|HAO WALA NAMAN TAKIAUS009920379B2 PILOT AT AN WA AINA TATTI (12 ) United States Patent (10 ) Patent No. : US 9 , 920 , 379 B2 Bentwich et al. (45 ) Date of Patent: Mar. 20 , 2018 ( 54 ) NUCLEIC ACIDS RELATED TO ( 2013. 01 ) ; C12N 2310 / 531 (2013 . 01 ) ; C12N MIR - 29B - 1 -5P AND USES THEREOF 2320 / 10 ( 2013 .01 ) ; C12N 2320 / 11 ( 2013 . 01 ) ; CI2N 2320 / 30 ( 2013 .01 ) ; C12N 2330 / 10 (71 ) Applicant : Rosetta Genomics Ltd ., Rehovot ( IL ) (2013 .01 ) ; C12Q 2600 / 106 (2013 .01 ) ; C12Q @ 2600 / 136 ( 2013 . 01 ) ; C12Q 2600 / 158 ( 72 ) Inventors : Itzhak Bentwich , Tel Aviv ( IL ) ; Amir (2013 . 01) ; C12Q 2600 / 16 (2013 . 01 ) ; C12Q Ayniel, Tel Aviv ( IL ) ; Yael Karov , Tel 2600 / 178 (2013 .01 ) Aviv ( IL ) ; Ranit Aharonov , Tel Aviv (58 ) Field of Classification Search None (IL ) See application file for complete search history . @( 73 ) Assignee : ROSETTA GENOMICS LTD ., Rehovot ( IL ) (56 ) References Cited U . S . PATENT DOCUMENTS @( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 7 , 250 , 289 B2 7 /2007 Zhou 7 , 407 , 784 B2 8 /2008 Butzke et al . U . S . C . 154 (b ) by 0 days . 7 ,655 , 785 B1 2 / 2010 Bentwich 7 , 820 , 809 B2 10 /2010 Khvorova et al . ( 21 ) Appl. No. : 15 /586 , 747 2005 /0075492 Al 4 /2005 Chen et al . 2005 /0261218 AL 11 / 2005 Esau ( 22 ) Filed : May 4 , 2017 2006 /0247193 AL 11 /2006 Kazunari 2008 /0125583 Al 5 /2008 Rigoutsos et al . 2008 /0269072 Al 10 / 2008 Hart et al. (65 ) Prior Publication Data 2012 / 0094374 Al 4 / 2012 Bentwich US 2017 / 0298447 A1 Oct. 19 , 2017 2014 /0017780 A11 /2014 Bentwich 2016 /0046935 A1 2 /2016 Bentwich et al . Related U . S . Application Data FOREIGN PATENT DOCUMENTS (60 ) Division of application No . 14 /756 , 185 , filed on Aug . 13 , 2015 , now Pat. No . 9 ,650 ,679 , which is a division wo 2003 /029459 A2 4 /2003 of application No. 13 /986 ,516 , filed on May 8 , 2013 , WO 2004 /016317 Al 2 / 2004 now Pat . No. 9 , 133 , 453 , which is a division of application No . 12 /661 , 041 , filed on Mar. 10 , 2010 , OTHER PUBLICATIONS now Pat. No . 8 ,461 , 315 , which is a division of Apr. 18 , 1997. “ EST28528 Cerebellum II Homo sapiens cDNA 5 ' application No. 11/ 130 ,645 , filed on May 16 , 2005, end .” XP002630735 . now Pat. No. 7 , 709, 616 , which is a continuation of May 16 , 2002 . “ Homo sapiens miR - 102 - precursor - 1 micro RNA , application No . PCT /US2005 /016986 , filed on May complete sequence . ” XP002630736 . 14 , 2005 , and a continuation - in -part of application Jan . 16 , 2001 . “ CM3- RT0006 -091200 -545 -505 RT0006 Homo sapi ens cDNA , mRNA sequence . ” XP002630737 . No. 10 /709 , 577 , filed on May 14 , 2004 , now Pat . No . May 16 , 2002 . “ Homo sapiens miR - 102 -precursor - 7 . 1 micro RNA , 7 ,687 ,616 , and a continuation - in - part of application complete sequence .” XP002630738 . No . 10 / 709, 572 , filed on May 14 , 2004 , now Pat. No . “ Human Genome, U95 Av2” , Oct . 2 , 2002 , XP002215481 , http :/ / 7 , 888 , 497 . www .affymetrix .com . “ GeneChip Human Genome U133 Set” , Feb . 26 , 2003 , (60 ) Provisional application No . 60 /666 ,340 , filed on Mar . XP002232760 , http :/ / www .affymetrix .com /support /technical / 30 , 2005 , provisional application No . 60 / 665 , 094 , datasheets / hgu 133 _ datasheet .pdf . filed on Mar . 25 , 2005 , provisional application No . Constantine L . et al ., “ Use of genechip high - density oligonucleotide arrays for gene expression monitoring” , Life Science News , 60 /662 ,742 , filed on Mar. 17 , 2005 , provisional Amersham Life Science, US , Jan . 1 , 1998 , pp . 11- 14 , application No. 60 /593 ,329 , filed on Jan . 6 , 2005, XP002964122 . provisional application No . 60 /593 ,081 , filed on Dec . Nov . 16 , 2001, “ Mus musculus 16 days neonate male diencephalon 8 , 2004 , provisional application No . 60 /522 , 860 , filed cDNA, Riken full - length enriched library , clone : G630058E01 , 3 ' on Nov. 15, 2004 , provisional application No . end partial sequence. ” , XP002630739 . 60 /522 , 457 , filed on Oct . 4 , 2004 , provisional application No . 60 /522 ,449 , filed on Oct. 3 , 2004 , (Continued ) provisional application No . 60 /522 ,452 , filed on Oct . Primary Examiner — Dana H Shin 3 , 2004 . (74 ) Attorney, Agent, or Firm — Polsinelli , PC ; Rob Ron Galant ( 51 ) Int. CI. C12N 15 / 11 ( 2006 . 01 ) (57 ) ABSTRACT C12Q 1/ 68 ( 2018 . 01 ) Described herein are polynucleotides associated with pros A61K 38 / 00 (2006 . 01 ) tate and lung cancer. The polynucleotides are miRNAs and C12N 15 / 113 ( 2010 .01 ) miRNA precursors . Related methods and compositions that (52 ) U . S . CI. can be used for diagnosis , prognosis , and treatment of those CPC . .. .. .. .. .. C120 1 /6886 ( 2013 .01 ) ; A61K 38 / 00 medical conditions are disclosed . Also described herein are (2013 .01 ) ; C12N 15 / 111 ( 2013 .01 ) ; C12N methods that can be used to identify modulators of prostate 15 / 113 (2013 . 01 ) ; C12Q 1 /6809 ( 2013 .01 ) ; and lung cancer . C12N 2310 / 14 (2013 .01 ) ; C12N 2310 / 141 3 Claims, 5 Drawing Sheets US 9 ,920 ,379 B2 Page 2 ( 56 ) References Cited OTHER PUBLICATIONS Dec . 6 , 2000 , “ UI- M - CG0p -bqm - b - 04 - 0 -UI . s1 NIH BMAP Ret4 S2 Mus musculus cDNA clone UI- M - CG0p -bqm - b - 04 - 0 -UI 3 ', mRNA sequence . ” XP002630740 . Bartel D . P ., “ MicroRNAs: Genomics , biogenesis , mechanism , and function ." , Cell, vol . 116 , No . 2 , Jan . 23 , 2004 , pp . 281- 297 , XP002359089. Lee R . C ., et al. , “ An extensive class of small RNAs in Caenorhabditis elegans ” , Science , American Association for the Advancement of Science ,US , vol . 294 , No. 5543, Oct . 26 , 2001, pp . 862 - 864 , XP002284273 . Lewis B . P . , “ Prediction of Mammalian MicroRNA Targets ” , Cell , Cell Press , Cambridge, NA , US , vol. 115 , No . 7 , Dec . 26 , 2003 , pp . 787 -798 , XP002295226 . Grad Y . et al ., “ Computational and Experimental Identification of C . Elegans Micrornas” , Molecular Cell, Cell Press , Cambridge, MA , US , vol . 11, No . 5 , May 1 , 2003 , pp . 1253 - 1263 , XP009032050 . McManus, M . T ., “ MicroRNAs and cancer, ” Seminars in Cancer Biology, 13 : 253 -258 ( 2003 ) . Calin , G . A . , Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers , PNAS , 101 ( 9 ) : 2999 - 3004 (2004 ) . Paul, et al. , “ Inosine exists in mRNA at tissue - specific levels and is most abundant in brain mRNA , ” 1998 , The EMBO Journal , vol . 17 , pp . 1120 - 1127 . GenBank Accession No. BB017822 , last updated Jun . 22 , 2000 . GenBank Accession No . BF019006 . 1 , last updated Dec . 29 , 2000 . Lagos - Quintana , et al. , Identification of tissue -specific microRNAs from mouse, 2002 , Current Biology , vol . 12, pp . 735 -739 . U . S . Patent Mar. 20, 2018 Sheet 1 of 5 US 9 ,920 ,379 B2 FIG . 10 FIG . 18 FIG . 10 TOHANA HR ANA CLEAR SGALL , SNOOR, Rus , , inte 20 iix is Antissists FrestiRNA PER ANNA . TENE ANA Osake SAMA Tags Mats egorise INN INNA Asso . ARRY ANNA wittin ASA | ature it it ! Mait rait T ai INTAS Nen int ite it text it NAANS TANIA U . S . Patent Mar. 20 , 2018 Sheet 2 of 5 US 9 ,920 ,379 B2 AK www . .. 23493430 . ... 412413414415 83 83 ** * * ** * ** ** 02431432 - - * * 40AT . - - WPQMOV 49 37837737 st 429430 - man . - A - - - 428 - 4 YRNA Quote 450:47 - . rrrrrrrrr 4552 000 414243 424425426 - - - - 4331 AJA - B 642 423 40 12 - - A 100910 437438439 619 420421422 436 - A18419 - - -- FIG.2A FIG.2B U . S . Patent Mar. 20 , 2018 Sheet 3 of 5 US 9 ,920 , 379 B2 800 . .. .. .. .. .. 600600 700 600 500500 11111111111111 i 400 300400 300400500 Locationonalignment 300 Locationonalignment ..da K 200200 .200 . Iwata ne 100 HomoSapiens 100 Pantroglodytes 0 FIG.3A de o There SCO FIG.3 Score U . S . Patent Mar. 20 , 2018 Sheet 4 of 5 US 9 ,920 ,379 B2 . MYYNY . SKOWEEN . voisirs WWW. * FIG.40 en Det ES COOTERSOMOCIO :* S * * : 1. M .XY *778 :.*234 :.* 7 * *26. .* Ort:30* *-7628 *O : :XY300* :7*, 3:20 :* ?38*. * * 26-28 *7: >*: * :* * :* 2* * :* * XXX* x *00x45086 17.30 :* * XXX* * 220:00 19: * *8 * * * * * * XXX FIG.4A FIG.45 U . S . Patent Mar. 20 , 2018 Sheet 5 of 5 US 9 ,920 ,379 B2 FIG . 5A BLAH A24 - 3p 419 - 30 asa - -08 HANAIRNA FIG . 58 5W www4444444444444444 80074418 wwwnnnnnnnnnnn 6FR * * * * 50014 : dajad Soowon FRI t a tatatatatatatatatatatatatatatatatate 1408 32 28 w mw 3257 bo Osovodu in here Een the R ? NM FIG . 5C S com en 2018 60 243 moment US 9 , 920 , 379 B2 NUCLEIC ACIDS RELATED TO invention satisfies this need and provides a significant num MIR - 29B - 1 -5P AND USES THEREOF ber of miRNAs and uses therefore . FIELD OF THE INVENTION SUMMARY OF THE INVENTION 5 The invention relates in general to microRNA molecules The present invention is related to an isolated nucleic acid as well as various nucleic acid molecules relating thereto or comprising a sequence of a pri- miRNA , pre -miRNA , derived therefrom . miRNA , miRNA * , anti -miRNA , or a miRNA binding site , or a variant thereof. The nucleic acid may comprise the REFERENCES TO THE SEQUENCE LISTING 10 sequence of a hairpin referred to in Table 1 ; the sequence of AND TABLES a miRNA referred to in Table 1 ; the sequence of a target gene binding site referred to in Table 4 ; or a sequence comprising Applicant hereby makes reference to the sequence listing at least 12 contiguous nucleotides at least 60 % identical and tables that were submitted electronically via EFS -Web . thereto . The isolated nucleic acid may be from 5 - 250 nucleo The sequence listing consists of a filed named “ Sequence - 15 tides in length . Listing .txt , ” ( 20 KB ) , created on May 3 , 2017 . The tables The present invention is also related to a probe compris consist of the following files : “ Table1.