Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
13 05 2021
Historique:
received: 17 01 2020
accepted: 06 04 2021
entrez: 14 5 2021
pubmed: 15 5 2021
medline: 1 6 2021
Statut: epublish

Résumé

CRISPR-based transcriptional activation is a powerful tool for functional gene interrogation; however, delivery difficulties have limited its applications in vivo. Here, we created a mouse model expressing all components of the CRISPR-Cas9 guide RNA-directed Synergistic Activation Mediator (SAM) from a single transcript that is capable of activating target genes in a tissue-specific manner. We optimized Lipid Nanoparticles and Adeno-Associated Virus guide RNA delivery approaches to achieve expression modulation of one or more genes in vivo. We utilized the SAM mouse model to generate a hypercholesteremia disease state that we could bidirectionally modulate with various guide RNAs. Additionally, we applied SAM to optimize gene expression in a humanized Transthyretin mouse model to recapitulate human expression levels. These results demonstrate that the SAM gene activation platform can facilitate in vivo research and drug discovery.

Identifiants

pubmed: 33986266
doi: 10.1038/s41467-021-22932-4
pii: 10.1038/s41467-021-22932-4
pmc: PMC8119962
doi:

Substances chimiques

Lipid Nanoparticles 0
Liposomes 0
Prealbumin 0
RNA, Guide 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

