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United States Patent (10) Patent No.: US 9,044,492 B2 Delacote Et Al

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United States Patent (10) Patent No.: US 9,044,492 B2 Delacote Et Al USOO9044492B2 (12) United States Patent (10) Patent No.: US 9,044,492 B2 Delacote et al. (45) Date of Patent: Jun. 2, 2015 (54) METHOD FORMODULATING THE 8,206,965 B2 6/2012 Arnould et al. EFFICIENCY OF DOUBLE-STRAND 8,211,685 B2 7/2012 Epinatet al. 8.426,177 B2 4/2013 Gouble BREAK-INDUCED MUTAGENESIS 8,476,072 B2 7/2013 Cabaniols et al. O O 8,530,214 B2 9/2013 Arnould et al. (75) Inventors: Fabien Delacote, Paris (FR); Philippe 2006, OO78552 A1 4/2006 Arnould et al. Duchateau, Livry Gargan (FR): 2006/0153826 A1 7/2006 Arnould et al. Christophe Perez-Michaut, Paris (FR) 2006/0206949 A1 9, 2006 Arnould et al. s 2009/0220476 A1 9/2009 Paques 2009/0222937 A1 9, 2009 Arnould et al. (73) Assignee. CELLECTISSA, Romainville (FR) 2009/0271881 A1 10, 2009 Arnould et al. - 2010/0086533 A1 4/2010 Montoya et al. (*) Notice: Subject to any disclaimer, the term of this 2010, 0146651 A1 6, 2010 Smith et al. patent is extended or adjusted under 35 2010, 0151556 Al 6, 2010 Arnould et al. U.S.C. 154(b) by 407 days. 2010.0167357 A1 7/2010 Fajardo Sanchez et al. 2010/02O3031 A1 8, 2010 Grizot et al. (21) Appl. No.: 13/367,098 2010/0229252 A1 9/2010 Perez-Michaut 9 (Continued) (22) Filed: Feb. 6, 2012 Primary Examiner — Terra C Gibbs (65) Prior Publication Data (74) Attorney, Agent, or Firm — Oblon, McClelland, US 2012/0244131 A1 Sep. 27, 2012 Maier & Neustadt, L.L.P. Related U.S. Application Data (57) ABSTRACT (60) Provisional application No. 61/439,739, filed on Feb. A method for modulating double-strand break-induced 4, 2011. mutagenesis at a genomic locus of interest in a cell, thereby giving new tools for genome engineering, including thera 51) Int. C peuticeut1C applicatiapol1Cat1OnS andd cellCell li1ne eng1neering.gi ing. A method fOr CI2O I/68 (2006.01) modulating double-strand break-induced mutagenesis, con A63/788 (2006.01) cerns the identification of effectors that modulate double CI2N IS/10 (2006.01) Strand break-induced mutagenesis by use of interfering (52) U.S. Cl. agents; these agents are capable of modulating double-strand CPC .......... A61K3I/7088 (2013.01); C12N 15/102 break-induced mutagenesis through their respective director (2013.01); C12N 15/1086 (2013.01) indirect actions on said effectors. Methods of using these (58) Field of Classification Search effectors, interfering agents and derivatives, respectively, by USPC .................. 435/6.1,911,325,375,536/24.5 introducing them into a cell in order to modulate and more See application file for complete search history. particularly to increase double-strand break-induced mutagenesis. Specific derivatives of identified effectors and (56)56 References Cited 1nterferinginterfering agagents, Vectors encodingding ththem, compositionspositi and kits comprising Such derivatives for modulating or increasing U.S. PATENT DOCUMENTS double-strand break-induced mutagenesis. 7,842,489 B2 11/2010 Arnould et al. 7,897,372 B2 3/2011 Duchateau et al. 9 Claims, 12 Drawing Sheets ----------- A :8: :x:g acroix: a sets ;32&ssi: US 9,044,492 B2 Page 2 (56) References Cited 2012/0272.348 A1 10, 2012 Danos et al. 2012/0288941 A1 11/2012 Arnould et al. U.S. PATENT DOCUMENTS 2012/0288942 A1 11/2012 Arnould et al. 2012/0288943 A1 11/2012 Arnould et al. 2011/0072527 A1 3f2011 Duchateau et al. 2012/030 1456 Al 1 1/2012 Tremblay et al. 2011/009 1441 A1 4/2011 Gouble et al. 2012/0304321 A1 11/2012 Arnould et al. 2011/O151539 A1 6/2011 Arnould et al. 2012/0317664 A1 12/2012 Arnould et al. 2011/0158974 A1 6, 2011 Duchateau et al. 2012/0322689 A1 12/2012 Epinatet al. 2011/0173710 A1 7, 2011 Grizot et al. 2012/0331574 A1 12/2012 Arnould et al. 2011/01795.06 A1 7, 2011 Grizot 2013,0059387 A1 3/2013 Smith et al. 2011/0179507 A1 7/2011 Paques 2013,0061341 A1 3/2013 Arnould et al. 2011 019 1870 A1 8/2011 Paques 2013, OO676O7 A1 3/2013 Arnould et al. 2011/02O7199 A1 8/2011 Paques et al. 2013,0203840 A1 8/2013 Arnould et al. 2011/0225664 A1 9, 2011 Smith 2013/0209437 A1 8/2013 Paques 2011/0239319 A1 9/2011 Danos et al. 2013/0227715 A1 8/2013 Danos et al. 2012. O159659 A1 6/2012 Arnould et al. 2013,0236946 A1 9/2013 Gouble 2012/0171191 A1 7, 2012 Choulika et al. 2013/0326644 Al 12/2013 Paques 2012fO258537 A1 10, 2012 Duchateau et al. 2014,0004608 A1 1/2014 Cabaniols et al. 2012fO26035.6 A1 10, 2012 Choulika et al. 2014, OO17731 A1 1/2014 Gouble et al. U.S. Patent Jun. 2, 2015 Sheet 1 of 12 US 9,044,492 B2 Figure •or . r DNA