US008962588B2 a2) United States Patent (0) Patent No.: US 8,962,588 B2 Olsonet al. (45) Date of Patent: *Feb. 24, 2015 (54) MICRO-RNAS THAT CONTROL MYOSIN 2009/0326049 Al 12/2009 Aristarkhovet al. EXPRESSION AND MYOFIBER IDENTITY 2010/0029003 Al 2/2010 Bartel et al. 2010/0280094 Al 11/2010 Beuvinketal. Applicant: The Board of Regents, The University (71) FOREIGN PATENT DOCUMENTS of Texas System, Austin, TX (US) EP 1777301 A2 4/2007 (72) Inventors: Erie N. Olson, Dallas, TX (US); Eva EP 1959012 A2 8/2008 van Rooij, Utrecht (NL) EP 2113567 Al 11/2009 JP 2004-522411 7/2004 (73) Assignee: The Board of Regents, The University JP 2006-502693 1/2006 of Texas System, Austin, TX (US) JP 2006-101790 4/2006 WO WO 02/10453 A2 2/2002 WO WO 03/065993 A2 8/2003 (*) Notice: Subject to any disclaimer, the term of this WO WO 2005/013901 A2 2/2005 patent is extended or adjusted under 35 WO WO 2005/017145 Al 2/2005 U.S.C. 154(b) by 147 days. WO WO 2005/078096 A2 8/2005 WO WO 2005/078139 A2 8/2005 This patent is subject to a terminal dis- WO WO 2005/079397 A2 9/2005 claimer. WO WO 2005/118806 A2 12/2005 = WO WO 2006/013561 A2 2/2006 Appl. No.: 13/796,884 WO WO 2006/047454 A2 5/2006 (21) WO WO 2006/063356 Al 6/2006 WO WO 2006/111512 Al 10/2006 (22) Filed: Mar. 12, 2013 WO WO 2006/137941 A2 12/2006 WO WO 2007/000668 A2 1/2007 (65) Prior Publication Data WO WO 2007/035684 A2 3/2007 WO WO 2007/070483 A2 6/2007 US 2013/0245092 Al Sep. 19, 2013 WO WO 2007/073737 Al 7/2007 WO WO 2007/090073 A2 8/2007 WO WO 2007/112754 A2 10/2007 Related U.S. Application Data WO WO 2008/016924 A2 2/2008 WO WO 2008/042231 A2 4/2008 (63) Continuation of application No. 12/671,436, filed as application No. PCT/US2008/071837 on Jul. 31, (Continued) 2008, now Pat. No. 8,481,507. OTHER PUBLICATIONS (60) Provisional application No. 60/952,911, filed on Jul. 31, 2007, provisional application No. 60/980,113, Chang, “International Search Report,” 4 pages, from International filed on Oct. 15, 2007, provisional application No. Patent Appl. No. PCT/US2008/071837, Korean Intellectual Property 60/980,3 14, filed on Oct. 16, 2007. Office, Daejon, Republic of Korea (mailed Nov. 27, 2009). Chenget al., “MicroRNAsare Aberrantly Expressed in Hypertrophic (51) Int. Cl. Heart,” Am.J. Pathol. 170(6):1831-1840 (2007). CIN 15/11 (2006.01) Sayedet al., “MicroRNAs Play and Essential Role in the Develop- C07H 21/02 (2006.01) ment of Cardiac Hypertrophy,” Cire. Res. 100(3):416-424 (2007). CO7H 21/04 (2006.01) Tatsuguchiet al., “Expression of MicroRNAsis Dynamically Regu- (52) US. Cl. lated During Cardiomyocyte Hypertrophy,” J. Mol. Cell. Cardiol. USPC oon ccc eesereeeeeneneenes 514/44 A; 536/24.5 42(6):1137-1141 (2007). (58) Field of Classification Search (Continued) None See application file for complete search history. Primary Examiner — Richard Schnizer (56) References Cited (74) Attorney, Agent, or Firm — Cooley LLP U.S. PATENT DOCUMENTS (57) ABSTRACT 7,232,806 B2 6/2007 Tuschlet al. 