US008940711B2 a2) United States Patent (10) Patent No.: US 8,940,711 B2 Olsonet al. (45) Date of Patent: Jan. 27, 2015 (54) MICRO-RNA FAMILY THAT MODULATES C1I2N 2310/321 (2013.01); C12N 2310/346 FIBROSIS AND USES THEREOF (2013.01); CI2N 2310/3515 (2013.01); C12N (71) Applicant: The Board of Regents, The University 2320/31 (2013.01); CI2N 2330/10 (2013.01) of Texas System, Austin, TX (US) USPC iececcsesseeseeesenensceesensessecsenesenscnseeee 514/444 (58) Field of Classification Search (72) Inventors: Erie N. Olson, Dallas, TX (US); Eva USPC iececcsesseeseeesenensceesensessecsenesenscnseeee 514/44A van Rooij, Utrecht (NL) See application file for complete search history. (56) References Cited (73) Assignee: The Board of Regents, The University of Texas System, Austin, TX (US) U.S. PATENT DOCUMENTS Notice: Subject to any disclaimer, the term of this 7,232,806 B2 6/2007 Tuschletal. (*) 7,674,617 B2 3/2010 Kim etal. patent is extended or adjusted under 35 2005/0059005 Al 3/2005 Tuschletal. U.S.C. 154(b) by 1 day. 2005/0222399 Al 10/2005 Bentwich 2005/0261218 Al 11/2005 Esau etal. (21) Appl. No.: 13/840,242 2006/0019286 Al 1/2006 Horvitz et al. 2006/0105360 Al 5/2006 Croceet al. Filed: Mar.15, 2013 2006/0185027 Al 8/2006 Bartel etal. (22) 2006/0247193 Al 11/2006 Taira etal. 2007/0087335 Al 4/2007 Brahmacharietal. (65) Prior Publication Data 2007/0092882 Al 4/2007 Wangetal. US 2013/0261169 Al Oct. 3, 2013 2008/0050722 Al 2/2008 Kim etal. 2008/0176766 Al 7/2008 Brown etal. 2009/0053718 Al 2/2009 Naguibnevaet al. Related U.S. Application Data 2009/0092980 Al 4/2009 Arenz etal. 2009/0143326 Al 6/2009 Obadetal. (62) Division of application No. 12/671,445, filed as 2009/0281167 Al 11/2009 Shenetal. application No. PCT/US2008/071839 on Jul. 31, (Continued) 2008, now Pat. No. 8,440,636. FOREIGN PATENT DOCUMENTS (60) Provisional application No. 60/952,917, filed on Jul. 31, 2007, provisional application No. 60/980,303, EP 1440981 A2 7/2004 filed on Oct. 16, 2007, provisional application No. EP 1627925 Al 2/2006 61/047,014,filed on Apr. 22, 2008. (Continued) OTHER PUBLICATIONS (51) Int. Cl. CIQN 15/11 (2006.01) Cheng et al, “MicroRNAs Are Aberrantly Expressed in A6IK 31/713 (2006.01) Hypertrophic Heart,” Am. J. Pathol. 170(6):183 1-1840 (2007). AOIK 67/027 (2006.01) Kim, “International Search Report,” 4 pages, from International A6IK 38/22 (2006.01) Patent Appl. No. PCT/US2008/071839, Korean Intellectual Property CI2N 9/16 (2006.01) Office, Daejon, Republic of Korea (mailed Jan. 6, 2009). CI2N 15/113 (2010.01) Rooij et al., “A signature pattern of stress-responsive microRNAsthat can evoke cardiac hypertrophy and heart failure,” Proc. Natl. Acad. CI2N 15/85 (2006.01) Sci. USA 103(48):18255-18260 (2006). A6IK 31/7105 (2006.01) Tatsuguchiet al., “Expression of MicroRNAsis Dynamically Regu- A6IK 31/712 (2006.01) lated During Cardiomyocyte Hypertrophy,” J. Mol. Cell. Cardiol. A6IK 31/7125 (2006.01) 42(6):1137-1141 (2007). A61K 39/395 (2006.01) Lagos-Quintanaet al., “New microRNAsfrom mouse and. human,” RNA,vol. 9:175-179, 2003. A6IK 45/06 (2006.01) Lagos-Quintanaet al., “Identification of tissue-specific microRNAs A6IK 31/07 (2006.01) from mouse,” Curent Biology, vol. 12:735-739, 2002. AGIK 31/355 (2006.01) (Continued) A6IK 31/375 (2006.01) (52) US. Cl. Primary Examiner — J. E. Angell CPC oc. A61LK 31/713 (2013.01); AOLK 67/0276 (74) Attorney, Agent, or Firm — Cooley LLP (2013.01); A6LK 38/2242 (2013.01); C12N (57) ABSTRACT 9/16 (2013.01); CI2N 15/113 (2013.01); CI2N The present invention relates to the identification of a 15/8509 (2013.01); AGLK 31/7105 (2013.01); microRNAfamily, designated miR-29a-c, that is a key regu- A61LK 31/712 (2013.01); A6LK 31/7125 lator of fibrosis in cardiac tissue. The inventors show that (2013.01); A6LK 39/3955 (2013.01); A61K members of the miR-29 family are down-regulated in the 45/06 (2013.01); A61K 31/07 (2013.01); A6LK heart tissue in responseto stress, and are up-regulatedin heart 31/355 (2013.01); A6LK 31/375 (2013.01); tissue of mice that are resistant to both stress and fibrosis. AOLK 2207/30 (2013.01); AOLK 2217/052 Also provided are methods of modulating expression and (2013.01); AOLK 2217/075 (2013.01); AOILK activity of the miR-29 family of miRNAsas a treatment for 2217/15 (2013.01); AOLK 2217/206 (2013.01); fibrotic disease, including cardiac hypertrophy, skeletal AOLK 2227/105 (2013.01); AOLK 2267/0375 muscle fibrosis other fibrosis related diseases and collagen (2013.01); CI2N 2310/113 (2013.01); C12N loss-related disease. 2310/141 (2013.01); CI2N 2310/315 (2013.01); 22 Claims, 29 Drawing Sheets US 8,940,711 B2 Page 2 (56) References Cited WO WO2007/081720 A2 7/2007 = WO WO 2007/081740 A2 7/2007 U.S. PATENT DOCUMENTS WO WO 2007/109236 A2 9/2007 WO WO 2007/112754 A2 10/2007 2009/0286969 Al 11/2009 Esauetal. WO WO 2008/016924 A2 2/2008 2009/0291906 Al 11/2009 Esauetal. WO WO 2008/043521 A2 4/2008 2009/0291907 Al 11/2009 Esau et al. WO WO 2008/061537 A2 5/2008 2009/0293148 Al 11/2009 Renetal. WO WO 2008/116267 Al 10/2008 2009/0317369 Al 12/2009 Hosodaet al. WO WO 2008/147839 Al 12/2008 2009/0326049 Al 12/2009 Aristarkhovetal. WO WO 2009/012263 A2 1/2009 —_ 2010/0029003 Al 2/2010 Barteletal. WO WO 2009/026576 Al 2/2009 2010/0087512 Al 4/2010 Tuschlet al. WO WO 2009/043353 A2 4/2009 — 2010/0087513 Al 4/2010 Tuschlet al. WO WO 2009/058818 A2 5/2009 2010/0093837 Al 4/2010 Tuschlet al. WO WO 2009/062169 A2 5/2009 2010/0099748 Al 4/2010 Tuschlet al. WO WO 2009/111375 A2 9/2009 2010/0113561 Al 5/2010 Tuschlet al. WO WO 2009/114681 A2 9/2009 WO WO 2009/121031 Al 10/2009 WO WO 2009/149182 Al 12/2009 FOREIGN PATENT DOCUMENTS WO WO 2010/036939 A2 4/2010 WO WO 2010/048585 A2 4/2010 EP 1777301 A2 4/2007 EP 1959012 A2 8/2008 EP 2113567 Al 11/2009 OTHER PUBLICATIONS — JP 2006-5 19008 8/2006 Sempere et al., “Expression profiling of mammalian microRNAs vo Wobolovoaee AQ oooos uncoversa subset