2770

Références

Prelich, G. Gene overexpression: uses, mechanisms, and interpretation. Genetics 190, 841–854 (2012).
pubmed: 22419077 pmcid: 3296252 doi: 10.1534/genetics.111.136911
Olalla Saad, S. T. et al. Comparison of different methods to overexpress large genes. J. Biol. Res. 91, https://doi.org/10.4081/jbr.2018.7249 (2018).
Guo, Y., Zhang, Y. & Hu, K. Sleeping Beauty transposon integrates into non-TA dinucleotides. Mob. DNA 9, 8 (2018).
pubmed: 29445422 pmcid: 5801840 doi: 10.1186/s13100-018-0113-8
Liu, C. Strategies for designing transgenic DNA constructs. Methods Mol. Biol. 1027, 183–201 (2013).
pubmed: 23912987 pmcid: 3815551 doi: 10.1007/978-1-60327-369-5_8
Groth, A. C., Olivares, E. C., Thyagarajan, B. & Calos, M. P. A phage integrase directs efficient site-specific integration in human cells. Proc. Natl Acad. Sci. USA 97, 5995–6000 (2000).
pubmed: 10801973 doi: 10.1073/pnas.090527097 pmcid: 18547
Kolot, M., Silberstein, N. & Yagil, E. Site-specific recombination in mammalian cells expressing the Int recombinase of bacteriophage HK022–site-specific recombination in mammalian cells promoted by a phage integrase. Mol. Biol. Rep. 26, 207–213 (1999).
pubmed: 10532317 doi: 10.1023/A:1007096701720
Tasic, B. et al. Site-specific integrase-mediated transgenesis in mice via pronuclear injection. Proc. Natl Acad. Sci. USA 108, 7902–7907 (2011).
pubmed: 21464299 doi: 10.1073/pnas.1019507108 pmcid: 3093482
Kim, M. J. & Ahituv, N. The hydrodynamic tail vein assay as a tool for the study of liver promoters and enhancers. Methods Mol. Biol. 1015, 279–289 (2013).
pubmed: 23824863 pmcid: 4096022 doi: 10.1007/978-1-62703-435-7_18
Tschaharganeh, D. F., Lowe, S. W., Garippa, R. J. & Livshits, G. Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J. 283, 3194–3203 (2016).
pubmed: 27149548 pmcid: 5120361 doi: 10.1111/febs.13750
Klug, A. The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q. Rev. Biophys. 43, 1–21 (2010).
pubmed: 20478078 doi: 10.1017/S0033583510000089
Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015).
doi: 10.1038/nature14136 pubmed: 25494202
Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17, 5–15 (2016).
pubmed: 26670017 doi: 10.1038/nrm.2015.2
Matharu, N. et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science 363, https://doi.org/10.1126/science.aau0629 (2019).
Lundh, M., Plucinska, K., Isidor, M. S., Petersen, P. S. S. & Emanuelli, B. Bidirectional manipulation of gene expression in adipocytes using CRISPRa and siRNA. Mol. Metab. 6, 1313–1320 (2017).
pubmed: 29031730 pmcid: 5641601 doi: 10.1016/j.molmet.2017.07.001
Dahlman, J. E. et al. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat. Biotechnol. 33, 1159–1161 (2015).
pubmed: 26436575 pmcid: 4747789 doi: 10.1038/nbt.3390
Liao, H. K. et al. In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation. Cell 171, 1495–1507 (2017). e1415.
pubmed: 29224783 pmcid: 5732045 doi: 10.1016/j.cell.2017.10.025
Ran, F. A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186–191 (2015).
pubmed: 25830891 pmcid: 4393360 doi: 10.1038/nature14299
Vora, S. et al. Rational design of a compact CRISPR-Cas9 activator for AAV- mediated delivery. Preprint at bioRxiv https://doi.org/10.1101/298620 (2018).
Lau, C. H., Ho, J. W., Lo, P. K. & Tin, C. Targeted transgene activation in the brain tissue by systemic delivery of engineered AAV1 expressing CRISPRa. Mol. Ther. Nucleic Acids 16, 637–649 (2019).
pubmed: 31108320 pmcid: 6526230 doi: 10.1016/j.omtn.2019.04.015
Wangensteen, K. J. et al. Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform. Hepatology 68, 663–676 (2018).
pubmed: 29091290 doi: 10.1002/hep.29626
Chavez, A. et al. Comparison of Cas9 activators in multiple species. Nat. Methods 13, 563–567 (2016).
pubmed: 27214048 pmcid: 4927356 doi: 10.1038/nmeth.3871
Zambrowicz, B. P. et al. Disruption of overlapping transcripts in the ROSA beta geo 26 gene trap strain leads to widespread expression of beta-galactosidase in mouse embryos and hematopoietic cells. Proc. Natl Acad. Sci. USA 94, 3789–3794 (1997).
pubmed: 9108056 doi: 10.1073/pnas.94.8.3789 pmcid: 20519
Friedrich, G. & Soriano, P. Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice. Genes Dev. 5, 1513–1523 (1991).
pubmed: 1653172 doi: 10.1101/gad.5.9.1513
Valenzuela, D. M. et al. High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat. Biotechnol. 21, 652–659 (2003).
pubmed: 12730667 doi: 10.1038/nbt822
Vihervaara, A. & Sistonen, L. HSF1 at a glance. J. Cell Sci. 127, 261–266 (2014).
pubmed: 24421309 doi: 10.1242/jcs.132605