2005/0059005 Al 3/2005 Tuschlet al. 2005/0261218 Al 11/2005 Esauetal. The present invention relates to the identification of two 2006/0019286 Al 1/2006 Horvitz et al. microRNAs, miR-499 and miR-208b, that repress fast skel- 2006/0185027 Al 8/2006 Bartel et al. etal muscle contractile protein genes. Expression ofmiR-499 2007/0287179 Al 12/2007 Tuschlet al. and/or miR-208b can be usedto repress fast fiber genes and 2007/0292878 Al 12/2007 Raymond activate slow fiber genes in the treatment of musculoskeletal 2008/0050744 Al 2/2008 Brownetal. 2008/0176766 Al 7/2008 Brownetal. disorders. Inhibition of miR-499 and/or miR-208b is pro- 2008/0214437 Al 9/2008 Mohapatraetal. posed as a treatment for cardiac hypertrophy, myocardial 2009/0137504 Al 5/2009 Echwaldet al. infarction, and/or heart failure. Pharmaceutical compositions 2009/0143326 Al 6/2009 Obadet al. comprising antagonists and agonists of miR-499 and miR- 2009/0286969 Al 11/2009 Esauetal. 2009/0291906 Al 11/2009 Esauetal. 208b function are also disclosed. 2009/0291907 Al 11/2009 Esauetal. 2009/0293148 Al 11/2009 Renet al. 2009/0317369 Al 12/2009 Hosodaetal. 41 Claims, 39 Drawing Sheets US 8,962,588 B2 Page 2 (56) References Cited Sempere et al., “Expression profiling of mammalian microRNAs uncoversa subset ofbrain-expressed microRNAswith possible roles in murine and human neuronal differentiation”’ Genome Biology, FOREIGN PATENT DOCUMENTS vol. 5:R13, 2004. WO WO 2008/043521 A2 4/2008 Van Rooij et al. “A signature pattern of stress-responsive WO WO 2008/061537 A2 5/2008 microRNAsthat can evoke cardiac hypertrophy and heart failure,” WO WO 2008/074328 A2 6/2008 Proc. Natl. Acad. Sci. USA, vol. 103: 18255-18260, 2006. WO WO 2008/076324 A2 6/2008 Landgrafet al., “A mammalian microRNAexpressionatlas based on WO WO 2008/147839 Al 12/2008 small RNAlibrary sequencing,” Cell, vol. 129: 1401-1414, 2007. — WO WO 2009/026576 Al 2/2009 Landgrafet al., “A mammalian microRNAexpressionatlas based on WO WO 2009/043353 A2 4/2009 small RNA library sequencing,” Cell, Supplementary Table S12, WO WO 2009/058818 A2 5/2009 WO WO 2009/062169 A2 5/2009 2007. WO WO 2009/114681 A2 9/2009 Van Rooij et al., “Control of stress-dependent cardiac growth and WO WO 2009/149182 Al 12/2009 gene expression by a microRNA,”Science, vol. 316: 575-579, 2007. — WO WO 2010/048585 A2 4/2010 Habedanck, Supplementary European Search Report for European OTHER PUBLICATIONS Application No. 08797004.2, 13 pages, European Patent Office, Munich, mailed Sep. 16, 2011. Thum etal., “MicroRNAsin the human Heart. A Clue to Fetal Gene Lorell et al., “Left Ventricular Hypertrophy: Pathogenesis, Detection, Reprogramming in Heart Failure,’ Circulation 116(3):258-267 and Prognosis,” Circulation, vol. 102: 470-479, 2000. (2007). Olson, “Transcriptional Control of Heart Developmentand Disease,” Lagos-Quintanaet al., “New microRNAsfrom mouse and. human,” Symposium Presentation at Duke University, Sep. 26, 2006. RNA,vol. 9:175-179, 2003. Olson, Genetic Pathways in Cardiovascular Development and Dis- Lagos-Quintanaet al., “Identification of tissue-specific microRNAs ease, Symposium Presentation at University of Cincinnati, Sep. from mouse,” Current Biology, vol. 12:735-739, 2002. 2006. B2 8,962,588 US “Dig 1 © © ADANDOVYVVWOONDOWDTERY ROS-HIL GIMCW (s ‘on aI Sas} O no Ov ¥ Y¥ a ¥ O’DY EAWOYY 3D DD Yyw¥HoOAnONA OND of PUTTOILIO 39 OU UU TP GL TERITERITTE TLE deomers (ce-on ar oas) 05 AnnnsewoeO OWO LS of mon ovnwin O29 PO a) a 9 38 @ oR 1 UOIO FREER EREELEY REE RES EREREREADE ERED BEEBE MESRE ERE KR BEHRPERERER RRR e WUIODTEOLLOOVYVCWIWOOOWESCLOWLOOLWOOOCULLOOOLODLLLCOOVOL, Bog {% ‘ON UI OusS} "ON GI O#S} Sheet LLLUOLODO 3ea fe PWOLDATLIOLLOOVIOSEPUELYLOOTOLILOVOLOOVEELLOODO DODO «sSSRoH POLOOLOLLOOUUYYOUDVDTULLOOVNLOLOVOLOOULELIOODOODDSLLEIOOUILDDOOYOEL {z 'ON aI Os) UDLOOLEDLLIOVLUCOUNDVOETOVOLOLALOULODOIOLELOOYOOOOOOVOE «BRUM (it 'ON UE O85} 4 2015 OHMS Sedaaees ueluny 24, Q4 9°Bh jwISPAS Feb. Q4 £9°Se SPS Patent U.S. B2 8,962,588 US 8 ft N oo © ¢ o 1OUIODILS aAne(ay WH 8 Aynoesuog = == = Aynoeuoes 39 yse4 SSS MOIS of 8 0 OHIN 2 oo on auL- aut | Sheet uoissaldxe a ° : loot 2015 24, Feb. ODUILU pesACSCLEO AVIVcto) = ML EeyUeema Patent U.S. B2 8,962,588 US 39 [aQuoA of 3 Ayinoesyuog OOS Aypoesu0E9 MOIS }se4 Sheet El 2015 vy ecenneerrnereveeemirninaecnesoenanematn 24, A A Feb. uisipioshyjodAH ssa STUTLE MNS 2t eg WAVi\to) = RET Esrey UES]78) Patent U.S. B2 8,962,588 US uolIssaidxe SHY eaAeyay 39 of 4 Sheet 2015 24, Feb. SLIvey UBWINY Ul Juesaid A UTEsLer eyYasLE Patent U.S. B2 y “OL 8,962,588 a)5lIv US jeds : : ' pexol-] . yeds ucIsIax3 PSE]Poy-s1D ay 39 ; poaebie of 5 4a uoneuiquosey Sheet snoBojowopy JOLOBA Sunebie; 2015 24, Feb. aohy odAy-PHM leds dq ¢¢ jedg Patent Le LelUb RLU IS MtAme Le U.S. B2 g “OL 8,962,588 US etpere seaSahn 39 of 6 Sheet 2015 Om ~/+ LM 24, yWeay jeyeucen Feb. LIBOLH IVIBUOSAY ul Patent tetehBe)imere orm le\ Bee ROvm transLL e U.S. B2 9 “SIg 8,962,588 US 39 of 7 Sheet 2015 24, Feb. DEGLISAG BINSSSig Buimojyjos SHA OX 80Z-Milu Ul Sisolgi4 pue AudosedAL pousiuimmig Patent U.S. B2 8,962,588 US 39 of 8 Sheet 2015 24, Feb. Oy 807-yIW sueBsuelL uunaulgje5 o1ueHsuel] ULNeUlsje9 LSTULES te TEs) fe)-s@ MexMri eletcroys Bey Patent oi Od eirApe | LUEEventBeeitrlenieelse estee| U.S. B2 8 “DIE 8,962,588 US MoOjs | 1SPJ OHIN-d «<—— SHI? 39 of re). LM 9 —]{_—_———— — :Bj-u9 + - + = ‘VL Sheet 2 3 2 02 e s or a 3a 09 3 2015 a g 8 3 24, a. ° oO = = Feb. OHI-9 OHW-d Och totPFTS OT MSs L610 to:be Eee Ee | Ue g Pet Ree Le Ral Remirage ise Patent U.S. B2 6 “OTs 8,962,588 US 39 of 10 Sheet Bi soz-yiw edAy-pyin = 2015 24, Feb. Toyictcreseb= Me) siiemayel eye) emer IUSIDILING SI GOZ-MIwW 10 UGISSIIAXA-1BAO Patent U.S. B2 OL “SIA eydyje jo uONeAIIe S}USABId pue e}Eq JO UOISSeldd/ SAADI}O1 Ld 8,962,588 US Oo» LM a8 a 39 es —_ + = :Ald oeuoos Ayipoequog ET Se7-S AnaeUOD 11 of OO£ oy ' t Sheet P 009 § aus mom ue - 006 g ~ ~ 2015 - 002) FZ 24, LE 00S} =a Feb.