ends & binding and protection DNA exis processing ------------------------ Nik &is igation K:::::::::::: 38: Kx: 88: 88k Ks xxxx-xx-x.: U.S. Patent Jun. 2, 2015 Sheet 2 of 12 US 9,044,492 B2 Figure 2 8 x 88883 : x -xxx x. $88: 8xxx xxxix. {y: $88.8.x: : x 8.8 xxixe: ki: cocions Ars .xxxx x88 - {{ 88: xxx xxxi-xxx xxx xx xxxx U.S. Patent Jun. 2, 2015 Sheet 3 of 12 US 9,044,492 B2 rigue 3 U.S. Patent US 9,044,492 B2 . × U.S. Patent Jun. 2, 2015 Sheet 5 of 12 US 9,044,492 B2 s As {K assssssssss........: *::::: ::::: ::::: 888 U.S. Patent Jun. 2, 2015 Sheet 6 of 12 US 9,044,492 B2 Figure 6 {& Ex.888 x -8x: ix.88883: xxxx xik cycine serine stretch x 8.8 xxix: e is exiers : ... to: : xix. text is 88. is Kreipes svopa pic or Amp 88.8.x is:x: xix {x : U.S. Patent Jun. 2, 2015 Sheet 8 of 12 US 9,044,492 B2 Figure 8: 8888 kept {x : ex orwar: pixer // x: 8:{{888 33 se 8. : i: 8:8 :::::::::: a six K preverse primer : Kp. it proseter origits sve 8: x8x: Figure 9 city forware prise civ promoter sco Races tax (8.3. : :::::::::: : xis: U.S. Patent Jun. 2, 2015 Sheet 9 of 12 US 9,044,492 B2 Figure 10 Ampr ORF EGFP pCLSOO99 6119 bp BGH polyA N f1 OR SV40 polyA o is 0. SV40 prom Neo R Figure 11 e APA P(LAC) APr pCLS0002G1. 2686 bp OR U.S. Patent Jun. 2, 2015 Sheet 10 of 12 US 9,044,492 B2 U.S. Patent Jun. 2, 2015 Sheet 11 of 12 US 9,044,492 B2 Figure 13 8 pronotor 888 {xx xxxx {8 &8::::::::::: :::::::::::: Exx 8x8x swept : Kg8. 8x8. is origs . 8x888: 888 88: 888 its grx 88:8: 8.8 x888 ::::::::::::: 8:8: 388: 888 $8xx:8: s: : N ... x: 8:8 88 grx 3 steps 88: 88: 8888 8 p. it origs U.S. Patent Jun. 2, 2015 Sheet 12 of 12 US 9,044,492 B2 Figure 15 & & & 3: 3: : & 3& & Figure 16 888 (8 x x: :::::::::: scies re-sex 8x8 $88.88: US 9,044,492 B2 1. 2 METHOD FOR MODULATING THE Osakabe et al. 2007). Typically, GT events occur in a fairly EFFICIENCY OF DOUBLE-STRAND small proportion of treated mammalian while GT efficiency is BREAK-INDUCED MUTAGENESIS extremely low in higher plant cells and range between 0.01 0.1% of the total number of random integration events CROSS-REFERENCE TO RELATED (Terada, Johzuka-Hisatomi et al. 2007). The low GT frequen APPLICATION cies reported in various organisms are thought to result from competition between HR and non homologous end joining This application claims priority under 35 U.S.C. S 119(e) to (NHEJ) for repair of dsDNA breaks (DSBs). As a conse U.S. Provisional Application No. U.S. 61/439,739, filed Feb. quence, the ends of a donor molecule are likely to be joined by 4, 2011, which is hereby incorporated by reference in its 10 NHEJ rather than participating in HR, thus reducing GT entirety. frequency. There is extensive data indicating that DSBs repair by NHEJ is error-prone. Often, DSBs are repaired by end FIELD OF THE INVENTION joining processes that generate insertions and/or deletions (Britt 1999). Thus, these NHEJ-based strategies might be The present invention relates to a method for modulating 15 more effective than HR-based strategies for targeted double-strand break-induced mutagenesis at a genomic locus mutagenesis into cells. Indeed, expression of I-Sce I, a rare of interest in a cell, thereby giving new tools for genome cutting restriction enzyme, has been shown to introduce engineering, including therapeutic applications and cell line mutations at I-Sce I cleavage sites in Arabidopsis and tobacco engineering. More specifically, the method of the present (Kirik, Salomon et al. 2000). Nevertheless, the use of restric invention for modulating double-strand break-induced tion enzymes is limited to rarely occurring natural recogni mutagenesis (DSB-induced mutagenesis), concerns the iden tion sites or to artificial target sites. To overcome this prob tification of effectors that modulate said DSB-induced lem, meganucleases with engineered specificity towards a mutagenesis by uses of interfering agents; these agents are chosen sequence have been developed. Meganucleases show capable of modulating DSB-induced mutagenesis through high specificity to their DNA target, these proteins being able their respective direct or indirect actions on said effectors. 25 to cleave a unique chromosomal sequence and therefore do The present invention also concerns the uses of these effec not affect global genome integrity. Natural meganucleases are tors, interfering agents and derivatives, respectively, by intro essentially represented by homing endonucleases, a wide ducing them into a cell in order to modulate and more par spread class of proteins found in eukaryotes, bacteria and ticularly to increase DSB-induced mutagenesis.
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