Graslund, T., Li, X., Magnenat, L., Popkov, M. & Barbas, C. F. 3rd Exploring strategies for the design of artificial transcription factors: targeting sites proximal to known regulatory regions for the induction of gamma-globin expression and the treatment of sickle cell disease. J. Biol. Chem. 280, 3707–3714 (2005).
pubmed: 15537646 doi: 10.1074/jbc.M406809200
Tutucci, E. et al. An improved MS2 system for accurate reporting of the mRNA life cycle. Nat. Methods 15, 81–89 (2018).
pubmed: 29131164 doi: 10.1038/nmeth.4502
Wu, C. et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 10, R130 (2009).
pubmed: 19919682 pmcid: 3091323 doi: 10.1186/gb-2009-10-11-r130
Lai, K. M. et al. Diverse phenotypes and specific transcription patterns in twenty mouse lines with ablated LincRNAs. PLoS ONE 10, e0125522 (2015).
pubmed: 25909911 pmcid: 4409293 doi: 10.1371/journal.pone.0125522
Su, A. I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062–6067 (2004).
pubmed: 15075390 doi: 10.1073/pnas.0400782101 pmcid: 395923
Jensen, M. K. Design principles for nuclease-deficient CRISPR-based transcriptional regulators. FEMS Yeast Res. 18, https://doi.org/10.1093/femsyr/foy039 (2018).
McGinn, J. & Marraffini, L. A. Molecular mechanisms of CRISPR-Cas spacer acquisition. Nat. Rev. Microbiol 17, 7–12 (2019).
pubmed: 30171202 doi: 10.1038/s41579-018-0071-7
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
pubmed: 12045153 pmcid: 186604 doi: 10.1101/gr.229102
Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
doi: 10.1038/nature11247
Davis, C. A. et al. The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. 46, D794–D801 (2018).
pubmed: 29126249 doi: 10.1093/nar/gkx1081
Zhou, H. et al. In vivo simultaneous transcriptional activation of multiple genes in the brain using CRISPR-dCas9-activator transgenic mice. Nat. Neurosci. 21, 440–446 (2018).
pubmed: 29335603 doi: 10.1038/s41593-017-0060-6
Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
pubmed: 11932250 pmcid: 187518
Gossler, A., Joyner, A. L., Rossant, J. & Skarnes, W. C. Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science 244, 463–465 (1989).
pubmed: 2497519 doi: 10.1126/science.2497519
Lau, C. H. & Suh, Y. In vivo genome editing in animals using AAV-CRISPR system: applications to translational research of human disease. F1000Res 6, 2153 (2017).
pubmed: 29333255 pmcid: 5749125 doi: 10.12688/f1000research.11243.1
Yin, H., Kauffman, K. J. & Anderson, D. G. Delivery technologies for genome editing. Nat. Rev. Drug Discov. 16, 387–399 (2017).
pubmed: 28337020 doi: 10.1038/nrd.2016.280
Senis, E. et al. CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnol. J. 9, 1402–1412 (2014).
pubmed: 25186301 doi: 10.1002/biot.201400046
Magami, Y. et al. Cell proliferation and renewal of normal hepatocytes and bile duct cells in adult mouse. Liver 22, 419–425 (2002).
pubmed: 12390477 doi: 10.1034/j.1600-0676.2002.01702.x
Malato, Y. et al. Fate tracing of mature hepatocytes in mouse liver homeostasis and regeneration. J. Clin. Invest. 121, 4850–4860 (2011).
pubmed: 22105172 pmcid: 3226005 doi: 10.1172/JCI59261
Furuyama, K. et al. Continuous cell supply from a Sox9-expressing progenitor zone in adult liver, exocrine pancreas and intestine. Nat. Genet. 43, 34–41 (2011).
doi: 10.1038/ng.722 pubmed: 21113154
Lattin, J. E. et al. Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res. 4, 5 (2008).
pubmed: 18442421 pmcid: 2394514 doi: 10.1186/1745-7580-4-5
Hordeaux, J. et al. The GPI-linked protein LY6A drives AAV-PHP.B transport across the blood-brain barrier. Mol. Ther. 27, 912–921 (2019).
pubmed: 30819613 pmcid: 6520463 doi: 10.1016/j.ymthe.2019.02.013
Chan, K. Y. et al. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci. 20, 1172–1179 (2017).
pubmed: 28671695 pmcid: 5529245 doi: 10.1038/nn.4593
Wise, P. M., Scarbrough, K., Weiland, N. G. & Larson, G. H. Diurnal pattern of proopiomelanocortin gene expression in the arcuate nucleus of proestrous, ovariectomized, and steroid-treated rats: a possible role in cyclic luteinizing hormone secretion. Mol. Endocrinol. 4, 886–892 (1990).
pubmed: 2233745 doi: 10.1210/mend-4-6-886
Goutman, J. D., Elgoyhen, A. B. & Gomez-Casati, M. E. Cochlear hair cells: the sound-sensing machines. FEBS Lett. 589, 3354–3361 (2015).
pubmed: 26335749 pmcid: 4641020 doi: 10.1016/j.febslet.2015.08.030
Ogier, J. M., Burt, R. A., Drury, H. R., Lim, R. & Nayagam, B. A. Organotypic culture of neonatal murine inner ear explants. Front. Cell Neurosci. 13, 170 (2019).
pubmed: 31130846 pmcid: 6509234 doi: 10.3389/fncel.2019.00170
Bas, E., Gupta, C. & Van De Water, T. R. A novel organ of corti explant model for the study of cochlear implantation trauma. Anat. Rec. (Hoboken) 295, 1944–1956 (2012).
doi: 10.1002/ar.22585
