US 20180305689A1 ( 19 ) United States (12 ) Patent Application Publication ( 10) Pub . No. : US 2018 /0305689 A1 Sætrom et al. ( 43 ) Pub . Date: Oct. 25 , 2018 ( 54 ) SARNA COMPOSITIONS AND METHODS OF plication No . 62 /150 , 895 , filed on Apr. 22 , 2015 , USE provisional application No . 62/ 150 ,904 , filed on Apr. 22 , 2015 , provisional application No. 62 / 150 , 908 , (71 ) Applicant: MINA THERAPEUTICS LIMITED , filed on Apr. 22 , 2015 , provisional application No. LONDON (GB ) 62 / 150 , 900 , filed on Apr. 22 , 2015 . (72 ) Inventors : Pål Sætrom , Trondheim (NO ) ; Endre Publication Classification Bakken Stovner , Trondheim (NO ) (51 ) Int . CI. C12N 15 / 113 (2006 .01 ) (21 ) Appl. No. : 15 /568 , 046 (52 ) U . S . CI. (22 ) PCT Filed : Apr. 21 , 2016 CPC .. .. .. C12N 15 / 113 ( 2013 .01 ) ; C12N 2310 / 34 ( 2013. 01 ) ; C12N 2310 /14 (2013 . 01 ) ; C12N ( 86 ) PCT No .: PCT/ GB2016 /051116 2310 / 11 (2013 .01 ) $ 371 ( c ) ( 1 ) , ( 2 ) Date : Oct . 20 , 2017 (57 ) ABSTRACT The invention relates to oligonucleotides , e . g . , saRNAS Related U . S . Application Data useful in upregulating the expression of a target gene and (60 ) Provisional application No . 62 / 150 ,892 , filed on Apr. therapeutic compositions comprising such oligonucleotides . 22 , 2015 , provisional application No . 62 / 150 ,893 , Methods of using the oligonucleotides and the therapeutic filed on Apr. 22 , 2015 , provisional application No . compositions are also provided . 62 / 150 ,897 , filed on Apr. 22 , 2015 , provisional ap Specification includes a Sequence Listing . SARNA sense strand (Fessenger 3 ' SARNA antisense strand (Guide ) Mathew, Si Target antisense RNA transcript, e . g . NAT Target Coding strand Gene Transcription start site ( T55 ) TY{ { ? ? Targeted Target transcript , e . MANA sequence Passenger strand (sense strand has sequence identity with a region on the ternplate strand located within + / - 2000 of TSS Patent Application Publication Oct. 25 , 2018 US 2018 / 0305689 A1 Codingstrand Templatestrand F16.1FIG.1 Targettranscript,2.3MRNA wwwSunTargetantisenseRNAtranscript,e.gNAT T55)site(startTranscription Passengerstrand(sense)hassequenceidentitywitharegionon thetemplatestrandlocatedwithin+/-2000ofTSS SORNAJensestrand(Passenger 3'SARNAantisensestrand(Guide) o Targeted Sequence Target Gene US 2018 /0305689 A1 Oct. 25 , 2018 SARNA COMPOSITIONS AND METHODS OF herein by reference in its entirety . Please refer to the end of USE the specification for access instructions. CROSS - REFERENCE TO RELATED FIELD OF THE INVENTION APPLICATIONS [0004 ] The invention relates to oligonucleotides , specifi cally SaRNA , compositions for modulating target gene [ 0001 ] This application is a 35 U . S . C . $ 371 U . S . National expression and to the methods of using the compositions in Stage Entry of International Application No . PCT /GB2016 / diagnostic and therapeutic applications. LENGTHY TABLES The patent application contains a lengthy table section . A copy of the table is available in electronic form from the USPTO web site (http : / / seqdata. uspto . gov / ? pageRequest = docDetail & DocID = US20180305689A1) . An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1 . 19 ( b ) ( 3 ) . 051116 filed Apr. 21 , 2016 , entitled SARNA COMPOSI BACKGROUND OF THE INVENTION TIONS AND METHODS OF USE , which claims the benefit of priority of U . S . Provisional Application No . 62 / 150 ,892 [0005 ] Recently it has been discovered that short RNAs filed Apr. 22 , 2015, entitled SARNA COMPOSITIONS can regulate transcription by destructing transcripts that are AND METHODS OF USE , U . S . Application No. 62 / 150 , sense or antisense to a given mRNA and which are presumed 893 filed Apr. 22 , 2015 , entitled SARNA COMPOSITIONS to be non - coding transcripts . Destruction of the non - coding AND METHODS OF USE , U . S . Application No . 62 / 150 , transcripts which are sense, or identical to , the given mRNA 897 filed Apr. 22 , 2015 , entitled SARNA COMPOSITIONS results in transcriptional repression of that mRNA , whereas AND METHODS OF USE , U . S . Application No. 62 / 150 , destruction of the non -coding transcripts which are antisense 895 filed Apr. 22 , 2015 , entitled SARNA COMPOSITIONS to the given mRNA results in transcriptional activation AND METHODS OF USE , U . S . Application No. 62 / 150 , and / or increased expression of the mRNA or the level of 904 filed Apr. 22 , 2015 , entitled SARNA COMPOSITIONS protein encoded by the mRNA . By targeting such non AND METHODS OF USE , U . S . Application No. 62 / 150 , coding transcripts , short RNAs can therefore be used to 908 filed Apr. 22 , 2015 , entitled SARNA COMPOSITIONS up - regulate specific genes at either the nucleic acid or AND METHODS OF USE and U . S . Application No. protein . Small duplex RNAs have also been discovered to 62/ 150 , 900 filed Apr. 22 , 2015 , entitled SARNA COMPO increase gene expression by targeting ncRNAs that overlap SITIONS AND METHODS OF USE the contents of which gene promoters (Janowski et al ., Nature Chemical Biology , are each incorporated herein by reference in their entirety . vol. 3 : 166 - 173 (2007 ) , the contents of which are incorpo rated herein by reference in their entirety ) . REFERENCE TO SEQUENCE LISTING [0006 ] Any short RNA which leads to up - regulation of the expression of a target gene by any mechanism is termed a [ 0002 ] The instant application contains a " lengthy ” short activating RNA or small activating RNA ( SARNA ) . Sequence Listing which has been submitted via DVD - R in Known methods of up -regulating a target gene by use of lieu of a printed paper copy, and is hereby incorporated by saRNAs can involve the detection of an RNA transcript reference in its entirety . This contains a sequence listing text which is antisense to the target gene of interest and design file as part of the originally filed subject matter as follows: ing short RNA molecules which down -regulate the identified File name: 20581300US371 _ SL . txt; File size : 974 , 266 , 368 transcript. For instance, U . S . Pat. No . 8 , 288 ,354 to Wahl bytes ; Date created : Oct. 19 , 2017 . These DVD - Rs are estedt, the contents of which are incorporated herein by labeled “ CRF, ” “ Copy 1 , ” and “ Copy 2 , ” respectively , and reference in their entirety , discloses a method of modulating each contain only one identical file , as identified immedi expression of a target gene comprising targeting a nucleic ately above . The machine- readable format of each DVD - R acid molecule to a naturally occurring anti - sense transcript is IBM -PC and the operating system of each disc is MS - (NAT ) of a sense strand of the targeted gene in a target cell , Windows. wherein the nucleic acid molecule targeting the NAT is complementary to the NAT. The NAT may be a coding RNA transcript or a non - coding RNA transcript lacking any REFERENCE TO LENGTHY TABLE extensive open reading frame . In another example , WO [ 0003 ] The specification includes a Lengthy Table 1 and a 2012 / 065143 to Krieg et al . , the contents of which are Lengthy Table 2 . Lengthy Table 1 has been submitted via incorporated herein by reference in their entirety, teaches a EFS -Web in electronic format as follows: File name: method of activating expression of a target gene comprising Tablel 1300US371 _ coding . txt, Date created : Oct. 19 , blocking the binding of a long non -coding RNA ( Inc -RNA ) 2017 ; File size : 2 ,916 ,312 bytes and is incorporated herein to Polycomb repressive complex 2 (PRC2 ) protein by a by reference in its entirety . Lengthy Table 2 has been single - stranded oligonucleotide, thereby preventing the Inc submitted via EFS -Web in electronic format as follows: File RNA from suppressing the target gene . name: Table2 _ 1300US371 _ noncoding . txt, Date created : [ 0007 ] There remains, however, a need for compositions Oct. 19 , 2017 ; File size : 802 ,071 bytes and is incorporated and methods for the targeted modulation of genes via US 2018 /0305689 A1 Oct. 25 , 2018 activation with saRNA which do not require the a priori invention means a single - stranded or double - stranded RNA identification of a NAT or rely on interactions at the poly that upregulates or has a positive effect on the expression of comb complex for prophylactic diagnostic and /or therapeu a specific gene . The saRNA may be single - stranded of 14 to tic purposes . 30 nucleotides . The saRNA may also be double - stranded , each strand comprising 14 to 30 nucleotides . The gene is BRIEF DESCRIPTION OF THE DRAWINGS called the target gene of the saRNA . As used herein , the [0008 ] The foregoing and other objects, features and target gene is a double - stranded DNA comprising a coding advantages will be apparent from the following description strand and a template strand . For example , an saRNA that of particular embodiments of the invention , as illustrated in upregulates the expression of the AGGALT2 gene is called the accompanying drawings in which like reference charac an “ A3GALT2 - saRNA ” and the A3GALT2 gene is the target ters refer to the same parts throughout the different views. gene of the A3GALT2 - saRNA . A target gene may be any The drawings are not necessarily to scale , emphasis instead gene of interest. In some embodiments , a target gene has a being placed upon illustrating the principles of various promoter region on the template strand . [0020 ] By " upregulation ” or “ activation ” of a gene is embodiments of the invention . meant an increase in the level of expression of a gene , or [ 0009 ] FIG . 1 is a schematic illustrating the relationships levels of the polypeptide ( s ) encoded by a gene or the activity among the nucleic acid moieties involved in the function of thereof , or levels of the RNA transcript( s ) transcribed from an saRNA of the invention . the template strand of a gene above that observed in the absence of the saRNA of the present invention . The saRNA SUMMARY OF THE INVENTION of the present invention may have a direct upregulating [ 0010 ] The present invention provides compositions, effect on the expression of the target gene .