Synthetic immunomodulation with a CRISPR super-repressor in vivo.


Journal

Nature cell biology
ISSN: 1476-4679
Titre abrégé: Nat Cell Biol
Pays: England
ID NLM: 100890575

Informations de publication

Date de publication:
09 2020
Historique:
received: 22 07 2019
accepted: 24 07 2020
entrez: 5 9 2020
pubmed: 5 9 2020
medline: 31 10 2020
Statut: ppublish

Résumé

Transient modulation of the genes involved in immunity, without exerting a permanent change in the DNA code, can be an effective strategy to modulate the course of many inflammatory conditions. CRISPR-Cas9 technology represents a promising platform for achieving this goal. Truncation of guide RNA (gRNA) from the 5' end enables the application of a nuclease competent Cas9 protein for transcriptional modulation of genes, allowing multifunctionality of CRISPR. Here, we introduce an enhanced CRISPR-based transcriptional repressor to reprogram immune homeostasis in vivo. In this repressor system, two transcriptional repressors-heterochromatin protein 1 (HP1a) and Krüppel-associated box (KRAB)-are fused to the MS2 coat protein and subsequently recruited by gRNA aptamer binding to a nuclease competent CRISPR complex containing truncated gRNAs. With the enhanced repressor, we demonstrate transcriptional repression of the Myeloid differentiation primary response 88 (Myd88) gene in vitro and in vivo. We demonstrate that this strategy can efficiently downregulate Myd88 expression in lung, blood and bone marrow of Cas9 transgenic mice that receive systemic injection of adeno-associated virus (AAV)2/1-carrying truncated gRNAs targeting Myd88 and the MS2-HP1a-KRAB cassette. This downregulation is accompanied by changes in downstream signalling elements such as TNF-α and ICAM-1. Myd88 repression leads to a decrease in immunoglobulin G (IgG) production against AAV2/1 and AAV2/9 and this strategy modulates the IgG response against AAV cargos. It improves the efficiency of a subsequent AAV9/CRISPR treatment for repression of proprotein convertase subtilisin/kexin type 9 (PCSK9), a gene that, when repressed, can lower blood cholesterol levels. We also demonstrate that CRISPR-mediated Myd88 repression can act as a prophylactic measure against septicaemia in both Cas9 transgenic and C57BL/6J mice. When delivered by nanoparticles, this repressor can serve as a therapeutic modality to influence the course of septicaemia. Collectively, we report that CRISPR-mediated repression of endogenous Myd88 can effectively modulate the host immune response against AAV-mediated gene therapy and influence the course of septicaemia. The ability to control Myd88 transcript levels using a CRISPR-based synthetic repressor can be an effective strategy for AAV-based CRISPR therapies, as this pathway serves as a key node in the induction of humoral immunity against AAV serotypes.

Identifiants

pubmed: 32884147
doi: 10.1038/s41556-020-0563-3
pii: 10.1038/s41556-020-0563-3
pmc: PMC7480217
mid: NIHMS1615043
doi:

Substances chimiques

Myeloid Differentiation Factor 88 0
RNA, Guide 0
Receptors, Cell Surface 0
Proprotein Convertase 9 EC 3.4.21.-

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

1143-1154

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL141805
Pays : United States
Organisme : NIBIB NIH HHS
ID : U01 EB029372
Pays : United States
Organisme : NIBIB NIH HHS
ID : T32 EB001026
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK127713
Pays : United States
Organisme : NIBIB NIH HHS
ID : R01 EB024562
Pays : United States
Organisme : NIBIB NIH HHS
ID : R01 EB028532
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK120531
Pays : United States