ofbrain-expressed microRNAswith possible roles Wo WO 2004/076622 A2 9/2004 in murine and human neuronal differentiation”’ Genome Biology, WO WO 2005/013901 A2 2/2005 vol. 5:R13, 2004. Wo WO 2005/017145 Al 2/2005 Mott et al., “miR-29 regulates Mcl-1 protein expression and. WO WO 2005/040419 Al 5/2005 apoptosis,” Oncogene,vol. 26: 6133-6140, 2007. WO WO2005/047505 A2 5/2005 He et al., “Overexpression of Micro Ribonucleic Acid 29, Highly WO WO 2005/056797 Al 6/2005 Up-Regulated in Diabetic Rats, Leads to Insulin Resistance in 3T3- WO WO 2005/118806 A2 12/2005 L1 Adipocytes,” Molecular Endocrinology, vol. 21: 2785-2794, — WO WO 2006/033020 A2 3/2006 2007 WO WO 2006/033928 A2 3/2006 , . wo WO 2006/081284 A2 8/2006 Zhaoet al., “Dysregulation of Cardiogenesis, Cardiac Conduction, Wo WO 2006/108473 Al 10/2006 and Cell Cycle in Mice Lacking miRNA-1-2,” Cell. vol. 129: 303- WO WO 2006/111512 Al 10/2006 317, 2007. WO WO 2006/128245 Al 12/2006 Van Rooij et al., “Dysregulation of microRNAsafter myocardial — WO WO 2006/133022 A2 12/2006 infarction reveals a role of miR-29 in cardiac fibrosis,” Proc. Natl. WO WO 2006/137941 A2 12/2006 Acad. Sci. USA,vol. 105: 13027-13032, 2008. — we we sooo ‘ seen Spindler, Supplementary European Search Report for European wo WO 2007/033023 A2 3/2007 Application No. 08797006.7, 10 pages, European Patent Office, The WO WO 2007/042899 A2 4/2007 Hague, mailed Aug. 17, 2011. WO WO 2007/067695 A2 6/2007 Pekarsky Y. et al., “Tell expression in chronic lymphocytic leukemia WO WO 2007/070483 A2 6/2007 is regulated by miR-29 and miR-181,’ Cancer Research, vol. WO WO 2007/081680 A2 7/2007 66:11590-11593, 2006. B2 8,940,711 US t “Sid i€ RONNOOVYYWWOSUpOVeLEAY .S BOZ-HyW SINVW (s son aI as) n 32 ov ¥ Y¥ > ¥ O°D¥ OAWAYY 35 DD VewEoonnonh pnd os 29 eu; villi dt el LIEITELEE EL PLR doonmueis (te ton aI ous) non oynynh O29 3D AnnnoSeWSDSS DW) OS of Woo £ 39 5 ® n 1 REAM EREMEER AR REREAD REED EK RERENE KEEPER EERE KL FPELSRETERES EREE UOLOOTLOLLOOVVWCWOVIOVOWULYELOOWOLIOLUDLOOULULLODOLOSTLLIOOVOR TIOOVOL Boa (7 ON GI O8S) WOLOOLIDLLODTIONWOOVOUULVIOOVO Sheet LOLOVS LODULULEADODDSLLELOOVOLOODOVeL wea (Ee ‘ON CI OmS) UOLOOLINOLLOOVWUTYOOUDO VDVVLYLOWLOLOVOLOOWLULLOODOOODDLLLIOOVALODDOVEL «=SSNOH (7 ‘ON CI OHS) UWOLOOLIDLLOOWUC WONVOOWOVVLOO WOLOOLYUOTOOUDULLODOOISOOLELOOVONONOOVOL «RUA (T ‘ON CI OS) 2015 _FeESUO SH 27, UCU oH 8h wee Jan. G4 £9°Se Patent U.S. U.S. Patent Jan. 27, 2015 Sheet 2 of 29 US 8,940,711 B2 £d — HUuIUd el: anon IMS UleUy WZ 00T o oO o o © oO © o 8 Oo mM r+ 4 NN wv AAPOPH s oO « “Sl uoIssaldxXs OHI SANEIAY Ayyoequoy yse2.] UISOAIN @JOUIOIILS Eas == 9/2 = AyNOeUOD Mois B2 8,940,711 US 29 of 3 Aywpoenuog Ors Aqynoe1u09 Sheet MOIS yse4 ol 2015 __vy 27, ern A A Jan. usipjosAyjodAH SSOS Patent TUTPNTIMUathe WAV)sme S|Le U.S. B2 oa od wy wed ay "7 we tt et ot up wn 8,940,711 US RA eR EK SKM EN Tee ERNE RTE St st > z 29 oF PST of S ; uoIssaidxe 4 | _< OHIN® eAneiay Sheet 2015 27, Jan.