1
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Cromer MK, Majeti KR, Rettig GR, Murugan K, Kurgan GL, Bode NM, Hampton JP, Vakulskas CA, Behlke MA, Porteus MH. Comparative analysis of CRISPR off-target discovery tools following ex vivo editing of CD34 + hematopoietic stem and progenitor cells. Mol Ther 2023; 31:1074-1087. [PMID: 36793210 PMCID: PMC10124080 DOI: 10.1016/j.ymthe.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
While a number of methods exist to investigate CRISPR off-target (OT) editing, few have been compared head-to-head in primary cells after clinically relevant editing processes. Therefore, we compared in silico tools (COSMID, CCTop, and Cas-OFFinder) and empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) after ex vivo hematopoietic stem and progenitor cell (HSPC) editing. We performed editing using 11 different gRNAs complexed with Cas9 protein (high-fidelity [HiFi] or wild-type versions), then performed targeted next-generation sequencing of nominated OT sites identified by in silico and empirical methods. We identified an average of less than one OT site per guide RNA (gRNA) and all OT sites generated using HiFi Cas9 and a 20-nt gRNA were identified by all OT detection methods with the exception of SITE-seq. This resulted in high sensitivity for the majority of OT nomination tools and COSMID, DISCOVER-Seq, and GUIDE-Seq attained the highest positive predictive value (PPV). We found that empirical methods did not identify OT sites that were not also identified by bioinformatic methods. This study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity and PPV, thereby enabling more efficient identification of potential OT sites without compromising a thorough examination for any given gRNA.
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Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Kiran R Majeti
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Karthik Murugan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Gavin L Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Jessica P Hampton
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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2
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Magis W, DeWitt MA, Wyman SK, Vu JT, Heo SJ, Shao SJ, Hennig F, Romero ZG, Campo-Fernandez B, Said S, McNeill MS, Rettig GR, Sun Y, Wang Y, Behlke MA, Kohn DB, Boffelli D, Walters MC, Corn JE, Martin DI. High-level correction of the sickle mutation is amplified in vivo during erythroid differentiation. iScience 2022; 25:104374. [PMID: 35633935 PMCID: PMC9130532 DOI: 10.1016/j.isci.2022.104374] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/21/2022] Open
Abstract
Background A point mutation in sickle cell disease (SCD) alters one amino acid in the β-globin subunit of hemoglobin, with resultant anemia and multiorgan damage that typically shortens lifespan by decades. Because SCD is caused by a single mutation, and hematopoietic stem cells (HSCs) can be harvested, manipulated, and returned to an individual, it is an attractive target for gene correction. Results An optimized Cas9 ribonucleoprotein (RNP) with an ssDNA oligonucleotide donor together generated correction of at least one β-globin allele in more than 30% of long-term engrafting human HSCs. After adopting a high-fidelity Cas9 variant, efficient correction with minimal off-target events also was observed. In vivo erythroid differentiation markedly enriches for corrected β-globin alleles, indicating that erythroblasts carrying one or more corrected alleles have a survival advantage. Significance These findings indicate that the sickle mutation can be corrected in autologous HSCs with an optimized protocol suitable for clinical translation. The gene editing protocol corrects the sickle mutation in ∼30% of engrafting cells Random assortment of engrafting stem cell clones without clonal dominance was shown Corrected erythroid cells are preferentially enriched compared with unedited cells
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3
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Aoki Y, Rocha CSJ, Lehto T, Miyatake S, Johansson H, Hashimoto Y, Nordin JZ, Mager I, Aoki M, Graham M, Sathyaprakash C, Roberts TC, Wood MJA, Behlke MA, Andaloussi SE. Fine Tuning of Phosphorothioate Inclusion in 2'-O-Methyl Oligonucleotides Contributes to Specific Cell Targeting for Splice-Switching Modulation. Front Physiol 2021; 12:689179. [PMID: 34721051 PMCID: PMC8548633 DOI: 10.3389/fphys.2021.689179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
Splice-switching antisense oligonucleotide- (SSO-) mediated correction of framedisrupting mutation-containing premessenger RNA (mRNA) transcripts using exon skipping is a highly promising treatment method for muscular diseases such as Duchenne muscular dystrophy (DMD). Phosphorothioate (PS) chemistry, a commonly used oligonucleotide modification, has been shown to increase the stability of and improve the pharmacokinetics of SSOs. However, the effect of PS inclusion in 2′-O-methyl SSOs (2OMe) on cellular uptake and splice switching is less well-understood. At present, we demonstrate that the modification of PS facilitates the uptake of 2OMe in H2k-mdx myoblasts. Furthermore, we found a dependency of SSO nuclear accumulation and high splice-switching activity on PS inclusion in 2OMe (2OMePS), as tested in various reporter cell lines carrying pLuc/705. Increased exon-inclusion activity was observed in muscle, neuronal, liver, and bone cell lineages via both the gymnotic uptake and lipofection of 2OMePS. Using the photoactivatable ribonucleoside-enhanced crosslinking and a subsequent proteomic approach, we identified several 2OMePS-binding proteins, which are likely to play a role in the trafficking of 2OMePS to the nucleus. Ablation of one of them, Ncl by small-interfering RNA (siRNA) enhanced 2OMePS uptake in C2C12 myoblasts and upregulated luciferase RNA splicing in the HeLa Luc/705 reporter cell line. Overall, we demonstrate that PS inclusion increases nuclear delivery and splice switching in muscle, neuronal, liver, and bone cell lineages and that the modulation of 2OMePS-binding partners may improve SSO delivery.
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Affiliation(s)
- Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.,Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Cristina S J Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Taavi Lehto
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Shouta Miyatake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Henrik Johansson
- Department of Oncology-Pathology, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Yasumasa Hashimoto
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Joel Z Nordin
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.,Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Imre Mager
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Misako Aoki
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - McClorey Graham
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Chaitra Sathyaprakash
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Samir El Andaloussi
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
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4
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Valentin R, Wong C, Alharbi AS, Pradeloux S, Morros MP, Lennox KA, Ellyard JI, Garcin AJ, Ullah TR, Kusuma GD, Pépin G, Li HM, Pearson JS, Ferrand J, Lim R, Veedu RN, Morand EF, Vinuesa CG, Behlke MA, Gantier MP. Sequence-dependent inhibition of cGAS and TLR9 DNA sensing by 2'-O-methyl gapmer oligonucleotides. Nucleic Acids Res 2021; 49:6082-6099. [PMID: 34057477 PMCID: PMC8216285 DOI: 10.1093/nar/gkab451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022] Open
Abstract
Oligonucleotide-based therapeutics have the capacity to engage with nucleic acid immune sensors to activate or block their response, but a detailed understanding of these immunomodulatory effects is currently lacking. We recently showed that 2′-O-methyl (2′OMe) gapmer antisense oligonucleotides (ASOs) exhibited sequence-dependent inhibition of sensing by the RNA sensor Toll-Like Receptor (TLR) 7. Here we discovered that 2′OMe ASOs can also display sequence-dependent inhibitory effects on two major sensors of DNA, namely cyclic GMP-AMP synthase (cGAS) and TLR9. Through a screen of 80 2′OMe ASOs and sequence mutants, we characterized key features within the 20-mer ASOs regulating cGAS and TLR9 inhibition, and identified a highly potent cGAS inhibitor. Importantly, we show that the features of ASOs inhibiting TLR9 differ from those inhibiting cGAS, with only a few sequences inhibiting both pathways. Together with our previous studies, our work reveals a complex pattern of immunomodulation where 95% of the ASOs tested inhibited at least one of TLR7, TLR9 or cGAS by ≥30%, which may confound interpretation of their in vivo functions. Our studies constitute the broadest analysis of the immunomodulatory effect of 2′OMe ASOs on nucleic acid sensing to date and will support refinement of their therapeutic development.
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Affiliation(s)
- Roxane Valentin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Christophe Wong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Arwaf S Alharbi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia.,The Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Turabah 29179, Saudi Arabia
| | - Solène Pradeloux
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Makala P Morros
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Kim A Lennox
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Julia I Ellyard
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.,Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Aurélie J Garcin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Tomalika R Ullah
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Gina D Kusuma
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria 3800, Australia
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Hong-Mei Li
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan Ferrand
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Rebecca Lim
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia.,Perron Institute for Neurological and Translational Science, Perth, Western Australia 6150, Australia
| | - Eric F Morand
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3168, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.,Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
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5
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Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, Florus K, Behlke MA, Wang Y, McNeill MS. CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing. Mol Ther Methods Clin Dev 2021; 21:478-491. [PMID: 33981780 PMCID: PMC8082044 DOI: 10.1016/j.omtm.2021.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
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Affiliation(s)
- Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | | | - Lauren Tso
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | | | | | | | | | - Yu Wang
- Integrated DNA Technologies, Coralville, IA 52241, USA
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6
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Cromer MK, Camarena J, Martin RM, Lesch BJ, Vakulskas CA, Bode NM, Kurgan G, Collingwood MA, Rettig GR, Behlke MA, Lemgart VT, Zhang Y, Goyal A, Zhao F, Ponce E, Srifa W, Bak RO, Uchida N, Majeti R, Sheehan VA, Tisdale JF, Dever DP, Porteus MH. Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells. Nat Med 2021; 27:677-687. [PMID: 33737751 PMCID: PMC8265212 DOI: 10.1038/s41591-021-01284-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
β-Thalassemia pathology is due not only to loss of β-globin (HBB), but also to erythrotoxic accumulation and aggregation of the β-globin-binding partner, α-globin (HBA1/2). Here we describe a Cas9/AAV6-mediated genome editing strategy that can replace the entire HBA1 gene with a full-length HBB transgene in β-thalassemia-derived hematopoietic stem and progenitor cells (HSPCs), which is sufficient to normalize β-globin:α-globin messenger RNA and protein ratios and restore functional adult hemoglobin tetramers in patient-derived red blood cells. Edited HSPCs were capable of long-term and bilineage hematopoietic reconstitution in mice, establishing proof of concept for replacement of HBA1 with HBB as a novel therapeutic strategy for curing β-thalassemia.
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Affiliation(s)
- M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Renata M Martin
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yankai Zhang
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ankush Goyal
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ezequiel Ponce
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Vivien A Sheehan
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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7
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Daher M, Basar R, Gokdemir E, Baran N, Uprety N, Nunez Cortes AK, Mendt M, Kerbauy LN, Banerjee PP, Shanley M, Imahashi N, Li L, Lim FLWI, Fathi M, Rezvan A, Mohanty V, Shen Y, Shaim H, Lu J, Ozcan G, Ensley E, Kaplan M, Nandivada V, Bdiwi M, Acharya S, Xi Y, Wan X, Mak D, Liu E, Jiang XR, Ang S, Muniz-Feliciano L, Li Y, Wang J, Kordasti S, Petrov N, Varadarajan N, Marin D, Brunetti L, Skinner RJ, Lyu S, Silva L, Turk R, Schubert MS, Rettig GR, McNeill MS, Kurgan G, Behlke MA, Li H, Fowlkes NW, Chen K, Konopleva M, Champlin RE, Shpall EJ, Rezvani K. Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells. Blood 2021; 137:624-636. [PMID: 32902645 PMCID: PMC7869185 DOI: 10.1182/blood.2020007748] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/29/2020] [Indexed: 12/22/2022] Open
Abstract
Immune checkpoint therapy has resulted in remarkable improvements in the outcome for certain cancers. To broaden the clinical impact of checkpoint targeting, we devised a strategy that couples targeting of the cytokine-inducible Src homology 2-containing (CIS) protein, a key negative regulator of interleukin 15 (IL-15) signaling, with fourth-generation "armored" chimeric antigen receptor (CAR) engineering of cord blood-derived natural killer (NK) cells. This combined strategy boosted NK cell effector function through enhancing the Akt/mTORC1 axis and c-MYC signaling, resulting in increased aerobic glycolysis. When tested in a lymphoma mouse model, this combined approach improved NK cell antitumor activity more than either alteration alone, eradicating lymphoma xenografts without signs of any measurable toxicity. We conclude that targeting a cytokine checkpoint further enhances the antitumor activity of IL-15-secreting armored CAR-NK cells by promoting their metabolic fitness and antitumor activity. This combined approach represents a promising milestone in the development of the next generation of NK cells for cancer immunotherapy.
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Affiliation(s)
- May Daher
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Elif Gokdemir
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Natalia Baran
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nadima Uprety
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mayela Mendt
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Lucila Nassif Kerbauy
- Department of Stem Cell Transplantation and Cellular Therapy and
- Department of Stem Cell Transplantation and Cellular Therapy, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Li Li
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mohsen Fathi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - Ali Rezvan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yifei Shen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Junjun Lu
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Gonca Ozcan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Emily Ensley
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Mecit Kaplan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mustafa Bdiwi
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Sunil Acharya
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xinhai Wan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Duncan Mak
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Enli Liu
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Xin Ru Jiang
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Sonny Ang
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Ye Li
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shahram Kordasti
- System Cancer Immunology, Comprehensive Cancer Centre, King's College London, London, United Kingdom
| | - Nedyalko Petrov
- System Cancer Immunology, Comprehensive Cancer Centre, King's College London, London, United Kingdom
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - David Marin
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Lorenzo Brunetti
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | | | - Shangrong Lyu
- C.T. Bauer College of Business, University of Houston, Houston, TX
| | - Leiser Silva
- C.T. Bauer College of Business, University of Houston, Houston, TX
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA
| | | | | | | | | | | | - Heng Li
- Dana-Farber/Harvard Cancer Center, Boston, MA; and
| | - Natalie W Fowlkes
- Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy and
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8
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Kow RL, Strovas TJ, McMillan PJ, Jacobi AM, Behlke MA, Saxton AD, Latimer CS, Keene CD, Kraemer BC. Distinct Poly(A) nucleases have differential impact on sut-2 dependent tauopathy phenotypes. Neurobiol Dis 2021; 147:105148. [PMID: 33184027 PMCID: PMC8092974 DOI: 10.1016/j.nbd.2020.105148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
Aging drives pathological accumulation of proteins such as tau, causing neurodegenerative dementia disorders like Alzheimer's disease. Previously we showed loss of function mutations in the gene encoding the poly(A) RNA binding protein SUT-2/MSUT2 suppress tau-mediated neurotoxicity in C. elegans neurons, cultured human cells, and mouse brain, while loss of PABPN1 had the opposite effect (Wheeler et al., 2019). Here we found that blocking poly(A) tail extension with cordycepin exacerbates tauopathy in cultured human cells, which is rescued by MSUT2 knockdown. To further investigate the molecular mechanisms of poly(A) RNA-mediated tauopathy suppression, we examined whether genes encoding poly(A) nucleases also modulated tauopathy in a C. elegans tauopathy model. We found that loss of function mutations in C. elegans ccr-4 and panl-2 genes enhanced tauopathy phenotypes in tau transgenic C. elegans while loss of parn-2 partially suppressed tauopathy. In addition, loss of parn-1 blocked tauopathy suppression by loss of parn-2. Epistasis analysis showed that sut-2 loss of function suppressed the tauopathy enhancement caused by loss of ccr-4 and SUT-2 overexpression exacerbated tauopathy even in the presence of parn-2 loss of function in tau transgenic C. elegans. Thus sut-2 modulation of tauopathy is epistatic to ccr-4 and parn-2. We found that human deadenylases do not colocalize with human MSUT2 in nuclear speckles; however, expression levels of TOE1, the homolog of parn-2, correlated with that of MSUT2 in post-mortem Alzheimer's disease patient brains. Alzheimer's disease patients with low TOE1 levels exhibited significantly increased pathological tau deposition and loss of NeuN staining. Taken together, this work suggests suppressing tauopathy cannot be accomplished by simply extending poly(A) tails, but rather a more complex relationship exists between tau, sut-2/MSUT2 function, and control of poly(A) RNA metabolism, and that parn-2/TOE1 may be altered in tauopathy in a similar way.
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Affiliation(s)
- Rebecca L. Kow
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health, Care System, Seattle, WA 98108, USA,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104, USA
| | - Timothy J. Strovas
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health, Care System, Seattle, WA 98108, USA
| | - Pamela J. McMillan
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | | | | | - Aleen D. Saxton
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health, Care System, Seattle, WA 98108, USA
| | - Caitlin S. Latimer
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brian C. Kraemer
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health, Care System, Seattle, WA 98108, USA,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA,Department of Pathology, University of Washington, Seattle, WA 98195, USA,Corresponding author at: Seattle Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA 98108, USA. (B.C. Kraemer)
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9
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Rosenblum D, Gutkin A, Kedmi R, Ramishetti S, Veiga N, Jacobi AM, Schubert MS, Friedmann-Morvinski D, Cohen ZR, Behlke MA, Lieberman J, Peer D. CRISPR-Cas9 genome editing using targeted lipid nanoparticles for cancer therapy. Sci Adv 2020; 6:6/47/eabc9450. [PMID: 33208369 PMCID: PMC7673804 DOI: 10.1126/sciadv.abc9450] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/02/2020] [Indexed: 05/19/2023]
Abstract
Harnessing CRISPR-Cas9 technology for cancer therapeutics has been hampered by low editing efficiency in tumors and potential toxicity of existing delivery systems. Here, we describe a safe and efficient lipid nanoparticle (LNP) for the delivery of Cas9 mRNA and sgRNAs that use a novel amino-ionizable lipid. A single intracerebral injection of CRISPR-LNPs against PLK1 (sgPLK1-cLNPs) into aggressive orthotopic glioblastoma enabled up to ~70% gene editing in vivo, which caused tumor cell apoptosis, inhibited tumor growth by 50%, and improved survival by 30%. To reach disseminated tumors, cLNPs were also engineered for antibody-targeted delivery. Intraperitoneal injections of EGFR-targeted sgPLK1-cLNPs caused their selective uptake into disseminated ovarian tumors, enabled up to ~80% gene editing in vivo, inhibited tumor growth, and increased survival by 80%. The ability to disrupt gene expression in vivo in tumors opens new avenues for cancer treatment and research and potential applications for targeted gene editing of noncancerous tissues.
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Affiliation(s)
- Daniel Rosenblum
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Anna Gutkin
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Ranit Kedmi
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Srinivas Ramishetti
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Nuphar Veiga
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Dinorah Friedmann-Morvinski
- Sagol School of Neuroscience, Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Zvi R Cohen
- Department of Neurosurgery, Sheba Medical Center, Ramat-Gan, and Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Dan Peer
- Laboratory of Precision Nanomedicine, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, Israel.
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
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10
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Alharbi AS, Garcin AJ, Lennox KA, Pradeloux S, Wong C, Straub S, Valentin R, Pépin G, Li HM, Nold MF, Nold-Petry CA, Behlke MA, Gantier MP. Rational design of antisense oligonucleotides modulating the activity of TLR7/8 agonists. Nucleic Acids Res 2020; 48:7052-7065. [PMID: 32544249 PMCID: PMC7367172 DOI: 10.1093/nar/gkaa523] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Oligonucleotide-based therapeutics have become a reality, and are set to transform management of many diseases. Nevertheless, the modulatory activities of these molecules on immune responses remain incompletely defined. Here, we show that gene targeting 2′-O-methyl (2′OMe) gapmer antisense oligonucleotides (ASOs) can have opposing activities on Toll-Like Receptors 7 and 8 (TLR7/8), leading to divergent suppression of TLR7 and activation of TLR8, in a sequence-dependent manner. Surprisingly, TLR8 potentiation by the gapmer ASOs was blunted by locked nucleic acid (LNA) and 2′-methoxyethyl (2′MOE) modifications. Through a screen of 192 2′OMe ASOs and sequence mutants, we characterized the structural and sequence determinants of these activities. Importantly, we identified core motifs preventing the immunosuppressive activities of 2′OMe ASOs on TLR7. Based on these observations, we designed oligonucleotides strongly potentiating TLR8 sensing of Resiquimod, which preserve TLR7 function, and promote strong activation of phagocytes and immune cells. We also provide proof-of-principle data that gene-targeting ASOs can be selected to synergize with TLR8 agonists currently under investigation as immunotherapies, and show that rational ASO selection can be used to prevent unintended immune suppression of TLR7. Taken together, our work characterizes the immumodulatory effects of ASOs to advance their therapeutic development.
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Affiliation(s)
- Arwaf S Alharbi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia.,The Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Taif University, Turabah 29179, Saudia Arabia
| | - Aurélie J Garcin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Kim A Lennox
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Solène Pradeloux
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Christophe Wong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Sarah Straub
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia.,Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn 53127, Germany
| | - Roxane Valentin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Hong-Mei Li
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Marcel F Nold
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Clayton, Victoria 3168, Australia
| | - Claudia A Nold-Petry
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria 3168, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
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11
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Reichenstein I, Eitan C, Diaz-Garcia S, Haim G, Magen I, Siany A, Hoye ML, Rivkin N, Olender T, Toth B, Ravid R, Mandelbaum AD, Yanowski E, Liang J, Rymer JK, Levy R, Beck G, Ainbinder E, Farhan SMK, Lennox KA, Bode NM, Behlke MA, Möller T, Saxena S, Moreno CAM, Costaguta G, van Eijk KR, Phatnani H, Al-Chalabi A, Başak AN, van den Berg LH, Hardiman O, Landers JE, Mora JS, Morrison KE, Shaw PJ, Veldink JH, Pfaff SL, Yizhar O, Gross C, Brown RH, Ravits JM, Harms MB, Miller TM, Hornstein E. Human genetics and neuropathology suggest a link between miR-218 and amyotrophic lateral sclerosis pathophysiology. Sci Transl Med 2020; 11:11/523/eaav5264. [PMID: 31852800 DOI: 10.1126/scitranslmed.aav5264] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 07/11/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022]
Abstract
Motor neuron-specific microRNA-218 (miR-218) has recently received attention because of its roles in mouse development. However, miR-218 relevance to human motor neuron disease was not yet explored. Here, we demonstrate by neuropathology that miR-218 is abundant in healthy human motor neurons. However, in amyotrophic lateral sclerosis (ALS) motor neurons, miR-218 is down-regulated and its mRNA targets are reciprocally up-regulated (derepressed). We further identify the potassium channel Kv10.1 as a new miR-218 direct target that controls neuronal activity. In addition, we screened thousands of ALS genomes and identified six rare variants in the human miR-218-2 sequence. miR-218 gene variants fail to regulate neuron activity, suggesting the importance of this small endogenous RNA for neuronal robustness. The underlying mechanisms involve inhibition of miR-218 biogenesis and reduced processing by DICER. Therefore, miR-218 activity in motor neurons may be susceptible to failure in human ALS, suggesting that miR-218 may be a potential therapeutic target in motor neuron disease.
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Affiliation(s)
- Irit Reichenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.,Project MinE ALS Sequencing Consortium
| | | | - Guy Haim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Iddo Magen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aviad Siany
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mariah L Hoye
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Natali Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Beata Toth
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Revital Ravid
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amitai D Mandelbaum
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eran Yanowski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jing Liang
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeffrey K Rymer
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rivka Levy
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Beck
- Stem Cell Core and Advanced Cell Technologies Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Stem Cell Core and Advanced Cell Technologies Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kimberly A Lennox
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Nicole M Bode
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Thomas Möller
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Smita Saxena
- Department of Neurology, Inselspital University Hospital, University of Bern, Freiburgstrasse 16, CH-3010 Bern, Bern, Switzerland.,Department for BioMedical Research, University of Bern, Murtenstrasse 40, CH-3008 Bern, Switzerland
| | | | - Giancarlo Costaguta
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kristel R van Eijk
- Project MinE ALS Sequencing Consortium.,Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease (CGND) and New York Genome Center (NYGC) ALS Consortium, New York, NY 10013, USA
| | - Ammar Al-Chalabi
- Project MinE ALS Sequencing Consortium.,Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute, Department of Basic and Clinical Neuroscience, Department of Neurology, King's College London, London SE5 9RX, UK.,Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - A Nazli Başak
- Project MinE ALS Sequencing Consortium.,Koç University Translational Medicine Research Center, NDAL, Istanbul 34010, Turkey
| | - Leonard H van den Berg
- Project MinE ALS Sequencing Consortium.,Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Orla Hardiman
- Project MinE ALS Sequencing Consortium.,Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Republic of Ireland.,Department of Neurology, Beaumont Hospital, Dublin 2, Republic of Ireland
| | - John E Landers
- Project MinE ALS Sequencing Consortium.,Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jesus S Mora
- Project MinE ALS Sequencing Consortium.,ALS Unit, Hospital San Rafael, Madrid 28016, Spain
| | - Karen E Morrison
- Project MinE ALS Sequencing Consortium.,Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Pamela J Shaw
- Project MinE ALS Sequencing Consortium.,Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Jan H Veldink
- Project MinE ALS Sequencing Consortium.,Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Samuel L Pfaff
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Christina Gross
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - John M Ravits
- Department of Neurosciences, UC San Diego, La Jolla, CA 92093, USA
| | - Matthew B Harms
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Timothy M Miller
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel. .,Project MinE ALS Sequencing Consortium
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12
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Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes. Nucleic Acids Res 2020; 48:5037-5053. [PMID: 32315032 PMCID: PMC7229833 DOI: 10.1093/nar/gkaa231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/06/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR RNA-guided endonucleases (RGEs) cut or direct activities to specific genomic loci, yet each has off-target activities that are often unpredictable. We developed a pair of simple in vitro assays to systematically measure the DNA-binding specificity (Spec-seq), catalytic activity specificity (SEAM-seq) and cleavage efficiency of RGEs. By separately quantifying binding and cleavage specificity, Spec/SEAM-seq provides detailed mechanistic insight into off-target activity. Feature-based models generated from Spec/SEAM-seq data for SpCas9 were consistent with previous reports of its in vitro and in vivo specificity, validating the approach. Spec/SEAM-seq is also useful for profiling less-well characterized RGEs. Application to an engineered SpCas9, HiFi-SpCas9, indicated that its enhanced target discrimination can be attributed to cleavage rather than binding specificity. The ortholog ScCas9, on the other hand, derives specificity from binding to an extended PAM. The decreased off-target activity of AsCas12a (Cpf1) appears to be primarily driven by DNA-binding specificity. Finally, we performed the first characterization of CasX specificity, revealing an all-or-nothing mechanism where mismatches can be bound, but not cleaved. Together, these applications establish Spec/SEAM-seq as an accessible method to rapidly and reliably evaluate the specificity of RGEs, Cas::gRNA pairs, and gain insight into the mechanism and thermodynamics of target discrimination.
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Affiliation(s)
- Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA.,Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - H Tomas Rube
- Department of Bioengineering, University of California, Merced, New York, NY 10027, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA
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13
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Shapiro J, Iancu O, Jacobi AM, McNeill MS, Turk R, Rettig GR, Amit I, Tovin-Recht A, Yakhini Z, Behlke MA, Hendel A. Increasing CRISPR Efficiency and Measuring Its Specificity in HSPCs Using a Clinically Relevant System. Mol Ther Methods Clin Dev 2020; 17:1097-1107. [PMID: 32478125 PMCID: PMC7251314 DOI: 10.1016/j.omtm.2020.04.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/29/2020] [Indexed: 12/26/2022]
Abstract
Genome editing of human cluster of differentiation 34+ (CD34+) hematopoietic stem and progenitor cells (HSPCs) holds great therapeutic potential. This study aimed to optimize on-target, ex vivo genome editing using the CRISPR-Cas9 system in CD34+ HSPCs and to create a clear workflow for precise identification of off-target effects. Modified synthetic guide RNAs (gRNAs), either 2-part gRNA or single-guide RNA (sgRNA), were delivered to CD34+ HSPCs as part of ribonucleoprotein (RNP) complexes, targeting therapeutically relevant genes. The addition of an Alt-R electroporation enhancer (EE), a short, single-stranded oligodeoxynucleotide (ssODN), significantly increased editing efficiency in CD34+ HSPCs. Notably, similar editing improvement was observed when excess gRNA over Cas9 protein was used, providing a DNA-free alternative suitable for therapeutic applications. Furthermore, we demonstrated that sgRNA may be preferable over 2-part gRNA in a locus-specific manner. Finally, we present a clear experimental framework suitable for the unbiased identification of bona fide off-target sites by Genome-Wide, Unbiased Identification of Double-Strand Breaks (DSBs) Enabled by Sequencing (GUIDE-seq), as well as subsequent editing quantification in CD34+ HSPCs using rhAmpSeq. These findings may facilitate the implementation of genome editing in CD34+ HSPCs for research and therapy and can be adapted for other hematopoietic cells.
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Affiliation(s)
- Jenny Shapiro
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Ortal Iancu
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | | | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | - Ido Amit
- Department of Computer Science, Interdisciplinary Center, Herzliya 4610101, Israel
| | - Adi Tovin-Recht
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Zohar Yakhini
- Department of Computer Science, Interdisciplinary Center, Herzliya 4610101, Israel.,Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Mark A Behlke
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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14
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Li W, Chan C, Zeng C, Turk R, Behlke MA, Cheng X, Dong Y. Rational Design of Small Molecules to Enhance Genome Editing Efficiency by Selectively Targeting Distinct Functional States of CRISPR-Cas12a. Bioconjug Chem 2020; 31:542-546. [PMID: 32119776 DOI: 10.1021/acs.bioconjchem.0c00062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a, a type-V CRISPR-Cas endonuclease, is an effective genome editing platform. To improve the gene editing efficiency of Cas12a, we rationally designed small molecule enhancers through a combined computational approach. First, we used extensive molecular dynamics (MD) simulations to explore the conformational landscape of Cas12a from Acidaminococcus (AsCas12a), revealing distinct conformational states that could be targeted by small molecules to modulate its genome editing function. We then identified 57 compounds that showed different binding behavior and stabilizing effects on these distinct conformational states using molecular docking. After experimental testing 6 of these 57 compounds, compound 1, quinazoline-2,4(1H,3H)-dione, was found particularly promising in enhancing the AsCas12a-mediated genome editing efficiency in human cells. Compound 1 was shown to act like a molecular "glue" at the interface between AsCas12a and crRNA near the 5'-handle region, thus specifically stabilizing the enzyme-crRNA complex. These results provide a new paradigm for future design of small molecules to modulate the genome editing of the CRISPR-Cas systems.
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Affiliation(s)
- Wenqing Li
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chun Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chunxi Zeng
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, Iowa 52241, United States
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa 52241, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center, Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Abstract
Chemically modified oligonucleotides (ONs) are routinely used in the laboratory to assess gene function, and clinical advances are rapidly progressing as continual efforts are being made to optimize ON efficacy. Over the years, RNA interference (RNAi) has become one of the main tools used to inhibit RNA expression across a wide variety of species. Efforts have been made to improve the exogenous delivery of the double-stranded RNA components to the endogenous intracellular RNAi machinery to direct efficacious degradation of a user-defined RNA target. More recently, synthetic RNA ONs are being used to mimic the bacterial-derived CRISPR/Cas system to direct specific editing of the mammalian genome. Both of these techniques rely on the use of various chemical modifications to the RNA phosphate backbone or sugar in specific positions throughout the ONs to improve the desired biological outcome. Relevant chemical modifications also include conjugated targeting ligands to assist ON delivery to specific cell types. Chemical modifications are most beneficial for therapeutically relevant ONs, as they serve to enhance target binding, increase drug longevity, facilitate cell-specific targeting, improve internalization into productive intracellular compartments, and mitigate both sequence-specific as well as immune-related off-target effects (OTEs). The knowledge gained from years of optimizing RNAi reagents and characterizing the biochemical and biophysical properties of each chemical modification will hopefully accelerate the CRISPR/Cas technology into the clinic, as well as further expand the use of RNAi to treat currently undruggable diseases. This review discusses the most commonly employed chemical modifications in RNAi reagents and CRISPR/Cas guide RNAs and provides an overview of select publications that have demonstrated success in improving ON efficacy and/or mitigating undesired OTEs.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA, USA.
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
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16
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Hoshijima K, Jurynec MJ, Klatt Shaw D, Jacobi AM, Behlke MA, Grunwald DJ. Highly Efficient CRISPR-Cas9-Based Methods for Generating Deletion Mutations and F0 Embryos that Lack Gene Function in Zebrafish. Dev Cell 2019; 51:645-657.e4. [PMID: 31708433 DOI: 10.1016/j.devcel.2019.10.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/13/2019] [Accepted: 10/03/2019] [Indexed: 11/24/2022]
Abstract
Inconsistent activity limits the use of CRISPR-Cas9 in zebrafish. We show supernumerary guanine nucleotides at the 5' ends of single guide RNAs (sgRNAs) account for diminished CRISPR-Cas9 activity in zebrafish embryos. Genomic sequences can be targeted consistently with extremely high efficiency using Cas9 ribonucleoproteins (RNPs) containing either a sgRNA molecule or a synthetic crRNA:tracrRNA duplex that perfectly matches the protospacer target site. Following injection of zebrafish eggs with such RNPs, virtually every copy of a targeted locus harbors an induced indel mutation. Loss of gene function is often complete, as F0 embryos closely resemble true null mutants without detectable non-specific effects. Mosaicism is sufficiently low in F0 embryos that cell non-autonomous gene functions can be probed effectively and redundant activities of genes can be uncovered when two genes are targeted simultaneously. Finally, heritable deletion mutations of at least 50 kbp can be readily induced using pairs of duplex guide RNPs targeted to a single chromosome.
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Affiliation(s)
- Kazuyuki Hoshijima
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael J Jurynec
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA; Department of Orthopaedics, University of Utah, Salt Lake City, UT 84112, USA
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Ashley M Jacobi
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - David Jonah Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
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17
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Veiga N, Goldsmith M, Diesendruck Y, Ramishetti S, Rosenblum D, Elinav E, Behlke MA, Benhar I, Peer D. Leukocyte-specific siRNA delivery revealing IRF8 as a potential anti-inflammatory target. J Control Release 2019; 313:33-41. [PMID: 31634546 DOI: 10.1016/j.jconrel.2019.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/27/2022]
Abstract
Interferon regulatory factor 8 (IRF8) protein plays a critical role in the differentiation, polarization, and activation of mononuclear phagocytic cells. In light of previous studies, we explored the therapeutic potential of IRF8 inhibition as immunomodulatory therapy for inflammatory bowel disease (IBD). To this end, we utilized siRNA-loaded lipid-based nanoparticles (siLNPs) and demonstrated a ∼90% reduction of IRF8 mRNA levels in vitro (PV < 0.0001), alongside a notable reduction in IRF8 protein. Moreover, silencing IRF8 ex vivo in splenocytes lead to a profound downregulation of IRF8 protein, followed by an immunomodulatory effect, as represented by a decrease in the secretion of TNFα, IL6 and IL12/IL23 (IL12p40) proinflammatory cytokines (PV = 0.0045, 0.0330, <0.0001, respectively). In order to silence IRF8 in vivo, selectively in inflammatory leukocytes, we used siLNPs that were coated with anti-Ly6C antibodies via our recently published ASSET targeting approach. Through this strategy, we have demonstrated a selective binding of the targeted-LNPs (T-LNPs) to Ly6C + inflammatory leukocytes. Finally, an immunomodulatory effect was demonstrated in vivo in an IBD mouse model with a profound decrease of TNFα, IL6, IL12/IL23, and IL1β pro-inflammatory cytokines (n = 5, PV < 0.0001, <0.0001, <0.0001, 0.02, respectively) and an improvement of colon-morphology as assessed by colon-length measurements and colonoscopy (PV < 0.0001). Overall, using antibody-targeted siLNPs, we showed a notable reduction of IRF8 mRNA and protein and demonstrated a targeted immunomodulation therapeutic effect ex vivo and in vivo, in the DSS colitis model. We claim that a selective silencing of IRF8 in inflammatory leukocytes (such as Ly6C+) may serve as a therapeutic approach for treating inflammatory disorders.