Références

Moreno, A. M. et al. In situ gene therapy via AAV-CRISPR-Cas9-mediated targeted gene regulation. Mol. Ther. 26, 1818–1827 (2018).
pubmed: 29754775 pmcid: 6035733 doi: 10.1016/j.ymthe.2018.04.017
Thakore, P. I. et al. RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat. Commun. 9, 1674 (2018).
pubmed: 29700298 pmcid: 5920046 doi: 10.1038/s41467-018-04048-4
Zheng, Y. et al. CRISPR interference-based specific and efficient gene inactivation in the brain. Nat. Neurosci. 21, 447–454 (2018).
pubmed: 29403034 doi: 10.1038/s41593-018-0077-5
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
Liao, H. K. et al. In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation. Cell 171, 1495–1507 (2017).
pubmed: 29224783 pmcid: 5732045 doi: 10.1016/j.cell.2017.10.025
Breinig, M. et al. Multiplexed orthogonal genome editing and transcriptional activation by Cas12a. Nat. Methods 16, 51–54 (2019).
pubmed: 30559432 doi: 10.1038/s41592-018-0262-1
Matharu, N. et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science 363, eaau0629 (2019).
pubmed: 30545847 doi: 10.1126/science.aau0629
Xu, L., Zhao, L., Gao, Y., Xu, J. & Han, R. Empower multiplex cell and tissue-specific CRISPR-mediated gene manipulation with self-cleaving ribozymes and tRNA. Nucleic Acids Res. 45, e28 (2017).
pubmed: 27799472
Xu, X. et al. High-fidelity CRISPR/Cas9-based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis. Nat. Commun. 9, 3509 (2018).
pubmed: 30158531 pmcid: 6115451 doi: 10.1038/s41467-018-05766-5
Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).
pubmed: 23849981 pmcid: 3770145 doi: 10.1016/j.cell.2013.06.044
Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).
pubmed: 25307932 pmcid: 4253859 doi: 10.1016/j.cell.2014.09.029
Kearns, N. A. et al. Functional annotation of native enhancers with a Cas9–histone demethylase fusion. Nat. Methods 12, 401–403 (2015).
pubmed: 25775043 pmcid: 4414811 doi: 10.1038/nmeth.3325
Thakore, P. I. et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12, 1143–1149 (2015).
pubmed: 26501517 pmcid: 4666778 doi: 10.1038/nmeth.3630
Thakore, P. I., Black, J. B., Hilton, I. B. & Gersbach, C. A. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods 13, 127–137 (2016).
pubmed: 26820547 pmcid: 4922638 doi: 10.1038/nmeth.3733
Konermann, S. et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472–476 (2013).
pubmed: 23877069 pmcid: 3856241 doi: 10.1038/nature12466
La Russa, M. F. & Qi, L. S. The new state of the art: Cas9 for gene activation and repression. Mol. Cell. Biol. 35, 3800–3809 (2015).
pubmed: 26370509 pmcid: 4609748 doi: 10.1128/MCB.00512-15
Evers, B. et al. CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. Nat. Biotechnol. 34, 631–633 (2016).
pubmed: 27111720 doi: 10.1038/nbt.3536
Yeo, N. C. et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat. Methods 15, 611–616 (2018).
pubmed: 30013045 pmcid: 6129399 doi: 10.1038/s41592-018-0048-5
Kiani, S. et al. Cas9 gRNA engineering for genome editing, activation and repression. Nat. Methods 12, 1051–1054 (2015).
pubmed: 26344044 pmcid: 4666719
Huang, X. & Yang, Y. Targeting the TLR9-MyD88 pathway in the regulation of adaptive immune responses. Expert Opin. Ther. Targets 14, 787–796 (2010).
pubmed: 20560798 pmcid: 2917181 doi: 10.1517/14728222.2010.501333
Janssens, S. & Beyaert, R. A universal role for MyD88 in TLR/IL-1R-mediated signaling. Trends Biochem. Sci. 27, 474–482 (2002).
pubmed: 12217523 doi: 10.1016/S0968-0004(02)02145-X
Warner, N. & Nunez, G. MyD88: a critical adaptor protein in innate immunity signal transduction. J. Immunol. 190, 3–4 (2013).
pubmed: 23264668 doi: 10.4049/jimmunol.1203103
Plant, L., Wan, H. & Jonsson, A.-B. MyD88-dependent signaling affects the development of meningococcal sepsis by nonlipooligosaccharide ligands. Infect. Immun. 74, 3538–3546 (2006).
pubmed: 16714586 pmcid: 1479290 doi: 10.1128/IAI.00128-06
Yu, X. et al. MYD88 L265P mutation in lymphoid malignancies. Cancer Res. 78, 2457–2462 (2018).
pubmed: 29703722 doi: 10.1158/0008-5472.CAN-18-0215
Liao, H.-K. et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat. Commun. 6, 6413 (2015).
pubmed: 25752527 doi: 10.1038/ncomms7413
Castle, M. J., Turunen, H. T., Vandenberghe, L. H. & Wolfe, J. H. in Gene Therapy for Neurological Disorders 133–149 (Springer, 2016).
Merkel, S. F. et al. Trafficking of adeno‐associated virus vectors across a model of the blood–brain barrier; a comparative study of transcytosis and transduction using primary human brain endothelial cells. J. Neurochem. 140, 216–230 (2017).
pubmed: 27718541 doi: 10.1111/jnc.13861
Chen, S. et al. Efficient transduction of vascular endothelial cells with recombinant adeno-associated virus serotype 1 and 5 vectors. Hum. Gene Ther. 16, 235–247 (2005).
pubmed: 15761263 doi: 10.1089/hum.2005.16.235
Veron, P. et al. Major subsets of human dendritic cells are efficiently transduced by self-complementary adeno-associated virus vectors 1 and 2. J. Virol. 81, 5385–5394 (2007).
pubmed: 17314166 pmcid: 1900227 doi: 10.1128/JVI.02516-06
Lu, Y. & Song, S. Distinct immune responses to transgene products from rAAV1 and rAAV8 vectors. Proc. Natl Acad. Sci. USA 106, 17158–17162 (2009).
pubmed: 19805176 doi: 10.1073/pnas.0909520106 pmcid: 2761323
Sudres, M. et al. MyD88 signaling in B cells regulates the production of Th1-dependent antibodies to AAV. Mol. Ther. 20, 1571–1581 (2012).
pubmed: 22643865 pmcid: 3412489 doi: 10.1038/mt.2012.101
Zhu, J., Huang, X. & Yang, Y. The TLR9-MyD88 pathway is critical for adaptive immune responses to adeno-associated virus gene therapy vectors in mice. J. Clin. Invest. 119, 2388–2398 (2009).
pubmed: 19587448 pmcid: 2719948 doi: 10.1172/JCI37607
Lin, X., Kong, J., Wu, Q., Yang, Y. & Ji, P. Effect of TLR4/MyD88 signaling pathway on expression of IL-1β and TNF-α in synovial fibroblasts from temporomandibular joint exposed to lipopolysaccharide. Mediators Inflamm. 2015, 329405 (2015).
pubmed: 25810567 pmcid: 4354974
Park, G. S. & Kim, J. H. LPS up-regulates ICAM-1 expression in breast cancer cells by stimulating a MyD88-BLT2-ERK-linked cascade, which promotes adhesion to monocytes. Mol. Cells 38, 821–828 (2015).
pubmed: 26299331 pmcid: 4588726 doi: 10.14348/molcells.2015.0174
Yu, M. et al. MyD88-dependent interplay between myeloid and endothelial cells in the initiation and progression of obesity-associated inflammatory diseases. J. Exp. Med. 211, 887–907 (2014).
pubmed: 24752299 pmcid: 4010914 doi: 10.1084/jem.20131314
Van den Akker, T. W., de Glopper-van der Veer, E., Radl, J. & Benner, R. The influence of genetic factors associated with the immunoglobulin heavy chain locus on the development of benign monoclonal gammapathy in ageing IgH-congenic mice. Immunology 65, 31–35 (1988).
pmcid: 1385015
Thakore, P. I. et al. RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat. Commun. 9, 1674 (2018).
pubmed: 29700298 pmcid: 5920046 doi: 10.1038/s41467-018-04048-4
Abifadel, M. et al. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat. Genet. 34, 154–156 (2003).
pubmed: 12730697 doi: 10.1038/ng1161
Maxwell, K. N. & Breslow, J. L. Adenoviral-mediated expression of Pcsk9 in mice results in a low-density lipoprotein receptor knockout phenotype. Proc. Natl Acad. Sci. USA 101, 7100–7105 (2004).
pubmed: 15118091 doi: 10.1073/pnas.0402133101 pmcid: 406472
Zhang, H. et al. Sepsis induces hematopoietic stem cell exhaustion and myelosuppression through distinct contributions of TRIF and MYD88. Stem Cell Rep. 6, 940–956 (2016).
doi: 10.1016/j.stemcr.2016.05.002
Ma, X.-Y., Tian, L.-X. & Liang, H.-P. Early prevention of trauma-related infection/sepsis. Mil. Med. Res. 3, 33 (2016).
pubmed: 27833759 pmcid: 5101695
Cho, S.-Y. & Choi, J.-H. Biomarkers of sepsis. Infect. Chemother. 46, 1–12 (2014).
pubmed: 24693464 pmcid: 3970312 doi: 10.3947/ic.2014.46.1.1
Yao, Z. et al. Blood-borne lipopolysaccharide is rapidly eliminated by liver sinusoidal endothelial cells via high-density lipoprotein. J. Immunol. 197, 2390–2399 (2016).
pubmed: 27534554 doi: 10.4049/jimmunol.1600702
Dandekar, A. et al. Toll-like receptor (TLR) signaling interacts with CREBH to modulate high-density lipoprotein (HDL) in response to bacterial endotoxin. J. Biol. Chem. 291, 23149–23158 (2016).
pubmed: 27637329 pmcid: 5087733 doi: 10.1074/jbc.M116.755728
Schnare, M. et al. Toll-like receptors control activation of adaptive immune responses. Nat. Immunol. 2, 947–950 (2001).
pubmed: 11547333 doi: 10.1038/ni712
Hiragami, K. & Festenstein, R. Heterochromatin protein 1: a pervasive controlling influence. Cell. Mol. Life Sci. 62, 2711–2726 (2005).
pubmed: 16261261 doi: 10.1007/s00018-005-5287-9
Schultz, D. C., Ayyanathan, K., Negorev, D., Maul, G. G. & Rauscher, F. J. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16, 919–932 (2002).
pubmed: 11959841 pmcid: 152359 doi: 10.1101/gad.973302
Canzio, D. et al. Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Mol. Cell 41, 67–81 (2011).
pubmed: 21211724 pmcid: 3752404 doi: 10.1016/j.molcel.2010.12.016
Meehan, R. R., Kao, C. F. & Pennings, S. HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain. EMBO J. 22, 3164–3174 (2003).
pubmed: 12805230 pmcid: 162158 doi: 10.1093/emboj/cdg306
Canzio, D., Larson, A. & Narlikar, G. J. Mechanisms of functional promiscuity by HP1 proteins. Trends Cell Biol. 24, 377–386 (2014).
pubmed: 24618358 pmcid: 4077871 doi: 10.1016/j.tcb.2014.01.002
Moghadam, F. et al. Synthetic immunomodulation with a CRISPR super-repressor in vivo. Protoc. Exch. https://doi.org/10.21203/rs.3.pex-1027/v1 (2020).
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
Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2014).
pubmed: 25494202 pmcid: 4420636 doi: 10.1038/nature14136
Duan, J. et al. The CRISPR/Cas9-created MDM2 T309G enhances vitreous-induced expression of MDM2 and proliferation and survival of cells. J. Biol. Chem. 291, 16339–16347 (2016).
pubmed: 27246850 pmcid: 4965581 doi: 10.1074/jbc.M116.729467

Auteurs

Farzaneh Moghadam (F)

Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Division of Experimental Pathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA.

Ryan LeGraw (R)

Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Division of Experimental Pathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA.

Jeremy J Velazquez (JJ)

Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Division of Experimental Pathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA.

Nan Cher Yeo (NC)

Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL, USA.
Precision Medicine Institute, University of Alabama, Birmingham, AL, USA.

Chenxi Xu (C)

Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.

Jin Park (J)

Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.

Alejandro Chavez (A)

Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA.

Mo R Ebrahimkhani (MR)

Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. mo.ebr@pitt.edu.
Division of Experimental Pathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. mo.ebr@pitt.edu.
School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA. mo.ebr@pitt.edu.
McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA. mo.ebr@pitt.edu.

Samira Kiani (S)

Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. skiani@pitt.edu.
Division of Experimental Pathology, Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. skiani@pitt.edu.
School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA. skiani@pitt.edu.
McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA. skiani@pitt.edu.

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