Shapiro, M. D., Tavori, H. & Fazio, S. PCSK9: from basic science discoveries to clinical trials. Circ. Res. 122, 1420–1438 (2018).
pubmed: 29748367 pmcid: 5976255 doi: 10.1161/CIRCRESAHA.118.311227
Melendez, Q. M., Krishnaji, S. T., Wooten, C. J. & Lopez, D. Hypercholesterolemia: the role of PCSK9. Arch. Biochem. Biophys. 625-626, 39–53 (2017).
pubmed: 28587771 doi: 10.1016/j.abb.2017.06.001
Hopkins, P. N. et al. Characterization of autosomal dominant hypercholesterolemia caused by PCSK9 gain of function mutations and its specific treatment with alirocumab, a PCSK9 monoclonal antibody. Circ. Cardiovasc. Genet. 8, 823–831 (2015).
pubmed: 26374825 pmcid: 5098466 doi: 10.1161/CIRCGENETICS.115.001129
Gertz, M. A. et al. Diagnosis, prognosis, and therapy of transthyretin amyloidosis. J. Am. Coll. Cardiol. 66, 2451–2466 (2015).
pubmed: 26610878 doi: 10.1016/j.jacc.2015.09.075
Ueda, M. & Ando, Y. Recent advances in transthyretin amyloidosis therapy. Transl. Neurodegener. 3, 19 (2014).
pubmed: 25228988 pmcid: 4165622 doi: 10.1186/2047-9158-3-19
Fu, L., Zhu, X., Yi, F., Liu, G. H. & Izpisua Belmonte, J. C. Regenerative medicine: transdifferentiation in vivo. Cell Res. 24, 141–142 (2014).
pubmed: 24343579 doi: 10.1038/cr.2013.165
Li, Y. Y. et al. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput. Biol. 2, e74 (2006).
pubmed: 16839196 pmcid: 1487180 doi: 10.1371/journal.pcbi.0020074
Kim, H. K., Pham, M. H. C., Ko, K. S., Rhee, B. D. & Han, J. Alternative splicing isoforms in health and disease. Pflug. Arch. 470, 995–1016 (2018).
doi: 10.1007/s00424-018-2136-x
Poueymirou, W. T. et al. F0 generation mice fully derived from gene-targeted embryonic stem cells allowing immediate phenotypic analyses. Nat. Biotechnol. 25, 91–99 (2007).
pubmed: 17187059 doi: 10.1038/nbt1263
Haeussler, M. et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 17, 148 (2016).
pubmed: 27380939 pmcid: 4934014 doi: 10.1186/s13059-016-1012-2
Arden, E. & Metzger, J. M. Inexpensive, serotype-independent protocol for native and bioengineered recombinant adeno-associated virus purification. J. Biol. Methods 3, https://doi.org/10.14440/jbm.2016.102 (2016).
Zolotukhin, S. et al. Recombinant adeno-associated virus purification using novel methods improves infectious titer and yield. Gene Ther. 6, 973–985 (1999).
pubmed: 10455399 doi: 10.1038/sj.gt.3300938
Liu, F., Song, Y. & Liu, D. Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA. Gene Ther. 6, 1258–1266 (1999).
pubmed: 10455434 doi: 10.1038/sj.gt.3300947
Altarejos, J. Y. et al. The Creb1 coactivator Crtc1 is required for energy balance and fertility. Nat. Med. 14, 1112–1117 (2008).
pubmed: 18758446 pmcid: 2667698 doi: 10.1038/nm.1866

Auteurs

Charleen Hunt (C)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Suzanne A Hartford (SA)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Derek White (D)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Evangelos Pefanis (E)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Timothy Hanna (T)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Clarissa Herman (C)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Jarrell Wiley (J)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Heather Brown (H)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Qi Su (Q)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Yurong Xin (Y)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Dennis Voronin (D)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Hien Nguyen (H)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Judith Altarejos (J)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Keith Crosby (K)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Jeffery Haines (J)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Sarah Cancelarich (S)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Meghan Drummond (M)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Sven Moller-Tank (S)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Ryan Malpass (R)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Jacqueline Buckley (J)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Maria Del Pilar Molina-Portela (M)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Gustavo Droguett (G)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

David Frendewey (D)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Eric Chiao (E)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Brian Zambrowicz (B)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.

Guochun Gong (G)

Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA. guochun.gong@regeneron.com.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH