US009856497B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,856 ,497 B2 Qi et al. (45 ) Date of Patent: Jan . 2 , 2018 ( 54 ) CHIMERIC PROTEINS AND METHODS OF 9 , 593 , 338 B2 3 / 2017 Liu et al . REGULATING GENE EXPRESSION 9 ,624 ,554 B2 4 /2017 Collins et al . 2004 /0197346 Al 10 / 2004 O 'Hare et al. 2006 /0182741 A1 8 / 2006 Bourel et al. @( 71 ) Applicant: THE BOARD OF TRUSTEES OF 2007 /0224615 Al 9 /2007 Lee et al. THE LELAND STANFORD JUNIOR 2007 /0231319 A1 10 /2007 Yednock et al. UNIVERSITY , Stanford , CA (US ) 2008 /0274913 AL 11 / 2008 Lee 2010 / 0076057 A1 3 / 2010 Sontheimer et al. 2010 / 0093617 AL 4 / 2010 Barrangou et al. @( 72 ) Inventors : Lei S . Qi, Stanford , CA (US ) ; P . C . 2011 / 0217739 AL 9 / 2011 Terns et al . Dave P . Dingal, Stanford , CA (US ) 2012 / 0077706 A1 * 3 / 2012 Lee . .. .. .. .. C12N 15 / 1055 506 / 11 @( 73 ) Assignee : The Board of Trustee of the Leland 2013 /0011828 A1 1 / 2013 Barrangou et al. Stanford Junior University , Stanford , 2014 / 0068797 Al 3 / 2014 Doudna et al. CA (US ) 2014 /0113376 Al 4 /2014 Sorek et al. 2014 /0179770 A1 * 6 /2014 * ZhangLilang . C12N 15 / 86 @ 514 /44 R ( * ) Notice: Subject to any disclaimer, the term of this 2014 /0199767 Al 7 / 2014 Barrangou et al . patent is extended or adjusted under 35 2014 /0234851 A1 8 / 2014 Leonard et al. U . S . C . 154 (b ) by 0 days . 2014 /0271635 Al 9 /2014 Brogdon et al . 2014 /0273226 AL 9 /2014 Wu ( 21 ) Appl. No .: 15 /403 , 058 2014 / 0294773 A1 10 / 2014 Brouns et al. 2014 /0295556 Al 10 /2014 Joung et al. 2014 / 0295557 A1 10 /2014 Joung et al . (22 ) Filed : Jan . 10 , 2017 2014 / 0315985 A 10 / 2014 May et al . 2014 /0342456 AL 11 /2014 Mali et al . (65 ) Prior Publication Data 2014 /0342457 AL 11/ 2014 Mali et al . 2014 /0342458 A1 11 /2014 Mali et al . US 2017 /0198308 A1 Jul. 13, 2017 (Continued ) Related U . S . Application Data FOREIGN PATENT DOCUMENTS ( 60 ) Provisional application No . 62/ 277 , 322 , filed on Jan . 11 , 2016 , provisional application No . 62 /351 ,522 , CA 2619833 Al 3 / 2007 filed on Jun . 17 , 2016 , provisional application No . EP 1916903 B1 7 /2010 62 /399 ,902 , filed on Sep . 26 , 2016 . (Continued ) (51 ) Int. CI. OTHER PUBLICATIONS CO7H 21/ 04 (2006 .01 ) ( 2006 .01 ) Cheng et al ( Cell Research , 2013 , 23 : 1163 - 1171 ). * C12N 15 / 90 Chavez et al (Nature Methods, 2015 , 12 : 326 - 310 ). * C12N 9 / 22 ( 2006 .01 ) Nunez et al ( ACS Chem . Biol .; Feb . 9 , 2016 ; 11: 681 -688 ). * ( 52 ) U .S . CI. Invitrogen “ TangoTM GPR21 - bla U2OS Cell -based Assay , " printed CPC .. .. C12N 15 / 907 (2013 .01 ) ; C12N 9 /22 2010 , p . 1 - 12 . ( 2013 .01 ) ; C12Y 301/ 00 (2013 .01 ) Lim et al (Nature Reviews, 2010 , 11 : 393 -403 ) * ( 58 ) Field of Classification Search Daringer et al (ACS Synthetic Biology , 2014 , 3 :892 - 902 ) .* None Wehr et al ( Chapter 8 ; G protein - Coupled Receptor Screening See application file for complete search history . Assays , Methods in Molecular Biology , Jan . 2015 ; vol. 1272 , p . 107 - 118 ). * (56 ) References Cited Qi et al ( Cell, 2013, 152 : 1173 - 1183 ) .* U . S . PATENT DOCUMENTS (Continued ) 5 , 888 , 813 A 3 / 1999 Endl et al. 7 , 049 , 076 B2 . 5 / 2006 Lee et al . Primary Examiner — Laura B Goddard 8 , 017 , 398 B2 9 / 2011 Lee et al. 8 , 546 , 553 B2 10 / 2013 Terns et al . (74 ) Attorney , Agent, or Firm — Kilpatrick Townsend & 8 , 697, 359 B1 4 / 2014 Zhang Stockton LLP 8 ,771 , 945 B1 . 7 / 2014 Zhang 8 , 795 , 965 B2 8 / 2014 Zhang 8 , 865 ,406 B2 10 / 2014 Zhang et al. (57 ) ABSTRACT 8 ,871 ,445 B2 10 / 2014 Le Cong et al . 8 , 889 , 356 B2 11/ 2014 Zhang The present disclosure provides systems, compositions and 8 , 895 ,308 B1 11/ 2014 Zhang et al. 8 , 906 , 616 B2 12 / 2014 Zhang et al. methods for regulating expression of a target polynucleotide 8 , 932 , 814 B2 1 /2015 Le Cong et al. in a cell. The systems, compositions and methods comprise 8 , 945, 839 B2 2 / 2015 Zhang a chimeric receptor polypeptide comprising a G -protein 8 , 993 , 233 B2 3 / 2015 Zhang et al. 8 , 999 , 641 B2 4 / 2015 Zhang et al. coupled receptor (GPCR ) or a fragment thereof, a chimeric 9 , 023 , 649 B2 5 / 2015 Mali et al . adaptor polypeptide, at least one actuator moiety and a 9 , 234 , 213 B2 1 / 2016 Wu cleavage moiety . 9 , 260 , 752 B1 2 / 2016 May et al. 9 , 580, 480 B2 2 / 2017 Lu et al. 9 , 587, 020 B2 3 /2017 Wu et al . 30 Claims, 49 Drawing Sheets US 9 ,856 ,497 B2 Page 2 References Cited WO 2015139139 9 / 2015 ( 56 ) WO 2015142661 9 /2015 U . S . PATENT DOCUMENTS WO 2015 / 148670 AL 10 / 2015 WO 2015 / 148863 A2 10 / 2015 2014 /0377868 A1 12 / 2014 Joung et al. WO 2015 / 155686 Al 10 / 2015 2015 / 0024499 AL 1 / 2015 Brouns et al . WO 2015150771 10 / 2015 2015 / 0044772 AL 2 / 2015 Zhao Wo 2016 /011210 A2 1 / 2016 2015 /0045546 Al 2 / 2015 Siksnys et al. wo 2016 / 070037 A2 5 / 2016 2015 /0056705 Al 2 / 2015 Conway et al . wo 2016 / 115033 Al 7 / 2016 2015 /0059010 A 2 / 2015 Cigan et al . WO 2016 / 138034 Al 9 / 2016 2015 /0211023 Al 7 / 2015 Shiboleth et al. WO 2016 / 149274 Al 9 / 2016 2015 /0232881 A1 8 / 2015 Glucksmann et al. WO 2017 /040694 A2 3 / 2017 2015 / 0259684 AL 9 / 2015 Church et al . wo 2017 / 044476 Al 3 / 2017 2015 / 0283265 A1 10 / 2015 Peyman WO 2017 /059187 A 4 / 2017 2015 /0284727 A 10 / 2015 Kim et al. WO 2017123556 7 / 2017 2015 /0291966 Al 10 / 2015 Zhang et al. 2015 / 0315576 A1 11/ 2015 Caliando et al. 2015 / 0322457 A1 11/ 2015 Kim et al . OTHER PUBLICATIONS 2015 / 0344912 Al 12 / 2015 Kim et al . Barnea , G . et al ., “ The genetic design of signaling cascades to 2016 / 0010076 Al 1 / 2016 Joung et al. record receptor activation ," PNAS , Jan . 2008 , 105 ( 1 ) :64 - 69 . 2016 /0017366 A1 1 / 2016 Chen et al. Daringer, N . et al. , “ Modular extracellular sensor architecture for 2016 / 0024523 AL 1 / 2016 Joung et al . engineering mammalian cell - based devices ,” ACS Synthetic Biol 2016 / 0024524 A1 1 / 2016 Joung et al . 2016 / 0046949 Al 2 / 2016 May et al. ogy, Feb . 2014 , 3 :892 - 902 . 2016 /0046961 Al 2 / 2016 Jinek et al. Dominguez , A . et al ., “ Beyond editing: repurposing CRISPR -Cas9 2016 /0046962 AL 2 / 2016 May et al. for precision genome regulation and interrogation ,” Nature Review 2016 / 0046963 A 2 / 2016 May et al. Molecular Cell Biology , Dec. 2015, 17 : 5 - 15 . 2016 / 0046978 A1 2 /2016 May et al. Du , D . and Qi, L ., “ CRISPR technology for genome activation and 2016 / 0060653 Al 3 / 2016 Doudna et al . repression in mammalian cells ,” Cold Spring Harbor Protocols, Jan . 2016 / 0060654 A1 3 / 2016 Doudna et al. 2016 , pp . 40 - 49 . 2016 / 0068864 Al 3 / 2016 Doudna et al . 2016 / 0068887 Al 3 / 2016 May et al. Gilbert , L . et al. , “ CRISPR -mediated modular RNA - guided regu 2016 / 0076020 A1 3 / 2016 May et al . lation of transcription in eukaryotes, ” Cell , Jul. 2013 , 154 ( 2 ) :442 2016 /0185862 A1 6 / 2016 Wu et al . 451 . 2016 /0186152 Al 6 / 2016 Brouns et al. Gilbert , L . et al. , “ Genome - scale CRISPR -mediated control of gene 2016 / 0186214 A 6 / 2016 Brouns et al . repression and activation ,” Cell, Oct. 2014 , 159 ( 3 ) :647 -661 . 2016 /0201089 Al 7 / 2016 Gersbach et al . Hawkins , J . et al . , “ Targeted transcriptional repression in bacteria 2017 / 0051310 A1 2 / 2017 Doudna et al. using CRISPR interference (CRISPRi ) ,” Methods Mol Biol. , 2015 , 2017 /0051312 A1 2 / 2017 Jinek et al. 1311: 349- 362. 2017 / 0058282 A1 3 / 2017 Lu et al . Kobilka, B . , “ G Protein Coupled Receptor Structure and Activa 2017 /0096680 A14 / 2017 Lu et al. tion , ” Biochimica et Biophysica Acta , 2007 , 1768 ( 4 ) :794 - 807 . Larson , M . et al. , " CRISPR interference (CRISPRI ) for sequence FOREIGN PATENT DOCUMENTS specific control of gene expression , ” Nature Protocols , Nov . 2013 , EP 2336362 A1 6 / 2011 8 ( 11 ) : 2180 - 2196 . EP 2341149 AL 7 / 2011 Liu , H . et al ., “ CRISPR - ERA : a comprehensive design tool for ?? 2002021 B1 10 / 2011 CRISPR -mediated gene editing , repression and activation , ” Bioin EP 1644734 B1 11 / 2011 formatics, 2015 , 31 ( 22 ) : 3676 - 3678 . EP 2325332 B1 10 / 2012 Lucks, J . et al. , “ Versatile RNA - sensing transcriptional regulators EP 2771468 B1 2 / 2015 GB 2518764 B 3 / 2016 for engineering genetic networks ,” PNAS , May 2011 , GB 2512246 B 7 /2016 108 ( 21) : 8617 -8622 . WO 2005 /007822 A2 1 / 2005 Mandegar , M . et al. , “ CRISPR interference efficiently induces WO 2007 /025097 A2 3 / 2007 specific and reversible gene silencing in human iPSCs, ” Cell Stem WO 2007 /032793 A1 3 / 2007 Cell , Apr. 2016 , 18 ( 4 ) :541 - 553 . WO 2007 / 127538 Al 11 / 2007 Morsut, L . et al ., “ Engineering Customized Cell Sensing and WO 2007 / 136815 A2 11 / 2007 Response Behaviors Using Synthetic Notch Receptors , " Cell , Feb . WO 2007 / 149807 AL 12 /2007 2016 , 164 :780 -791 . WO 2012 / 164565 Al 12 /2012 WO 2013 /088446 Al 6 / 2013 Qi, L . et al. , “ Repurposing CRISPR as an RNA - guided platform for WO 2013 /098244 AL 7 / 2013 sequence - specific control of gene expression ,” Cell, Feb . 2013 , WO 2013 / 141680 Al 9 /2013 152 ( 5 ) : 1173 - 1183 .
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