US 20090232893A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0232893 A1 Bader et al. (43) Pub. Date: Sep. 17, 2009 (54) MIR-143 REGULATED GENES AND Related U.S. Application Data PATHWAYS AS TARGETS FOR (60) Provisional application No. 60/939,573, filed on May THERAPEUTIC INTERVENTION 22, 2007. (76) Inventors: Andreas G. Bader, Austin, TX Publication Classification (US); Mike W. Byrom, Austin, TX (51) Int. Cl. (US); Charles D. Johnson, Austin, A6IR 9/14 (2006.01) TX (US); David Brown, Austin, TX CI2N 5/02 (2006.01) (US) A63L/7088 (2006.01) CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl. ............. 424/489: 435/375; 514/44 R; 435/6 Fulbright & Jaworski L.L.P. 600 Congress Avenue, Suite 2400 (57) ABSTRACT Austin, TX 78701 (US) The present invention concerns methods and compositions for identifying genes or genetic pathways modulated by miR (21) Appl. No.: 12/125,412 143, using miR-143 to modulate a gene or gene pathway, using this profile in assessing the condition of a patient and/or (22) Filed: May 22, 2008 treating the patient with an appropriate miRNA. Patent Application Publication Sep. 17, 2009 US 2009/0232893 A1 9||#7|Z||09 uo?e|noou??sodsÁed 07|| OZ|. 00|| 08 09 07 (uu) eZSJOun US 2009/0232893 A1 Sep. 17, 2009 MR-143 REGULATED GENES AND sion is lower in many human cancer tumor samples including PATHWAYS AS TARGETS FOR lung, colon, breast, bladder, and thyroid tumors, than in nor THERAPEUTIC INTERVENTION mal cells from the same patients. Overexpression of hsa-miR 143 in human leukemia cells (Jurkat) increased proliferation of those cells. The inventors also found hsa-miR-143 to be 0001. This application claims Priority to U.S. Provisional up-regulated in brain tissues of Alzheimer's patients. Other Patent Application Ser. No. 60/939,573, filed May 22, 2007 investigators have also observed that miR-143 is down-regu and PCT application No. PCT/US07/78859 filed Sep. 19, lated in colorectal tumors when compared with matched nor 2007, each of which are hereby incorporated by reference in mal samples (Michael et al., 2003: Akao et al., 2006) and that their entirety. miR-143 may be involved in the differentiation of human adipocytes (fat storage cells) (Esau et al., 2004). BACKGROUND OF THE INVENTION 0009 Bioinformatics analyses suggest that any given 0002 I. Field of the Invention miRNA may bind to and alter the expression of up to several 0003. The present invention relates to the fields of molecu hundred different genes. In addition, a single gene may be lar biology and medicine. More specifically, the invention regulated by several miRNAs. Thus, each miRNA may regu relates to methods and compositions for the treatment of late a complex interaction among genes, gene pathways, and diseases or conditions that are affected by miR-143 microR gene networks. Mis-regulation or alteration of these regula NAS, microRNA expression, and genes and cellular pathways tory pathways and networks, involving miRNAS, are likely to directly and indirectly modulated by such. contribute to the development of disorders and diseases such 0004 II. Background as cancer. Although bioinformatics tools are helpful in pre 0005. In 2001, several groups used a cloning method to dicting miRNA binding targets, all have limitations. Because isolate and identify a large group of “microRNAs (miRNAs) of the imperfect complementarity with their target binding from C. elegans, Drosophila, and humans (Lagos-Quintana et sites, it is difficult to accurately predict the mRNA targets of al., 2001; Lau et al., 2001; Lee and Ambros, 2001). Several miRNAs with bioinformatics tools alone. Furthermore, the hundred miRNAs have been identified in plants and ani complicated interactive regulatory networks among miRNAS mals—including humans—that do not appear to have endog and target genes make it difficult to accurately predict which enous siRNAs. Thus, while similar to siRNAs, miRNAs are genes will actually be mis-regulated in response to a given distinct. miRNA. 0006 miRNAs thus far observed have been approximately 0010 Correcting gene expression errors by manipulating 21-22 nucleotides in length, and they arise from longer pre miRNA expression or by repairing miRNA mis-regulation cursors transcribed from non-protein-encoding genes. See represent promising methods to repair genetic disorders and review of Carrington et al. (2003). The precursors form struc cure diseases like cancer. A current, disabling limitation of tures that fold back on themselves in self-complementary this approach is that, as mentioned above, the details of the regions; they are then processed by the nuclease Dicer (in regulatory pathways and networks that are affected by any animals) or DCL1 (in plants) to generate the short double given miRNA, including miR-143, remain largely unknown. stranded miRNA. One of the miRNA strands is incorporated This represents a significant limitation for treatment of can into a complex of proteins and miRNA called the RNA cers in which miR-143 may play a role. A need exists to induced silencing complex (RISC). The miRNA guides the identify the genes, genetic pathways, and genetic networks RISC complex to a target mRNA, which is then cleaved or that are regulated by or that may regulate hsa-miR-143 translationally silenced, depending on the degree of sequence expression. complementarity of the miRNA to its target mRNA. Cur rently, it is believed that perfect or nearly perfect complemen SUMMARY OF THE INVENTION tarity leads to mRNA degradation, as is most commonly 0011. The present invention provides additional composi observed in plants. In contrast, imperfect base pairing, as is tions and methods by identifying genes that are direct targets primarily found in animals, leads to translational silencing. for miR-143 regulation or that are indirect or downstream However, recent data Suggest additional complexity (Bagga targets of regulation following the miR-143-mediated modi et al., 2005; Lim et al., 2005), and mechanisms of gene fication of another gene(s) expression. Furthermore, the silencing by miRNAS remain under intense study. invention describes gene, disease, and/or physiologic path 0007 Recent studies have shown that expression levels of ways and networks influenced by miR-143 and its family numerous miRNAS are associated with various cancers (re members. In certain aspects, compositions of the invention viewed in Esquela-Kerscher and Slack, 2006; Calin and are administered to a Subject having, Suspected of having, or Croce, 2006). miRNAs have also been implicated in regulat at risk of developing a metabolic, an immunologic, an infec ing cell growth and cell and tissue differentiation—cellular tious, a cardiovascular, a digestive, an endocrine, an ocular, a processes that are associated with the development of cancer. genitourinary, a blood, a musculoskeletal, a nervous system, 0008. The inventors previously demonstrated that hsa a congenital, a respiratory, a skin, or a cancerous disease or miR-143 is involved with the regulation of numerous cell condition. activities that represent intervention points for cancer therapy 0012. In particular aspects, a subject or patient may be and for therapy of other diseases and disorders (U.S. patent selected for treatment based on expression and/or aberrant application Ser. No. 1 1/141,707 filed May 31, 2005 and Ser. expression of one or more miRNA or mRNA. In a further No. 1 1/273,640 filed Nov. 14, 2005, each of which are incor aspect, a subject or patient may be selected for treatment porated herein by reference in their entirety). Upon evaluation based on aberrations in one or more biologic or physiologic of 24 different human tissues, hsa-miR-143 was found to be pathway(s), including aberrant expression of one or more preferentially expressed in human prostate and colon tissue gene associated with a pathway, or the aberrant expression of samples. The inventors observed that hsa-miR-143 expres one or more protein encoded by one or more gene associated US 2009/0232893 A1 Sep. 17, 2009 with a pathway. In still a further aspect, a Subject or patient miR-143 could be used as a therapeutic target for any of these may be selected based on aberrations in miRNA expression, diseases. In certain embodiments miR-143 can be used to or biologic and/or physiologic pathway(s). A subject may be modulate the activity of miR-143 in a Subject, organ, tissue, or assessed for sensitivity, resistance, and/or efficacy of a cell. therapy or treatment regime based on the evaluation and/or 0015. A cell, tissue, or subject may be a cancer cell, a analysis of miRNA or mRNA expression or lack thereof. A cancerous tissue, harbor cancerous tissue, or be a Subject or subject may be evaluated for amenability to certain therapy patient diagnosed or at risk of developing a disease or condi prior to, during, or after administration of one or therapy to a tion. In certain aspects a cancer cell is a neuronal, glial, lung, Subject or patient. Typically, evaluation or assessment may be liver, brain, breast, bladder, blood, leukemic, lymphoid, done by analysis of miRNA and/or mRNA, as well as com colon, endometrial, stomach, skin, ovarian, fat, bone, cervi bination of other assessment methods that include but are not cal, esophageal, pancreatic, prostate, kidney, testicular, intes limited to histology, immunohistochemistry, blood work, etc. tinal, colorectal, or thyroid cell. In still a further aspect cancer 0013. In some embodiments, an infectious disease or con includes, but is not limited to astrocytoma, acute myelog dition includes a bacterial, viral, parasite, or fungal infection. enous leukemia, acute lymphoblastic leukemia, anaplastic Many of these genes and pathways are associated with vari large cell lymphoma, B-cell lymphoma, breast carcinoma, ous cancers and other diseases.