetical protein LOC54752 NM OO5252 V-fos FBJ murine osteosarcoma viral oncogene US 2009/0227533 A1 Sep. 10, 2009 34

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description FOSB NM OO6732 FBJ murine osteosarcoma viral oncogene homolog FOSL1 NM 005438 FOS-like antigen 1 FOSL2 NM O05253 FOS-like antigen 2 FOXE1 NM 004473 orkhead box E1 FOXG1B NM OO5249 orkhead box G1B FOX1 NM 01218.8 orkhead box I1 isoform a FOX1 NM OO1454 orkhead box J1 FOXJ2 NM 018416 orkhead box J2 FOXK2 NM 004514 orkhead box K2 isoform 1 FOXL2 NM 023067 orkhead box L2 FOXM1 NM O21953 orkhead boxM1 isoform 2 FOXP1 NM 032682 orkhead box P1 isoform 1 FOXO1 NM 033260 orkhead box Q1 FOXR2 NM 198451 orkhead box R2 FOXRED1 NM 017547 FAD-dependent oxidoreductase domain containing FRAG1 NM O14489 FGF receptor activating protein 1 FREM1 NM 144966 FRAS1 related 1 FRK NM 002031 yn-related kinase FRMD1 NM 024919 FERM domain containing 1 FRMD4A NM 018027 FERM domain containing 4A FSD1 L, NM 207647 fibronectin type III and SPRY domain containing FSTL1 NM 007085 ollistatin-like 1 precursor FSTL3 NM OO5860 ollistatin-like 3 glycoprotein precursor FSTL4 NM O15082 ollistatin-like 4 FSTL5 NM O2O116 ollistatin-like 5 FTS NM 00101.2398 used toes homolog FUK NM 145059 lucokinase FUNDC1 NM 173794 FUN14 domain containing 1 FURIN NM OO2569 urin preproprotein FUT1 NM 000148 lucosyltransferase 1 FUT10 NM 032664 lucosyltransferase 10 FUT5 NM 002034 lucosyltransferase 5 FUT8 NM 004480 lucosyltransferase 8 isoform b NM 012192 racture callus 1 homolog NM 000144 rataxin isoform 1 preproprotein NM OO1680 FXYD domain-containing ion transport regulator 2 NM O24513 FYVE and coiled-coil domain containing 1 NM 003505 rizzled 1 NM 0121.93 rizzled 4 FZR1 NM O16263 FZrl protein GABARAPL2 NM OO7285 GABA(A) receptor-associated protein-like 2 GABBR2 NM 005458 G protein-coupled receptor 51 GABRA1 NM 000806 gamma-aminobutyric acid (GABA) A receptor, alpha GABRE NM 004961 gamma-aminobutyric acid (GABA) A receptor, GABRG1 NM 173536 gamma-aminobutyric acid A receptor, gamma 1 GADD4SG NM OO6705 growth arrest and DNA-damage-inducible, gamma GALM NM 1388O1 galactose mutarotase (aldose 1-epimerase) GALNT2 NM 004481 polypeptide N-acetylgalactosaminyltransferase 2 GALNT7 NM O17423 polypeptide N-acetylgalactosaminyltransferase 7 GALNTL1 NM 020692 UDP-N-acetyl-alpha-D-galactosamine: polypeptide GARNLA NM O15085 GTPase activating Rap/RangAP domain-like 4 GAS1 NM 002048 growth arrest-specific 1 GAS8 NM 001481 growth arrest-specific 8 GATA3 NM OO1002295 GATA binding protein 3 isoform 1 GATAS NM 080473 GATA binding protein 5 GATAD2A NM O17660 GATA zinc finger domain containing 2A GATAD2B NM 020699 GATA zinc finger domain containing 2B GATS NM 178831 opposite strand transcription unit to STAG3 GBA3 NM 020973 cytosolic beta-glucosidase GBF1 NM OO4193 golgi-specific brefeldin A resistance factor 1 GBL NM 022372 G protein beta subunit-like GBP2 NM 004120 guanylate binding protein 2, GBP4. NM 052941 guanylate binding protein 4 GCAT NM O14291 glycine C-acetyltransferase precursor GCH1 NM 00016.1 GTP cyclohydrolase 1 isoform 1 GCLM NM 002061 glutamate-cysteine ligase 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) transferase 2, Gcom1 NM 001018097 GRINL1A combined protein isoform 8 US 2009/0227533 A1 Sep. 10, 2009 35

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description DA NM OO4293 guanine deaminase DAP1L1 NM 024034 ganglioside-induced differentiation-associated DF2 NM 016204 growth differentiation factor 2 DF5 NM 000557 growth differentiation factor 5 preproprotein DF8 NM OO5259 growth differentiation factor 8 Gene symbol has-miR-34a target Gene name ENX-3414 NM OO3943 genethonin 1 FAP NM 002055 glial fibrillary acidic protein FER NM OO5262 erv1-like growth factor FRA3 NM OO1496 GDNF family receptor alpha 3 preproprotein MAP6 NM OO1007224 GTPase, IMAP family member 6 isoform 3 NS3 NM O2.2770 hypothetical protein LOC64785 PC1 NM OO5716 regulator of G-protein signalling 19 interacting PC2 NM O17655 PDZ domain protein GIPC2 AS NM OO5266 gap junction protein, alpha 5 NM 152219 gap junction protein, chi 1, 31.9 kDa (connexin LCE NM O15554 D-glucuronyl C5-epimerase L14 NM 138465 GLI-Kruppel family member GLI4 NM 032575 GLIS family Zinc finger 2 NM 002062 glucagon-like peptide 1 receptor NM OO6529 glycine receptor, alpha 3 NM 002064 glutaredoxin (thioltransferase) NM 016417 glutaredoxin 5 NM O14905 glutaminase C NM O24656 glycosyltransferase 25 domain containing 1 NM O15101 glycosyltransferase 25 domain containing 2 NMOO1.010983 glycosyltransferase 8 domain containing 1 NM 016433 glycolipid transfer protein NM 000405 GM2 ganglioside activator precursor NM 020713 hypothetical protein LOC57473 NM 004124 glia maturation factor, beta NM O16573 GEM interacting protein NM O15895 geminin NM OO7353 guanine nucleotide binding protein (G protein) NM 002070 guanine nucleotide binding protein (G protein), NM OO2O71 guanine nucleotide binding protein (G protein), NM O16592 guanine nucleotide binding protein, alpha NM 002073 guanine nucleotide binding protein, alpha Z NM 002075 guanine nucleotide-binding protein, beta-3 NM 001017998 guanine nucleotide binding protein (G protein), NM 018841 G-protein gamma-12 subunit NM 053064 guanine nucleotide binding protein (G protein), NM 052847 guanine nucleotide binding protein (G protein), NM 005471 glucosamine-6-phosphate deaminase 1 NM 198066 glucosamine-phosphate N-acetyltransferase 1 NM 024312 N-acetylglucosamine-1-phosphate transferase GNRHR NM 0004O6 gonadotropin-releasing hormone receptor isoform GNS NM OO2O76 glucosamine (N-acetyl)-6-sulfatase precursor GOLGA4 NM 002078 golgi autoantigen, golgin subfamily a 4 GOLGB1 NM OO4487 golgi autoantigen, golgin subfamily b, GOLPH3 NM 0221.30 golgi phosphoprotein 3 GOLPH3L NM 018178 GPP34-related protein GOLT1B NM 016072 golgi transport 1 homolog B GORASP2 NM O15530 golgi reassembly stacking protein 2 GOSR1 NM OO1007024 golgi SNAP receptor complex member 1 isoform 3 GOSR2 NM 001012511 golgi SNAP receptor complex member 2 isoform C GP5 NM 004488 glycoprotein V (platelet) GPATC3 NM O22078 G patch domain containing 3 GPC4 NM OO1448 glypican 4 GPHBS NM 145171 glycoprotein beta 5 GPR124 NM 032777 protein-coupled receptor 124 GPR135 NM O22571 protein-coupled receptor 135 GPR143 NM OOO273 protein-coupled receptor 143 GPR17 NM 005291 protein-coupled receptor 17 GPR26 NM 153442 protein-coupled receptor 26 GPR3 NM OO5281 protein-coupled receptor 3 GPR37L1 NM 004767 -protein coupled receptor 37 like 1 GPR4 NM OO5282 protein-coupled receptor 4 GPR44 NM 004778 protein-coupled receptor 44 GPR55 NM 005683 protein-coupled receptor 55 US 2009/0227533 A1 Sep. 10, 2009 36

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description PR56 NM 005682 G protein-coupled receptor 56 isoform a PR6 NM OO5284 G protein-coupled receptor 6 PR64 NM O05756 G protein-coupled receptor 64 PR83 NM O16540 G protein-coupled receptor 83 PR84 NM O2O370 inflammation-related G protein-coupled receptor PR85 NM 018970 G protein-coupled receptor 85 PR97 NM 170776 G protein-coupled receptor 97 PRCSB NM O16235 G protein-coupled receptor, family C, group 5, PS2 NM 004489 G protein pathway suppressor 2 PX3 NM 002084 plasma glutathione peroxidase 3 precursor RAMD2 NM 001012642 hypothetical protein LOC196996 RAP NM OO6613 GRB2-related adaptor protein RB10 NM OO1 OO1549 growth factor receptor-bound protein 10 isoform REM2 NM 022469 gremlin 2 precursor RHL1 NM 014552 leader-binding protein 32 isoform 1 RHL2 NM O24915 transcription factor CP2-like 3 RHL3 NM 02118O sister-of-mammalian grainy head protein isoform RID1 NM 017551 glutamate receptor, ionotropic, delta 1 RIN1 NM 000832 NMDA receptor 1 isoform NR1-1 precursor RIN3A NM 133445 glutamate receptor, ionotropic, RK6 NM 001004106 G protein-coupled receptor kinase 6 isoform A RM1 NM 000838 glutamate receptor, metabotropic 1 RM2 NM 000839 glutamate receptor, metabotropic 2 precursor RM7 NM 000844 glutamate receptor, metabotropic 7 isoform a RSF1 NM O02092 G-rich RNA sequence bmdin factor 1 GSDML NM 018530 hypothetical protein LOC55876 GSG1 NMO31289 erm cell associated 1 isoform 1 GSPT2 NM 018094 eptide chain release factor 3 GSTM3 NM OOO849 utathione S-transferase M3 GSTMS NM OOO851 utathione S-transferase M5 GTF2F1 NM OO2.096 eneral transcription factor hF, polypeptide 1, GTF3C4 NM 012204 eneral transcription factor IIIC, polypeptide GTSE1 NM 016426 G-2 and S-phase expressed 1 GUCA2A NM 033553 guanylate cyclase activator 2A GYG1 NM 004130 glycogenin GYG2 NM OO3918 glycogenin 2 GYPE NM 198682 glycophorin E precursor H2AFV NM 1386.35 H2A histone family, member V isoform 2 H2AFX NM 002105 H2A histone family, member X H6PD NM OO4285 hexose-6-phosphate dehydrogenase precursor HAAO NM 012205 3-hydroxyanthranilate 3,4-dioxygenase HABP2 NM 004132 yaluronan binding protein 2 HACE1 NM 020771 HECT domain and ankyrin repeat containing, E3 HADH2 NM 004493 hydroxyacyl-Coenzyme A dehydrogenase, type II HAP1 NM OO3949 huntingtin-associated protein 1 isoform 1 HAPLN3 NM 178232 hyaluronan and proteoglycan link protein 3 HAPLN4 NM 0230O2 brain link protein 2 HARS2 NM 080820 histidyl-tRNA synthetase 2 HAS3 NM 005329 hyaluronan synthase 3 isoform a HAVCR2 NM 032782 T cell immunoglobulin mucin 3 HBG1 NM 000559 A-gamma globin HBG2 NM 000184 G-gamma globin HBS1L NM O06620 HBS1-like HCFC1 NM 005334 host cell factor Cl (VP16-accessory protein) NM 005844 hypothetical protein LOC10255 NM 020897 hyperpolarization activated cyclic NM 002111 huntingtin NM 004964 histone deacetylase 1 NM OO6037 histone deacetylase 4 NM O15401 histone deacetylase 7A isoform a NM 138574 hepatoma derived growth factor-like 1 NM 005336 high density lipoprotein binding protein NM O15987 heme binding protein 1 NM O16217 headcase NM O15052 NEDD4-like ubiguitin-protein ligase 1 NM 020760 HECT, C2 and WW domain containing E3 ubiquitin NM O16173 HemK methyltransferase family member 1 NM 00101.3000 hect domain and RLD 6 isoform c NM O19089 hairy and enhancer of split homolog 2 NM 001024598 hairy and enhancer of split 3 US 2009/0227533 A1 Sep. 10, 2009 37

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 018645 hairy and enhancer of split 6 NM 012258 hairyienhancer-of-split related with YRPW motif NM 014571 hairyienhancer-of-split related with YRPW NM 001010934 hepatocyte growth factor isoform 5 precursor NM 004712 hepatocyte growth factor-regulated tyrosine NM 032558 hypothetical protein LOC84641 NM O15094 hypermethylated in cancer 2 HIF1AN NM O17902 hypoxia-inducible factor 1, alpha Subunit HIF3A NM 152794 hypoxia-inducible factor-3 alpha isoform a HIP1 NM 005338 huntingtin interacting protein 1 HIP1R NM OO3959 huntingtin interacting protein-1-related HIP2 NM 005339 huntingtin interacting protein 2 HIPK1 NM 181358 homeodomain-interacting protein kinase 1 isoform HK1 NM 000188 hexokinase 1 isoform HKI HKR2 NM 181846 GLI-Kruppel family member HKR2 HLA-DQA1 NM 002122 major histocompatibility complex, class II, DQ HLA-DQA2 NM 020056 major histocompatibility complex, class II, DQ HLX1 NM O21958 H2.0-like homeo box HM13 NM 178580 minor histocompatibility antigen 13 isoform 2 HMBOX1 NM O24567 hypothetical protein LOC79618 HMBS NM OOO190 hydroxymethylbilane synthase isoform 1 HMG20A NM 018200 high-mobility group 20A HMGA1 NM 002131 high mobility group AT-hook 1 isoform b HMGB1 NM 002128 high-mobility group box. 1 HMGCS1 NM 002130 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 HMGN4 NM OO6353 high mobility group nucleosomal binding domain HMMR NMO12484 hyaluronan-mediated motility receptor isoform a HMP19 NM O15980 HMP19 protein HMX1 NM 018942 homeo box (H6 family) 1 HN1 NM OO1002032 hematological and neurological expressed 1 HNF4A NM 000457 hepatocyte nuclear factor 4 alpha isoform b HNF4G NM 004.133 hepatocyte nuclear factor 4, gamma HNRPUL1 NM 007040 E1B-55 kDa-associated protein 5 isoform a HOMER2 NM OO4839 homer 2 isoform 1 HOXA13 NM 000522 homeobox A13 HOXA3 NM 030661 homeobox A3 isoform a HOXB4 NM 024015 homeobox B4 HOXB8 NM 024016 homeobox B8 HOXC13 NM O17410 homeobox C13 HOXC8 NM 022658 homeobox C8 HOXD9 NM O14213 homeobox D9 HPCAL1 NM 002149 hippocalcin-like 1 HPCAL4 NM O16257 hippocalcin-like protein 4 HPS1 NM 182637 Hermansky-Pudlak syndrome 1 protein isoform b HPSE NM OO6665 heparanase HR NM 005144 hairless protein isoform a HRH3 NM OO7232 histamine receptor H3 HRH4 NM 021624 histamine H4 receptor HS1BP3 NM 022460 HS1-binding protein 3 HS2ST1 NM 012262 heparan sulfate 2-O-sulfotransferase 1 HS6ST1 NM OO4807 heparan sulfate 6-O-sulfotransferase HSBP1 NM OO1537 binding protein 1 D11B2 NM OOO196 hydroxysteroid (11-beta) dehydrogenase 2 PA12B NM 052970 heat shock 70 kD protein 12B PA1A NM OO5345 heat shock 70 kDa protein 1A PA1B NM OO5346 heat shock 70 kDa protein 1B PA5 NM OO5347 heat shock 70 kDa protein 5 (glucose-regulated PB6 NM 144617 heat shock protein, alpha-crystallin-related, PBP1 NM 012267 hsp70-interacting protein PC117 NM 014306 hypothetical protein LOC51493 PG2 NM 005529 heparan Sulfate proteoglycan 2 ATIP NM OO6388 HIV-1 Tat interactive protein, 60 kDa isoform 2 LF NM 002158 T-cell leukemia virus enhancer factor R2A NM 000621 5-hydroxytryptamine (serotonin) receptor 2A R2C NM OOO868 5-hydroxytryptamine (serotonin) receptor 2C NM 1994.53 serotonin 5-HT4 receptor isoform g NM 002775 Htra serine peptidase 1 NM OO4507 HUS1 checkpoint protein NM 003549 hyaluronoglucosaminidase 3 NM 182757 IBR domain containing 2 US 2009/0227533 A1 Sep. 10, 2009 38

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 004968 islet cell autoantigen 1 NM 012405 isoprenylcysteine carboxyl methyltransferase NM 012092 inducible T-cell co-stimulator precursor NM O15259 inducible T-cell co-stimulator ligand NM OO5896 isocitrate dehydrogenase 1 (NADP+), soluble NM 005530 isocitrate dehydrogenase 3 (NAD+) alpha NM O16545 immediate early response 5 NM 005533 interferon-induced protein 35 NM 00101.0987 interferon-induced protein with NM 000629 interferon-alpha receptor 1 precursor NM 000619 interferon, gamma NM 000618 insulin-like growth factor 1 (Somatomedin C) NM OOO875 insulin-like growth factor 1 receptor precursor NM 016412 insulin-like growth factor 2 antisense NM OO6546 insulin-like growth factor 2 mRNA binding NM OO1007225 insulin-like growth factor 2 mRNA binding NM OO6547 insulin-like growth factor 2 mRNA binding NM 000596 insulin-like growth factor binding protein 1 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 20583.3 immunoglobulin Superfamily, member 1 isoform 2 NM OO1007237 immunoglobulin Superfamily, member 3 isoform 2 NM 021189 immunoglobulin Superfamily, member 4B NM 145296 immunoglobulin Superfamily, member 4C NM 153184 immunoglobulin Superfamily, member 4D NM O2O789 immunoglobulin Superfamily, member 9 NM 001025374 invasion inhibitory protein 45 isoform 2 NM 003640 inhibitor of kappa light polypeptide gene NM OO1556 inhibitor of kappa light polypeptide gene NM O14002 IKK-related kinase epsilon NM 003639 inhibitor of kappa light polypeptide gene NM 000628 interleukin 10 receptor, beta precursor NM 147162 interleukin 11 receptor, alpha isoform 2 NM 0021.89 interleukin 15 receptor, alpha isoform 1 NM 172217 interleukin 16 isoform 2 NM 032732 interleukin 17 receptor C isoform 3 precursor NM 017563 interleukin 17 receptor D NM 173042 interleukin 18 binding protein precursor NM 000576 interleukin 1, beta proprotein NM OOO877 interleukin 1 receptor, type 1 precursor NM OO3856 interleukin 1 receptor-like 1 isoform 2 NM 000577 interleukin 1 receptor antagonist isoform 3 NM 021258 interleukin 22 receptor, alpha 1 NM 052962 interleukin 22-binding protein isoform 1 NM 170743 interleukin 28 receptor, alpha isoform 1 NM OOO878 receptor beta precursor NM 000418 interleukin 4 receptor alpha chain isoform a NM OOO565 interleukin 6 receptor isoform 1 precursor NM 000634 interleukin 8 receptor alpha NM 176786 interleukin 9 receptor isoform 2 NM 175924 immunoglobulin-like domain containing receptor NM 012218 interleukin enhancer binding factor 3 isoform a NM 176799 integrin-linked kinase-associated protein NM 032549 IMP2 inner mitochondrial membrane protease-like NM OOO883 inosine monophosphate dehydrogenase 1 isoform a NM 032727 neuronal NM O2O238 inner centromere protein antigens 135/155 kDa NM 005537 inhibitor of growth family, member 1 isoform D NM 198267 inhibitor of growth family, member 3 isoform 3 NM 032329 inhibitor of growth family, member 5 NM 002193 inhibin beta B subunit precursor NM OO6774 indolethylamine N-methyltransferase NM 017553 INO80 complex homolog 1 NM 005540 inositol polyphosphate-5-phosphatase, 75 kDa NM 001017915 SH2 containing inositol phosphatase isoform a NM 005542 insulin induced gene 1 isoform 1 NM 005478 insulin-like 5 precursor NM 0021.96 insulinoma-associated 1 NM 032594 insulinoma-associated protein IA-6 US 2009/0227533 A1 Sep. 10, 2009 39

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NTS2 NM 020748 integrator complex subunit 2 NTS3 NM O23015 hypothetical protein LOC65123 PLA2(GAMMA) NM O15723 intracellular membrane-associated PO11 NM 016338 Ranbinding protein 11 PPK NM O22755 inositol 1,3,4,5,6-pentakisphosphate 2-kinase QCE NM 152558 IQ motif containing E QGAP1 NM OO3870 IQ motif containing GTPase activating protein 1 QGAP3 NM 178229 IQ motif containing GTPase activating protein 3 QSEC1 NM O14869 IQ motif and Sec7 domain 1 QSEC2 NM O15075 IQ motif and Sec7 domain 2 RAK2 NM OO1570 interleukin-1 receptor-associated kinase 2 RAK4 NM 016123 interleukin-1 receptor-associated kinase 4 RF1 NM 002198 interferon regulatory factor 1 RF2BP1 NM O15649 interferon regulatory factor 2 binding protein RF4 NM 002460 interferon regulatory factor 4 RF6 NM OO6147 interferon regulatory factor 6 SG2OL1 NM O22767 interferon stimulated exonuclease gene SG2OL2 NM 030980 interferon stimulated exonuclease gene TCH NM 031483 itchy homolog E3 ubiquitin protein ligase TFG3 NM 032039 integrin alpha FG-GAP repeat containing 3 TGA10 NM 003637 integrin, alpha 10 precursor TGA11 NM 001004439 integrin, alpha 11 precursor TGAL NM OO2209 integrin alpha L precursor TGAM NM 000632 integrin alpha M precursor TGB8 NM 002214 integrin, beta 8 precursor TIHS NM O30569 inter-alpha trypsin inhibitor heavy chain TPK1 NMO14216 inositol 1,3,4-triphosphate 5/6 kinase TPKB NM OO2221 1D-myo-inositol-trisphosphate 3-kinase B TPR2 NM OO2223 inositol 14,5-triphosphate receptor, type 2 TPR3 NM 002224 inositol 14,5-triphosphate receptor, type 3 TSN1 NM 001001132 intersectin 1 isoform ITSN-s XL NM 017592 intersex-like AG1 NM 000214 jagged 1 precursor AK2 NM OO4972 anus kinase 2 AKMIP1 NM 144720 multiple coiled-coil GABABR1-binding protein AM3 NM 0328O1 junctional adhesion molecule 3 precursor ARID2 NM OO4973 jumonji, AT rich interactive domain 2 protein AZF1 NM 175061 juxtaposed with another Zinc finger gene 1 MD1C NM 004241 jumonji domain containing 1C MD2C NM O15061 jumonji domain containing 2C MD2D NM 018039 jumonji domain containing 2D MD4 NM 023007 jumonji domain containing 4 MDS NM O24773 hypothetical protein LOC79831 OSD2 NM 138334 osephin domain containing 2 PH1 NM 020647 iunctophilin 1 PH3 NM O2O655 iunctophilin 3 PH4 NM 032452 iunctophilin 4 RK NM 003724 jerky homolog JUP NM OO2230 junction K6HF NM 004693 type II K6IRS4 NM 175053 6 irs4 KA36 NM 182497 type I keratin KA36 KAZALD1 NM 030929 Kazal-type serine protease inhibitor domain 1 KBTBD11 NM O14867 kelch repeat and BTB (POZ) domain containing 11 KBTBD6 NM 152903 kelch repeat and BTB (POZ) domain-containing 6 KCNA6 NM OO2235 potassium voltage-gated channel, shaker-related KCNAB2 NM 003636 potassium voltage-gated channel, shaker-related KCNC3 NM OO4977 Shaw-related voltage-gated potassium channel KCNC4 NM OO4978 Shaw-related voltage-gated potassium channel KCNE1 NM 000219 potassium voltage-gated channel, Isk-related KCNE1L, NM 012282 potassium voltage-gated channel, Isk-related KCNE3 NM 005472 potassium voltage-gated channel, Isk-related KCNG1 NM 172318 potassium voltage-gated channel, Subfamily G, KCNH2 NM OOO238 voltage-gated potassium channel, Subfamily H, KCNHS NM 172375 potassium voltage-gated channel, Subfamily H, KCNH7 NM 033272 potassium voltage-gated channel, Subfamily H, KCNIP1 NM 014592 KV channel interacting protein 1 isoform 2 KCNJ 10 NM 002241 potassium inwardly-rectifying channel, Subfamily KCNJ11 NM 000525 potassium inwardly-rectifying channel J11 KCNJ14 NM 013348 potassium inwardly-rectifying channel J 14 US 2009/0227533 A1 Sep. 10, 2009 40

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description KCNV2 NM OOO891 potassium inwardly-rectifying channel J2 KCN4 NM 004981 potassium inwardly-rectifying channel J4 KCNJ8 NM 004982 potassium inwardly-rectifying channel J8 KCNK2 NM 001017424 potassium channel, Subfamily K, member 2 isoform KCNK3 NM 002246 potassium channel, Subfamily K, member 3 KCNKS NM 003740 potassium channel, Subfamily K, member 5 KCNK6 NM 004823 potassium channel, Subfamily K, member 6 KCNK9 NM 016601 potassium channel, Subfamily K, member 9 KCNMA1 NM 001014797 arge conductance cal cium-activated potassium KCNN1 NM 002248 potassium intermedia eismall conductance KCNQ1 NM 000218 potassium voltage-ga ed channel, KQT-like KCNQ2 NM OO4518 potassium voltage-ga ed channel KQT-like protein KCNQ4 NM 004700 potassium voltage-ga ed channel KQT-like protein KCNS2 NM 020697 potassium voltage-ga ed channel, KCTD10 NM 031954 potassium channel tetramerisation domain KCTD16 NM O2O768 potassium channel tetramerisation domain KCTD17 NM O24681 potassium channel tetramerisation domain KCTD2 NM O15353 potassium channel tetramerisation domain KCTDS NM 018992 potassium channel tetramerisation domain KCTD7 NM 153033 potassium channel tetramerisation domain DELR3 NM OO6855 KDEL receptor 3 iso Oil 8 HK NM 000221 ketohexokinase isoform a AAOO40 NM 014656 hypothetical protein LOC9674 AAO082 NM O15050 hypothetical protein LOC23070 AAO090 NM O15047 hypothetical protein LOC23065 AAO125 NM 014792 hypothetical protein LOC9834 AAO152 NMO14730 hypothetical protein LOC9761 AAO157 NM 032182 hypothetical protein LOC23172 AAO179 NM O15056 hypothetical protein LOC23076 AAO182 NM 014615 hypothetical protein LOC23199 AAO251 NM O15027 hypothetical protein LOC23042 AAO265 NM O14997 hypothetical protein LOC23008 AAO286 NM O15257 hypothetical protein LOC23306 AAO319 NM 014.809 KIAAO319 AAO319L. NM O24874 polycystic kidney disease 1-like isoform a AAO329 NM O14844 hypothetical protein LOC9895 AAO3SS NM 014686 hypothetical protein LOC9710 AAO376 NM O15330 cytospin A AAO404 NM O15104 hypothetical protein LOC23130 AAO4O6 NM 014657 hypothetical protein LOC9675 AAO427 NM 014772 hypothetical protein LOC9811 AA0446 NM 014655 hypothetical protein LOC9673 AAO495 NM 207306 KIAAO495 AAOS13 NM 014732 hypothetical protein LOC9764 AAOS23 NM O15253 hypothetical protein LOC23302 AAO556 NM O152O2 hypothetical protein LOC23247 AAO652 NM 014741 hypothetical protein LOC9776 AAO672 NM O14859 hypothetical protein LOC9912 AAO683 NM 016111 hypothetical protein LOC9894 AAO753 NM 014804 hypothetical protein LOC9851 AAO773 NM OO1031690 hypothetical protein LOC9715 AAO789 NM 014653 hypothetical protein LOC9671 AAO8O2 NM O15210 hypothetical protein LOC23255 AAO828 NM O15328 KIAAO828 protein AAO892 NM O15329 hypothetical protein LOC23383 AAO971 NM O14929 hypothetical protein LOC22868 AA1005 NM O15272 hypothetical protein LOC23322 AA1008 NM O14953 KIAA1008 AA1009 NM O14895 hypothetical protein LOC22832 AA1018 NM O14967 hypothetical protein LOC22909 AA1024 NM O15206 hypothetical protein LOC23251 AA1160 NM 020701 hypothetical protein LOC57461 AA1166 NM 018684 hepatocellular carcinoma-associated antigen 127 AA1212 NM 018084 Hook-related protein 1 AA1217 NM 019590 hypothetical protein LOC56243 AA1267 NM 015443 hypothetical protein LOC284.058 AA1274 NM O14431 KIAA1274 AA1303 NM 020761 AA1324 NM O2O775 hypothetical protein LOC57535 AA1333 NM O17769 hypothetical protein LOC55632 US 2009/0227533 A1 Sep. 10, 2009 41

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description AA1522 NM 020888 hypothetical protein LOC57648 AA1609 NM 020947 hypothetical protein LOC57707 AA1729 NM 053042 hypothetical protein LOC85460 AA1787 NM 001005408 hypothetical protein LOC84461 isoform 2 AA1815 NM 024896 hypothetical protein LOC79956 AA1853 NM 194286 KIAA1853 protein AA1875 NM 032529 KIAA1875 protein AA1904 NM 052906 hypothetical protein LOC114794 AA1909 NM 052909 hypothetical protein LOC153478 AA1919 NM 153369 KIAA1919 protein AA1920 NM 052919 hypothetical protein LOC114817 AA1924 NM 145294 hypothetical protein LOC197335 AA1958 NM 133465 hypothetical protein LOC1584.05 NM 021174 p30 DBC protein NM OO10O8537 hypothetical protein LOC340533 NM OO4523 family member 11 NM 022113 kinesin family member 13A NM 020816 kinesin family member 17 NM 004321 axonal transport of synaptic vesicles 1 B NM O15074 kinesin family member IB isoform b NM O14218 killer cell immunoglobulin-like receptor, two NM O14219 killer cell immunoglobulin-like receptor, two NM 014511 killer cell immunoglobulin-like receptor, two NM OO2255 killer cell immunoglobulin-like receptor, two NM 020535 killer cell immunoglobulin-like receptor, two DLS B NM 001018081 killer cell immunoglobulin-like receptor, two NMO12312 killer cell immunoglobulin-like receptor, two NM 012314 killer cell immunoglobulin-like receptor, two NM 014513 killer cell immunoglobulin-like receptor, two NM 013289 killer cell immunoglobulin-like receptor, three NM OO6737 killer cell immunoglobulin-like receptor, three NM 153443 killer cell immunoglobulin-like receptor, three NM 000222 v-kit Hardy-Zuckerman 4 feline sarcoma viral I LG NM OOO899 KIT ligand isoform b precursor NM 153683 klotho isoform b LC2 NM 022822 ikely ortholog of kinesin light chain 2 NM 003597 Kruppel-like factor 11 NM OO7249 Kruppel-like factor 12 isoform a NM O15995 Kruppel-like factor 13 NM 173484 Zinc finger protein 393 4 NM OO4235 Kruppel-like factor 4 (Rubin and Gutmann, 2005) NM OO1730 Kruppel-like factor 5 NM OO1008490 Kruppel-like factor 6 NM 057161 estis intracellular mediator protein NM 207335 hypothetical protein LOC166348 NM 152375 hypothetical protein LOC127707 NM 173546 hypothetical protein LOC200942 NM 021633 kelch-like 12 NM 020805 kelch-like 14 NM 198317 kelch-like 17 NM O25010 kelch-like 18 NM O14851 kelch-like 21 NM 022480 BTB/POZ KELCH domain protein NM O17415 kelch-like 3 (Drosophila) NM O15596 kallikrein 13 precursor NM OO2262 killer cell lectin-like receptor subfamily D, NM OO7360 NKG2-D type II integral membrane protein NM 152643 kinase non-catalytic C-lobe domain (Lopez-Beltran et al., 2006) REMEN2 NM 024507 kringle-containing transmembrane protein 2 RIT1 NM 001013406 krew interaction trapped 1 isoform 2 RT2O NM O19010 RTS NM 000424 RTAP3-1 NM 031958 keratin associated protein 3.1 RTAP4-14 NM 033059 keratin associated protein 4-14 RTAP4-7 NM 033061 keratin associated protein 4-7 RTAPS-10 NM 001012710 keratin associated protein 5-10 RTAPS-2 NM OO10043.25 keratin associated protein 5-2 RTHB1 NM OO2281 keratin, hair, basic, 1 RTHB2 NM 033033 keratin, hair, basic, 2 US 2009/0227533 A1 Sep. 10, 2009 42

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description KRTHB3 NM O02282 keratin, hair, basic, 3 KSR1 NM O14238 kinase Suppressor of ras KTN1 NM 182926 kinectin 1 L1 CAM NM 000425 L1 cell adhesion molecule isoform 1 precursor LAD1 NM OO5558 adinin 1 LAMB2 NM 002292 aminin, beta 2 precursor LAMC1 NM 002293 aminin, gamma 1 precursor LANCL1 NM OO6055 anthionine synthetase C-like protein 1 LARPS NM O15155 La ribonucleoprotein domain family, member 5 LASP1 NM 006148 LIM and SH3 protein 1 LASS1 NM 021267 ongevity assurance gene 1 isoform 1 LASS2 NM 013384 LAG1 longevity assurance homolog 2 isoform 2 LASS3 NM 178842 hypothetical protein LOC204219 LASSS NM 147190 LAG1 longevity assurance homolog 5 LASS6 NM 203463 ongevity assurance homolog 6 LCE1C NM 178351 ate cornified envelope 1C LCMT2 NM 014793 eucine carboxyl methyltransferase 2 LCP1 NM 002298 L-plastin NM 007078 LIM domain binding 3 NM 005566 actate dehydrogenase A NM 1534.86 D-lactate dehydrogenase isoform 1 precursor R NM 000527 ow density lipoprotein receptor precursor NM 001013693 hypothetical protein LOC4O1944 NM 032287 hypothetical protein LOC84247 F1 NM O16269 ymphoid enhancer binding factor-1 NM 001010857 ate cornified envelope-like proline-rich 1 NM 018655 ens epithelial protein NM 018192 eprecan-like 1 NM 018471 erythropoietin 4 immediate early response NM 001024668 LETM1 domain containing 1 isoform 2 NM 005097 eucine-rich, glioma inactivated 1 precursor NM 018176 eucine-rich repeat LGI family, member 2 NM 139278 eucine-rich repeat LGI family, member 3 NM 018490 eucine-rich repeat-containing G protein-coupled NM OOO233 uteinizing hormone? choriogonadotropin receptor NM 005779 ipoma HMGIC fusion partner-like 2 NM 022126 phospholysine phosphohistidine inorganic NM OO4789 LIM homeobox protein 2 NM 014564 LIM homeobox protein 3 isoform b NM 002309 eukemia inhibitory factor (cholinergic NM OO6847 eukocyte immunoglobulin-like receptor, NM 016357 epithelial protein lost in neoplasm beta NM 014240 LIM domains containing 1 NM O30576 LIM domain containing 2 NM O16735 LIM domain kinase 1 isoform dLIMK NM O24674 in-28 homolog NM OO1004317 in-28 homolog B NM 181740 ines homolog 1 isoform 3 LPS-induced TNF-alpha factor imb expression 1 ethal giant larvae homolog 1 ectin, mannose-binding 2-like ipocalin-interacting membrane receptor amin AC isoform 1 precursor amin B2 eiomodin 1 (Smooth muscle) ymphocyte adaptor protein multi-PDZ-domain-containing protein PDZ domain containing ring finger 1 LOC113386 hypothetical protein LOC113386 LOC115648 hypothetical protein LOC115648 LOC128439 hypothetical protein LOC128439 LOC128,977 hypothetical protein LOC128977 LOC1291.38 hypothetical protein LOC1291.38 LOC130576 hypothetical protein LOC130576 LOC134145 hypothetical protein LOC134145 LOC134147 NM 1388.09 hypothetical protein LOC134147 LOC1476SO NM 207324 hypothetical protein LOC147650 LOC147808 NM 203374 hypothetical protein LOC147808 LOC14962O NM 001013621 hypothetical protein LOC149620 US 2009/0227533 A1 Sep. 10, 2009 43

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description LOC150223 NM 001017964 hypothetical protein LOC150223 isoform a LOC1SO383 NM 001.008917 hypothetical protein LOC150383 isoform 2 LOC152485 NM 178835 hypothetical protein LOC152485 LOC153222 NM 1536O7 hypothetical protein LOC153222 LOC153364 NM 203406 similar to metallo-beta-lactamase Superfamily LOC158318 NM 001024608 hypothetical protein LOC158318 LOC159090 NM 145284 hypothetical protein LOC159090 LOC162427 NM 178126 hypothetical protein LOC162427 LOC1651.86 NM 19928O hypothetical protein LOC165186 LOC1688SO NM 176814 hypothetical protein LOC168850 LOC200261 NM 182535 hypothetical protein LOC200261 LOC2OO312 NM 001017981 similar to RIKEN cDNA 0610009J22 LOC2O1181 NM 001013624 hypothetical protein LOC201181 LOC2O1895 NM 174921 hypothetical protein LOC201895 LOC221442 NM 001010871 hypothetical protein LOC221442 LOC221955 NM 139179 hypothetical protein LOC221955 LOC222171 NM 175887 hypothetical protein LOC222171 LOC255374 NM 203397 hypothetical protein LOC255374 LOC283174 NM 001001873 hypothetical protein LOC283174 LOC2832.19 NM 001029859 hypothetical protein LOC283219 LOC283487 NM 178514 hypothetical protein LOC283487 LOC283SS1 NM 001012706 hypothetical protein LOC283551 LOC284296 NM 175908 hypothetical protein LOC284296 LOC284739 NM 207349 hypothetical protein LOC284739 LOC285382 NM 001025266 hypothetical protein LOC285382 LOC28S636 NM 175921 hypothetical protein LOC285636 LOC28S989 NM 001013258 hypothetical protein LOC28.5989 isoform 2 LOC338328 NM 178172 high density lipoprotein-binding protein LOC339.123 NM 001005920 hypothetical LOC339123 LOC339524 NM 207357 hypothetical protein LOC339524 LOC34OO61 NM 198282 hypothetical protein LOC340061 LOC34O156 NM 001012418 hypothetical protein LOC34.0156 LOC340527 NM 001013627 hypothetical protein LOC340527 LOC345222 NM 001012982 hypothetical protein LOC345222 LOC348262 NM 207368 hypothetical protein LOC348262 LOC349136 NM 198285 hypothetical protein LOC349136 LOC387646 NM 001006604 hypothetical protein LOC387646 LOC387856 NM 001013635 hypothetical protein LOC387856 LOC388O22 NM 001013637 hypothetical protein LOC388022 LOC38861O NM 001013642 hypothetical protein LOC388610 LOC388886 NM 207644 hypothetical protein LOC388886 LOC388910 NM 001012986 hypothetical protein LOC388910 LOC3891.51 NM 001013650 hypothetical protein LOC389151 LOC389432 NM 001030060 hypothetical protein LOC389432 LOC389634 NM 001012988 hypothetical protein LOC389634 LOC3898.33 NM 001033515 hypothetical protein LOC3898.33 LOC389936 NM 001013656 hypothetical protein LOC389936 LOC390980 NM 001023563 similar to Zinc finger protein 264 LOC4OO145 NM 001013669 hypothetical protein LOC4001.45 LOC4OO258 NM 001008404 hypothetical protein LOC400258 LOC400464 NM 001013670 hypothetical protein LOC400464 LOC4OOSO9 NM 001012391 hypothetical protein LOC400509 LOC400696 NM 207646 hypothetical protein LOC400696 LOC40O891 NM 001013675 hypothetical protein LOC400891 LOC4OO96S NM 001013677 hypothetical protein LOC400965 LOC4OO968 NM 001013678 hypothetical protein LOC400968 LOC4O1252 NM 001013681 hypothetical protein LOC4O1252 LOC4O128O NM 001013682 hypothetical protein LOC4O1280 LOC4O1286 NM 001023565 hypothetical protein LOC4.01286 LOC4O1296 NM 001024677 hypothetical protein LOC4O1296 LOC4O1357 NM 001013685 hypothetical protein LOC4O1357 LOC4O1431 NM 001008745 hypothetical protein LOC4O1431 LOC4O1589 NM 001013687 hypothetical protein LOC4O1589 LOC4O162O NM 001013688 hypothetical protein LOC4O1620 LOC4O1622 NM 001013689 hypothetical protein LOC4O1622 LOC4O1623 NM 001018158 hypothetical protein LOC4O1623 LOC4O1720 NM 001013690 hypothetical protein LOC401720 LOC43998S NM 001013696 hypothetical protein LOC439985 LOC44O295 NM 1981.81 hypothetical protein LOC440295 LOC440313 NM 001013704 hypothetical protein LOC440313 US 2009/0227533 A1 Sep. 10, 2009 44

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description LOC44O742 NM 001013710 hypothetical protein LOC440742 LOC44.0836 NM 001014440 similar to MGC52679 protein LOC440944 NM 001013713 hypothetical protein LOC440944 LOC441046 NM 00101.1539 hypothetical protein LOC441046 LOC44112O NM 001013718 hypothetical protein LOC441120 LOC441179 NM 001013721 hypothetical protein LOC441179 LOCSO4.188 NM 001013404 hypothetical protein LOC504.188 LOCS1149 NM 001018061 hypothetical protein LOC51149 isoform 4 LOCS1333 NM 016643 mesenchymal stem cell protein DSC43 LOCSS2891 NM 004125 hypothetical protein LOC552891 LOC55565 NM 017530 hypothetical protein LOC55565 LOC619208 NM OO1033564 hypothetical protein LOC619208 LOC6392O NM O22090 transposon-derived Buster3 transposase-like LOC89944 NM 138342 hypothetical protein LOC89944 LOC90321 NM 00101.0851 hypothetical protein LOC90321 LOC933.49 NM 138402 hypothetical protein LOC93349 LOH11CR2A NM 014622 BCSC-1 isoform 1 LONRF3 NM OO1031855 LON peptidase N-terminal domain and ring finger LOXL3 NM 032603 ySyl oxidase-like 3 precursor LPAL2 NM 145727 ipoprotein, Lp(a)-like 2 precursor LPGAT1 NM O14873 ySophosphatidylglycerol acyltransferase 1 LPHN1 NM OO1008701 atrophilin 1 isoform 1 precursor LPIN1 NM 145693 ipin LPIN2 NM 014646 ipin 2 LPIN3 NM O22896 ipin 3 LPO NM OO6151 actoperoxidase LPP NMOO5578 LIM domain containing preferred translocation LPPR2 NM O22737 ipid phosphate phosphatase-related protein type LRAT NM 004744 ecithin retinol acyltransferase LRCH1 NM O15116 eucine-rich repeats and calponin homology (CH) LRCH2 NM 020871 eucine-rich repeats and calponin homology (CH) LRCH4 NM 002319 eucine-rich repeats and calponin homology (CH) LRIG1 NM O15541 eucine-rich repeats and immunoglobulin-like LRP1 NM 002332 ow density lipoprotein-related protein 1 LRP2BP NM 018409 LRP2 binding protein LRP4 NM 002334 ow density lipoprotein receptor-related protein LRRC1 NM 018214 eucine rich repeat containing 1 LRRC14 NM 014665 eucine rich repeat containing 14 LRRC18 NM OO1 OO6939 eucine rich repeat containing 18 LRRC2 NM O24512 eucine rich repeat containing 2 LRRC40 NM O17768 eucine rich repeat containing 40 LRRC44 NM 145258 eucine rich repeat containing 44 LRRCSS NM 001005210 hypothetical protein LOC219527 LRRC56 NM 1980.75 hypothetical protein LOC115399 LRRFIP1 NM OO4735 eucine rich repeat (in FLII) interacting LRRTM2 NM O15564 eucine rich repeat transmembrane neuronal 2 LRSAM1 NM 001005373 eucine rich repeat and sterile alpha motif LSS NM 002340 anosterol synthase LTBP2 NM 000428 atent transforming growth factor beta binding LTBR NM 002342 ymphotoxin beta receptor LTF NM 002343 actotransferrin LUZP1 NM 033631 eucine Zipper protein 1 LUZP4 NM 016383 eucine Zipper protein 4 LY6GSB NM 021221 ymphocyte antigen 6 complex G5B LY6G5C NM 001002848 ymphocyte antigen 6 complex G5C isoform C LY6K NM 017527 ymphocyte antigen 6 complex, locus K LY75 NM 002349 ymphocyte antigen 75 LY9 NM OO1033667 ymphocyte antigen 9 isoform b LYCAT NM OO10O2257 ySocardiolipin acyltransferase isoform 2 LYPD3 NM O14400 GPI-anchored metastasis-associated protein LY PLA1 NM OO6330 ySophospholipase I LY PLA3 NM 012320 ySophospholipase 3 (lysosomal phospholipase LY PLAL1 NM 138794 ySophospholipase-like 1 LYSMD4 NM 152449 hypothetical protein LOC145748 LYST NM 000081 ysosomal trafficking regulator isoform 1 LYZ NM OOO239 ysozyme precursor LZTS1 NM 021020 eucine Zipper, putative tumor Suppressor 1 LZTS2 NM 032429 eucine Zipper, putative tumor Suppressor 2 M6PR NM 002355 cation-dependent mannose-6-phosphate receptor MADD NM OO3682 MAP-kinase activating death domain-containing US 2009/0227533 A1 Sep. 10, 2009 45

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description MAF1 NM 032272 MAF1 protein MAFF NM 012323 transcription factor MAFF MAFK NM 002360 V- musculoaponeurotic fibrosarcoma oncogene MAGEA12 NM OO5367 melanoma antigen family A, 12 MAGEA2 NM OO5361 melanoma antigen family A, 2 MAGEA2B NM 153488 melanoma antigen family A, 2B MAGEA3 NM OO5362 melanoma antigen family A, 3 MAGEA6 NM OO5363 melanoma antigen family A, 6 MAGEB2 NM 002364 melanoma antigen family B, 2 MAGEC3 NM 177456 melanoma antigen family C, 3 isoform 2 MAGI1 NM OO1033057 membrane associated guanylate kinase, WW and PDZ MAK3 NM O251.46 Mak3 homolog NM 002371 T-lymphocyte maturation-associated protein NM 018717 mastermind-like 3 NM 006122 mannosidase, alpha, class 2A, member 2 NM 000240 monoamine oxidase A NM 002373 microtubule-associated protein 1A NM 002374 microtubule-associated protein 2 isoform 1 NM OO2755 mitogen-activated protein kinase kinase 1 NM OO2756 mitogen-activated protein kinase kinase 3 NM OO3954 mitogen-activated protein kinase kinase kinase NM 001001671 mitogen-activated protein kinase kinase kinase NM 002401 mitogen-activated protein kinase kinase kinase 3 NM OO3188 mitogen-activated protein kinase kinase kinase 7 MAP3K7IP1 NM OO6116 mitogen-activated protein kinase kinase kinase 7 MAP3K7IP2 NM O15093 mitogen-activated protein kinase kinase kinase 7 MAP3K9 NMO33141 mitogen-activated protein kinase kinase kinase MAP4 NM 002375 microtubule-associated protein 4 isoform 1 MAP4K4 NM 004834 mitogen-activated protein kinase kinase kinase MAP6 NM 207577 microtubule-associated protein 6 isoform 2 MAP6D1 NM O24871 MAP6 domain containing 1 MAP7 NM OO3980 microtubule-associated protein 7 MAPK1 NM OO2745 mitogen-activated protein kinase MAPK10 NM OO2753 mitogen-activated protein kinase 10 isoform 1 MAPK13 NM 002754 mitogen-activated protein kinase 13 MAPK15 NM 139021 mitogen-activated protein kinase 15 MAPKAPK3 NM 004635 mitogen-activated protein kinase-activated MAPRE2 NM O14268 microtubule-associated protein, RP/EB family, MAPT NM 005910 microtubule-associated protein tau isoform 2 MARCH4 NM 020814 membrane-associated ring finger (C3HC4) 4 MARCHS NM 017824 ring finger protein 153 MARCH8 NM OO10O2265 cellular modulator of immune recognition MARCH9 NM 138396 membrane-associated RING-CH protein IX MARCKSL1 NM O23009 MARCKS-like 1 MARK4 NM 031417 MAP microtubule affinity-regulating kinase 4 MARVELD1 NM 031484 MARVEL domain containing I MARVELD3 NM 052858 MARVEL domain containing 3 isoform 2 MASP1 NM OO 1031849 mannan-binding lectin serine protease 1 isoform MASP2 NM OO6610 mannan-binding lectin serine protease 2 isoform MAT2A NM 005911 methionine adenosyltransferase II, alpha MAWBP NM OO1033083 MAWD binding protein isoform b MAX NM 002382 MAX protein isoform a MBD1 NM 002384 methyl-CpG binding domain protein 1 isoform 4 MBD3 NM OO3926 methyl-CpG binding domain protein 3 MBD6 NM 052897 methyl-CpG binding domain protein 6 MBP NM 001025081 myelin basic protein isoform 1 MC2R NM 000529 melanocortin 2 receptor MCART6 NM 001012755 hypothetical protein LOC4O1612 MCFD2 NM 139279 multiple coagulation factor deficiency 2 MCL1 NM O21960 myeloid cell leukemia sequence 1 isoform 1 MCOLN1 NM 020533 mucolipin 1 MDGA1 NM 153487 MAM domain containing MECP2 NM OO4992 methyl CpG binding protein 2 MECR NM 001024732 -binding factor 1 isoform b MED19 NM 153450 mediator of RNA polymerase II transcription, MED4 NM 014166 mediator of RNA polymerase II transcription, MED8 NM 001001651 mediator of RNA polymerase II transcription MEGF10 NM 0324.46 MEGF10 protein MEOX1 NM OO4527 mesenchyme homeobox 1 isoform 1 MESP1 NM 018670 mesoderm posterior 1 US 2009/0227533 A1 Sep. 10, 2009 46

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description MEST NM 002402 mesoderm specific transcript isoform a MET NM OOO245 met proto-oncogene precursor METAP1 NM O15143 methionyl aminopeptidase 1 METT1 OD NM 024086 hypothetical protein LOC79066 METTL1 NM OO5371 methyltransferase-like protein 1 isoform a METTL4 NM 022840 methyltransferase like 4 MFAP2 NM OO2403 microfibrillar-associated protein 2 precursor MFAP4 NM 002404 microfibrillar-associated protein 4 MFN2 NM O14874 mitofusin 2 MFRP NM 031433 membrane frizzled-related protein MGAT1 NM 002406 mannosyl (alpha-1,3-)-glycoprotein MGAT3 NM 0024.09 mannosyl (beta-1,4-)-glycoprotein MGAT4B NM O14275 mannosyl (alpha-1,3-)-glycoprotein MGATSB NM 144677 beta(1,6)-N-acetylglucosaminyltransferase V MGC11102 NM 032325 hypothetical protein LOC84285 MGC12981 NM 032357 hypothetical protein LOC84317 MGC13024 NM 152288 hypothetical protein LOC93129 MGC13114 NM 032366 hypothetical protein LOC84326 isoform a MGC13138 NM 033410 hypothetical protein LOC92595 MGC16169 NM 033115 hypothetical protein LOC93627 MGC16291 NM 032770 hypothetical protein LOC84856 MGC17330 NM 052880 HGFL protein MGC21644 NM 138492 hypothetical protein LOC153768 isoform c MGC21675 hypothetical protein LOC92070 MGC2328O hypothetical protein LOC147015 MGC24039 hypothetical protein LOC160518 MGC26694 hypothetical protein LOC284439 MGC2752 hypothetical protein LOC65996 MGC3123 hypothetical protein LOC79089 isoform 1 MGC33556 hypothetical protein LOC339541 MGC34774 hypothetical protein LOC399670 MGC3S440 hypothetical protein LOC147990 MGC39518 hypothetical protein LOC285172 MGC42367 hypothetical protein LOC343990 MGC4268 hypothetical protein LOC83607 MGC43122 hypothetical protein LOC151477 MGC44328 hypothetical protein LOC440757 MGC4S491 hypothetical protein LOC221416 MGCSO722 hypothetical protein LOC399693 MGC52057 NM 194317 hypothetical protein LOC130574 MGCS242 NM 024033 hypothetical protein LOC78996 MGC70857 NM 001001795 hypothetical protein LOC414919 MGCfO870 NM 203481 hypothetical LOC403340 MGLL NM 001003794 monoglyceride lipase isoform 2 MIB1 NM 020774 mind bomb homolog 1 MICAL-L1 NM 03.3386 molecule interacting with Rab13 MIER2 NM 017550 hypothetical protein LOC54531 MIER3 NM 152622 hypothetical protein LOC166968 MIR16 NM 016641 membrane interacting protein of RGS16 MITF NM 000248 microphthalmia-associated transcription factor MK167 NM 002417 antigen identified by monoclonal antibody Ki-67 MKL2 NM 014048 megakaryoblastic leukemia 2 protein MKLN1. NM 013255 muskelin 1, intracellular mediator containing MKNK2 NM 199054 MAP kinase-interacting serine threonine kinase 2 MKX NM 173576 hypothetical protein LOC283078 MLANA NM OO5511 melan-A MLC1 NM O15166 megalencephalic leukoencephalopathy with MLL NM 005933 myeloid lymphoid or mixed-lineage leukemia MLLT3 NM OO4529 myeloid lymphoid or mixed-lineage leukemia MMAB NM 052845 cob (I)alamin adenosyltransferase MMP11 NM OO5940 matrix metalloproteinase 11 preproprotein MMP14 NM OO4995 matrix metalloproteinase 14 preproprotein MMP15 NM OO2428 matrix metalloproteinase 15 preproprotein MMP19 NM OO1032360 matrix metalloproteinase 19 isoform 2 precursor MMP2 NM 004530 matrix metalloproteinase 2 preproprotein MMP25 NM 022468 matrix metalloproteinase 25 preproprotem MMS19L. NM O22362 MMSI9-like (MET18 homolog, S. cerevisiae) MNT NM 020310 MAX binding protein MOAP1 NM 022151 modulator of apoptosis 1 MOBKL1A NM 173468 MOB1, Mps One Binder kinase activator-like 1A US 2009/0227533 A1 Sep. 10, 2009 47

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description MOBKL2A NM 130807 MOB-LAK MOBKL2C NM 145279 MOB1, Mps One Binder kinase activator-like 2C MOV10 NM 020963 Mov10, Moloney leukemia virus 10, homolog MOV1 OL1 NM 018995 MOV10-like 1 PHOSPH6 NM OO5792 M-phase phosphoprotein 6 NM OO2435 mannose-6-phosphate isomerase NM OO5373 myeloproliferative leukemia virus oncogene NM OOO250 myeloperoxidase NM OO5374 palmitoylated membrane protein 2 NM 022474 membrane protein, palmitoylated 5 NM OO1585 hypothetical protein LOC758 NM OO1584 hypothetical protein LOC744 NM 012219 muscle RAS oncogene homolog NM 054030 MAS-related GPR, member X2 RI P NM O15134 phosphatase-Rho interacting protein NM 145255 mitochondrial ribosomal protein L10 isoform a NM 145212 mitochondrial ribosomal protein L30 NM 004891 mitochondrial ribosomal protein L33 isoform a NM 020409 mitochondrial ribosomal protein L47 isoform a NM 178336 mitochondrial ribosomal protein L52 isoform a NM 021107 mitochondrial ribosomal protein S12 precursor NM O22497 mitochondrial ribosomal protein S25 NM O15084 mitochondrial ribosomal protein S27 NM O15971 mitochondrial ribosomal protein S7 NM OO6069 JAW1-related protein isoform a NM 206893 membrane-spanning 4-domains, Subfamily A, member NMOOO139 membrane-spanning 4-domains, Subfamily A, member NM 002442 musashi 1 NM 018133 ring finger protein 184 NM O78628 male-specific lethal 3-like 1 isoform d MSR1 NM 138715 macrophage scavenger receptor 1 isoform type 1 MST1SO NM 032947 putative Small membrane protein NID67 MSX2 NM 002449 msh homeobox2 MT1E NM 175617 metallothionein 1E MTA2 NM OO4739 metastasis-associated protein 2 MTAP NM OO2451 5-methylthioadenosine phosphorylase MTERFD2 NM 1825O1 MTERF domain containing 2 MTFR1 NM 014637 chondrocyte protein with a poly-proline region MTHFR NM OO5957 5,10-methylenetetrahydrofolate reductase 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 MTMR4 NM 004687 myotubularin related protein 4 MTMR9 NM O15458 myotubularin-related protein 9 MTUS1 NM 001001924 mitochondrial tumor suppressor 1 isoform 1 MUCDHL NM 03.1265 mu-protocadherin isoform 4 MUM1 NM 032853 melanoma ubiquitous mutated protein NM OO6454 MAD4 MYADM NM 001020818 myeloid-associated differentiation marker MYADML NM 207329 myeloid-associated differentiation marker-like MY B NM OO5375 v- myeloblastosis viral oncogene homolog NM OO2467 myc proto-oncogene protein MYCBP2 NM O15057 MYC binding protein 2 MYCN NM OO5378 v-myc myelocytomatosis viral related oncogene, MY NM OO2471 myosin heavy chain 6 MY NM OO2473 myosin, heavy polypeptide 9, non-muscle MY NM 001002841 atrial embryonic alkali MY NM OO6097 myosin regulatory light polypeptide 9 isoform a MY NM 005965 myosin light chain kinase isoform 6 MY NM 033118 skeletal myosin light chain kinase MYO10 NM 012334 myosin X MYO15A NM O16239 myosin XV MYO18A NM O78471 myosin 18A isoform a MYO1C NM 033375 myosin IC MYO1D NM O15194 myosin ID MYO1F NM 012335 myosin IF MYOZ3 NM 133371 myozen in 3 MYRIP NM O15460 myosin VIIA and Rab interacting protein MYT1 NM OO4535 myelin transcription factor 1 US 2009/0227533 A1 Sep. 10, 2009 48

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description N4BP1 NM 153029 Nedd4 binding protein 1 NAGPA NM O16256 N-acetylglucosamine-1-phosphodiester NALP2 NM O17852 NACHT, leucine rich repeat and PYD containing 2 NAP1L2 NM O21963 nucleosome assembly protein 1-like 2 NAP1LS NM 153757 nucleosome assembly protein 1-like 5 NAPE-PLD NM 1989.90 N-acyl-phosphatidylethanolamine-hydrolyzing NAT NM 024662 N-acetyltransferase-like protein NAT NM O24771 hypothetical protein LOC79829 NAV NM 020443 neuron navigator 1 NAV2 NM 145117 neuron navigator 2 isoform 2 NAV3 NM O14903 neuron navigator 3 NBL NM O05380 neuroblastoma, Suppression of tumorigenicity 1 NBN NM 001024688 nibrin isoform 2 NBP NM 183372 hypothetical protein LOC200030 NBP NM 152488 hypothetical protein LOC1485.45 NBR NM O05899 neighbor of BRCA1 gene 1 NCBP2 NM OO7362 nuclear cap binding protein subunit 2, 20 kDa NCDN NM 001014839 neurochondrin isoform 1 NCK2 NM OO1004720 NCK adaptor protein 2 isoform A NCLN NM O2O170 nicalin NCOA1 NM 003743 nuclear receptor coactivator 1 isoform 1 NCOA4 NM 005437 nuclear receptor coactivator 4 NCOA6IP NM 024831 PRIP-interacting protein PIPMT NM OO6312 nuclear receptor co-repressor 2 NM 1471.30 natural cytotoxicity triggering receptor 3 NM O14434 NADPH dependent diflavin oxidoreductase 1 NMOO6096 N-myc downstream regulated gene 1 NM 020465 NDRG family member 4 ST NM OO1543 N-deacetylase/N-sulfotransferase (heparan NM 020142 NADH:ubiguinone oxidoreductase MLRQ subunit NM OO4549 NADH dehydrogenase (ubiquinone) 1, Subcomplex NM OO4553 NADH dehydrogenase (ubiquinone) Fe—S protein 6, NM OO6154 neural precursor cell expressed, developmentally NM O15277 ubiquitin-protein ligase NEDD4-like NM OO6156 neural precursor cell expressed, developmentally NM 182966 neural precursor cell expressed, developmentally NM 173808 neuronal growth regulator 1 NM 024800 NIMA (never in mitosis genea)-related kinase NM 033116 NIMA related kinase 9 gR 1 NM 138966 neuropilin-and tolloid-like protein 1 isoform 3 T 2 NM 018092 neuropilin-and tolloid-like protein 2 NM 000434 neuraminidase precursor NM 004210 neuralized-like 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 OO4554 cytoplasmic nuclear factor of activated T-cells NM OO3204 nuclear factor (erythroid-derived 2)-like 1 NM OO25O1 nuclear factor IX (CCAAT-binding transcription NM 020529 nuclear factor of kappa light polypeptide gene NM OO4556 nuclear factor of kappa light polypeptide gene NM 147134 nuclear transcription factor, X-box binding 1 NM OO2505 nuclear transcription factor Y, alpha isoform 1 NM O14223 nuclear transcription factorY. gamma NM 021257 neuroglobin NM OO2507 nerve growth factor receptor precursor HLRC1 NM 198586 malin HS NM 19827O Nance-Horan syndrome protein N NM 020921 ninein isoform 2 NM 004148 ninjurin 1 NJ2 NM O16533 ninjurin 2 PSNAP1 NM 003634 nipSnap homolog 1 PSNAP3B NM 018376 nipSnap homolog 3B KD2 NM 033120 naked cuticle homolog 2 KTR NM 00101.2651 natural killer-tumor recognition sequence KX3-1 NM OO6167 NK3 transcription factor related, locus 1 LE1 NM 001014445 Notchless gene homolog isoform b NMNAT3 NM 178177 nicotinamide nucleotide adenylyltransferase 3 NMT1 NM 021079 N-myristoyltransferase 1 US 2009/0227533 A1 Sep. 10, 2009 49

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NMT2 NM 004.808 glycylpeptide N-tetradecanoyltransferase 2 NMUR1 NM OO6056 neuromedin U receptor 1 NNAT NM OO5386 neuronatin isoform alpha NOL1 NM OO1033714 nucleolar protein 1, 120 kDa NOL10 NM 024894 nucleolar protein 10 NOL6 NM 022917 nucleolar RNA-associated protein alpha isoform NONO NM OO7363 non-POU domain containing, octamer-binding NOS1AP NM 014697 nitric oxide synthase 1 (neuronal) adaptor NOS2A NM OOO625 nitric oxide synthase 2A isoform 1 NOS3 NM OOO603 nitric oxide synthase 3 (endothelial cell) NOTCH1 NM O17617 notchl preproprotein NOTCH2 NM 024408 notch 2 preproprotein NOTCH3 NM OOO435 Notch homolog 3 NOTCH4 NM OO4557 notch4 preproprotein NM 178493 hypothetical protein LOC147111 NM 032569 cytokine-like nuclear factorn-pac NM 178864 HLH-PAS transcription factor NXF NM 013389 NPC-like 1 NM O17921 nuclear protein localization 4 NM OO1033047 nephronectin NM OO2522 neuronal pentraxin I precursor NM OO2523 neuronal pentraxin II NM OOO903 NAD(P)H menadione oxidoreductase 1, NM OO3889 isoform 1 NM 016346 photoreceptor-specific nuclear receptor isoform NM 173158 nuclear receptor Subfamily 4, group A, member 1 NMOO6186 nuclear receptor subfamily 4, group A, member 2 NM OO3822 nuclear receptor Subfamily 5, group A, member 2 NM 178564 nuclear receptor binding protein 2 NM O13958 neuregulin 1 isoform HRG-beta3 NM 031474 nuclear receptor interacting protein 2 NM O2O645 nuclear receptor interacting protein 3 NM 198465 Nik related kinase NM O16588 neuritin precursor NM OO3872 neuropilin 2 isoform 2 precursor NM O15080 neurexin 2 isoform alpha-1 precursor NM 012229 5'-nucleotidase, cytosolic II NM OO1031701 hypothetical protein LOC51559 isoform 1 NM 032536 netrin G2 NM 001018.064 neurotrophic tyrosine kinase, receptor, type 2 NM OO2531 neurotensin receptor 1 NM O15332 Nudic domain containing 3 NM O15901 nudix-type motif 13 DT16L1 NM 032349 Syndesmos DT4 NM O19094 nudix-type motif 4 isoform alpha DT8 NM 181843 nudix-type motif 8 FIP1 NM 012345 nuclear fragile X mental retardation protein FIP2 NM O2O772 82-kD FMRP Interacting Protein MB NM 001005743 numb homolog isoform 1 MBL NM OO4756 numb homolog (Drosophila)-like P188 NM O15354 nucleoporin 188 kDa P210 NM 024923 nucleoporin 210 P43 NM 198887 nucleoporin 43 kDa PL1 NM OO10O8564 nucleoporin like 1 isoform b D-SP18 NM 032599 testes development-related NYD-SP18 D-SP21 NM 032597 testes development-related NYD-SP21 REN18 NM 016118 NEDD8 ultimate buster-1 S3 NM OO61.87 2'-5"oligoadenylate synthetase 3 OATL1 NM OO1OO6113 ornithine aminotransferase-like 1 isoform 1 OAZ2 NM OO2537 ornithine decarboxylase antizyme 2 OCRL NM 000276 phosphatidylinositol polyphosphate 5-phosphatase ODF3L1 NM 175881 Outer dense fiber of sperm tails 3-like 1 ODZ.1 NM O14253 odz, Odd OZ ten-m homolog 1 OGDH NM OO2541 oxoglutarate (alpha-ketoglutarate) dehydrogenase OGFOD1 NM 018233 hypothetical protein LOC55239 OGT NM OO3605 O-linked GlcNAc transferase isoform 3 OLFM4 NM OO6418 olfactomedin 4 precursor OLFML.1 NM 1984.74 olfactomedin-like 1 OLIG2 NM OO5806 oligodendrocyte lineage transcription factor 2 OLIG3 NM 175747 oligodendrocyte transcription factor 3 US 2009/0227533 A1 Sep. 10, 2009 50

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description PCML NM 00101.2393 opioid binding protein cell adhesion PHN1 NM OO2547 oligophrenin 1 PN4 NM OO103.0015 opsin 4 isoform 2 PN5 NM OO1030051 opsin 5 isoform 2 PRL1 NM OOO913 opiate receptor-like 1 PRM1 NM OO1008505 opioid receptor, mu 1 isoform MOR-1X PRS1 NM OO5866 opioid receptor, Sigma 1 isoform 1 R2E1 NM O3O883 olfactory receptor, family 2, Subfamily H, RS1E2 NM 030774 olfactory receptor, family 51, subfamily E, RAOV1 NM 153451 oral cancer overexpressed 1 RMDL3 NM 13928O ORM1-like 3 PL7 NM O17731 oxysterol-binding protein-like protein 7 SCAR NM 130771 Osteoclast-associated receptor isoform 3 NM 020530 oncostatin M precursor NM 004.802 otoferlin isoform b s B2 NM 023112 OTU domain, ubiguitin aldehyde binding 2 O TX NM 014562 orthodenticle 1 OVCA2 NM 080822 candidate tumor suppressor in ovarian cancer 2 OVOL1 NM 004561 OVO-like 1 binding protein OVOL2 NM 021220 Zinc finger protein 339 OXSR1 NM 005109 oxidative-stress responsive 1 P15RS NM 018170 hypothetical protein FLJ10656 P18SRP NM 173829 P18SRP protein NM 175567 purinergic receptor P2X4 isoform b NM 177427 purinergic receptor P2X7 isoform b NM 005446 purinergic receptor P2X-like 1, orphan receptor NMO14879 purinergic receptor P2Y, G-protein coupled, 14 NM OO2564 urinergic receptor P2Y2 NM 178129 G-protein coupled purinergic receptor P2Y8 NM 182904 prolyl 4-hydroxylase, alpha III subunit PACS1 NM 018026 phosphofurin acidic cluster sorting protein 1 PACSIN1 NM 020804 protein kinase C and casein kinase Substrate in PAG1 NM 018440 phosphoprotein associated with glycosphingolipid PAICS NM OO6452 phosphoribosylaminoimidazole carboxylase PAK1 NM OO2576 p21-activated kinase 1 PAK4 NM 001014831 p21-activated kinase 4 isoform 1 PALLD NM 016081 palladin PALM2-AKAP2 NM OO72O3 PALM2-AKAP2 rotein isoform 1 PAN3 NM 175854 PABPI-dependent poly A-specific ribonuclease PAPOLB NM O2O144 poly(A) polymerase beta (testis specific) PAPOLG NM 022894 poly(A) polymerase gamma PAPPA NM OO2581 pregnancy-associated plasma protein A PAPPA2 NM 020318 pappalysin 2 isoform 1 NM 001015880 3'-phosphoadenosine 5'-phosphosulfate synthase 2 NM O17705 membrane progestin receptor gamma NM 178422 progestin and adipoQ receptor family member VII NM 133367 progestin and adipoCR receptor family member NM 032521 PAR-6 beta NM OO2582 poly(A)-specific ribonuclease (deadenylation NM 032789 poly (ADP-ribose) polymerase family, member 10 NM O2O367 poly (ADP-ribose) polymerase family, member 11 NM 017554 poly (ADP-ribose) polymerase family, member 14 NM 152268 prolyl-tRNA synthetase NM 018222 parvin, alpha NM 022141 parvin, gamma NM OOO278 paired box protein 2 isoform b PAX8 NM O13952 paired box gene 8 isoform PAX8C PBEF1 NM O05746 pre-B-cell colony enhancing factor 1 isoform a PCBP4. NM 020418 poly(rC) binding protein 4 isoform a PCDH11X NM 032968 protocadherin 11 X-linked isoform c PCDH11 Y NM 032973 protocadherin 11 Y-linked isoform c PCDH17 NM O14459 protocadherin 17 PCDH21 NM 033100 protocadherin 21 precursor PCDHGA1 NM 018912 protocadheringamma Subfamily A, 1 isoform 1 PCDHGA10 NM 018913 protocadheringamma Subfamily A, 10 isoform 1 PCDHGA11 NM 018914 protocadheringamma Subfamily A, 11 isoform 1 PCDHGA12 NM 003735 protocadheringamma Subfamily A, 12 isoform 1 PCDHGA2 NM 018915 protocadheringamma Subfamily A, 2 isoform 1 PCDHGA3 NM 018916 protocadheringamma Subfamily A, 3 isoform 1 PCDHGA4 NM 018917 protocadheringamma Subfamily A, 4 isoform 1 US 2009/0227533 A1 Sep. 10, 2009 51

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq Transcript ID Gene Symbol (Pruitt et al., 2005) Description PC NM 018918 protocadheringamma Su bfamily A, 5 isoform 1 PC NM 018919 protocadheringamma Su b amily A, 6 isoform 1 PC NM 018920 protocadheringamma Su b amily A, 7 isoform 1 PC NM 032088 protocadheringamma Su b amily A, 8 isoform 1 PC NM 018921 protocadheringamma Su b amily A, 9 isoform 1 PC NM 018922 protocadheringamma Subfamilyb B, 1 isoform 1 PC NM 018923 protocadheringamma Subfamilyb B, 2 isoform 1 PC NM 018924 protocadheringamma Subfamily B, 3 isoform 1 PC NM 003736 protocadheringamma Subfamilyb B, 4 isoform 1 PC NM 018925 protocadheringamma Subfamilyb B, 5 isoform 1 PC NM 018926 protocadheringamma Subfamilyb B, 6 isoform 1 PC NM 018927 protocadheringamma Subfamilyb B, 7 isoform 1 PC NM OO2588 protocadheringamma Subfamilyb C, 3 isoform 1 PC NM 018928 protocadheringamma Subfamilyb C, 4 isoform 1 PC NM 018929 protocadheringamma Subfamilyb C, 5 isoform 1 PC NM OO6315 ring finger protein 3 PC 2 NM 001018073 mitochondrial phosphoenolpyruvate carboxykinase PCMTD1 NM 052937 hypothetical protein LOC115294 PCNXL2 NM 014801 pecanex-like 2 PCSK1N NM 013271 proprotein convertase subtilisinkexin type 1 PCSK7 NM 004716 proprotein convertase subtilisin?kexin type 7 PCTK3 NM OO2596 PCTAIRE protein kinase 3 isoform b PCYOX1 NM O16297 prenylcysteine oxidase 1 PCYT2 NM 002861 phosphate cytidylyltransferase 2, ethanolamine DCD10 NM 007217 programmed cell death 10 DCD2 NM 144781 programmed cell death 2 isoform 2 DCD4 NMO14456 programmed cell death 4 isoform 1 DE1B NM 000924 phosphodiesterase 1B, calmodulin-dependent DE4A NM OO62O2 phosphodiesterase 4A, cAMP-specific DESA NM 001083 phosphodiesterase 5A isoform 1 DE7A NM 002603 phosphodiesterase 7A isoform a DE7B NM 018945 phosphodiesterase 7B DGFB NM 002608 platelet-derived growth factor beta isoform 1, DGFRA NM OO62O6 platelet-derived growth factor receptor alpha DGFRB NM 002609 platelet-derived growth factor receptor beta DK2 NM 002611 pyruvate dehydrogenase kinase, isoenzyme 2 DLIM2 NM 021630 PDZ and LIM domain 2 isoform 2 DLIM7 NM 213636 PDZ and LIM domain 7 isoform 4 DPN NM 001006624 ung type-I cell membrane-associated DPR NM O17990 pyruvate dehydrogenase phosphatase regulatory DRG1 NM O3O815 and DNA damage-regulated protein DXK NM OO3681 pyridoxal kinase DZD11 NM 016484 PDZ domain containing 11 DZRN3 NM O15009 PDZ domain containing RING finger 3 EA15 NM 003768 phosphoprotein enriched in astrocytes 15 NM 002616 period 1 NM 022817 period 2 isoform 1 NM O16831 period 3 NM 033419 CAB2 protein NM O14303 pescadillo homolog 1, containing BRCT domain EX11B NM 003846 peroxisomal biogenesis factor 11B EX11G NM 080662 peroxisomal biogenesis factor 11 gamma EX14 NM 004565 peroxisomal biogenesis factor 14 EXSL NM O16559 PXR2b protein EX7 NM 000288 peroxisomal biogenesis factor 7 FKFB1 NM OO2625 6-phosphofructo-2-kinasef fructose-2, FKFB3 NM 004566 6-phosphofructo-2-kinasef fructose-2, FTK NM 012395 PFTAIRE protein kinase 1 PGAM1 NM OO2629 phosphoglycerate mutase 1 (brain) PGAM4 NM 001029891 phosphoglycerate mutase family 3 PGAP NM O24989 GPI deacylase PGD NM 002631 phosphogluconate dehydrogenase PGDS NM O14485 prostaglandin-D synthase PGEA NM OO1002880 PKD2 interactor, golgi and endoplasmic reticulum PGF NM 002632 placental growth factor, vascular endothelial PGLYRP2 NM 052890 peptidoglycan recognition protein L precursor PGLYRP3 NM 052891 peptidoglycan recognition protein-I-alpha PGM1 NM 002633 phosphoglucomutase 1 PGM2L1 NM 173582 phosphoglucomutase 2-like 1 PGMS NM O21965 phosphoglucomutase 5 US 2009/0227533 A1 Sep. 10, 2009 52

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description PGRMC2 NM OO6320 progesterone membrane binding protein HACTR4 NM 023923 phosphatase and actin regulator 4 HB NM 002634 prohibitin HF13 NM 153812 PHD finger protein 13 HF15 NM O15288 HD finger protein 15 HF19 NM O15651 HD finger protein 19 isoform a HF6 NM 001015877 HD finger protein 6 isoform 1 NM O15107 HD finger protein 8 NM 177967 hypothetical protein LOC337867 NM OOO293 phosphorylase kinase, beta isoform a NM 014759 phytanoyl-CoA hydroxylase interacting protein NM 153370 protease inhibitor 16 precursor NM 012407 protein interacting with C kinase 1 NM 004204 hosphatidylinositol glycan, class Q isoform 2 NM O25163 MP3 mannosyltransferase NM OO5026 hosphoinositide-3-kinase, catalytic, delta NM 005O27 hosphoinositide-3-kinase, regulatory subunit 2 NM OO3629 hosphoinositide-3-kinase, regulatory subunit 3 NM 002651 hosphatidylinositol 4-kinase, catalytic, beta NM O15553 hosphoinositide-binding protein PIP3-E NM 003557 hosphatidylinositol-4-phosphate 5-kinase, type NM 012398 hosphatidylinositol-4-phosphate 5-kinase, type NM 003559 hosphatidylinositol-4-phosphate 5-kinase type NM OO10O2881 hosphatidylinositol-3- NM 018068 piwi-like 2 NM O14819 praja 2, R1NG-H2 motif containing NM 138694 polyductin isoform 1 NM OO6823 cAMP-dependent protein kinase inhibitor alpha NM 004571 BX knotted 1 homeobox 1 isoform 1 NM O22062 BX knotted 1 homeobox2 NM OOO299 akophilin 1 isoform 1b NM 001005242 akophilin 2 isoform 2a NM 001005476 akophilin 4 isoform b NM 012400 hospholipase A2, group IID NM 022819 hospholipase A2, group IIF NM 178034 hospholipase A2, group IVD NM 001004426 hospholipase A2, group VI isoform b NM 182832 acenta-specific 4 NM 002655 eiomorphic adenoma gene 1 NM 002656 eiomorphic adenoma gene-like 1 isoform 1 NM 002657 eiomorphic adenoma gene-like 2 NM 153021 hospholipase B1 NM O15192 hosphoinositide-specific phospholipase C beta 1 NM 133373 hospholipase C delta 3 NM 016341 ancreas-enriched phospholipase C NM 002660 hospholipase C gamma 1 isoform a NM 001005473 hosphatidylinositol-specific phospholipase C, X NM 012388 allidin NM 002664 eckstrin LEKHA1 NM OO1 OO1974 eckstrin homology domain containing, family A LEKHAS NM O19012 eckstrin homology domain containing, family A LEKHA6 NM O14935 osphoinositol 3-phosphate-binding protein-3 LEKHF1 NM 024310 poptosis-inducing protein D LEKHGS NM 020631 ll 8. ive NFkB activating protein isoform a LEKHG6 NM 018173 eckstrin homology domain containing, family G LEKHH2 NM 172069 eckstrin homology domain containing, family H LEKHJ1 NM 018049 eckstrin homology domain containing, family J LEKHK1 NM 145307 eckstrin homology domain containing, family K LEKHM1 NM 014798 eckstrin homology domain containing, family M LEKHQ1 NM O252O1 H domain-containing protein NM 002666 perilipin NM 002667 phospholamban LOD1 NM OOO3O2 ySylhydroxylase precursor NM 002670 plastin 1 NM 020405 plexin domain containing 1 precursor NM 032242 plexin A1 NM 017514 plexin A3 NM 031887 pro-melanin-concentrating hormone-like 1 NM OO7221 polyamine-modulated factor 1 NM 033238 promyelocytic leukemia protein isoform 1 US 2009/0227533 A1 Sep. 10, 2009 53

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description PNMA3 NM 013364 paraneoplastic cancer-testis-brain antigen PNOC NM OO6228 prepronociceptin PNRC2 NM O17761 proline-rich nuclear receptor coactivator 2 PODXL NM 001018111 podocalyxin-like precursor isoform 1 POFUT1 NM O15352 protein O-fucosyltransferase 1 isoform 1 POFUT2 NM O15227 protein O-fucosyltransferase 2 isoform A POGZ. NM O15100 pogo transposable element with ZNF domain POLD3 NM OO6591 polymerase (DNA directed), delta 3 POLG NM 002693 polymerase (DNA directed), gamma POLL NM 013274 polymerase (DNA directed), lambda POLQ NM 199420 DNA polymerase theta POLR2G. NM 002696 DNA directed RNA polymerase II polypeptide G POLR22 NM 032958 DNA directed RNA polymerase II polypeptide POLR3H NM 001018050 polymerase (RNA) III (DNA directed) polypeptide POLS NM OO6999 DNA polymerase sigma POMT1 NM 007171 protein-O-mannosyltransferase 1 POMT2 NM 013382 putative protein O-mannosyltransferase POMZP3 NM 012230 POMZP3 fusion protein isoform 1 PON2 NM OOO305 paraOXonase 2 isoform 1 POTE14 NM 001005356 protein expressed in prostate, ovary, testis, POU2F1 NM 002697 POU domain, class 2, transcription factor 1 POU4F1 NM OO6237 POU domain, class 4, transcription factor 1 POU6F1 NM OO2702 POU domain, class 6, transcription factor 1 PAP2B NM 003713 phosphatidic acid phosphatase type 2B PAPDC3 NM 032728 phosphatidic acid phosphatase type 2 domain PARA NM 001001928 peroxisome proliferative activated receptor, PARD NMOO6238 peroxisome proliferative activated receptor, PARG NM 005037 peroxisome proliferative activated receptor PEF2 NM 152933 serine/threonine protein phosphatase with PFLA1 NM OO3626 PTPRF interacting protein alpha 1 isoform b PFLA4 NM O15053 protein tyrosine phosphatase, receptor type, f PGB NM OOO3O8 protective protein for beta-galactosidase PIE NM OO6112 peptidylprolyl isomerase E isoform 1 PIL2 NM 148175 peptidylprolyl isomerase-like 2 isoform a NM OO2705 periplakin NM 021003 protein phos hatase 1A isoform 1 NM 014634 protein phos hatase 1F NM 1392.45 protein phos hatase 1 (formerly 2C)-like NM 144641 protein phos hatase 1M (PP2C domain containing) NM 002710 protein phos hatase 1, catalytic Subunit, gamma NM 002714 protein phos hatase 1, regulatory Subunit 10 NM O21959 protein phos hatase 1, regulatory (inhibitor) NM 002481 protein phos hatase 1, regulatory (inhibitor) NM O15316 protein phos hatase 1, regulatory (inhibitor) NM O17726 protein phos hatase 1, regulatory Subunit 14D NM 032833 protein phos hatase 1, regulatory subunit 15B NM O15568 protein phosphatase 1 regulatory inhibitor NM 002713 protein phosphatase 1 regulatory inhibitor NM 002716 beta isoform of regulatory subunit A, protein NM 020416 gamma isoform of regulatory subunit B55, protein NM 002718 protein phosphatase 2, regulatory subunit B", NM 021131 protein phosphatase 2A, regulatory subunit B' NM OO6243 protein phosphatase 2, regulatory subunit B NM 002719 gamma isoform of regulatory subunit B56, protein NM OO6245 delta isoform of regulatory subunit B56, protein NM OOO945 protein phosphatase 3, regulatory subunit B, NM 14718O protein phosphatase 3 regulatory subunit B, beta NM 018498 hypothetical protein LOC55370 NM 139283 T-cell activation protein phosphatase 2C NM O25078 PQ loop repeat containing 1 NM 1452O2 proline-rich acidic protein 1 NM OO3981 protein regulator of cytokinesis 1 isoform 1 NM 021620 PR domain containing 13 NM 022114 PR domain containing 16 isoform 1 NM 013388 prolactin regulatory element binding protein NM O15387 preimplantation protein 3 isoform 1 NM 002725 proline arginine-rich end leucine-rich repeat NM 002726 prolyl endopeptidase NM OO6036 prolyl endopeptidase-like NM 198859 prickle-like 2 US 2009/0227533 A1 Sep. 10, 2009 54

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description MA1 NM 178013 proline rich membrane anchor 1 KACB NM OO2731 cAMP-dependent protein kinase catalytic subunit KAG1 NM OO2733 AMP-activated protein kinase, noncatalytic KAG3 NM O17431 AMP-activated protein kinase, non-catalytic KAR1B NM OO2735 protein kinase, cAMP-dependent, regulatory, type KCA NM OO2737 protein kinase C, alpha KCB1 NM OO2738 protein kinase C, beta isoform 2 KCE NM OO5400 protein kinase C, epsilon KCH NM OO6255 protein kinase C, eta KCQ NM OO6257 protein kinase C, theta KD1 NM OO2742 protein kinase D1 KD3 NM OO5813 protein kinase D3 KG2 NM OO6259 protein kinase, c0MP-dependent, type II KRIP1 NM O24653 PRKR interacting protein 1 (IL11 inducible) KRIR NM 004705 protein-kinase, interferon-inducible double KX NM 005044 protein kinase, X-linked KY NM 002760 protein kinase, Y-linked LR NM OOO949 prolactin receptor RMT2 NM OO1535 HMT1 hnRNP methyltransferase-like 1 RMT3 NM OO5788 HMT1 hnRNP methyltransferase-like 3 RMTS NM OO6109 protein arginine methyltransferase 5 isoform a RND NM 012409 prion-like protein doppel preproprotein ROM2 NM 144707 prominin 2 roSAPP1 NM 014731 ProSAPiP1 protein ROSC NM 007198 proline synthetase co-transcribed homolog ROZ NM OO3891 protein Z, vitamin K-dependent plasma RPF31 NMO15629 pre-mRNA processing factor 31 homolog RPF38B NM 018061 PRP38 pre-mRNA processing factor 38 (yeast) RPS1 NM OO2764 phosphoribosyl pyrophosphate synthetase 1 RR11 NM 018304 hypothetical protein LOC55771 RSS21 NM OO6799 estisin isoform 1 RSS7 NM 002772 enterokinase precursor RSS8 NM OO2773 prostasin preproprotein RX NM 020956 periaxin isoform 1 RY NM 004676 PTPN13-like, Y-linked RY2 NM OO1002758 PTPN13-like, Y-linked 2 PSCD3 NM OO4227 pleckstrin homology, Sect and coiled coil PSCD4 NM 013385 pleckstrin homology, Sect and coiled coil PSD2 NM 032289 pleckstrin and Sect domain containing 2 PSD3 NM O15310 ADP-ribosylation factor guanine nucleotide PSD4 NM 012455 pleckstrin and Sect domain containing 4 PSKH1 NM OO6742 protein serine kinase H1 PSMD5 NM 005047 proteasome 26S non-ATPase subunit 5 PSMD9 NM 002813 proteasome 26S non-ATPase subunit 9 PSME1 NM OO6263 proteasome activator Subunit 1 isoform 1 PSME3 NM OO5789 proteasome activator subunit 3 isoform 1 PSRC2 NM 144982 hypothetical protein LOC196441 PTGER4 NM OOO958 prostaglandin E receptor 4, subtype EP4 PTGES2 NM O25072 prostaglandin E synthase 2 isoform 1 PTGFR NM OOO959 prostaglandin F receptor isoform a precursor PTGFRN NM 020440 prostaglandin F2 receptor negative regulator PTGIR NM OOO960 prostaglandin I2 (prostacyclin) receptor (IP) PTGIS NM OOO961 prostaglandin I2 (prostacyclin) synthase PTGS1 NM OOO962 prostaglandin-endoperoxide synthase 1 isoform 1 PTK6 NM OO5975 PTK6 protein tyrosine kinase 6 PTK7 NM 152883 PTK7 protein tyrosine kinase 7 isoform e PTOV1 NM O17432 prostate tumor overexpressed gene 1 PTPDC1 NM 152422 protein tyrosine phosphatase domain containing 1 PTPLAD2 NM 00101.0915 hypothetical protein LOC4O1494 PLB NM 1984.02 protein tyrosinep hosphatase-like (proline PN2 NM 080422 protein tyrosinep hosphatase, non-receptor type PN5 NM 032781 protein tyrosinep hosphatase, non-receptor type PRE NM O06504 protein tyrosinep hosphatase, receptor type, E PRG NM 002841 protein tyrosinep hosphatase, receptor type, G PRM NM 002845 protein tyrosinep hosphatase, receptor type, M PRN NM 002846 protein tyrosinep hosphatase, receptor type, N PRR NM 002849 protein tyrosinep hosphatase, receptor type, R PRT NM 007050 protein tyrosinep hosphatase, receptor type, T PRU NM 005704 protein tyrosinep hosphatase, receptor type, U PRZ1 NM 002851 protein tyrosinep hosphatase, receptor-type, US 2009/0227533 A1 Sep. 10, 2009 55

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 012232 polymerase I and transcript release factor NM OO10O2.913 hypothetical protein LOC138428 NM 001020658 pumilio 1 isoform 1 NM 033224 purine-rich element binding protein B NM 001015508 purine-rich element binding protein G isoform B NM 031292 hypothetical protein LOC83448 NM O06505 poliovirus receptor NM 002856 poliovirus receptor-related 2 (herpesvirus entry NM OO7238 peroxisomal membrane protein 4 isoform a NM 002859 paxillin NM 152901 pyrin domain containing 1 NM 138300 pygopus homolog 2 NM O16131 ras-related GTP-binding protein RAB10 NM O14904 B11 family interacting protein 2 (class I) NM 032932 B11 family interacting protein 4 (class II) NM 016322 Pase Rab14 NM 022449 B17, member RAS oncogene family NM 030981 B1B, member RAS oncogene family NM O14999 B21, member RAS oncogene family NM O14353 B26, member RAS oncogene family NM O14488 B30, member RAS oncogene family NM OO6868 B31, member RAS oncogene family NM 03.1934 B39 NM OO6861 B35, member RAS oncogene family NM 004914 B36, member RAS oncogene family NM 171998 B39B, member RAS oncogene family NM 002867 B3B, member RAS oncogene family NM 138453 B3C, member RAS oncogene family NM 013401 B3A interacting protein (rabin3)-like 1 NM 198490 B43 protein NM 004578 B4A, member RAS oncogene family NM 002868 B5B, member RAS oncogene family NM O16577 B6B, member RAS oncogene family NM O15064 B6-interacting protein 2 isoform alpha NM 177403 B7B, member RAS oncogene family NM O16530 B8E3, member RAS oncogene family NM 002871 B-interacting factor NM 1738.25 B, member of RAS oncogene family-like 3 NM O22777 B, member RAS oncogene family-like 5 C 2 NM 002872 related C3 botulinum toxin substrate 2 NM 002874 excision repair protein RAD23 homolog B NM OO5732 D50 homolog isoform 1 NM 002875 D51 homolog protein isoform 1 NM 002878 D51-like 3 isoform 1 NM 004.584 D9 homolog NM 152442 D9 homolog B NM 001015885 E.1 (RNA export 1, S. pombe) homolog F1 NM 002880 v-raf-1 murine leukemia viral oncogene homolog 14 NM O15577 retinoic acid induced 14 16 NM O22749 retinoic acid induced 16 NM 020338 retinoic acid induced 17 NM 002881 v-ral simian leukemia viral oncogene homolog B NM OO6266 ral guanine nucleotide dissociation stimulator NM 014636 Ral GEF with PH domain and SH3 binding motif 1 NM 152663 Ral GEF with PH domain and SH3 binding motif 2 NM OO7367 RNA binding protein (autoantigenic, NM 020850 RAN binding protein 10 NM 022897 RAN binding protein 17 NM 003624 RAN binding protein 3 isoform RANBP3-a NM 002883 Ran GTPase activating protein 1 NM 002885 RAP1, GTPase activating protein 1 NM 002886 RAP2B, member of RAS oncogene family NM 016340 PDZ domain-containing guanine nucleotide NM 213589 Ras association and pleckstrin homology domains NM 000964 , alpha isoform a NM OOO965 retinoic acid receptor, beta isoform 1 NM OOO966 retinoic acid receptor, gamma NM OO7368 RAS p21 protein activator 3 NM OO6989 RAS p21 protein activator 4 NM 014310 RASD family, member 2 US 2009/0227533 A1 Sep. 10, 2009 56

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description RASGEF1A NM 145313 RasGEF domain family, member 1A RASGEF1C NM OO 1031799 RasGEF domain family, member 1C isoform 2 RASGRP3 NM 170672 RAS guanyl releasing protein 3 (calcium and RASGRP4 NM 170604 RAS guanyl releasing protein 4 isoform 1 RASL1 OB NM 033315 RAS-like, family 10, member B RASL12 NM O16563 RAS-like, family 12 protein RASSF2 NM 014737 Ras association domain family 2 RASSFS NM 031437 Ras association (RalGDSA F-6) domain family 5 RASSF6 NM 177532 Ras association (RalGDSA F-6) domain family 6 RASSF7 NM OO3475 Ras association (RalGDSA F-6) domain family 7 BAK NM 021163 RB-associated KRAB repressor BBP5 NM 005057 retinoblastoma binding protein 5 NM O16544 Ras-associated protein Rap1 BM12 NM OO6047 RNA binding motif protein 12 BM13 NM 032509 RNA binding motif protein 13 BM1SB NM 013286 RNA binding motif protein 15B BM17 NM 032.905 RNA binding motif protein 17 BM19 NM 0161.96 RNA binding motif protein 19 BM23 NM 0181.07 hypothetical protein LOC55147 BM24 NM 153020 hypothetical protein LOC221662 BM28 NM 018077 RNA binding motif protein 28 BM33 NM OO10O8408 hypothetical protein LOC155435 BP2 NM 004164 retinol binding protein 2, cellular BP5 NM 031491 retinol binding protein 5, cellular BPMS2 NM 194272 RNA binding protein with multiple splicing 2 CC2 NM 018715 RCC1-like DH11 NMO16026 androgen-regulated short-chain DH12 NM 152443 retinol dehydrogenase 12 (all-trans and 9-cis) DH13 NM 138412 retinol dehydrogenase 13 (all-trans and 9-cis) DHS NM OO2905 retinol dehydrogenase 5 (11-cis and 9-cis) ECK NM 021111 RECK protein precursor EEP5 NM O05669 receptor accessory protein 5 ELN NM 005045 reelin isoform a EM1 NM 014012 RAS-like GTP-binding protein REM EPIN1 NM 013400 replication initiator 1 isoform 1 EXO1L1 NM 172239 exonuclease GOR EXO4 NM O2O385 XPMC2 prevents mitotic catastrophe 2 homolog FP2 NM OO1007278 ret finger protein 2 isoform 2 NM OO2918 regulatory factor X1 RG AG.4 NM 001024455 retrotransposon gag domain containing 4 RGL1 NM O15149 ral guanine nucleotide dissociation RGMB NM 001012761 RGM domain family, member B isoform 1 precursor RGS11 NM OO3834 regulator of G-pro ein signalling 11 isoform 2 RGS17 NM 012419 regulator of G-pro ein signalling 17 RGS3 NM 021106 regulator of G-pro ein signalling 3 isoform 2 RGS4 NM OO5613 regulator of G-pro ein signaling 4 RGSS NM OO3617 regulator of G-pro ein signalling 5 RGS6 NM 004296 regulator of G-pro ein signalling 6 RGS9BP NM 207391 RGS9 anchor protein HBDL3 NM 138328 rhomboid, veinlet ike 3 HBG NM 020407 Rhesus blood grou p, B glycoprotein HEB NM OO5614 Ras homolog enric hed in brain HEBL1 NM 144593 Ras homolog enric hed in brain like 1 HO NM 000539 rhodopsin HOBTB3 NM O14899 rho-related BTB domain containing 3 HOJ NM 020663 TC10-like Rho GT Pase HOT1 NM OO1033567 ras homolog gene family, member T1 isoform 4 HOT2 NM 138769 ras homolog gene family, member T2 HOU NM 021205 ras homolog gene family, member U. HOV NM 133639 ras homolog gene family, member V C3 NM O24557 resistance to inhibitors of cholinesterase 3 C8B NM 018157 resistance to inhibitors of cholinesterase 8 CS NM 014715 Rho GTPase-activating protein LP NM 031430 Rab interacting lysosomal protein MBP2 NM O15347 RIM-binding protein 2 MS3 NM 014747 regulating synaptic membrane exocytosis 3 MS4 NM 182970 regulating synaptic membrane exocytosis 4 N1 NM 004292 ras inhibitor RIN1 NM OO10330O2 RPA interacting protein isoform 1 NM O15375 receptor interacting protein kinase 5 isoform 1 US 2009/0227533 A1 Sep. 10, 2009 57

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 016626 ring finger and KH domain containing 2 NM 145250 ribonuclease, RNase A family, 11 (non-active) NM 021133 ribonuclease L. NM O24539 ring finger protein 128 isoform 2 NM 014746 ring finger protein 144 NM 152470 ring finger protein 165 NM 152737 ring finger protein 182 NM 152267 ring finger protein 185 NM O15435 ring finger protein 19 NM 007219 ring finger protein 24 NM O17999 ring finger protein 31 NM O25126 ring finger protein 34 isoform 2 NM O22781 ring finger protein 38 isoform 1 NM OO2938 ring finger protein 4 NM 014771 ring finger protein 40 NM OO5785 ring finger protein 41 isoform 1 NM O14901 ring finger protein 44 NM OO3958 ring finger protein 8 isoform 1 NM O17495 RNA-binding region containing protein 1 isoform NM OO5156 ROD1 regulator of differentiation 1 ROGDI NM O24589 leucine Zipper domain protein P11-193.3 NM 001012267 hypothetical protein LOC401541 P13-1SM17.2 NM 001010866 hypothetical protein LOC199953 P1-32F7.2 NM 173698 hypothetical protein LOC286499 P13-36OB22.2 NM 032227 hypothetical protein LOC84187 R PH3A NM O14954 rabphilin 3A homolog R PH3AL NM OO6987 rabphilin 3A-like (without C2 domains) R PLA NM 144563 ribose 5-phosphate isomerase A (ribose R PL13A NM 012423 ribosomal protein L13a R PL28 NM OOO991 ribosomal protein L28 R PL32 NM OOO994 ribosomal protein L32 RPL7L1C NM 198486 ribosomal protein L7-like 1 RPS23 NM 001025 ribosomal protein S23 RPS29 NM OO1030001 ribosomal protein S29 isoform 2 RPS6KA4 NM 001006944 ribosomal protein S6 kinase, 90 kDa, polypeptide RPS6KB1 NM OO3161 ribosomal protein S6 kinase, 70 kDa, polypeptide RPS6KL1 NM 031464 ribosomal protein S6 kinase-like 1 RPUSD1 NM 058.192 RNA pseudouridylate synthase domain containing RRAD NM 004165 Ras-related associated with diabetes RRAS NM OO6270 related RAS viral (r-ras) oncogene homolog R NM 012250 related RAS viral (r-ras) oncogene homolog 2 R NM 080657 radical S-adenosyl methionine domain containing R NM 178565 R-spondin family, member 2 R NM 001029871 R-spondin family, member 4 isoform 1 precursor NM O15138 Paf1/RNA polymerase II complex component NM 007008 reticulon 4 isoform C NM 178568 reticulon 4 receptor-like 1 NM 001015051 runt-related transcription factor 2 isoform b RUNX3 NM OO1031680 runt-related transcription factor 3 isoform 1 RUTBC1 NM O14853 RUN and TBC1 domain containing 1 RWDD1 NM OO1007464 RWD domain containing 1 isoform b RXRA NM OO2957 , alpha S100A7L1 NM 1768.23 S100 calcium binding protein A7-like 1 S1OOPBP NM O22753 S100P binding protein Riken isoform a SACM1L, NM 014O16 Suppressor of actin 1 SAMD3 NM 152552 sterile alpha motif domain containing 3 isoform SAMD4B NM 018028 sterile alpha motif domain containing 4B SAP3 OBP NM 013260 transcriptional regulator protein SAPS2 NM 014678 hypothetical protein LOC9701 SAR1A NM O2O150 SAR1a gene homolog 1 SARM1 NM O15.077 sterile alpha and TIR motif containing 1 SART1 NM OO5146 Squamous cell carcinoma antigen recognized by T SATB1 NM OO2971 special AT-rich sequence binding protein 1 SATB2 NM O15265 SATB family member 2 SAV1 NM 021818 WW45 protein SBK1 NM 001024401 SH3-binding domain kinase 1 SCAMPS NM 138967 secretory carrier membrane protein S SCARA3 NM 016240 Scavenger receptor class A, member 3 isoform 1 SCARAS NM 173833 hypothetical protein LOC286133 SCARF1 NM 145349 Scavenger receptor class F, member 1 isoform 2 US 2009/0227533 A1 Sep. 10, 2009 58

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description SCARF2 NM 153334 Scavenger receptor class F, member 2 isoform 1 SCCPDH NM 016002 Saccharopine dehydrogenase (putative) SCD NM 005063 Stearoyl-CoA desaturase SCMH1 NM OO1031694 sex comb on midleg homolog 1 isoform 1 SCML2 NM OO6089 sex comb on midleg-like 2 SCN1B NM OO1037 Sodium channel, voltage-gated, type I, beta SCN2B NM OO4588 Sodium channel, voltage-gated, type II, beta SCN3A NM OO6922 Sodium channel, voltage-gated, type III, alpha SCN3B NM 018400 voltage-gated sodium channel beta-3 subunit SCN4A NM OOO334 voltage-gated sodium channel type 4 alpha SCN4B NM 174934 Sodium channel, voltage-gated, type IV, beta SCNSA NM 000335 voltage-gated sodium channel type Valpha SCNN1A NM OO 1038 Sodium channel, nonvoltage-gated 1 alpha SCNN1D NM OO2978 Sodium channel, nonvoltage-gated 1, delta SCNN1G NM OO1039 Sodium channel, nonvoltage-gated 1, gamma SCP2 NM OO1007098 sterol carrier protein 2 isoform 2 SCRIB 5356 scribble isoform b SCUBE3 NM 152753 signal peptide, CUB domain, EGF-like 3 SDAD1 SDA1 domain containing 1 DC1 NM 001006946 Syndecan 1 precursor DHC Succinate dehydrogenase complex, Subunit C DK2 9064 sidekick 2 EC13L1 NM 030673 SEC13-like 1 isoform a EC31L2 NM O S490 S. cerevisiae SEC3 1-like 2 isoform a EC61A1 NM O 3336 Sec61 alpha 1 subunit EH1L, NM 03.1216 sec13-like protein isoform 2 ELPLG NMOO3OO6 selecti EMA3E 2431 Sel8) EMA3G NM O2O163 Semaphorin Sem2 EMA4B NM 020210 Semaphorin 4B precursor EMA4C NM O 7789 semaphorin 4C EMA4D NM OO6378 semaphorin 4D EMA4F NM 004263 semaphorin W EMA4G 7893 semaphorin 4G EMASA NM OO3966 semaphorin 5A EMA6A NM 020796 Sema domain, transmembrane domain (TM), and EMA6C NM 030913 semaphorin Y EMA6D NM 020858 semaphorin 6D isoform 1 precursor ENP2 NM 021627 SUMO1/sentrin SMT3 specific protease 2 E P3 NM O15670 SUMO1/sentrin SMT3 specific protease 3 P6 NM O15571 SUMO1/sentrin specific protease 6 PN1 NM 020451 selenoprotein N, 1 isoform 1 precursor PT1 NM 052838 Septin 1 PT11 NM 018243 Septin 11 PT3 NM 019106 septin 3 isoform B PT4 NM 004574 septin 4 isoform 1 PT6 NM 145800 septin 6 isoform A PT9 NM OO6640 septin 9 RINC1 NM 020755 tumor differentially expressed 2 RPINB2 NM OO2575 serine (or cysteine) proteinase inhibitor, clade RPINB5 NM 002639 serine (or cysteine) proteinase inhibitor, clade RPINB8 NM 002640 serine (or cysteine) proteinase inhibitor, clade RPINE1 NM OOO602 plasminogen activator inhibitor-1 RPINF2 NM OOO934 alpha-2-plasmin inhibitor SN2 NM 031459 sestrin 2 NM OO1007258 hypothetical protein LOC54093 isoform b NM 007165 splicing factor 3a, Subunit 2 NM 012426 splicing factor 3b, Subunit 3 NM 152235 splicing factor, arginine?serine-rich 8 isoform NM 032740 SFT2 domain containing 3 NM OO6926 Surfactant, pulmonary-associated protein A2 NM 178858 sideroflexin 2 NM 030971 sideroflexin 3 NM 144579 sideroflexin 5 NM 030791 sphingosine-1-phosphatase NM OOO199 N-sulfoglucosamine Sulfohydrolase (sulfamidase) NM OO3021 Small glutamine-rich tetratricopeptide NM 031469 SH3 domain binding glutamic acid-rich protein NM OO3O23 SH3-domain binding protein 2 NM 014521 SH3-domain binding protein 4 US 2009/0227533 A1 Sep. 10, 2009 59

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM OO3O25 SH3-domain GRB2-like 1 NM 153271 SH3 and PX domain containing 3 NM 014631 SH3 multiple domains 1 NM 001017995 SH3 and PX domains 2B NM O24577 SH3 domain and tetratricopeptide repeats 2 NM 012309 SH3 and multiple ankyrin repeat domains 2 NM 203349 rai-like protein NM 001010846 Src homology 2 domain containing E NM 138392 SH3KBP1 binding protein 1 NM 004169 serine hydroxymethyltransferase 1 (soluble) NM OO7373 Soc-2 Suppressor of clear homolog NM OO6883 short stature homeobox isoform b NM 170601 cytosolic sialic acid 9-O-acetylesterase NM O17699 SID1 transmembrane family, member 1 NM 052884 sialic acid binding Ig-like lectin 11 NM OO9586 single-minded homolog 2 short isoform NM OO6747 signal-induced proliferation-associated protein NM 080792 signal-regulatory protein alpha precursor NM OO6065 signal-regulatory protein beta 1 precursor NM 012238 sirtuin 1 NM 031244 sirtuin 5 isoform 2 NM O16539 sirtuin 6 NM O14450 SHP2-interacting transmembrane adaptor protein NM 175875 sine oculis homeobox homolog 5 NM OO3036 v-ski sarcoma viral oncogene homolog NM O16532 skeletal muscle and kidney enriched inositol NM 052931 activating NK receptor precursor NM 000452 solute carrier family 10 (sodium/bile acid NM 001046 solute carrier family 12 NM OO6598 Solute carrier family 12 (potassium chloride NM 021082 solute carrier family 15 (H+ peptide NM OO3051 solute carrier family 16, member 1 NM 152527 Solute carrier family 16 (monocarboxylic acid NM O06517 solute carrier family 16, member 2 NM 013356 solute carrier family 16, member 8 NM OO5495 Solute carrier family 17 (sodium phosphate), NM OO3053 Solute carrier family 18 (vesicular monoamine), NM OO6996 solute carrier family 19, member 2 NM OO3O38 solute carrier family 1, member 4 NM 144585 urate anion exchanger 1 isoform a NM 018420 Solute carrier family 22 (organic cation NM O21977 solute carrier family 22 member 3 NM OO6672 solute carrier family 22 member 7 isoform a NM 08O866 Solute carrier family 22 (organic anion cation NM O24959 solute carrier family 24 member 6 NM O14251 solute carrier family 25, member 13 (citrin) NM OO6358 solute carrier family 25 (mitochondrial carrier; NM O24698 mitochondrial glutamate carrier 1 NM 024103 solute carrier family 25 (mitochondrial carrier; NM 207348 solute carrier family 25, member 34 NM 022042 solute carrier family 26, member 1 isoform a NM 133489 solute carrier family 26, member 10 isoform 2 NM OOO112 solute carrier family 26 member 2 NM 052832 solute carrier family 26, member 7 isoform a NM 052934 solute carrier family 26, member 9 isoform a NM 005094 solute carrier family 27 (fatty acid NM OO4955 solute carrier family 29 (nucleoside NM 018344 solute carrier family 29 (nucleoside NM 153247 solute carrier family 29 (nucleoside NM 145176 Solute carrier family 2 (facilitated glucose NM 052885 Solute carrier family 2 (facilitated glucose NM 020062 SLC2A4 regulator NM 014580 Solute carrier family 2, (facilitated glucose NM 001004433 solute carrier family 30 (zinc transporter), NM 001004434 solute carrier family 30, member 2 isoform 1 NM OO3459 solute carrier family 30 (zinc transporter), NM 013309 solute carrier family 30 (zinc transporter), NM 133496 Zinc transporter like 2 NM OO6345 solute carrier family 30 (zinc transporter), NM OO1860 Solute carrier family 31 (copper transporters), US 2009/0227533 A1 Sep. 10, 2009 60

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 007001 solute carrier family 35, member D2 NM O78483 solute carrier family 36 member 1 NM 198277 solute carrier family 37 (glycerol-3-phosphate NM 207113 solute carrier family 37 (glycerol-3-phosphate NM 030674 amino acid transporter system A1 NM 018018 solute carrier family 38, member 4 NM O2O342 solute carrier family 39 (zinc transporter), NM 152264 solute carrier family 39 (zinc transporter), NM O15359 solute carrier family 39 (zinc transporter), NM 213568 solute carrier family 39 (zinc transporter), NM 152346 solute carrier family 43, member 2 NM 020428 CTL2 protein NM 033102 prostein NM 003040 Solute carrier family 4, anion exchanger, member NM OO3615 Solute carrier family 4, Sodium bicarbonate NM 152351 Solute carrier family 5 (sodium glucose NM 178498 Solute carrier family 5 (sodium glucose NM 145913 solute carrier family 5 (iodide transporter), NM 003042 solute carrier family 6 (neurotransmitter NM 003044 solute carrier family 6 (neurotransmitter NM OO7231 Solute carrier family 6 (amino acid NM 001010898 solute carrier family 6, member 17 NM 001044 solute carrier family 6 (neurotransmitter NM 003043 solute carrier family 6 (neurotransmitter NM 001024845 solute carrier family 6 member 9 isoform 3 NM OO3O45 Solute carrier family 7 (cationic amino acid NMO19849 solute carrier family 7, member 10 NM 001008539 solute carrier family 7, member 2 isoform 1 NM OO3983 Solute carrier family 7 (cationic amino acid NM 032178 solute carrier family 7, member 6 opposite NM 012244 Solute carrier family 7 (cationic amino acid NM 033262 solute carrier family 8 member 3 isoform A NM OO4252 Solute carrier family 9 (sodium hydrogen NM O15266 Na+ H+ exchanger isoform 8 NM O17435 Solute carrier organic anion transporter family, NM OO5630 Solute carrier organic anion transporter family, NM 013272 Solute carrier organic anion transporter family, NM 144975 schlafen family member 5 NM OO5902 MAD, mothers against decapentaplegic homolog 3 NM 001001419 SMAD, mothers against DPP homolog 5 NM OO5904 MAD, mothers against decapentaplegic homolog 7 NM 021940 stromal membrane-associated protein NM O2O159 SWI/SNF-related, matrix-associated NM 003074 SWISNF-related matrix-associated NM OO6306 SMC1 structural maintenance of NM 004653 Smcy homolog, Y-linked SMO NM OO5631 Smoothened SMOC1 NM 0221.37 Secreted modular calcium-binding protein 1 SMOX NM 1758.39 polyamine oxidase isoform 1 SMPD1 NM 000543 sphingomyelin phosphodiesterase 1, acid SMPD3 NM 018667 sphingomyelin phosphodiesterase 3, neutral SMTN NM 134270 Smoothelin isoform a SMTNL2 NM 1985O1 hypothetical protein LOC342527 SMURF1 NM 020429 Smad ubiguitination regulatory factor 1 isoform SMYD1 NM 1982.74 SET and MYND domain containing 1 SNAI1 NM OO5985 Snail 1 homolog SNAI3 NM 178310 Snail homolog 3 SNAP2S NM OO3O81 synaptosomal-associated protein 25 isoform SNAP29 NM OO4782 synaptosomal-associated protein 29 SNAPC1 NM OO3O82 Small nuclear RNA activating complex, SNAPC2 NM OO3O83 Small nuclear RNA activating complex, SNCA NM OOO345 alpha-synuclein isoform NACP140 SNCG NM OO3O87 Synuclein, gamma (breast cancer-specific protein SND NM O14390 staphylococcal nuclease domain containing 1 SNF1LK2 NM O15191 SNF1-like kinase 2 SNPH NM 014723 Syntaphilin SNTA1 NM 003098 acidic alpha 1 syntrophin SNURF NM OO5678 SNRPN upstream reading frame protein SNX NM OO3099 Sorting nexin 1 isoform a SNX10 NM 013322 Sorting nexin 10 US 2009/0227533 A1 Sep. 10, 2009 61

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq Transcript ID Gene Symbol (Pruitt et al., 2005) Description SNX13 NM O15132 Sorting nexin 13 SNX15 NM 013306 Sorting nexin 15 isoform A SNX19 NM 014758 Sorting nexin 19 SNX4 NM 003794 Sorting nexin 4 SNX9 NM 016224 Sorting nexin 9 SOCS3 NM OO3955 Suppressor of cytokine signaling 3 SOCS4 NM 08O867 Suppressor of cytokine signaling 4 SOD3 NM 003102 Superoxide dismutase 3, extracellular SORBS1 NM O15385 Sorbin and SH3 domain containing 1 isoform 2 SORCS2 NM O2O777 VPS10 domain receptor protein SORCS 2 SOST NM O25237 Sclerostin precursor SOX10 NM OO6941 SRY (sex determining region Y)-box 10 SOX4 NM OO3107 SRY (sex determining region Y)-box 4 SOX6 NM 017508 SRY (sex determining region Y)-box 6 isoform 1 SOX9 NM 000346 transcription factor SOX9 P1 NM 138473 P2 NM OO3110 P7 NM 152860 osterix PAG11 NM 0582OO sperm associated antigen 11 isoform G precursor PARC NM OO3118 Secreted protein, acidic, cysteine-rich PATA12 NM 181727 spermatogenesis associated 12 PATA2 NM OO6038 spermatogenesis associated 2 PATA20 NM 022827 sperm protein SSP411 PATA3 NM 139073 testis and spermatogenesis cell apoptosis PBC24 NM 182513 spindle pole body component 24 homolog PCS2 NM 014752 signal peptidase complex subunit 2 homolog PDEF NMO12391 SAM pointed domain containingets transcription PEN NM O15001 spen homolog, transcriptional regulator PFH1 NM OO6459 SPFH domain family, member 1 PG21 NM 016630 acid cluster protein 33 PG7 NM 003119 paraplegin isoform 1 PI1 NM 003120 spleen focus forming virus (SFFV) proviral PINK2 NM 021114 serine protease inhibitor, Kazal type 2 PINKS NM OO6846 serine peptidase inhibitor, Kazal type 5 PINLW1 NM O2O398 serine peptidase inhibitor-like, with Kunitz and PN NM OO 1030288 sialophorin POCK1 NM 004598 sparcosteonectin, cwcv and kazal-like domains POCK2 NM 014767 sparcosteonectin, cwcv and kazal-like domains PON1 NM OO6108 spondin 1, extracellular matrix protein PO C NM OO1007226 speckle-type POZ protein PP NM OOO582 secreted phosphoprotein 1 isoform b PPL3 NM 139015 SPPL3 protein PRN NM 001012508 shadow of prion protein PRR2A NM 005.988 Small proline-rich protein 2A PRR2B NM 001017418 Small proline-rich protein 2B PRR2D NM OO6945 Small proline-rich protein 2D PRR2F NM 001014450 Small proline-rich protein 2F PRY1 NM 005841 sprouty homolog 1, antagonist of FGF signaling PRY3 NM 005840 sprouty homolog 3 PRYD4 NM 207344 hypothetical protein LOC283377 PSB3 NM 08O861 SPRY domain-containing SOCS box protein SSB-3 PSB4 NM 08O862 SPRY domain-containing SOCS box protein SSB-4 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 RC NM 005417 proto-oncogene tyrosine-protein kinase SRC RF NM OO3131 (c-fos serum response RGAP1 NM O2O762 SLIT-ROBO Rho GTPase-activating protein 1 RGAP2 NM O15326 SLIT-ROBO Rho GTPase RGAP3 NM OO1033116 SLIT-ROBO Rho GTPase activating protein 3 RPR NM OO3139 signal recognition particle receptor ("docking RR NM O21947 serine racemase S NM 080725 Sulfiredoxin 1 homolog SSR2 NM OO3145 signal sequence receptor, beta precursor SSR3 NM 007107 signal sequence receptor gamma Subunit SSTR2 NM 001050 Somatostatin receptor 2 SSX2IP NM 014021 synovial sarcoma, X breakpoint 2 interacting SSX5 NM 021015 synovial sarcoma, X breakpoint 5 isoform a SSX6 NM 173357 synovial sarcoma, X breakpoint 6 US 2009/0227533 A1 Sep. 10, 2009 62

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description ST18 NM 014682 Suppression of tumorigenicity 18 ST3GAL3 NM OO6279 sialyltransferase 6 isoform ST6GAL1 NM OO3O32 sialyltransferase 1 isoform a ST6GALNAC4 NM 175039 sialyltransferase 7D isoform a ST6GALNAC6 NM 013443 ST6 ST8SLA2 NM OO6011 ST8 alpha-N-acetyl-neuraminide STAB2 NM 017564 stabilin 2 precursor STAC NM OO3149 SH3 and cysteine rich domain STAC2 NM 1989.93 SH3 and cysteine rich domain 2 STAG2 NM OO6603 stromal antigen 2 STARD3 NM OO6804 steroidogenic acute regulatory protein related STARD8 NM 014725 START domain containing 8 STAT1 NM 139266 signal transducer and activator of transcription STAT3 NM OO3150 signal transducer and activator of transcription STC1 NM OO3155 Stanniocalcin 1 precursor STC2 NM 003714 Stanniocalcin 2 precursor STCH NM OO6948 stress 70 protein chaperone, STEAP2 NM 152999 six transmembrane epithelial antigen of the STIL NM OO3035 SCLTAL1 interrupting locus STIM1 NM OO3156 stromal interaction molecule 1 precursor STK10 NM OO5990 serine/threonine kinase 10 STK2S NM OO6374 serine/threonine kinase 25 STK35 NM 08.0836 serine/threonine kinase 35 STK39 NM 013233 serine threonine kinase 39 (STE20/SPS1 homolog, STK4 NM OO6282 serine/threonine kinase 4 STMN3 NM O15894 SCG10-like-protein STOM NMOO4099 stomatin isoform a STON1 NM OO6873 stonin 1 STRAP NM 007178 serine/threonine kinase receptor associated STRBP NM 018387 spermatid perinuclear RNA-binding protein STRN3 NM 014574 nuclear autoantigen STS NM 000351 steryl-sulfatase precursor STS-1 NM 032873 Cbl-interacting protein Sts-1 STX17 NM O17919 Syntaxin 17 STX1A NM 004603 Syntaxin 1A (brain) STX5 NM OO3164 Syntaxin 5 STXBP1 NM OO1032221 Syntaxin binding protein 1 isoform b SU NM 016169 Suppressor of fused SU NM 080764 Suppressor of hairy wing homolog 2 SU NM O15170 Sulfatase 1 SU NM 018837 Sulfatase 2 isoform a precursor SU NM O1435 Sulfotransferase family 4A, member 1 SUOX NM 000456 sulfite oxidase SU NM 007192 chromatin-specific transcription elongation SU NM OO3170 Suppressor of Ty 6 homolog SU NM OO3172 Surfeit 1 SU NM 03.316 Surfeit 4 SU NM OO6753 Surfeit 6 NM OO3173 Suppressor of variegation 3-9 homolog 1 NM 016028 Suppressor of variegation 4-20 homolog 1 isoform NM 03270 Suppressor of variegation 4-20 homolog 2 NM O14849 synaptic vesicle glycoprotein 2 SV L NM OO3174 Supervillin isoform 1 SVOP NM 01871 SV2 related protein SWAP70 NM O15055 SWAP-70 protein SYN2 NM OO3178 synapsin II isoform IIb SYNC1 NM 030786 , intermediate filament 1 SYNGR1 NM 00471 synaptogyrin 1 isoform 1 a SYNGR2 NM 004710 synaptogyrin 2 SYNGR3 NM 004209 synaptogyrin 3 SYNJ1 NM OO3895 synaptoanin 1 isoform a SYNPR NM 144642 synaptoporin SYT1 NM OO5639 synaptotagmin I SYT11 NM 152280 synaptotagmin 12 SYT13 NM 020826 synaptotagmin XIII SYT15 NM 03.1912 synaptotagmin XV isoform a SYT4 NM 020783 synaptotagmin IV SYT6 NM 205848 synaptotagmin VI SYT9 NM 175733 synaptotagmin IX SYVN1 NM 032431 synoviolin 1 isoform a US 2009/0227533 A1 Sep. 10, 2009 63

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description TACC1 NM OO6283 transforming, acidic coiled-coil containing TACR1 NM 001058 tachykinin receptor 1 isoform long TACSTD2 NM 002353 tumor-associated calcium signal transducer 2 TAF1A NM 005681 TBP-associated factor 1A isoform 1 TAF2 NM 003184 TBP-associated factor 2 TAF5 NM OO6951 TBP-associated factor 5 TAFSL NM 001025247 PCAF associated factor 65 beta isoform b TAGAP NM 054114 T-cell activation Rho GTPase-activating protein TAGLN NM 001001522 transgelin TAIP-2 NM 024969 TGF-beta induced apoptosis protein 2 TAL NM OO3189 T-cell acute lymphocytic leukemia 1 TAOK1 NM 020791 TAOkinase 1 TAPBP NM OO3190 apasin isoform 1 precursor TARBP2 NM 0041 78 TAR RNA binding protein 2 isoform b TARP NM 001003799 TCRgamma alternate reading frame protein TAS1R1 NM 177539 Sweet taste receptor T1r isoform a TATDN2 NM 014760 TatD DNase domain containing 2 TAX1BP3 NM 014604 Tax1 (human T-cell leukemia virus type I) TBC1D13 NM 0182O1 TBC1 domain family, member 13 TBC1D2 NM 018421 TBC1 domain family, member 2 TBC1D22B NM 017772 TBC1 domain family, member 22B TBC1D2B NM O15079 TBC1 domain family, member 2B TBC1D5 NM 014744 TBC1 domain family, member 5 TBCD NM OO1033052 beta- cofactor D isoform 2 TBL1XR1 NM O24665 nuclear receptor co-repressor? HDAC3 complex TBRG1 NM 032811 transforming growth factor beta regulator 1 TBX4 NMO18488 T-box 4 TCF NM 000545 transcription factor 1, hepatic TCF12 NM OO3205 transcription factor 12 isoform b TCF2 NM OO6481 transcription factor 2 isoform b TCF3 NM OO3200 transcription factor 3 TCF7 NM OO32O2 transcription factor 7 (T-cell specific, TCOF1 NM OO10O8657 Treacher Collins-Franceschetti syndrome 1 TCTA NM 022171 T-cell leukemia translocation altered gene TCTEX1D1 NM 152665 hypothetical protein LOC200132 TEF NM OO3216 hyrotrophic embryonic factor TENC1 NM O15319 ensin like C1 domain containing phosphatase TERT NM 198253 elomerase reverse transcriptase isoform 3 TESK1 NM OO6285 estis-specific protein kinase 1 TETRAN NM OO1120 etracycline transporter-like protein TEX13B NM 031273 estis expressed sequence 13B TEX261 NM 144582 estis expressed sequence 261 TEX264 NM O15926 estis expressed sequence 264 TFAP2A NM OO 1032280 transcription factor AP-2 alpha isoform b TFCP2L1 NM 014553 LBP-9 TFDP2 NM OO6286 transcription factor Dp-2 (E2F dimerization TFE3 NM OO6521 transcription factor binding to IGHM enhancer 3 TFEB NM 007162 transcription factor EB TFRC NM OO3234 transferrin receptor TGFA NM OO3236 transforming growth factor, alpha TGFB3 NM OO3239 transforming growth factor, beta 3 TGFBI NM OOO358 transforming growth factor, beta-induced, 68 kDa TGFBR1 NM 004612 transforming growth factor, beta receptor I TGFBR2 NM 001024847 TGF-beta type II receptor isoform A precursor TGFBR3 NM OO3243 transforming growth factor, beta receptor III TGIF2 NM O21809 TGFB-induced factor 2 TGM2 NM 004613 transglutaminase 2 isoform a TGOLN2 NM OO6464 trans-golgi network protein 2 TH NM OOO360 tyrosine hydroxylase isoform b TH1L, NM 198976 TH1-like protein THADA NM 198554 hyroid adenoma associated isoform 2 NM OOO361 hrombomodulin precursor NM OO3246 hrombospondin 1 precursor NM 176853 hioesterase Superfamily member 4 isoform b NM 182578 hioesterase Superfamily member 5 NM OO3249 himet oligopeptidase 1 NM 000460 hrombopoietin isoform 1 precursor NM 1993.34 hyroid hormone receptor, alpha isoform 1 NM OO5121 hyroid hormone receptor associated protein 1 THSD4 NM O24817 hypothetical protein LOC79875 US 2009/0227533 A1 Sep. 10, 2009 64

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description TICAM2 NM 021649 oll-like receptor adaptor molecule 2 TIGD6 NM 030953 hypothetical protein LOC81789 TIMM10 NM 012456 translocase of inner mitochondrial membrane 10 TIMM13 NM 012458 translocase of inner mitochondrial membrane 13 TIMM17B NM OO5834 translocase of inner mitochondrial membrane 17 TIMM22 NM 013337 translocase of inner mitochondrial membrane 22 TIMM8A NM 004085 translocase of inner mitochondrial membrane 8 TINP1 NM O14886 TGF beta-inducible nuclear protein 1 TK1 NM OO3258 hymidine kinase 1, Soluble TLK1 NM 012290 Ousled-like kinase 1 TLR4 NM 138554 oll-like receptor 4 precursor TLX1 NM 005521 T-cell leukemia, homeobox 1 TLX2 NM O16170 T-cell leukemia, homeobox2 TM4SF1 NM O14220 transmembrane 4Superfamily member 1 TM4SF4 NM 004617 transmembrane 4Superfamily member 4 TM9SF2 NM 004800 transmembrane 9 superfamily member 2 TM9SF3 NM O2O123 endomembrane protein emp70 precursor isolog TM9SF4 NM 014742 transmembrane 9 superfamily protein member 4 TMBIM1 NM 022152 transmembrane BAX inhibitor motif containin 1 TMC2 NM 080751 transmembrane cochlear-expressed protein 2 TMC5 NM O24780 transmembrane channel-like 5 TMCC1 NM 001017395 transmembrane and coiled-coil domains 1 isoform TMCC3 NM 020698 transmembrane and coiled-coil domains 3 TMED10 NM OO6827 transmembrane trafficking protein TMEFF1 NM OO3692 transmembrane protein with EGF-like and two TMEM104 NM O17728 hypothetical protein LOC54868 TM NMO24092 transmembrane protein 109 TM NM 138385 hypothetical protein LOC92305 TM NM 152913 hypothetical protein LOC222865 TM NM 032021 hypothetical protein LOC83935 TM NM 032928 transmembrane protein 141 TM NM 018273 hypothetical protein LOC55260 TM NM 018342 hypothetical protein LOC55314 TM NM 018075 hypothetical protein LOC55129 TM NM O25246 transmembrane protein 22 TM NM 032780 transmembrane protein 25 TM NM O15686 transmembrane protein 28 TM NM 014138 hypothetical protein LOC29057 TM NM 018126 transmembrane protein 33 TM NM 021637 transmembrane protein 35 TM NM 018266 transmembrane protein 39A TM NM 024334 transmembrane protein 43 TM NM 018087 transmembrane protein 48 TM NM 018710 transmembrane protein 55A TM NM 0182O2 transmembrane protein 57 TM NM 014698 transmembrane protein 63A TM NM 020431 transmembrane protein 63C TM NM 032323 hypothetical protein LOC84283 TM NM 174940 hypothetical protein LOC283232 TM NM 153347 hypothetical protein LOC144110 TM NM O15497 hypothetical protein LOC25963 TM NM O2O182 transmembrane prostate androgen-induced protein TM NM 018196 trimethyllysine hydroxylase, epsilon TMOD2 NM 014548 2 (neuronal) TMPRSS13 NM 032046 transmembrane protease, serine 13 TMPRSS4 NM 019894 transmembrane protease, serine 4 isoform 1 TMPRSS5 NM 030770 transmembrane protease, serine 5 TMPRSS6 NM 153609 transmembrane protease, serine 6 TMSB10 NM 021103 hymosin, beta 10 TMTC2 NM 152588 hypothetical protein LOC160335 TNFAIP1 NM 021137 tumor necrosis factor, alpha-induced protein 1 TNFAIP8L2 NM O24575 tumor necrosis factor, alpha-induced protein TNFRSF1OD NM OO3840 tumor necrosis factor receptor Superfamily, TNFRSF11B NM OO2546 Osteoprotegerin precursor TNFRSF14 NM OO3820 tumor necrosis factor receptor Superfamily, TNFRSF19 NM 148957 tumor necrosis factor receptor Superfamily, TNFRSF19L. NM 032871 tumor necrosis factor receptor Superfamily, TNFRSF8 NM 001243 tumor necrosis factor receptor Superfamily, TNFRSF9 NM OO1561 tumor necrosis factor receptor Superfamily, TNIP2 NM O24309 A20-binding inhibitor of NF-kappaB activation 2 US 2009/0227533 A1 Sep. 10, 2009 65

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description TNK1 NM OO3985 tyrosine kinase, non-receptor, 1 TNNI1 NM OO3281 I, skeletal, slow TNNI3 NM OOO363 , cardiac TNP1 NM 003284 transition protein 1 (during histone to TNPO2 NM 013433 transportin 2 (importin 3, karyopherin beta 2b) TNRC4 NM 007185 Erinucleotide repeat containing 4 TNRC6B NM 001024843 Erinucleotide repeat containing 6B isoform 2 TNS3 NM O22748 ensin-like SH2 domain containing 1 TNS4 NM 032865 C-terminal tensin-like TNT NM 182831 hypothetical protein LOC162083 TNXB NM 019105 enascin XB isoform 1 TOB2 NM O16272 transducer of ERBB2, 2 TOLLIP NM O19009 oll interacting protein TOM1 NM 005488 arget of myb1 TOM1L2 NM OO1033551 arget of myb1-like 2 isoform 1 TOMM22 NM O2O243 mitochondrial import receptor Tom 22 TOMM4OL NM 032174 translocase of Outer mitochondrial membrane 40 TOP2B NM OO1068 DNA topoisomerase II, beta isozyme TOPORS NM OO58O2 opoisomerase I binding, arginine?serine-rich TOR1A NM 000113 orsin A TOR1B NM 014506 orsin family 1, member B (torsin B) TOR3A NM 022371 orsin family 3, member A TOX NM 014729 hymus high mobility group box protein TOX TP53I11 NM OO6034 p53-induced protein TP53INP1 NM 033285 tumor protein p53 inducible nuclear protein 1 TP53INP2 NM 021202 tumor protein p53 inducible nuclear protein 2 TP53TG3 NMO16212 hypothetical protein LOC24150 TP73L NM 003722 tumor protein -like TPD52 NM 001025252 tumor protein D52 isoform 1 TPD52L3 NM 001001875 protein kinase NYD-SP25 isoform 3 TPI1 NM OOO365 triosephosphate isomerase 1 TPP1 NM OOO391 tripeptidyl-peptidase I precursor TPPP NM 007030 brain-specific protein p25 alpha TPSAB1 NM OO3294 tryptase alphabeta 1 precursor TPSB2 NM 024164 tryptase beta 2 precursor TRAF1 NM OO5658 TNF receptor-associated factor 1 TRAF3IP3 NM O25228 TRAF3-interacting JNK-activating modulator TRAF7 NM 206835 ring finger and WD repeat domain 1 isoform 2 TRAFD1 NM OO6700 FLN29 gene product TRAPPC6A NM 024.108 trafficking protein particle complex 6A EML4 NM 198153 triggering receptor expressed on myeloid ERF1 NM 018415 transcriptional regulating factor 1 isoform 3 EX1 NM 032166 hree prime repair exonuclease 1 isoform c AD3 NM 207111 TRIAD3 protein isoform a B2 NM 021643 tribbles homolog 2 M10 NM 052828 tripartite motif-containing 10 isoform 2 M14 NM 014788 tripartite motif protein TRIM14 isoform alpha M2 NM O15271 tripartite motif-containing 2 M21 NM 003141 52 kD Ro/SSA autoantigen M22 NM OO6074 tripartite motif-containing 22 M2S NM 005082 tripartite motif-containing 25 M29 NM 012101 tripartite motif protein TRIM29 isoform alpha M32 NM 012210 TAT-interactive protein, 72-KD M33 NM O15906 tripartite motif-containing 33 protein isoform M35 NM O15066 tripartite motif-containing 35 isoform 1 M37 NM O15294 tripartite motif-containing 37 protein M41 NM 03.3549 tripartite motif-containing 41 isform 1 MS4 NM 032546 ring finger protein 30 isoform 1 M62 NM 0182O7 tripartite motif-containing 62 M67 NM 001004342 hypothetical protein LOC440730 M68 NM 018073 ring finger protein 137 M9 NM 052978 tripartite motif protein 9 isoform 2 O NM 007118 triple functional domain (PTPRF interacting) TRM T5 NM 020810 RNA-(N1G37) methyltransferase PC3 NM OO3305 transient receptor potential cation channel, PC5 NM 012471 transient receptor potential cation channel, PV4 NM 021625 transient receptor potential cation channel, TSC1 NM OOO368 tuberous sclerosis 1 protein isoform 1 TSHR NM OOO369 hyroid stimulating hormone receptor isoform 1 TSHZ2 NM 173485 Zinc finger protein 218 US 2009/0227533 A1 Sep. 10, 2009 66

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description TSN NM 004622 translin TSPAN14 NM 030927 etraspanin 14 TSPAN17 NM 001006616 transmembrane 4 superfamily member 17 isoform c TSPAN18 NM 130783 etraspanin 18 isoform 2 TSPAN32 NM 139024 tumor-suppressing Subtransferable candidate 6 TSPAN33 NM 178562 penumbra TSPYL1 NM OO3309 TSPY-like 1 TSPYL4 NM 021648 TSPY-like 4 TSPYL5 NM 033512 TSPY-like S TSPYL6 NM OO10O3937 TSPY-like 6 TSR NM 018128 hypothetical protein LOC55720 TSSC4 NM 005706 tumor Suppressing subtransferable candidate 4 TTBK1 NM 032538 autubulin kinase 1 TTC NM OO3314 etratricopeptide repeat domain 1 TTC19 NM O17775 etratricopeptide repeat domain 19 TTL NM 153712 tubulin tyrosine ligase TTLL12 NM O15140 hypothetical protein LOC23170 TTLL3 NM O15644 tubulin tyrosine ligase-like family, member 3 TTMB NM 001003682 hypothetical protein LOC399474 TTYH2 NM 032.646 weety 2 isoform 1 TTYH3 NM O2S250 weety 3 TUBA2 NM OO6001 tubulin, alpha 2 isoform 1 TUBA4 NM O25019 tubulin, alpha 4 TUBB NM 178O14 tubulin, beta polypeptide TUBB1 NM 030773 beta tubulin 1, class VI TUFT NM O2O127 tuftelin 1 NMOO3322 tubby like protein 1 NM OO3324 tubby like protein 3 NM OO1007466 tubby like protein 4 isoform 2 NM 172367 LOST NM 012473 hioredoxin 2 precursor NM 021156 hioredoxin domain containing 13 NM O15051 hioredoxin domain containing 4 (endoplasmic NM OO5783 ATP binding protein associated with cell NM OO6472 hioredoxin interacting protein NM 0010O8224 uveal autoantigen with coiled-coil domains and NM 018449 ubiquitin associated protein 2 NM 001001895 ubiquitin associated and SH3 domain containing, NM OO3334 ubiquitin-activating enzyme E1 NM O24818 ubiquitin-activating enzyme E1-domain containing NM OO3342 biquitin-conjugating enzyme E2G 1 isoform 1 NM 0581.67 l biquitin conjugating enzyme E2, J2 isoform 2 NM OO3347 l biquitin-conjugating enzyme E2L 3 isoform 1 NM 001012989 hypothetical protein LOC389898 NM 022066 ubiquitin-conjugating enzyme E2O NM 017582 ubiquitin-conjugating enzyme E2O NM 017811 ubiquitin-conjugating enzyme UBC3B NM 001001481 hypothetical protein LOC55284 isoform 1 NM 183414 l biquitin protein ligase E3B isoform b NM O14235 l biquitin-like 4 NM 032907 l biquitin-like 7 (bone marrow stromal NM 016936 l binuclein 1 OX5 NM O14948 U-box domain containing 5 isoform a NM 014517 upstream binding protein 1 (LBP-1a) NM O2O131 ataxin-1 ubiquitin-like interacting protein NM O14233 upstream binding transcription factor, RNA NM 152376 UBX domain containing 3 NM 014613 UBX domain containing 8 NM 033199 urocortin 2 preproprotein NM OO3356 uncoupling protein 3 isoform UCP3L NM OO5659 ubiquitin fusion degradation 1-like isoform A NM 152404 UDP glycosyltransferase 3 family, polypeptide NM 152896 Np95-like ring finger protein isoform b NM O25217 UL16 binding protein 2 NM 003565 unc-51-like kinase 1 NM O05148 unc119 (C. elegans) homolog isoform a NM O06377 UNC13 (C. elegans)-like UNC45A NM 018671 Smooth muscle cell associated protein-1 isoform UNC4SB NM OO1033576 cardiomyopathy associated 4 isoform 2 UNCSA NM 133369 netrin receptor Unc5h1 US 2009/0227533 A1 Sep. 10, 2009 67

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description UNC5C NM 003728 UNCSD NM 080872 netrin receptor Unc5h4 UNC84A NM O25154 unc-84 homolog A UNG NM OO3362 uracil-DNA glycosylase isoform UNG1 precursor UQCR NM OO6830 ubiquinol-cytochrome c reductase, 6.4 kDa UROC1 NM 144639 urocanase domain containing 1 UROS NM OOO375 uroporphyrinogen III synthase URP2 NM 031471 UNC-112 related protein 2 short form USF1 NM 007122 upstream stimulatory factor 1 isoform 1 USP15 NM OO6313 ubiguitin specific protease 15 USP25 NM 013396 ubiguitin specific protease 25 USP3 NM OO6537 ubiquitin specific protease 3 USP47 NM O17944 ubiquitin specific protease 47 UST NM OO5715 uronyl-2-sulfotransferase UTS2D NM 198152 urotensin 2 domain containing JTY NM 007125 tetratricopeptide repeat protein isoform 3 WAMP1 NM O14231 vesicle-associated membrane protein 1 isoform 1 WAMP2 NM O14232 vesicle-associated membrane protein 2 WAMP3 NM OO4781 vesicle-associated membrane protein 3 WANGL2 NM 020335 yang-like 2 (van gogh, Drosophila) WAPA NM 003574 vesicle-associated membrane protein-associated VARSL NM 020442 valyl-tRNA synthetase 2-like WASH1 NM O14909 vasohibin 1 WAT1 NM OO6373 vesicle amine transport protein 1 WAV2 NM OO3371 vaV 2 oncogene WAX1 NM 1991.31 ventral anterior homeobox 1 WCAM1 NM 001078 vascular cell adhesion molecule 1 isoform a VCL. NM OO3373 winculin isoform VCL VCP NM 007126 valosin-containing protein VCPIP1 NM O25054 valosin containing protein (p97), p.47 complex WDR NM OOO376 vitamin D (1,25-dihydroxyvitamin D3) receptor VEGF NM 001025366 vascular endothelial growth factor isoform a VEZT NM O transmembrane protein vezatin WGLL3 NM O colon carcinoma related protein VISA NM 020746 virus-induced signaling adapter WMD2 NM 004183 bestrophin WMD2L1 7682 vitelliform macular dystrophy 2-like 1 WMD2L2 NM 153274 vitelliform macular dystrophy 2-like 2 VMP NM 080723 vesicular membrane protein p24 VPS13A NM 001018037 vacuolar protein sorting 13A isoform C VPS13B NM O 7890 vacuolar protein sorting 13B isoform 5 VPS13C NM O 7684 vacuolar protein sorting 13C protein isoform 1A VPS13D NM O 5378 vacuolar protein sorting 13D isoform 1 VPS24 NM 001005753 vacuolar rotein sortin 24 isoform 2 VPS36 vacuolar protein sorting 36 VPS37A NM 152415 hepatocellular carcinoma related protein 1 VPS37B NM 024667 vacuolar protein sorting 37B VPS39 NM O 5289 vacuolar protein sorting 39 VPS41 NM O 4396 vacuolar protein sorting 41 (yeast homolog) VPS4A NM O 3245 vacuolar protein sorting factor 4A VPS52 NM O22553 Suppressor of actin mutations 2-like WSIG1 NM 1826O7 V-set and immunoglobulin domain containing 1 VTCN1 NM O24626 V-set domain containing T cell activation WWA1 NM 022834 von Willebrand factor A domain-related protein VWCE NM 152718 hypothetical protein LOC220001 WASF1 NM 001024934 Wiskott-Aldrich syndrome protein family member WASF2 NM OO6990 WAS protein family, member 2 WASL NM OO3941 Wiskott-Aldrich syndrome gene-like protein WBSCR16 NM 030798 Williams-Beuren syndrome chromosome region 16 WBSCR17 NM O22479 UDP-GalNAc:polypeptide WBSCR18 NM 032317 Williams Beuren syndrome chromosome region 18 WDFY3 NM 014991 WD repeat and FYVE domain containing 3 isoform WDR22 NM OO3861 Breakpoint cluster region protein, uterine WDR23 NM O25230 WD repeat domain 23 isoform 1 WDR3 NM OO6784 WD repeat-containing protein 3 WDR33 NM OO1006623 WD repeat domain 33 isoform 3 WDR35 NM OO1OO6657 WD repeat domain 35 isoform 1 WDR37 NM 014023 WD repeat domain 37 WDR39 NM 004804 WD repeat domain 39 WDR41 NM 018268 WD repeat domain 41 US 2009/0227533 A1 Sep. 10, 2009 68

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description WDRSB NM O19069 WD repeat domain 5B WDR68 WD-repeat protein WDR77 NM 024102 methylosome protein 50 WFDC5 NM 145652 WAP four-disulfide core domain 5 precursor WFIKKN2 NM 175575 WFIKKN2 protein WHSC1 NM OO7331 Wolf-Hirschhorn syndrome candidate 1 protein WHSC1L1 NM O23O34 WHSC1L1 protein isoform long WIPI2 NM OO1033518 hypothetical protein LOC26100 isoform c WIRE NM 133264 WIRE protein WISP2 NM 003881 WNT1 inducible signaling pathway protein 2 WIT1 NM O15855 Wilms tumor upstream neighbor 1 WNT1 NM 005430 wingless-type MMTV integration site family, WNT2 NM OO3391 wingless-type MMTV integration site family WNT2B NM 004.185 wingless-type MMTV integration site family, WNTSB NM 030775 wingless-type MMTV integration site family, WNT9B NM OO3396 wingless-type MMTV integration site family, WTAP NM 004906 Wilms' tumour 1-associating protein isoform 1 WWC3 NM O15691 hypothetical protein LOC55841 NM 005080 X-box binding protein 1 NM 207411 XK-related protein 5a NM 00101.1720 XK-related protein 9 NM OO6691 extracellular link domain containing 1 NM 004628 Xeroderma pigmentosum, complementation group C NM 020750 exportin 5 NM O 5171 exportin 6 NM 004.736 Xenotropic and polytropic retrovirus receptor NM005431 X-ray repair cross complementing protein 2 NM 005432 X-ray repair cross complementing protein 3 9001 5'-3' exoribonuclease 1 NM 005108 xylulokinase homolog NM 022166 xylosyltransferase I 8023 YEATS domain containing 2 NM 024029 Yipl domain family, member 2 NM 030799 Smooth muscle cell associated protein 5 NM OO6555 YKT6 v-SNARE protein 3313 yippee-like 1 NM 0010054.04 yippee-like 2 NM 145008 yippee-like 4 NM OO1031732 splicing factor YT521-B isoform 1 NM O 7798 YTH domain family, member 1 NM O 2479 tyrosine 3-monooxygenase/tryptophan NM 003406 tyrosine 3, tryptophan 5-monooxygenase NM OO3403 YY1 transcription factor NM OO4729 Ac-like transposable element 4830 Zinc finger and BTB domain containing 39 NM 020899 Zinc finger and BTB domain containing 4 NM O 4870 Zinc finger and BTB domain containing 40 NM O 4007 Zinc finger protein 297B NM O 4872 Zinc finger and BTB domain containing 5 NM 152735 Zinc finger and BTB domain containing 9 4827 hypothetical protein LOC9877 NM 001010888 hypothetical protein LOC340554 NM O 5117 Zinc finger CCCH-type domain containing 3 NM O 4153 Zinc finger CCCH-type domain containing 7 NM O 7590 Zinc finger CCCH-type containing 7B Zinc finger antiviral protein isoform 1 6505 putative S1 RNA binding domain protein NM 181706 Zinc finger, CSL domain containing 3 NM 032327 Abl-philin 2 isoform 1 5336 huntingtin interacting protein 14 NM 032.283 Zinc finger, DHHC domain containing 18 NM 174976 Zinc finger, DHHC domain containing 22 NM 173570 Zinc finger, DHHC domain containing 23 NM O 6598 DHHC1 protein NM O 3373 Zinc finger, DHHC domain containing 8 NM 033400 Zinc finger homeobox2 NM O24721 Zinc finger homeodomain 4 NM 03.0613 Zinc finger protein 2 homolog NM OO3407 Zinc finger protein 36, C3H type, homolog NM 173832 Zinc finger protein 41 homolog US 2009/0227533 A1 Sep. 10, 2009 69

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM 133458 Zinc finger protein 90 homolog NM 170768 Zinc finger protein 91 isoform 2 NM OO6782 Zinc finger protein-like 1 NM 181484 Zinc finger, CCCH-type with G patch domain NM O14943 Zinc fingers and 2 NM O15035 Zinc fingers and homeoboxes 3 ZMPSTE24 NM OO5857 Zinc metalloproteinase STE24 homolog ZMYM3 NM 005096 Zinc finger protein 261 ZMYM4 NM 00509S Zinc finger protein 262 ZMYND11 NM OO6624 Zinc finger, MYND domain containing 11 isoform F137 NM OO3438 Zinc finger protein 137 (clone pHZ-30) F148 NM 021964 Zinc finger protein 148 (pHZ-52) F16 NM 00102.9976 Zinc finger protein 16 isoform 2 F179 NM 007148 Zinc finger protein 179 F18O NM 013256 Zinc finger protein 180 (HHZ168) F182 NM OO1007088 Zinc finger protein 21 isoform 2 F184 NM 007149 Zinc finger protein 184 (Kruppel-like) F189 NM OO3452 Zinc finger protein 189 isoform 1 F193 NM OO6299 Zinc finger protein 193 F2 NM 001017396 Zinc finger protein 2 isoform b F2O7 NM OO3457 Zinc finger protein 207 isoform a F213 NM 004220 Zinc finger protein 213 F235 NM 004234 Zinc finger protein 93 homolog F238 NM OO6352 Zinc finger protein 238 isoform 2 F248 NM 021045 Zinc finger protein 248 F264 NM OO3417 Zinc finger protein 264 F274 NMO16324 Zinc finger protein 274 isoform b F276 NM 152287 Zinc finger protein 276 homolog F281 NM 012482 Zinc finger protein 281 F282 NM 003575 Zinc finger protein 282 F285 NM 152354 Zinc finger protein 285 F3 NM O17715 Zinc finger protein 3 isoform 1 F302 NM 00101.2320 Zinc finger protein 302 F304 NM O2O657 Zinc finger protein 304 F312 NM 018008 Zinc finger protein 312 F317 NM 020933 Zinc finger protein 317 F324 NM O14347 Zinc finger protein 324 F329 NM O24620 Zinc finger protein 329 F33B NM OO6955 Zinc finger protein 33B F346 NM 012279 Zinc finger protein 346 F358 NM 018083 Zinc finger protein 358 F365 NM 1994.51 Zinc finger protein 365 isoform C F367 NM 153695 Zinc finger protein 367 F37A NM OO1007094 Zinc finger protein 37a F395 NM 018660 Zinc finger protein 395 F397 NM 032347 Zinc finger protein 397 F398 NM 020781 Zinc finger 398 isoform b F406 NM 00102993.9 Zinc finger protein 406 isoform TR-ZFAT F418 NM Zinc finger protein 418 F436 Zinc finger protein 436 F445 Zinc finger protein 445 F446 Zinc finger protein 446 F449 Zinc finger protein 449 F45 Zinc finger protein 45 F471 Zinc finger protein 471 F480 Zinc finger protein 480 F493 Zinc finger protein 493 F497 Zinc finger protein 497 F5O1 Zinc finger protein 501 F502 Zinc finger protein 502 F510 Zinc finger protein 510 F512 Zinc finger protein 512 F513 Zinc finger protein 513 F526 Zinc finger protein 526 F530 Zinc finger protein 530 F532 Zinc finger protein 532 F540 Zinc finger protein 540 F551 Zinc finger protein 551 F553 Zinc finger protein 553 Zinc finger protein 561 US 2009/0227533 A1 Sep. 10, 2009 70

TABLE 3-continued Predicted target genes of hsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description NM O17656 Zinc finger protein 562 NM 152600 Zinc finger protein 579 NM 016202 Zinc finger protein 580 NM 032828 Zinc finger protein 587 NM 198457 Zinc finger protein 600 NM 1832.38 Zinc finger protein 605 NM O25040 Zinc finger protein 614 NM 198484 Zinc finger protein 621 NM 014789 Zinc finger protein 623 NM 033113 Zinc finger protein 628 NM 152320 Zinc finger protein 641 NM 016620 Zinc finger protein 644 isoform 2 NM 145166 Zinc finger protein 651 NM O14897 Zinc finger protein 652 NM 2074.04 Zinc finger protein 662 NM O24833 Zinc finger protein 671 NM O24836 Zinc finger protein 672 NM 138447 Zinc finger protein HIT-39 NM 001012.981 Zinc finger protein 694 NM 021916 Zinc finger protein 70 NM 016096 HSPCO38 protein NM 173831 Zinc finger protein 707 NM 198526 Zinc finger protein 710 NM OO3427 Zinc finger protein 76 (expressed in testis) NM OO6060 Zinc finger protein, Subfamily 1A, 1 (Ikaros) NM O22465 Zinc finger protein, Subfamily 1A, 4 NM 021035 Zinc finger, NFX1-type containing 1 NM OO6349 Zinc finger, HIT domain containing 1 ZSCAN2 NM 181877 Zinc finger protein 29 isoform 1 ZSWIM4 NM 023072 Zinc finger, SWIM domain containing 4 DB NM 007157 Zinc finger, X-linked, duplicated B DC NM O25112 ZXD family Zinc finger C NM O24646 hypo hetical protein LOC79699 NM O06336 zyg 1 homolog B (C. elegans)-like ZZEF1 NM O15113 ZC. finger, ZZ type with EF hand domain 1 ZZZ3 NM O15534 Zinc finger, ZZ domain containing 3

TABLE 4 Predicted hsa-miR-34a targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miR hSa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description BCA1 NM OO55O2 ATP-binding cassette, Sub-family A member 1 LIM3 NM O14945 actin binding LIM protein family, member 3 K3 NM 001149 ankyrin 3 isoform 2 PPBP2 NM OO6380 amyloid beta precursor protein-binding protein P3 NM 004925 aquaporin 3 EG NM OO1657 amphiregulin preproprotein HGAP1 NM 004308 Rho GTPase activating protein 1 HGDIB NM 001175 Rho GDP dissociation inhibitor (GDI) beta RTS-1 NM 016442 type 1 tumor necrosis factor receptor shedding NM OO1679 Na+K+-ATPase beta 3 subunit NM OOO332 ataxin 1 NM OO1699 receptor tyrosine kinase isoform 2 NM OO1497 UDP-Gal:betaGlcNAc beta 14 C NM OO3921 B-cell CLL/lymphoma 10 NM 001012270 baculoviral IAP repeat-containing protein 5 NM OO7306 breast cancer 1, early onset isoform R NM O14299 bromodomain-containing protein 4 isoform short NM 007047 butyrophilin, Subfamily 3, member A2 precursor NM 013279 hypothetical protein LOC745 NM 173481 hypothetical protein LOC126353 NM OO6688 complement component 1, q. Subcomponent-like 1 US 2009/0227533 A1 Sep. 10, 2009 71

TABLE 4-continued Predicted hsa-miR-34a targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miRhsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description C8orf1 NM 004337 hypothetical protein LOC734 CAP1 NM OO6367 adenylyl cyclase-associated protein CASP2 NM 032982 caspase 2 isoform 1 preproprotein CASP7 NM OO1227 caspase 7 isoform alpha precursor CCND1 NM 053056 cyclin D1 CCND3 NM OO1760 cyclin D3 CDC23 NM 004661 cell division cycle protein 23 CDH17 NM 004O63 cadherin 17 precursor CHES1 NM 005197 checkpoint Suppressor 1 CLDN1 NM 021101 claudin 1 COLSA1 NM 000093 alpha 1 type V collagen preproprotein COL6A2 NM 058175 alpha 2 type VI collagen isoform 2C2a precursor CRIP2 NM 001312 cysteine-rich protein 2 CRISPLD2 NM 031476 cysteine-rich Secretory protein LCCL domain CTDSPL NM OO1008392 Small CTD phosphatase 3 isoform 1 CTNND1 NM OO1331 catenin (cadherin-associated protein), delta 1 CTSB NM OO1908 cathepsin B preproprotein CXCL1 NM OO1511 chemokine (C-X-C motif) ligand 1 XCL2 NM O02089 chemokine (C-X-C motif) ligand 2 XCLS NM OO2994 chemokine (C-X-C motif) ligand 5 precursor YR61 NM OO1554 cysteine-rich, angiogenic inducer, 61 DX58 NM 014314 DEAD H (Asp-Glu-Ala-Asp/His) box polypeptide GAT1 NM 012079 diacylglycerol O-acyltransferase 1 KFZp564K142 NM 03.2121 implantation-associated protein PYSL3 NM OO1387 dihydropyrimidinase-like 3 2F5 NMOO1951 E2F transcription factor 5 FHD2 NM O24329 EF hand domain family, member D2 24 NM OO1007 277 etoposide induced 2.4 isoform 2 NM OOO132 coagulation factor VIII isoform a precursor NM OOOO43 tumor necrosis factor receptor Superfamily, NM 024907 F-box protein FBG4 isoform 2 NM 004116 FK506-binding protein 1B isoform a NM 024845 hypothetical protein LOC79903 NM O19008 hypothetical protein LOC54471 NM O17842 hypothetical protein LOC55652 NM 004475 lotill in 2 NM 013281 fibronectin leucine rich transmembrane protein 3 NM 005438 FOS-like antigen 1 NM O21953 orkhead boxM1 isoform 2 NM 007085 ollistatin-like 1 precursor NM OO1680 FXYD domain-containing ion transport regulator 2 NM O17423 polypeptide N-acetylgalactosaminyltransferase 7 NM O14905 glutaminase C GMNN NM O15895 geminin GNPDA1 NM 005471 glucosamine-6-phosphate deaminase 1 GORASP2 NM O15530 golgi reassembly stacking protein 2 GPR64 NM O05756 G protein-coupled receptor 64 GTSE NM 016426 G-2 and S-phase expressed 1 GYG2 NM OO3918 glycogenin 2 HDAC1 NM 004964 histone deacetylase 1 HIC2 NM O15094 hypermethylated in cancer 2 HLX1 NM O21958 H2.0-like homeo box 1 HMGCS1 NM 002130 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 HMGN4 NM OO6353 high mobility group nucleosomal binding domain HMMR NM 012484 hyaluronan-mediated motility receptor isoform a L1RL1 NM OO3856 interleukin 1 receptor-like 1 isoform 2 NHBB NM 002193 inhibin beta B subunit precursor RF1 NM 002198 interferon regulatory factor 1 TGAM NM 000632 integrin alpha M precursor TPR2 NM OO2223 inositol 14,5-triphosphate receptor, type 2 KCNK3 NM 002246 potassium channel, Subfamily K, member 3 KCNMA1 NM 001014797 large conductance calcium-activated potassium KIF11 NM OO4523 kinesin family member 11 KLC2 NM 022822 likely ortholog of kinesin light chain 2 NM OO4235 Kruppel-like factor 4 KRT20 NM O19010 keratin 20 LEPREL1 NM 018192 -like 1 LGR4 NM 018490 leucine-rich repeat-containing G protein-coupled LHX2 NM OO4789 LIM homeobox protein 2 US 2009/0227533 A1 Sep. 10, 2009 72

TABLE 4-continued Predicted hsa-miR-34a targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miRhsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description LITAF NM 004862 LPS-induced TNF-alpha factor LMAN2L. NM O3O805 lectin, mannose-binding 2-like LNK NM 005475 lymphocyte adaptor protein LOC933.49 NM 138402 hypothetical protein LOC93349 LPIN1 NM 145693 lipin 1 NM O17768 leucine rich repeat containing 40 LYST NM 000081 lysosomal trafficking regulator isoform 1 MAFF NM 012323 transcription factor MAFF MAP7 NM OO398O microtubule-associated protein 7 MARCH8 NM OO10O2265 cellular modulator of immune recognition MCL1 NM O21960 myeloid cell leukemia sequence 1 isoform 1 MET NM OOO245 met proto-oncogene precursor NM O14874 mitofusin 2 MK167 NM 002417 antigen identified by monoclonal antibody Ki-67 MPHOSPH6 NM OO5792 M-phase phosphoprotein 6 MTUS1 NM 001001924 mitochondrial tumor suppressor 1 isoform 1 NM OO6454 MAD4 MYL9 NM OO6097 myosin regulatory light polypeptide 9 isoform a NAV3 NM O14903 neuron navigator 3 NM 000268 neurofibromin 2 isoform 1 NM O14223 nuclear transcription factorY. gamma NINJ1 NM 004148 ninjurin 1 NMT2 NM 004.808 glycylpeptide N-tetradecanoyltransferase 2 NM OO2522 neuronal pentraxin I precursor NM 00618.6 nuclear receptor Subfamily 4, group A, member 2 NRP2 NMOO3872 neuropilin 2 isoform 2 precursor NUP210 NM 024923 nucleoporin 210 PALM2-AKAP2 NM OO72O3 PALM2-AKAP2 protein isoform 1 PDCD2 NM 144781 programmed cell death 2 isoform 2 PER2 NM 022817 period 2 isoform 1 PIK3CD NM OO5026 phosphoinositide-3-kinase, catalytic, delta PODXL NM 001018111 podocalyxin-like precursor isoform 1 PPL NM OO2705 Periplakin PPP1R11 NM O21959 protein phosphatase 1, regulatory (inhibitor) PROSC NM 007198 proline synthetase co-transcribed homolog PSME3 NM OO5789 proteasome activator subunit 3 isoform 1 PTPRE NM O06504 protein tyrosine phosphatase, receptor type, E RAI14 NM O15577 retinoic acid induced 14 RASSF2 NM 014737 Ras association domain family 2 RHEB NM OO5614 Rashomolog enriched in brain RIP NM OO10330O2 RPA interacting protein isoform 1 RRAD NM 004165 Ras-related associated with diabetes NM OO6270 related RAS viral (r-ras) oncogene homolog NM OOO602 plasminogen activator inhibitor-1 NM 030791 sphingosine-1-phosphatase NM OOO199 N-sulfoglucosamine Sulfohydrolase (sulfamidase) NM OO3O25 SH3-domain GRB2-like 1 NM 012238 sirtuin 1 NM OO4955 solute carrier family 29 (nucleoside NM 003043 solute carrier family 6 (neurotransmitter NM OO5902 MAD, mothers against decapentaplegic homolog 3 NM OO3118 Secreted protein, acidic, cysteine-rich NM OO6459 SPFH domain family, member 1 NM OO3155 Stanniocalcin 1 precursor NM OO3174 Supervillin isoform 1 NM O15055 SWAP-70 protein NM OO5639 synaptotagmin I NM 001024847 TGF-beta type II receptor isoform A precursor NM OOO361 thrombomodulin precursor NM 012458 translocase of inner mitochondrial membrane 13 NM OO3258 thymidine kinase 1, Soluble NM 004617 transmembrane 4 Superfamily member 4 NM 018087 transmembrane protein 48 NM OO1561 tumor necrosis factor receptor Superfamily, NM 001025252 tumor protein D52 isoform 1 NM OOO365 triosephosphate isomerase 1 NM 014788 tripartite motif protein TRIM14 isoform alpha NM OO6074 tripartite motif-containing 22 NM 007118 triple functional domain (PTPRF interacting) US 2009/0227533 A1 Sep. 10, 2009 73

TABLE 4-continued Predicted hsa-miR-34a targets that exhibited altered mRNA expression levels in human cancer cells after transfection with pre-miRhsa-miR-34a. RefSeq, Transcript ID Gene Symbol (Pruitt et al., 2005) Description TSN NM 004622 Translin TUBB NM 178O14 tubulin, beta polypeptide UBE2IL3 NM OO3347 ubiquitin-conjugating enzyme E2L 3 isoform 1 UROS NM OOO375 uroporphyrinogen III synthase VPS4A NM 013245 vacuolar protein sorting factor 4A WHSC1 NM OO7331 Wolf-Hirschhorn syndrome candidate 1 protein XBP1 NM 005080 X-box binding protein 1 YKT6 NM OO6555 YKT6 v-SNARE protein ZNF238 NM OO6352 Zinc finger protein 238 isoform 2 ZNF281 NM 012482 Zinc finger protein 281 ZNF551 NM 138347 Zinc finger protein 551 ZNF58O NM O16202 Zinc finger protein 580 ZNF652 NM O14897 Zinc finger protein 652

0061 Predicted gene targets are shown in Table 3. Target embodiments, a component is provided individually in the genes whose mRNA expression levels are affected by hsa same concentration as it would be in a solution with other miR-34 represent particularly useful candidates for cancer components. Concentrations of components may be provided therapy and therapy of other diseases or conditions through as 1x, 2x, 5x, 10x, or 20x or more. Kits for using probes, manipulation of their expression levels. synthetic nucleic acids, recombinant nucleic acids, or non 0062 Certain embodiments of the invention include deter synthetic nucleic acids of the invention for therapeutic, prog mining expression of one or more marker, gene, or nucleic nostic, or diagnostic applications are included as part of the acid segment representative of one or more genes, by using an invention. Specifically contemplated are any such molecules amplification assay, a hybridization assay, or protein assay, a corresponding to any miRNA reported to influence biological variety of which are well known to one of ordinary skill in the activity or expression of one or more marker gene or gene art. In certain aspects, an amplification assay can be a quan pathway described herein. In certain aspects, negative and/or titative amplification assay, such as quantitative RT-PCR or positive controls are included in some kit embodiments. The the like. In still further aspects, a hybridization assay can control molecules can be used to verify transfection effi include array hybridization assays or Solution hybridization ciency and/or control for transfection-induced changes in assays. The nucleic acids from a sample may be labeled from cells. the sample and/or hybridizing the labeled nucleic acid to one 0064 Certain embodiments are directed to a kit for assess or more nucleic acid probes. Nucleic acids, mRNA, and/or ment of a pathological condition or the risk of developing a nucleic acid probes may be coupled to a Support. Such Sup pathological condition in a patient by nucleic acid profiling of ports are well known to those of ordinary skill in the art and a sample comprising, in Suitable container means, two or include, but are not limited to glass, plastic, metal, or latex. In more nucleic acid hybridization or amplification reagents. particular aspects of the invention, the Support can be planar The kit can comprise reagents for labeling nucleic acids in a or in the form of a bead or other geometric shapes or configu sample and/or nucleic acid hybridization reagents. The rations known in the art. Proteins are typically assayed by hybridization reagents typically comprise hybridization immunoblotting, chromatography, or mass spectrometry or probes. Amplification reagents include, but are not limited to other methods known to those of ordinary skill in the art. amplification primers, reagents, and enzymes. 0063. The present invention also concerns kits containing 0065. In some embodiments of the invention, an expres compositions of the invention or compositions to implement sion profile is generated by steps that include: (a) labeling methods of the invention. In some embodiments, kits can be nucleic acid in the sample; (b) hybridizing the nucleic acid to used to evaluate one or more marker molecules, and/or a number of probes, or amplifying a number of nucleic acids, express one or more miRNA or miRNA inhibitor. In certain and (c) determining and/or quantitating nucleic acid hybrid embodiments, a kit contains, contains at least or contains at ization to the probes or detecting and quantitating amplifica most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, tion products, wherein an expression profile is generated. See 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, U.S. Provisional Patent Application 60/575,743 and the U.S. 36, 37,38, 39, 40, 41,42, 43,44, 45,46, 47,48, 49, 50, 51, 52, Provisional Patent Application 60/649.584, and U.S. patent 53, 54, 55, 56, 57, 58, 59, 60, 61, 100, 150, 200 or more application Ser. No. 1 1/141,707 and U.S. patent application probes, recombinant nucleic acid, or synthetic nucleic acid Ser. No. 1 1/273,640, all of which are hereby incorporated by molecules related to the markers to be assessed oran miRNA reference. or miRNA inhibitor to be expressed or modulated, and may 0.066 Methods of the invention involve diagnosing and/or include any range or combination derivable therein. Kits may assessing the prognosis of a patient based on a miRNA and/or comprise components, which may be individually packaged a marker nucleic acid expression profile. In certain embodi or placed in a container, Such as a tube, bottle, vial, Syringe, or ments, the elevation or reduction in the level of expression of other Suitable container means. Individual components may a particular gene or genetic pathway or set of nucleic acids in also be provided in a kit in concentrated amounts; in some a cell is correlated with a disease State or pathological condi US 2009/0227533 A1 Sep. 10, 2009 74 tion compared to the expression level of the same in a normal oforsets of the miRNAs and/or nucleic acids discussed in this or non-pathologic cell or tissue sample. This correlation application. The expression profile that is generated from the allows for diagnostic and/or prognostic methods to be carried patient will be one that provides information regarding the out when the expression level of one or more nucleic acid is measured in a biological sample being assessed and then particular disease or condition. In many embodiments, the compared to the expression level of a normal or non-patho profile is generated using nucleic acid hybridization or ampli logic cell or tissue sample. It is specifically contemplated that fication, (e.g., array hybridization or RT-PCR). In certain expression profiles for patients, particularly those Suspected aspects, an expression profile can be used in conjunction with of having or having a propensity for a particular disease or other diagnostic and/or prognostic tests, such as histology, condition Such as cancer, can be generated by evaluating any protein profiles in the serum and/or cytogenetic assessment.

TABLE 5 Tumor associated mRNAs altered by hsa-miR-34a 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, (Xia et al., 2001: Wikman et al., 2002; Boultwood et al., SSeCKSGravin transduction CML 2004; Choi et al., 2004: Mori et al., 2006) ANG Angiogenin angiogenesis BC, OC, M, PaC, UC, CeC (Barton et al., 1997: Montero et al., 1998; Hartmann et al., 1999; Miyake et al., 1999; Shimoyama et al., 1999; Bodner Adler et al., 2001) AREG Amphiregulin signal HCC, NSCLC, MM, PC, (Kitadai et al., 1993: Ebert et al., 1994: Solic and Davies, transduction OC, CRC, PaC, GC 1997; D'Antonio et al., 2002; Bostwicket al., 2004: Ishikawa et al., 2005; Mahtouk et al., 2005; Castillo et al., 2006) AURKB aurora kinase B chromosomal PC, NSCLC, BC, CRC (Keen and Taylor, 2004; Smith et al., 2005; Chieffi et al., STK12 stability 2006) BCL10 BCL-10 signal MALT BCL (Thome, 2004) transduction BRCA1 BRCA-1 chromosomal BC, OC (Wooster and Weber, 2003) stability BRCA2 BRCA-2 chromosomal BC, OC (Wooster and Weber, 2003) stability BUB1 BUB1 chromosomal AML. SGT, ALL HL, L, (Cahill et al., 1998; Qian et al., 2002; Ru et al., 2002; stability CRC, GC Grabsch et al., 2003: Shigeishi et al., 2006) CCNA2 cyclin A2 cell cycle AML (Qian et al., 2002) CCND1 cyclin D1 cell cycle MCL, BC, SCCHN, OepC, (Donnellan and Chetty, 1998) HCC, CRC, BldC, EC, OC, M, AC, GB, GC, PaC CCND3 cyclin D3 cell cycle EC, TC, BldC, CRC, LSCC, (Florenes et al., 2000; Ito et al., 2001; Filipits et al., 2002; Bai BCL, PaC, M et al., 2003; Pruneri et al., 2005; Tanami et al., 2005; Lopez Beltran et al., 2006; Troncone et al., 2007: Wu et al., 2006) CDK4 CDK-4 cell cycle G, GB, BC, LC, GC, EC, L, (Malumbres and Barbacid, 2001) OS, OC, TT, HCC, CHN CDKN2C CDK inhibitor 2C cell cycle HB, MB, HCC, HL, MM ( olascon et al., 1998: Kulkami et al., 2002: Morishita et al., 2 004: Sanchez-Aguilera et al., 2004) CTGF CTGF, IGFBP-8 cell adhesion, BC, GB, OepC, RMS, CRC, ( Hishikawa et al., 1999; Shimo et al., 2001; Koliopanos et al., migration PC, 2 002: Pan et al., 2002: Croci et al., 2004; Lin et al., 2005: Yang et al., 2005) EIF3S3 eIF-3 subunit 3g translation BC, PC, HCC (Nupponen et at., 1999; Nupponen et al., 2000; Okamoto et al., 2003) FAS Fas apoptosis NSCLC, G, L, CRC, OepC Moller et al., 1994; Gratas et al., 1998: Martinez-Lorenzo et al., 1998; Shinoura et al., 2000; Viard-Leveugle et al., 2003) FOXM1 forkhead box M1 transcription GB, LC, PC (Kalin et al., 2006; Kim et al., 2006; Liu et al., 2006) GMNN Geminin DNA CRC, BC, CeC (Wohlschlegel et al., 2002; Bravou et al., 2005; Shetty et al., replication 2005) HDAC1 HDAC-1 transcription BC, PC (Kawai et al., 2003; Halkidou et al., 2004) IL8 IL-8 signal BC, CRC, PaC, NSCLC, PC, (Akiba et al., 2001; Sparmann and Bar-Sagi, 2004) transduction HCC JUN c-Jun transcription HL, HCC Eferl et al., 2003; Weiss and Bohmann, 2004) LMO4 Lmo-4 transcription BC, SCCHN, SCLC Visvader et al., 2001; Mizunuma et al., 2003: Taniwaki et .., 2006) MCAM MCAM cell adhesion M, AS, KS, LMS Boccaccia and Comoglio, 2006) MCL1 McI-1 apoptosis HCC, MM, TT, CLL, Krajewska et al., 1996; Kitada et al., 1998; Cho-Vega et al., ALCL, BCL, PC 004: Rust et al., 2005; Sano et al., 2005; Wuilleme-Toumi et .., 2005; Fleischer et al., 2006: Sieghart et al., 2006) MET c-Met signal SPRC, HCC, GC, SCCHN, Boccaccio and Comoglio, 2006) transduction OS, RMS, GB, BC, M, CRC, GI, PaC, PC, OC MLF1 myeloid leukemia cell cycle AML (Matsumoto et al., 2000) factor 1 MYBL2 Myb L2 transcription BC, NSCLC, PC, OC (Tanner et al., 2000; Bar-Shira et al., 2002; Borczuk et al., 2003; Ginestier et al., 2006) NF1 NF-1 signal G, AC, NF, PCC, ML (Rubin and Gutmann, 2005) transduction US 2009/0227533 A1 Sep. 10, 2009 75

TABLE 5-continued Tumor associated mRNAs altered by hsa-miR-34a having prognostic or therapeutic value for the treatment of various malignancies.

Gene Cellular Symbol Gene Title Process Cancer Type Reference NF2 Merlin. NF-2 cell adhesion Schw, TC, HCC, MG, MT (McClatchey and Giovannini, 2005) of lung PBX1 PBX-1 transcription ALL (Aspland et al., 2001) PIK3CD PI 3-kinase IA signa AML, MSS, GI (Vogt et al., 2006) delta (p110 delta) transduction PLK1 polo-like kinase 1 chromosomal NSCLC, OrpC, OepC, GC, (Strebhardt and Ullrich, 2006) stability M, BC, OC, EC, CRC, GB, PapC, PaC, PC, HB, NHL RASSF2 RASSF2 signa GC, CRC, OC (Akino et al., 2005; Endoh et al., 2005; Lambros et al., 2005) transduction RBL1 b107 cell cycle BCL, PC, CRC, TC (Takimoto et al., 1998; Claudio et al., 2002; Wu et al., 2002; signa Ito et al., 2003) RRAS R-RAS transduction CeC, BC (Yu and Feig, 2002; Rincon-Arano et al., 2003) SMAD3 SMAD-3 signa GC, CRC, HCC, BC, ALL (Zhu et al., 1998; Han et al., 2004; Liu and Matsuura, 2005; transduction Yamagata et al., 2005; Yang et al., 2006) TACSTD1 tumor-associated cell adhesion, NSCLC, CRC (Xi et al., 2006a, Xi et al., 2006b) calcium signal vesicle transducer 1 trafficking TGFB2 TGFbeta-2 signa PaC, CRC, BC, M (Krasagakis et al., 1998; Jonson et al., 2001; Nakagawa et al., transduction 2004: Beisner et al., 2006) TGFBR2 TGF beta receptor signa BC, CRC type II transduction (Markowitz, 2000; Lucke et al., 2001; Biswas et al., 2004) TPD52 tumor protein D52 signa BC, LC, PC, OC, EC, HCC (Boutros et al., 2004) transduction TXN hioredoxin (trx) hioredoxin LC, PaC, CeC, HCC (Marks, 2006) redox system WNT7B Wnt-7b signa BC, BldC (Huguet et al., 1994: Buiet al., 1998) transduction

Abbreviations: AC, astrocytoma; ALCL, anaplastic large cell lymphoma; ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; AS, angiosarcoma; BC, breast carcinoma; BCL, B-cell lymphoma; BldC., bladder carcinoma: CeC, cervical carcinoma; CHN, carcinoma of the head and neck; CLL, chronic lymphocytic leukemia; CML, chronic myeloid leukemia; CRC, colorectal carcinoma; EC, endometrial carcinoma; G, glioma: GB, glioblastoma; GC, gastric carcinoma; GI, gastrinoma; HB, hepatoblastoma: HCC, hepatocellular carcinoma; HL, Hodgkin lymphoma; KS, Kaposi's sarcoma; L. leukemia; LC, lung carcinoma; LMS, leiomyosarcoma; LSCC, laryngeal squamous cell carcinoma; M, melanoma; MALT BCL, mucosa-associated lymphoid tissue B-cell lymphoma; MB, medulloblastoma: MCL, mantle cell lymphoma; MG, meningioma: ML, myeloid leukemia; MM, multiple myeloma; MSS, high-risk myelodysplastic syndrome: MT, mesothelioma: NF, neurofibroma: NHL, non-Hodgkin lymphoma; NSCLC, non-Small cell lung carcinoma; OC, ovarian carcinoma; US 2009/0227533 A1 Sep. 10, 2009 76

TABLE 5-continued Tumor associated mRNAs altered by hsa-miR-34a having prognostic or therapeutic value for the treatment of various malignancies.

Gene Cellular Symbol Gene Title Process Cancer Type Reference OepC, esophageal carcinoma; OrpC, oropharyngeal carcinoma; OS, Osteosarcoma; PaC, pancreatic carcinoma; PapC, papillary carcinoma; PC, prostate carcinoma; PCC, pheochromocytoma; RMS, rhabdomyosarcoma; SCCHN, Squamous cell carcinoma of the head and neck; Schw, Schwannoma; SCLC, Small cell lung cancer; SGT, salivary gland tumor; SPRC, sporadic papillary renal carcinoma; TC, thyroid carcinoma; TT, testicular tumor; UC, urothelial carcinoma

0067. The methods can further comprise one or more of 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, 36, 37,38, 39, 40, 41, the steps including: (a) obtaining a sample from the patient, 42, 43,44, 45,46, 47, 48,49, 50, 51, 52,53,54, 55,56, 57,58, (b) isolating nucleic acids from the sample, (c) labeling the 59, 60, 61,100, 150, 200 or more probes, recombinant nucleic nucleic acids isolated from the sample, and (d) hybridizing acid, or synthetic nucleic acid molecules related to the mark the labeled nucleic acids to one or more probes. Nucleic acids ers to be assessed oran miRNA to be expressed or modulated, of the invention include one or more nucleic acid comprising and may include any range or combination derivable therein. at least one segment having a sequence or complementary Kits may comprise components, which may be individually sequence of to a nucleic acid representative of one or more of packaged or placed in a container, such as a tube, bottle, vial, genes or markers in Table 1, 3, 4, and/or 5. Syringe, or other Suitable container means. Individual com 0068. It is contemplated that any method or composition ponents may also be provided in a kit in concentrated described herein can be implemented with respect to any amounts; in some embodiments, a component is provided other method or composition described herein and that dif individually in the same concentration as it would be in a ferent embodiments may be combined. It is specifically con Solution with other components. Concentrations of compo templated that any methods and compositions discussed nents may be provided as 1x, 2x, 5x, 10x, or 20x or more. Kits herein with respect to miRNA molecules, miRNA, genes, and for using probes, synthetic nucleic acids, recombinant nucleic Certain embodiments of the invention include determining acids, or non-synthetic nucleic acids of the invention for expression of one or more marker, gene, or nucleic acid therapeutic, prognostic, or diagnostic applications are representative thereof, by using an amplification assay, a included as part of the invention. Specifically contemplated hybridization assay, or protein assay, a variety of which are are any such molecules corresponding to any miRNA well known to one of ordinary skill in the art. In certain reported to influence biological activity or expression of one aspects, an amplification assay can be a quantitative amplifi or more marker gene or gene pathway described herein. In cation assay, such as quantitative RT-PCR or the like. In still certain aspects, negative and/or positive controls are included further aspects, a hybridization assay can include array in Some kit embodiments. The control molecules can be used hybridization assays or solution hybridization assays. The to verify transfection efficiency and/or control for transfec nucleic acids from a sample may be labeled from the sample tion-induced changes in cells. and/or hybridizing the labeled nucleic acid to one or more 0070 Certain embodiments are directed to a kit for assess nucleic acid probes. Nucleic acids, mRNA, and/or nucleic ment of a pathological condition or the risk of developing a acid probes may be coupled to a Support. Such supports are pathological condition in a patient by nucleic acid profiling of well known to those of ordinary skill in the art and include, but a sample comprising, in Suitable container means, two or are not limited to glass, plastic, metal, or latex. In particular more nucleic acid hybridization or amplification reagents. aspects of the invention, the Support can be planar or in the The kit can comprise reagents for labeling nucleic acids in a form of a bead or other geometric shapes or configurations sample and/or nucleic acid hybridization reagents. The known in the art. Protein are typically assayed by immunob hybridization reagents typically comprise hybridization lotting, chromatography, or mass spectrometry or other meth probes. Amplification reagents include, but are not limited to ods known to those of ordinary skill in the art. amplification primers, reagents, and enzymes. 0069. The present invention also concerns kits containing 0071. In some embodiments of the invention, an expres compositions of the invention or compositions to implement sion profile is generated by steps that include: (a) labeling methods of the invention. In some embodiments, kits can be nucleic acid in the sample; (b) hybridizing the nucleic acid to used to evaluate one or more marker molecules, and/or a number of probes, or amplifying a number of nucleic acids, express one or more miRNA. In certain embodiments, a kit and (c) determining and/or quantitating nucleic acid hybrid contains, contains at least or contains at most 1, 2, 3, 4, 5, 6, ization to the probes or detecting and quantitating amplifica 7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, tion products, wherein an expression profile is generated. See US 2009/0227533 A1 Sep. 10, 2009 77

U.S. Provisional Patent Application 60/575,743 and the U.S. ments thereof, unless otherwise indicated. It is understood by Provisional Patent Application 60/649.584, and U.S. patent those of skill in the art that a “gene family’ refers to a group application Ser. No. 1 1/141,707 and U.S. patent application of genes having the same coding sequence or miRNA coding Ser. No. 1 1/273,640, all of which are hereby incorporated by sequence. Typically, miRNA members of a gene family are reference. identified by a number following the initial designation. For 0072 Methods of the invention involve diagnosing and/or example, miR-16-1 and miR-16-2 are members of the miR assessing the prognosis of a patient based on a miRNA and/or 16 gene family and “mir-7 refers to miR-7-1, miR-7-2 and a marker nucleic acid expression profile. In certain embodi miR-7-3. Moreover, unless otherwise indicated, a shorthand ments, the elevation or reduction in the level of expression of notation refers to related miRNAs (distinguished by a letter). a particular gene or genetic pathway or set of nucleic acids in Exceptions to these shorthand notations will be otherwise a cell is correlated with a disease state or pathological condi identified. tion compared to the expression level of the same in a normal 0077. Other embodiments of the invention are discussed or non-pathologic cell or tissue sample. This correlation throughout this application. Any embodiment discussed with allows for diagnostic and/or prognostic methods to be carried respect to one aspect of the invention applies to other aspects out when the expression level of one or more nucleic acid is of the invention as well and vice versa. The embodiments in measured in a biological sample being assessed and then the Example and Detailed Description section are understood compared to the expression level of a normal or non-patho to be embodiments of the invention that are applicable to all logic cell or tissue sample. It is specifically contemplated that aspects of the invention. expression profiles for patients, particularly those Suspected (0078. The terms “inhibiting,” “reducing,” or “prevention.” of having or having a propensity for a particular disease or or any variation of these terms, when used in the claims and/or condition Such as cancer, can be generated by evaluating any the specification includes any measurable decrease or com oforsets of the miRNAs and/or nucleic acids discussed in this plete inhibition to achieve a desired result. application. The expression profile that is generated from the 007.9 The use of the word “a” or “an when used in con patient will be one that provides information regarding the junction with the term “comprising in the claims and/or the particular disease or condition. In many embodiments, the specification may mean “one but it is also consistent with profile is generated using nucleic acid hybridization or ampli the meaning of"one or more.” “at least one.” and “one or more fication, (e.g., array hybridization or RT-PCR). In certain than one.” aspects, an expression profile can be used in conjunction with 0080. Throughout this application, the term “about is other diagnostic and/or prognostic tests, such as histology, used to indicate that a value includes the standard deviation of protein profiles in the serum and/or cytogenetic assessment. error for the device or method being employed to determine 0073. The methods can further comprise one or more of the value. the steps including: (a) obtaining a sample from the patient, 0081. The use of the term “or” in the claims is used to (b) isolating nucleic acids from the sample, (c) labeling the mean “and/or unless explicitly indicated to refer to alterna nucleic acids isolated from the sample, and (d) hybridizing tives only or the alternatives are mutually exclusive, although the labeled nucleic acids to one or more probes. Nucleic acids the disclosure supports a definition that refers to only alter of the invention include one or more nucleic acid comprising natives and “and/or.” at least one segment having a sequence or complementary I0082. As used in this specification and claim(s), the words sequence of to a nucleic acid representative of one or more of “comprising (and any form of comprising, such as "com genes or markers in Table 1, 3, 4, and/or 5. prise' and "comprises”), “having (and any form of having, 0074. It is contemplated that any method or composition such as “have and “has'), “including' (and any form of described herein can be implemented with respect to any including, such as “includes and “include’) or “containing other method or composition described herein and that dif (and any form of containing, such as “contains and “con ferent embodiments may be combined. It is specifically con tain’) are inclusive or open-ended and do not exclude addi templated that any methods and compositions discussed tional, unrecited elements or method steps. herein with respect to miRNA molecules, miRNA, genes and I0083. Other objects, features and advantages of the nucleic acids representative of genes may be implemented present invention will become apparent from the following with respect to synthetic nucleic acids. In some embodiments detailed description. It should be understood, however, that the synthetic nucleic acid is exposed to the proper conditions the detailed description and the specific examples, while indi to allow it to become a processed or mature nucleic acid, Such cating specific embodiments of the invention, are given by as a miRNA under physiological circumstances. The claims way of illustration only, since various changes and modifica originally filed are contemplated to cover claims that are tions within the spirit and scope of the invention will become multiply dependent on any filed claim or combination of filed apparent to those skilled in the art from this detailed descrip claims. tion. 0075 Also, any embodiment of the invention involving specific genes (including representative fragments there of), DESCRIPTION OF THE DRAWINGS mRNA, or miRNAs by name is contemplated also to cover I0084. The following drawings form part of the present embodiments involving miRNAS whose sequences are at specification and are included to further demonstrate certain least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,90,91, 92,93, 94, aspects of the present invention. The invention may be better 95, 96, 97,98, 99% identical to the mature sequence of the understood by reference to one or more of these drawings in specified miRNA. combination with the detailed description of specific embodi 0076. It will be further understood that shorthand nota ments presented herein. tions are employed Such that a generic description of a gene or I0085 FIG. 1. Percent (%) proliferation of eight human marker thereof, or of a miRNA refers to any of its gene family lung cancer cell lines treated with hsa-miR-34a and other members (distinguished by a number) or representative frag compounds, relative to cells treated with negative control US 2009/0227533 A1 Sep. 10, 2009

miRNA (100%). Abbreviations: miR-34a, hsa-miR-34a: 0092 FIG. 8. Histology of tumors that developed from siEg5, siRNA against the motor protein kinesin 11 (Eg5); PPC-1 prostate cancer cells treated with negative control Etopo, etoposide: NC, negative control miRNA. Standard miRNA (right) or hsa-miR-34a (left). Images show tumors deviations are indicated in the graph. stained with hematoxylin and eosin. The arrow indicates a I0086 FIG. 2. Long-term effects of hsa-miR-34a on cul pocket with seemingly viable cells. Abbreviation: miR-34a, tured human H226 lung cancer cell numbers. Equal numbers hsa-miR-34a: NC, negative control miRNA. of H226 cells were electroporated with 1.6 uMhsa-miR-34a (0093 FIG. 9. Immunohistochemistry of PPC-1 tumors (white squares) or negative control miRNA (NC, black dia treated with negative control miRNA (top panels) or hsa monds), seeded and propagated in regular growth medium. miR-34a (bottom panels). For hsa-miR-34a-treated tumors, When the control cells reached confluence (days 6, 17 and the analysis is limited to areas with seemingly viable cells as 25), cells were harvested, counted and electroporated again shown in FIG. 8. Left images show tumor cells stained with with the respective miRNAs. The population doubling and hematoxylin and eosin (H&E); center images show an immu cumulative cell counts was calculated and plotted on a linear nohistochemistry analysis using antibodies against the Ki-67 scale. Arrows represent electroporation days. Abbreviation: antigen (dark spotted areas); right images show an immuno miR-34a, hsa-miR-34a, NC, negative control miRNA. histochemistry analysis using antibodies against caspase 3. I0087 FIG. 3. Percent (%) proliferation of H460 lung can Areas with increased apoptotic activity are exemplarily cer cells following administration of various combinations of denoted by arrows. Abbreviation: miR-34a, hsa-miR-34a: microRNAs. A positive sign under each bar in the graph NC, negative control miRNA. indicates that the miRNA was present in the administered combination. Standard deviations are shown in the graph. DETAILED DESCRIPTION OF THE INVENTION Abbreviations: miR-34a, hsa-miR-34a: miR-124a, hsa-miR 0094. The present invention is directed to compositions 124a: miR-126, hsa-miR-126; miR-147, hsa-miR-147; let and methods relating to the identification and characteriza 7b, hsa-let-7b; let-7c, hsa-let-7c; let-7g, hsa-let-7g; Etopo, tion of genes and biological pathways related to these genes etoposide: NC, negative control miRNA. as represented by the expression of the identified genes, as 0088 FIG. 4. Average tumor volumes in groups of six well as use of miRNAs related to such, for therapeutic, prog (n-6) mice carrying human H460 lung cancer Xenografts. nostic, and diagnostic applications, particularly those meth Palpable tumors were treated with hsa-miR-34a (white ods and compositions related to assessing and/or identifying squares) or with a negative control miRNA (NC, black dia pathological conditions directly or indirectly related to miR monds) on days 11, 14, and 17 (arrows). Standard deviations 34 expression or the aberrant expression thereof. are shown in the graph. Data points with p values.<0.1, <0.05 0095. In certain aspects, the invention is directed to meth and <0.01 are indicated by a cross, an asterisk or circles, ods for the assessment, analysis, and/or therapy of a cell or respectively. Abbreviation: miR-34a, hsa-miR-34a: NC, Subject where certain genes have a reduced or increased negative control miRNA. expression (relative to normal) as a result of an increased or I0089 FIG. 5. Percent (%) proliferation of hsa-miR-34a decreased expression of any one or a combination of miR-34 treated human prostate cancer cells relative to cells treated family members (including, but not limited to SEQID NO:1 with negative control miRNA (100%). Abbreviations: miR to SEQID NO:71) and/or genes with an increased expression 34a, hsa-miR-34a: siEg5, siRNA against the motor protein (relative to normal) as a result of an increased or decreased kinesin 11 (Eg5); NC, negative control miRNA. Standard expression of one or a combination of miR-34 family mem deviations are indicated in the graph. bers. The expression profile and/or response to miR-34 0090 FIG. 6. Long-term effects of hsa-miR-34a on cul expression or inhibition may be indicative of a disease or an tured human PPC-1, PC3 and Du145 prostate cancer cells. individual with a condition, e.g., cancer. Equal numbers cells were electroporated with 1.6 uM hsa 0096 Prognostic assays featuring any one or combination miR-34a (white squares) or negative control miRNA (NC, of the miRNAs listed or the markers listed (including nucleic black diamonds), seeded and propagated in regular growth acids representative thereof) could be used in assessment of a medium. When the control cells reached confluence (days 4 patient to determine what if any treatment regimen is justi and 11 for PPC-1, days 7 and 14 for PC3 and Du145), cells fied. As with the diagnostic assays mentioned above, the were harvested, counted and electroporated again with the absolute values that define low expression will depend on the respective miRNAs. The population doubling and cumulative platform used to measure the miRNA(s). The same methods cell counts was calculated and plotted on a linear scale. described for the diagnostic assays could be used for prog Arrows represent electroporation days. Experiments with nostic assays. PC3 and Du 145 cells were carried out in triplicates. Standard deviations are shown in the graphs. Abbreviation: miR-34a, I. Therapeutic Methods hsa-miR-34a: NC, negative control miRNA. 0091 FIG. 7. Average tumor volumes in groups of seven 0097 Embodiments of the invention concern nucleic (n=7) mice carrying human PPC-1 prostate cancer acids that perform the activities of or inhibit endogenous xenografts. Human PPC-1 prostate tumor cells were treated miRNAs when introduced into cells. In certain aspects, with hsa-miR-34a (white squares) or with a negative control nucleic acids are synthetic or non-synthetic miRNA. miRNA (NC, black diamonds) on days 0, 7, 13, 20, and 25 Sequence-specific miRNA inhibitors can be used to inhibit (arrows). Tumor growth was determined by caliper measure sequentially or in combination the activities of one or more ments for 32 days. Standard deviations are shown in the endogenous miRNAS in cells, as well those genes and asso graph. All data points yielded p values <0.01. The p value ciated pathways modulated by the endogenous miRNA. obtained from data on day 22 is indicated by a circle. Abbre 0098. The present invention concerns, in some embodi viation: miR-34a, hsa-miR-34a: NC, negative control ments, short nucleic acid molecules that function as miRNAS miRNA. or as inhibitors of miRNA in a cell. The term "short” refers to US 2009/0227533 A1 Sep. 10, 2009 79 a length of a single polynucleotide that is 15, 16, 17, 18, 19. the miRNA region is or is at least 90,91, 92,93, 94.95, 96.97, 20, 21, 22, 23, 24, 25, 50, 100, or 150 nucleotides or fewer, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or including all integers or ranges derivable there between. The 100% identical to the sequence of a naturally-occurring nucleic acid molecules are typically synthetic. The term "syn miRNA or complement thereof. thetic' refers to nucleic acid molecule that is isolated and not 0101 The term “complementary region' or “comple produced naturally in a cell. In certain aspects the sequence ment” refers to a region of a nucleic acid or mimetic that is or (the entire sequence) and/or chemical structure deviates from is at least 60% complementary to the mature, naturally occur a naturally-occurring nucleic acid molecule, such as an ring miRNA sequence. The complementary region is or is at endogenous precursor miRNA or miRNA molecule or least 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, complement thereof. While in some embodiments, nucleic 75, 76, 77,78, 79,80, 81,82, 83, 84,85, 86,87, 88, 89,90,91, acids of the invention do not have an entire sequence that is 92,93,94, 95, 96, 97,98,99,99.1,99.2, 99.3,99.4,99.5, 99.6, identical or complementary to a sequence of a naturally 99.7. 99.8, 99.9 or 100% complementary, or any range deriv occurring nucleic acid, Such molecules may encompass all or able therein. With single polynucleotide sequences, there 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 0102. 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, 99.3,994, 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 miRNA and miRNA inhibitors of the invention are collec prises the appropriate percentage of complementarity to the tively referred to as “synthetic nucleic acids.” sequence of a mature miRNA. 0099. In some embodiments, there is a miRNA or a syn 0103) In some embodiments, of the invention, a synthetic thetic miRNA having a length of between 17 and 130 resi miRNA or inhibitor contains one or more design element(s). dues. The present invention concerns miRNA or synthetic These design elements include, but are not limited to: (i) a miRNA molecules that are, are at least, or are at most 15, 16, replacement group for the phosphate or hydroxyl of the nucle 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, otide at the 5' terminus of the complementary region; (ii) one 34,35,36, 37,38, 39, 40, 41,42, 43,44, 45,46, 47, 48,49, 50, or more Sugar modifications in the first or last 1 to 6 residues 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 65,66, 67, of the complementary region; or, (iii) noncomplementarity 68, 69,70, 71,72, 73,74, 75,76, 77,78, 79,80, 81, 82, 83, 84, between one or more nucleotides in the last 1 to 5 residues at 85, 86, 87, 88, 89,90,91, 92,93, 94, 95, 96, 97,98, 99, 100, the 3' end of the complementary region and the corresponding 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, nucleotides of the miRNA region. A variety of design modi 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, fications are known in the art, see below. 125, 126, 127, 128, 129, 130, 140, 145, 150, 160, 170, 180, 0104. In certain embodiments, a synthetic miRNA has a 190, 200 or more residues in length, including any integer or nucleotide at its 5' end of the complementary region in which any range there between. the phosphate and/or hydroxyl group has been replaced with 0100. In certain embodiments, synthetic miRNA have (a) another chemical group (referred to as the “replacement a “miRNA region' whose sequence or binding region from 5' design). In some cases, the phosphate group is replaced, to 3' is identical or complementary to all or a segment of a while in others, the hydroxyl group has been replaced. In mature miRNA sequence, and (b) a “complementary region' particular embodiments, the replacement group is biotin, an whose sequence from 5' to 3' is between 60% and 100% amine group, a lower alkylamine group, an aminohexyl phos complementary to the miRNA sequence in (a). In certain phate group, an acetyl group, 2"O-Me (2'oxygen-methyl), embodiments, these synthetic miRNA are also isolated, as DMTO (4,4'-dimethoxytrity1 with oxygen), fluorescein, a defined above. The term “miRNA region” refers to a region thiol, or acridine, though other replacement groups are well on the synthetic miRNA that is at least 75, 80, 85,90, 95, or known to those of skill in the art and can be used as well. This 100% identical, including all integers there between, to the design element can also be used with a miRNA inhibitor. entire sequence of a mature, naturally occurring miRNA 0105. Additional embodiments concern a synthetic sequence or a complement thereof. In certain embodiments, miRNA having one or more Sugar modifications in the first or US 2009/0227533 A1 Sep. 10, 2009 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 0112 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 function. It is contemplated, however, that the 0106. In other embodiments of the invention, there is a miRNA molecule introduced into a cell is not a mature synthetic miRNA or inhibitor in which one or more nucle miRNA but is capable of becoming or functioning as a mature otides in the last 1 to 5 residues at the 3' end of the comple miRNA under the appropriate physiological conditions. In mentary region are not complementary to the corresponding cases in which a particular corresponding miRNA is being nucleotides of the miRNA region (“noncomplementarity”) inhibited by a miRNA inhibitor, the particular miRNA will be (referred to as the “noncomplementarity design). The non referred to as the “targeted miRNA. It is contemplated that complementarity may be in the last 1,2,3,4, and/or 5 residues multiple corresponding miRNAs may be involved. In particu of the complementary miRNA. In certain embodiments, there lar embodiments, more than one miRNA molecule is intro is noncomplementarity with at least 2 nucleotides in the duced into a cell. Moreover, in other embodiments, more than complementary region. one miRNA inhibitor is introduced into a cell. Furthermore, a 0107. It is contemplated that synthetic miRNA of the combination of miRNA molecule(s) and miRNA inhibitor(s) invention have one or more of the replacement, Sugar modi may be introduced into a cell. The inventors contemplate that fication, or noncomplementarity designs. In certain cases, a combination of miRNA may act at one or more points in synthetic RNA molecules have two of them, while in others cellular pathways of cells with aberrant phenotypes and that these molecules have all three designs in place. Such combination may have increased efficacy on the target 0108. The miRNA region and the complementary region cell while not adversely effecting normal cells. Thus, a com may be on the same or separate polynucleotides. In cases in bination of miRNA may have a minimal adverse effect on a which they are contained on or in the same polynucleotide, Subject or patient while Supplying a sufficient therapeutic the miRNA molecule will be considered a single polynucle effect, Such as amelioration of a condition, growth inhibition otide. In embodiments in which the different regions are on of a cell, death of a targeted cell, alteration of cell phenotype separate polynucleotides, the synthetic miRNA will be con or physiology, slowing of cellular growth, sensitization to a sidered to be comprised of two polynucleotides. second therapy, sensitization to a particular therapy, and the 0109 When the RNA molecule is a single polynucleotide, like. there can be a linker region between the miRNA region and 0113 Methods include identifying a cell or patient in need the complementary region. In some embodiments, the single of inducing those cellular characteristics. Also, it will be polynucleotide is capable of forming a hairpin loop structure understood that an amount of a synthetic nucleic acid that is as a result of bonding between the miRNA region and the provided to a cellor organism is an “effective amount,” which complementary region. The linker constitutes the hairpin refers to an amount needed (or a Sufficient amount) to achieve loop. It is contemplated that in some embodiments, the linker a desired goal. Such as inducing a particular cellular charac region is, is at least, or is at most 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, teristic(s). 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 0114. In certain embodiments of the methods include pro 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 residues in viding or introducing to a cell a nucleic acid molecule corre length, or any range derivable therein. In certain embodi sponding to a mature miRNA in the cell in an amount effec ments, the linker is between 3 and 30 residues (inclusive) in tive to achieve a desired physiological result. length. 0115 Moreover, methods can involve providing synthetic 0110. In addition to having a miRNA or inhibitor region or nonsynthetic miRNA molecules. It is contemplated that in and a complementary region, there may be flanking these embodiments, that methods may or may not be limited sequences as well at either the 5' or 3' end of the region. In to providing only one or more synthetic miRNA molecules or some embodiments, there is or is at least 1, 2, 3, 4, 5, 6, 7, 8, only one or more nonsynthetic miRNA molecules. Thus, in 9, 10 nucleotides or more, or any range derivable therein, certain embodiments, methods may involve providing both flanking one or both sides of these regions. synthetic and nonsynthetic miRNA molecules. In this situa 0111 Methods of the invention include reducing or elimi tion, a cell or cells are most likely provided a synthetic nating activity of one or more miRNAS in a cell comprising miRNA molecule corresponding to a particular miRNA and a US 2009/0227533 A1 Sep. 10, 2009

nonsynthetic miRNA molecule corresponding to a different of the invention, and vice versa. It will be understand that the miRNA. Furthermore, any method articulated using a list of term “providing an agent is used to include “administering miRNAS using Markush group language may be articulated the agent to a patient. without the Markush group language and a disjunctive article 0.120. In certain embodiments, methods also include tar (i.e., or) instead, and vice versa. geting a miRNA to modulate in a cell or organism. The term 0116. In some embodiments, there is a method for reduc “targeting a miRNA to modulate” means a nucleic acid of the ing or inhibiting cell proliferation in a cell comprising intro invention will be employed so as to modulate the selected ducing into or providing to the cell an effective amount of (i) miRNA. In some embodiments the modulation is achieved an miRNA inhibitor molecule or (ii) a synthetic or nonsyn with a synthetic or non-synthetic miRNA that corresponds to thetic miRNA molecule that corresponds to a miRNA the targeted miRNA, which effectively provides the targeted sequence. In certain embodiments the methods involves miRNA to the cellor organism (positive modulation). In other introducing into the cell an effective amount of (i) a miRNA embodiments, the modulation is achieved with a miRNA inhibitor molecule having a 5' to 3' sequence that is at least inhibitor, which effectively inhibits the targeted miRNA in 90% complementary to the 5' to 3' sequence of one or more the cell or organism (negative modulation). mature miRNA. I0121. In some embodiments, the miRNA targeted to be 0117 Certain embodiments of the invention include meth modulated is a miRNA that affects a disease, condition, or ods of treating a pathologic condition, in particular cancer, pathway. In certain embodiments, the miRNA is targeted e.g., lung or liver cancer. In one aspect, the method comprises because a treatment can be provided by negative modulation contacting a target cell with one or more nucleic acid, Syn of the targeted miRNA. In other embodiments, the miRNA is thetic miRNA, or miRNA comprising at least one nucleic acid targeted because a treatment can be provided by positive segment having all or a portion of a miRNA sequence. The modulation of the targeted miRNA or its targets. segment may be 5, 6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 0.122. In certain methods of the invention, there is a further 19, 20, 21, 22, 23, 24, 25, 30 or more nucleotides or nucleotide step of administering the selected miRNA modulator to a cell, analog, including all integers there between. An aspect of the tissue, organ, or organism (collectively “biological matter”) invention includes the modulation of gene expression, in need of treatment related to modulation of the targeted miRNA expression or function or mRNA expression or func miRNA or in need of the physiological or biological results tion within a target cell. Such as a cancer cell. discussed herein (such as with respect to a particular cellular 0118. Typically, an endogenous gene, miRNA or mRNA is pathway or result like decrease in cell viability). Conse modulated in the cell. In particular embodiments, the nucleic quently, in some methods of the invention there is a step of acid sequence comprises at least one segment that is at least identifying a patient in need of treatment that can be provided 70, 75, 80, 85, 90, 95, or 100% identical in nucleic acid by the miRNA modulator(s). It is contemplated that an effec sequence to one or more miRNA or gene sequence. Modula tive amount of a miRNA modulator can be administered in tion of the expression or processing of an endogenous gene, Some embodiments. In particular embodiments, there is a miRNA, or mRNA can be through modulation of the process therapeutic benefit conferred on the biological matter, where ing of a mRNA, such processing including transcription, a “therapeutic benefit” refers to an improvement in the one or transportation and/or translation with in a cell. Modulation more conditions or symptoms associated with a disease or may also be effected by the inhibition or enhancement of condition or an improvement in the prognosis, duration, or miRNA activity with a cell, tissue, or organ. Such processing status with respect to the disease. It is contemplated that a may affect the expression of an encoded product or the sta therapeutic benefit includes, but is not limited to, a decrease in bility of the mRNA. In still other embodiments, a nucleic acid pain, a decrease in morbidity, a decrease in a symptom. For sequence can comprise a modified nucleic acid sequence. In example, with respect to cancer, it is contemplated that a certain aspects, one or more miRNA sequence may include or therapeutic benefit can be inhibition of tumor growth, preven comprise a modified nucleobase or nucleic acid sequence. tion of metastasis, reduction in number of metastases, inhi 0119. It will be understood in methods of the invention bition of cancer cell proliferation, induction of cell death in that a cell or other biological matter Such as an organism cancer cells, inhibition of angiogenesis near cancer cells, (including patients) can be provided a miRNA or miRNA induction of apoptosis of cancer cells, reduction in pain, molecule corresponding to a particular miRNA by adminis reduction in risk of recurrence, induction of chemo- or radi tering to the cell or organism a nucleic acid molecule that osensitivity in cancer cells, prolongation of life, and/or delay functions as the corresponding miRNA once inside the cell. of death directly or indirectly related to cancer. The form of the molecule provided to the cell may not be the I0123. Furthermore, it is contemplated that the miRNA form that acts a miRNA once inside the cell. Thus, it is compositions may be provided as part of a therapy to a contemplated that in some embodiments, a synthetic miRNA patient, in conjunction with traditional therapies or preventa or a nonsynthetic miRNA is provided such that it becomes tive agents. Moreover, it is contemplated that any method processed into a mature and active miRNA once it has access discussed in the context of therapy may be applied as preven to the cell's miRNA processing machinery. In certain tatively, particularly in a patient identified to be potentially in embodiments, it is specifically contemplated that the miRNA need of the therapy or at risk of the condition or disease for molecule provided is not a mature miRNA molecule but a which a therapy is needed. nucleic acid molecule that can be processed into the mature 0.124. In addition, methods of the invention concern miRNA once it is accessible to miRNA processing machin employing one or more nucleic acids corresponding to a ery. The term “nonsynthetic' in the context of miRNA means miRNA and a therapeutic drug. The nucleic acid can enhance that the miRNA is not “synthetic.' as defined herein. Further the effect or efficacy of the drug, reduce any side effects or more, it is contemplated that in embodiments of the invention toxicity, modify its bioavailability, and/or decrease the dos that concern the use of synthetic miRNAs, the use of corre age or frequency needed. In certain embodiments, the thera sponding nonsynthetic miRNAS is also considered an aspect peutic drug is a cancer therapeutic. Consequently, in some US 2009/0227533 A1 Sep. 10, 2009

embodiments, there is a method of treating cancer in a patient pharmaceutical composition, generally, is defined as that comprising administering to the patient the cancer therapeu amount sufficient to detectably and repeatedly to achieve the tic and an effective amount of at least one miRNA molecule stated desired result, for example, to ameliorate, reduce, that improves the efficacy of the cancertherapeutic or protects minimize or limit the extent of the disease or its symptoms. non-cancer cells. Cancer therapies also include a variety of Other more rigorous definitions may apply, including elimi combination therapies with both chemical and radiation nation, eradication or cure of disease. based treatments. Combination chemotherapies include but 0127. A. Administration are not limited to, for example, 5-fluorouracil, alemtuzumab, 0128. In certain embodiments, it is desired to kill cells, amrubicin, bevacizumab, bleomycin, bortezomib, buSulfan, inhibit cell growth, inhibit metastasis, decrease tumor or tis camptothecin, capecitabine, cisplatin (CDDP), carboplatin, Sue size, and/or reverse or reduce the malignant or disease cetuximab, chlorambucil, cisplatin (CDDP), cyclophospha phenotype of cells. The routes of administration will vary, mide, camptothecin, COX-2 inhibitors (e.g., celecoxib), naturally, with the location and nature of the lesion or site to cyclophosphamide, cytarabine, dactinomycin, dasatinib, be targeted, and include, e.g., intradermal, Subcutaneous, daunorubicin, dexamethasone, docetaxel, doxorubicin regional, parenteral, intravenous, intramuscular, intranasal, (adriamycin), EGFR inhibitors (gefitinib and cetuximab), systemic, and oral administration and formulation. Direct erlotinib, binding agents, etoposide injection, intratumoral injection, or injection into tumor vas (VP16), everolimus, farnesyl-protein transferase inhibitors, culature is specifically contemplated for discrete, Solid, gefitinib, gemcitabine, gemtuzumab, ibritumomab, ifosfa accessible tumors, or other accessible target areas. Local, mide, imatinib mesylate, larotaxel, lapatinib, lonafarnib, regional, or systemic administration also may be appropriate. mechlorethamine, melphalan, methotrexate, mitomycin, For tumors of>4 cm, the volume to be administered will be navelbine, nitroSurea, nocodazole, Oxaliplatin, paclitaxel, pli about 4-10 ml (preferably 10 ml), while for tumors of <4 cm, comycin, procarbazine, raloxifene, rituximab, sirolimus, Sor a volume of about 1-3 ml will be used (preferably 3 ml). afenib, Sunitinib, tamoxifen, taxol, taxotere, temsirolimus, I0129 Multiple injections delivered as a single dose com tipifarnib, to situmomab, transplatinum, trastuzumab, Vin prise about 0.1 to about 0.5 ml volumes. Compositions of the blastin, Vincristin, or vinorelbine or any analog or derivative invention may be administered in multiple injections to a variant of the foregoing. tumor or a targeted site. In certain aspects, injections may be 0.125 Generally, inhibitors of miRNAs can be given to spaced at approximately 1 cm intervals. decrease the activity of an endogenous miRNA. Similarly, 0.130. In the case of surgical intervention, the present nucleic acid molecules corresponding to the mature miRNA invention may be used preoperatively, to renderan inoperable can be given to achieve the opposite effect as compared to tumor Subject to resection. Alternatively, the present inven when inhibitors of the miRNA are given. For example, inhibi tion may be used at the time of Surgery, and/or thereafter, to tors of miRNA molecules that increase cell proliferation can treat residual or metastatic disease. For example, a resected be provided to cells to increase proliferation or decrease cell tumor bed may be injected or perfused with a formulation proliferation. The present invention contemplates these comprising a miRNA or combinations thereof. Administra embodiments in the context of the different physiological tion may be continued post-resection, for example, by leaving effects observed with the different miRNA molecules and a catheter implanted at the site of the surgery. Periodic post miRNA inhibitors disclosed herein. These include, but are not Surgical treatment also is envisioned. Continuous perfusion limited to, the following physiological effects: increase and of an expression construct or a viral construct also is contem decreasing cell proliferation, increasing or decreasing apop plated. tosis, increasing transformation, increasing or decreasing cell I0131 Continuous administration also may be applied viability, activating or inhibiting a kinase (e.g., Erk), activat where appropriate, for example, where a tumor or other ing/inducing or inhibitinghTert, inhibit stimulation of growth undesired affected area is excised and the tumor bed or tar promoting pathway (e.g., Stat 3 signaling), reduce or increase geted site is treated to eliminate residual, microscopic dis viable cell number, and increase or decrease number of cells ease. Delivery via Syringe or catherization is contemplated. at a particular phase of the cell cycle. Methods of the inven Such continuous perfusion may take place for a period from tion are generally contemplated to include providing or intro about 1-2 hours, to about 2-6 hours, to about 6-12 hours, to ducing one or more different nucleic acid molecules corre about 12-24 hours, to about 1-2 days, to about 1-2 wk or sponding to one or more different miRNA molecules. It is longer following the initiation of treatment. Generally, the contemplated that the following, at least the following, or at dose of the therapeutic composition via continuous perfusion most the following number of different nucleic acid or will be equivalent to that given by a single or multiple injec miRNA molecules may be provided or introduced: 1, 2, 3, 4, tions, adjusted over a period of time during which the perfu 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, sion occurs. 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34,35, 36, 37,38, 39, I0132 Treatment regimens may vary as well and often 40, 41,42, 43,44, 45,46,47, 48,49, 50, 51, 52,53,54, 55,56, depend on tumor type, tumor location, immune condition, 57,58, 59, 60, 61, 62,63, 64, 65, 66, 67,68, 69,70, 71, 72,73, target site, disease progression, and health and age of the 74, 75,76, 77,78, 79,80, 81, 82, 83, 84, 85,86, 87,88, 89,90, patient. Certain tumor types will require more aggressive 91, 92,93, 94, 95, 96, 97,98, 99, 100, or any range derivable treatment. The clinician will be best Suited to make such therein. This also applies to the number of different miRNA decisions based on the known efficacy and toxicity (if any) of molecules that can be provided or introduced into a cell. the therapeutic formulations. 0133. In certain embodiments, the tumor or affected area II. Pharmaceutical Formulations and Delivery being treated may not, at least initially, be resectable. Treat 0126 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 construct encoding the same. An "effective amount of the by elimination of certain particularly invasive portions. Fol US 2009/0227533 A1 Sep. 10, 2009 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, 0134) 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, 0135 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, 0140. 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. 0141 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 0.136 B. Injectable Compositions and Formulations artin light of the present disclosure. For example, one dosage 0.137 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 0.138. 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 0142. 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. 0139 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 0143. 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 0144. 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., all cases the form must be sterile and must be fluid to the the aggressiveness of the disease or cancer, the size of any US 2009/0227533 A1 Sep. 10, 2009

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. 0149. 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, 0145 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 0150. 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 0151. A/B/AB/A/BB/B/A A/A/BA/B/BB/A/AA/B/B/B system can be injected into a tissue or fluid Surrounding the BFAFBFB cell, or administered by diffusion of the nucleic acid delivery system across the cell membrane, or by any active or passive 0152 B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A transport mechanism across the cell membrane. Additionally, B/B/A/A the nucleic acid delivery system can be provided to the cell O153 B/A/B/A B/A/A/B A/A/A/B B/A/A/A A/B/A/A using techniques such as antibody-related targeting and anti A/A/B/A body-mediated immobilization of a viral vector. 0154 Administration of any compound or therapy of the 0146 C. Combination Treatments present invention to a patient will follow general protocols for 0147 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 0.155. 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, 0156 1. Chemotherapy or by contacting the cell with two or more distinct composi 0157. 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 0148. 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 extend the time period for treatment significantly, however, aberrations by affecting nucleic acid synthesis. Most chemo US 2009/0227533 A1 Sep. 10, 2009 therapeutic agents fall into the following categories: alkylat (0169. 2. Radiotherapy ing agents, antimetabolites, antitumor antibiotics, mitotic 0170 Radiotherapy, also called radiation therapy, is the inhibitors, and nitrosoureas. treatment of cancer and other diseases with ionizing radia 0158 a. Alkylating Agents tion. Ionizing radiation deposits energy that injures or destroys cells in the area being treated by damaging their 0159 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 0171 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 (0160 b. Antimetabolites plated such as microwaves, proton beam irradiation (U.S. Pat. 0161 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 gastrointestinal tract. 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 methotrexate. to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage 0162 5-Fluorouracil (5-FU) has the chemical name of ranges for radioisotopes vary widely, and depend on the half 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 antibodies 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 thymidine deficiency leading to cell death. Thus, the risk of radiation damage to healthy cells. effect of 5-FU is found in cells that rapidly divide, a charac 0172 Stereotactic radio-surgery (gamma knife) for brain teristic of metastatic cancers. and other tumors does not use a knife, but very precisely 016.3 c. Antitumor Antibiotics targeted beams of gamma radiotherapy from hundreds of 0164 Antitumor antibiotics have both antimicrobial and different angles. Only one session of radiotherapy, taking cytotoxic activity. These drugs also interfere with DNA by about four to five hours, is needed. For this treatment a spe chemically inhibiting enzymes and mitosis or altering cellu cially made metal frame is attached to the head. Then, several lar membranes. These agents are not phase specific So they scans and X-rays are carried out to find the precise area where work in all phases of the cell cycle. Thus, they are widely used the treatment is needed. During the radiotherapy for brain for a variety of cancers. Examples of antitumor antibiotics tumors, the patient lies with their head in a large helmet, include bleomycin, dactinomycin, daunorubicin, doxorubi which has hundreds of holes in it to allow the radiotherapy cin (Adriamycin), and idarubicin, Some of which are dis beams through. Related approaches permit positioning for cussed in more detail below. Widely used in clinical setting the treatment of tumors in other areas of the body. for the treatment of neoplasms, these compounds are admin 0173 J. Immunotherapy istered through bolus injections intravenously at doses rang 0.174. 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 0.165 d. Mitotic Inhibitors be, for example, an antibody specific for Some marker on the 0166 Mitotic inhibitors include plant 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 (0167 e. Nitrosureas cyte carrying a surface molecule that interacts, either directly 016.8 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 2009/0227533 A1 Sep. 10, 2009

0.175. 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 Cancer immunotherapeutics and their targets. the context of the present invention. Common tumor markers include carcinoembryonic antigen, prostate specific antigen, Generic Name Target urinary tumor associated antigen, fetal antigen, tyrosinase MORAb-009 Mesothelin G2SO carbonic anhydrase IX (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, mAb 8H9 8H9 antigen Much3, PLAP, estrogen receptor, receptor, erb Band M195 CD33 p155. An alternative aspect of immunotherapy is to combine pilimumab CTLA4 HuLuc63 CS1 anticancer effects with immune stimulatory effects. Immune Alemtuzumab CD53 stimulating molecules also exist including: cytokines such as Epratuzumab CD22 IL-2, IL-4, IL-12, GM-CSF, gamma-IFN. chemokines such BC8 CD45 as MIP-1, MCP-1, IL-8 and growth factors such as FLT3 HuJS91 Prostate specific membrane antigen ligand. Combining immune stimulating molecules, either as Lexatumumab TRAIL receptor-2 proteins or using gene delivery in combination with a tumor Pertuzumab HER-2 receptor Suppressor Such as MDA-7 has been shown to enhance anti Mik-beta-1 IL-2R tumor effects (Ju et al., 2000). Moreover, antibodies against RAV12 RAAG12 any of these compounds can be used to target the anti-cancer SGN-30 CD30 AME-133w CD2O agents discussed herein. HeFi-1 CD30 0176 Examples of immunotherapies currently under BMS-663S13 CD137 investigation or in use are immune adjuvants e.g., Mycobac Volociximab anti-C531 integrin GC1008 TGFB terium bovis, Plasmodium falciparum, dinitrochlorobenzene HCD122 CD40 and aromatic compounds (U.S. Pat. Nos. 5,801,005 and Siplizumab CD2 5,739,169: Hui and Hashimoto, 1998; Christodoulides et al., MORAb-003 Folate receptor alpha 1998), cytokine therapy e.g., interferons C, B and Y: IL-1, CNTO 328 IL-6 MDX-060 CD30 GM-CSF and TNF (Bukowski et al., 1998; Davidson et al., Ofatumumab CD2O 1998: Hellstrand et al., 1998) gene therapy e.g., TNF, IL-1, SGN-33 CD33 IL-2, p53 (Qinet al., 1998; Austin-Ward and Villaseca, 1998: U.S. Pat. Nos. 5,830,880 and 5,846,945) and monoclonal antibodies e.g., anti-ganglioside GM2, anti-HER-2, anti (0178 4. Gene Therapy p185; Pietras et al., 1998: Hanibuchietal., 1998: U.S. Pat. No. 0179. In yet another embodiment, a combination treat 5,824.311). Herceptin (trastuzumab) is a chimeric (mouse ment involves gene therapy in which atherapeutic polynucle human) monoclonal antibody that blocks the HER2-neu receptor. It possesses anti-tumor activity and has been otide is administered before, after, or at the same time as one approved for use in the treatment of malignant tumors or more therapeutic miRNA. Delivery of a therapeutic (Dillman, 1999). Table 6 is a non-limiting list of several polypeptide or encoding nucleic acid in conjunction with a known anti-cancer immunotherapeutic agents and their tar miRNA may have a combined therapeutic effect on target gets. It is contemplated that one or more of these therapies tissues. A variety of proteins are encompassed within the may be employed with the miRNA therapies described invention, some of which are described below. Various genes herein. that may be targeted for gene therapy of some form in com 0177. A number of different approaches for passive immu bination with the present invention include, but are not lim notherapy of cancer exist. They may be broadly categorized ited to inducers of cellular proliferation, inhibitors of cellular into the following: injection of antibodies alone; injection of proliferation, regulators of programmed cell death, cytokines antibodies coupled to toxins or chemotherapeutic agents; and other therapeutic nucleic acids or nucleic acid that encode injection of antibodies coupled to radioactive isotopes; injec therapeutic proteins. tion of anti-idiotype antibodies; and finally, purging of tumor 0180. The tumor suppressor oncogenes function to inhibit cells in bone marrow. excessive cellular proliferation. The inactivation of these genes destroys their inhibitory activity, resulting in unregu TABLE 6 lated proliferation. The tumor Suppressors (e.g., therapeutic Cancer immunotherapeutics and their targets. polypeptides) p53, FHIT, p16 and C-CAM can be employed. 0181. In addition to p53, another inhibitor of cellular pro Generic Name Target liferation is p16. The major transitions of the eukaryotic cell Cetuximab EGFR cycle are triggered by cyclin-dependent kinases, or CDKs. Panitumumab EGFR One CDK, cyclin-dependent kinase 4 (CDK4), regulates pro Trastuzumab erbB2 receptor gression through the G1. The activity of this enzyme may be Bevacizumab VEGF Alemtuzumab CD52 to phosphorylate Rb at late G1. The activity of CDK4 is Gemtuzumab ozogamicin CD33 controlled by an activating Subunit, D-type cyclin, and by an Rituximab CD2O inhibitory subunit, the p16INK4 has been biochemically Tositumomab CD2O characterized as a protein that specifically binds to and inhib Matuzumab EGFR Ibritumomab tiuxetan CD2O its CDK4, and thus may regulate Rb phosphorylation (Ser Tositumomab CD2O rano et al., 1993: Serrano et al., 1995). Since the p16INK4 HuPAM4 MUC1 protein is a CDK4 inhibitor (Serrano, 1993), deletion of this gene may increase the activity of CDK4, resulting in hyper US 2009/0227533 A1 Sep. 10, 2009 phosphorylation of the Rb protein. p16 also is known to cytokine analogs; or MIP-1, MIP-1beta, MCP-1, RANTES, regulate the function of CDK6. and other chemokines. It is further contemplated that the 0182 p16INK4 belongs to a newly described class of upregulation of cell Surface receptors or their ligands such as CDK-inhibitory proteins that also includes p16B, p19. Fas/Fas ligand, DR4 or DR5/TRAIL (Apo-2 ligand) would p21WAF1, and p27KIP1. The p16INK4 gene maps to 9p21, a potentiate the apoptotic inducing abilities of the present chromosome region frequently deleted in many tumor types. invention by establishment of an autocrine or paracrine effect Homozygous deletions and mutations of the p16INK4 gene on hyperproliferative cells. Increases intercellular signaling are frequent in human tumor cell lines. This evidence Sug by elevating the number of GAPjunctions would increase the gests that the p16INK4 gene is a tumor Suppressor gene. This anti-hyperproliferative effects on the neighboring hyperpro interpretation has been challenged, however, by the observa liferative cell population. In other embodiments, cytostatic or tion that the frequency of the p16INK4 gene alterations is differentiation agents can be used in combination with the much lower in primary uncultured tumors than in cultured present invention to improve the anti-hyperproliferative effi cell lines (Caldas et al., 1994; Cheng et al., 1994; Hussussian cacy of the treatments. Inhibitors of cell adhesion are con et al., 1994; Kamb et al., 1994; Mori et al., 1994: Okamoto et templated to improve the efficacy of the present invention. al., 1994: Nobori et al., 1995: Orlow et al., 1994; Arap et al., Examples of cell adhesion inhibitors are focal adhesion 1995). Restoration of wild-type p16INK4 function by trans kinase (FAKs) inhibitors and Lovastatin. It is further contem fection with a plasmid expression vector reduced colony for plated that other agents that increase the sensitivity of a hyper mation by some human cancer cell lines (Okamoto, 1994: proliferative cell to apoptosis, such as the antibody c225, Arap, 1995). could be used in combination with the present invention to 0183. Other genes that may be employed according to the improve the treatment efficacy. present invention include Rb, APC, DCC, NF-1, NF-2, WT-1, 0190. Apo2 ligand (Apo2L, also called TRAIL) is a mem MEN-I, MEN-II, Zac1, p73, VHL, MMAC1/PTEN, DBCCR ber of the tumor necrosis factor (TNF) cytokine family. 1. FCC, rsk-3, p27, p27/p16 fusions, p21/p27 fusions, anti TRAIL activates rapid apoptosis in many types of cancer thrombotic genes (e.g., COX-1, TFPI), PGS, Dp, E2F, ras, cells, yet is not toxic to normal cells. TRAIL mRNA occurs in myc, neu, raf, erb, fms, trk, ret, gsp, hist, abl, E1A, p300, genes a wide variety of tissues. Most normal cells appear to be involved in angiogenesis (e.g., VEGF, FGF, thrombospondin, resistant to TRAIL's cytotoxic action, Suggesting the exist BAI-1, GDAIF, or their receptors) and MCC. ence of mechanisms that can protect againstapoptosis induc 018.4 5. Surgery tion by TRAIL. The first receptor described for TRAIL, 0185. Approximately 60% of persons with cancer will called death receptor 4 (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 0186 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 0191 There have been many advances in the therapy of cers, precancers, or incidental amounts of normal tissue. cancer following the introduction of cytotoxic chemothera 0187 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 0.192 Another form of therapy for use in conjunction with be of varying dosages as well. chemotherapy, radiation therapy or biological therapy 0188 6. Other Agents includes hyperthermia, which is a procedure in which a 0189 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. US 2009/0227533 A1 Sep. 10, 2009

0193 A patient's organ or a limb is heated for regional otide sequences in situ on a Substrate. Spotted or fabricated therapy, which is accomplished using devices that produce nucleic acid molecules can be applied in a high density matrix high energy, such as magnets. Alternatively, some of the pattern of up to about 30 non-identical nucleic acid molecules patient's blood may be removed and heated before being per square centimeter or higher, e.g. up to about 100 or even 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 0194 Hormonal therapy may also be used in conjunction linked to the original sample. with the present invention or in combination with any other 0200 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 0.195. 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 III. Mirna Molecules types of nucleic acid arrays. (0196) MicroRNA molecules (“miRNAs) are generally 0201 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; (0197) 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 (0198 A. Array Preparation 803 000; the disclosures of which are all herein incorporated 0199 Certain embodiments of the present invention con by reference. cerns the preparation and use of mRNA or nucleic acid arrays, 0202. 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-34 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 0203 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 US 2009/0227533 A1 Sep. 10, 2009 otide probes per cm. The surface area of the array can be condition, or between two differently treated samples. Also, about or less than about 1, 1.6,2,3,4,5,6,7,8,9, or 10 cm. miRNA or gene expression may be compared between a 0204 Moreover, a person of ordinary skill in the art could sample believed to be susceptible to a particular disease or readily analyze data generated using an array. Such protocols condition and one believed to be not susceptible or resistant to 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 0205 B. Sample Preparation traits include symptoms of, or Susceptibility to, a disease or 0206. 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 0213. 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 0207 C. Hybridization as fiber optics, glass or any other appropriate Substrate, see 0208 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. 0214 Particularly, arrays can be used to evaluate samples 0209. 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 0215 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 0210. 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 0216. 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 0211 D. Differential Expression Analyses during treatment to determine if there are miRNA or genes 0212 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 US 2009/0227533 A1 Sep. 10, 2009 90 profile is determined to be correlated with drug efficacy or 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, drug toxicity, that profile is relevant to whether that patient is 31, 32,33, 34,35,36, 37,38, 39, 40, 41, 42,43, 44, 45, 46,47, an appropriate patient for receiving a drug, for receiving a 48, 49, 50, 51, 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, combination of drugs, or for a particular dosage of the drug. 65, 66,67,68, 69,70, 71,72, 73,74, 75,76, 77,78, 79,80, 81, 0217. In addition to the above prognostic assay, samples 82, 83, 84,85, 86, 87, 88, 89,90,91, 92,93,94, 95, 96, 97,98, from patients with a variety of diseases can be evaluated to 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, determine if different diseases can be identified based on 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, miRNA and/or related gene expression levels. A diagnostic 240, 250, 260, 270, 280, 290, 300, 310,320, 330, 340, 350, assay can be created based on the profiles that doctors can use 360, 370, 380,390, 400, 410, 420, 430, 440, 450, 460, 470, to identify individuals with a disease or who are at risk to 480,490,500, 510,520, 530, 540, 550,560,570,580,590, develop a disease. Alternatively, treatments can be designed 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, based on miRNA profiling. Examples of such methods and 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 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 in the names of David Brown, Lance Ford, Angie Cheng processed miRNA, miRNA probes, precursor miRNA, and Rich Jarvis, which is hereby incorporated by reference in miRNA containing vectors, mRNA, mRNA probes, control its entirety. nucleic acids, and other probes and primers. 0218 E. Other Assays 0223) In many embodiments, miRNA are 19-24 nucle 0219. In addition to the use of arrays and microarrays, it is otides in length, while miRNA probes are 19-35 nucleotides contemplated that a number of different assays could be in length, depending on the length of the processed miRNA employed to analyze miRNAs or related genes, their activi and any flanking regions added. miRNA precursors are gen ties, and their effects. Such assays include, but are not limited erally between 62 and 110 nucleotides in humans. to, nucleic acid amplification, polymerase chain reaction, 0224 Nucleic acids of the invention may have regions of quantitative PCR, RT-PCR, in situ hybridization, Northern identity or complementarity to another nucleic acid. It is hybridization, hybridization protection assay (HPA) (Gen contemplated that the region of complementarity or identity Probe), branched DNA (bDNA) assay (Chiron), rolling circle can be at least 5 contiguous residues, though it is specifically amplification (RCA), single molecule hybridization detec contemplated that the region is, is at least, or is at most 6, 7, 8, tion (US Genomics), Invader assay (ThirdWave Technolo 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, gies), and/or Bridge Litigation Assay (Genaco). 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, IV. Nucleic Acids 60, 61, 62,63, 64, 65, 66, 67,68, 69,70, 71,72, 73,74, 75,76, 0220. The present invention concerns nucleic acids, modi 77,78, 79,80, 81, 82, 83, 84,85, 86, 87, 88,89,90,91, 92,93, fied or mimetic nucleic acids, miRNAS, mRNAS, genes, and 94, 95, 96, 97,98, 99, 100, 110, 120, 130, 140, 150, 160, 170, representative fragments thereof that can be labeled, used in 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, array analysis, or employed in diagnostic, therapeutic, or 300, 310,320, 330, 340, 350, 360, 370, 380,390, 400, 410, prognostic applications, particularly those related to patho 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510,520, logical conditions such as cancer. The molecules may have 530, 540, 550,560,570,580,590, 600, 610, 620, 630, 640, been endogenously produced by a cell, or been synthesized or 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, produced chemically or recombinantly. They may be isolated 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, and/or purified. Each of the miRNAs described herein and 890,900,910,920,930,940,950,960,970,980,990, or 1000 includes the corresponding SEQID NO and accession num contiguous nucleotides. It is further understood that the bers for these miRNA sequences. The name of a miRNA is length of complementarity within a precursor miRNA or often abbreviated and referred to without a “hsa- prefix and other nucleic acid or between a miRNA probe and a miRNA will be understood as such, depending on the context. Unless or a miRNA gene are such lengths. Moreover, the comple otherwise indicated, miRNAs referred to in the application mentarity may be expressed as a percentage, meaning that the are human sequences identified as miR-X or let-X, where X is complementarity between a probe and its target is 90% or a number and/or letter. greater over the length of the probe. In some embodiments, 0221. In certain aspects, a miRNA probe designated by a complementarity is or is at least 90%. 95% or 100%. In Suffix '5P or “3P can be used. “5P indicates that the particular, Such lengths may be applied to any nucleic acid mature miRNA derives from the 5' end of the precursor and a comprising a nucleic acid sequence identified in any of SEQ corresponding “3P indicates that it derives from the 3' end of ID NOS described herein, accession number, or any other the precursor, as described on the world wide web at sanger. sequence disclosed herein. Typically, the commonly used ac.uk. Moreover, in some embodiments, a miRNA probe is name of the miRNA is given (with its identifying source in the used that does not correspond to a known human miRNA. It prefix, for example, "hsa' for human sequences) and the is contemplated that these non-human miRNA probes may be processed miRNA sequence. Unless otherwise indicated, a used in embodiments of the invention or that there may exist miRNA without a prefix will be understood to refer to a a human miRNA that is homologous to the non-human human miRNA. Moreover, a lowercase letter in a miRNA miRNA. In other embodiments, any mammaliancell, biologi name may or may not be lowercase; for example, hsa-mir cal sample, or preparation thereof may be employed. 130b can also be referred to as miR-130B. The term “miRNA 0222. In some embodiments of the invention, methods and probe' refers to a nucleic acid probe that can identify a par compositions involving miRNA may concern miRNA, mark ticular miRNA or structurally related miRNAs. ers (mRNAs), and/or other nucleic acids. Nucleic acids may 0225. It is understood that some nucleic acids are derived be, beat least, or beat most 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, from genomic sequences or a gene. In this respect, the term