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Affiliation(s)
- Nuphar Veiga
- Laboratory of Precision NanoMedicine, Tel Aviv, 69978, Israel; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, 69978, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv, 69978, Israel; Cancer Biology Research Center, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Meir Goldsmith
- Laboratory of Precision NanoMedicine, Tel Aviv, 69978, Israel; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, 69978, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv, 69978, Israel; Cancer Biology Research Center, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yael Diesendruck
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel
| | - Srinivas Ramishetti
- Laboratory of Precision NanoMedicine, Tel Aviv, 69978, Israel; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, 69978, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv, 69978, Israel; Cancer Biology Research Center, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Daniel Rosenblum
- Laboratory of Precision NanoMedicine, Tel Aviv, 69978, Israel; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, 69978, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv, 69978, Israel; Cancer Biology Research Center, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Itai Benhar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel
| | - Dan Peer
- Laboratory of Precision NanoMedicine, Tel Aviv, 69978, Israel; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv, 69978, Israel; Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, 69978, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv, 69978, Israel; Cancer Biology Research Center, Tel Aviv University, Tel Aviv, 69978, Israel.
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18
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Abstract
Introduction of CRISPR/Cas9 methods (clustered regularly interspaced short palindromic repeats, CRISPR-associated protein 9) have led to a huge surge in the use of precision genome editing for research applications. Translational medical efforts are likewise rapidly progressing, and Phase I clinical trials using these techniques have already started. As with any new technology that is applied to medical therapeutics, risks must be carefully defined and steps taken to mitigate side effects wherever possible. Effective methods are now available that permit identification of off-target cleavage events, a major class of potential side effects seen in mammalian genome editing. Off-target prediction algorithms are improving and have utility, but are insufficient to use alone. Empiric methods to define the off-target profile must also be used. Once defined, the frequency of off-target cleavage can be minimized using methods that limit the duration of exposure of the genome to the active genome editing complex, for example, using the ribonucleoprotein (RNP) approach. In addition, Cas9 mutants have been developed that markedly reduce the rate of off-target cleavage compared to the wild-type enzyme. Use of these new tools should become standard practice for medical applications.
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19
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Lueck JD, Yoon JS, Perales-Puchalt A, Mackey AL, Infield DT, Behlke MA, Pope MR, Weiner DB, Skach WR, McCray PB, Ahern CA. Engineered transfer RNAs for suppression of premature termination codons. Nat Commun 2019; 10:822. [PMID: 30778053 PMCID: PMC6379413 DOI: 10.1038/s41467-019-08329-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/21/2018] [Indexed: 12/28/2022] Open
Abstract
Premature termination codons (PTCs) are responsible for 10–15% of all inherited disease. PTC suppression during translation offers a promising approach to treat a variety of genetic disorders, yet small molecules that promote PTC read-through have yielded mixed performance in clinical trials. Here we present a high-throughput, cell-based assay to identify anticodon engineered transfer RNAs (ACE-tRNA) which can effectively suppress in-frame PTCs and faithfully encode their cognate amino acid. In total, we identify ACE-tRNA with a high degree of suppression activity targeting the most common human disease-causing nonsense codons. Genome-wide transcriptome ribosome profiling of cells expressing ACE-tRNA at levels which repair PTC indicate that there are limited interactions with translation termination codons. These ACE-tRNAs display high suppression potency in mammalian cells, Xenopus oocytes and mice in vivo, producing PTC repair in multiple genes, including disease causing mutations within cystic fibrosis transmembrane conductance regulator (CFTR). Premature termination codon suppression therapy could be used to treat a range of genetic disorders. Here the authors present a high-throughput cell-based assay to identify anticodon engineered tRNAs with high suppression activity.
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Affiliation(s)
- John D Lueck
- Department of Physiology and Pharmacology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
| | - Jae Seok Yoon
- CFFT Lab, Cystic Fibrosis Foundation Therapeutics, Lexington, 02421, MA, USA
| | | | - Adam L Mackey
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, 52241, USA
| | - Marshall R Pope
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | | | - William R Skach
- CFFT Lab, Cystic Fibrosis Foundation Therapeutics, Lexington, 02421, MA, USA.,Cystic Fibrosis Foundation, Bethesda, 20814, MD, USA
| | - Paul B McCray
- Stead Family Department of Pediatrics, Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, 52242, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
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20
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Charlesworth CT, Deshpande PS, Dever DP, Camarena J, Lemgart VT, Cromer MK, Vakulskas CA, Collingwood MA, Zhang L, Bode NM, Behlke MA, Dejene B, Cieniewicz B, Romano R, Lesch BJ, Gomez-Ospina N, Mantri S, Pavel-Dinu M, Weinberg KI, Porteus MH. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat Med 2019; 25:249-254. [PMID: 30692695 PMCID: PMC7199589 DOI: 10.1038/s41591-018-0326-x] [Citation(s) in RCA: 517] [Impact Index Per Article: 103.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022]
Abstract
The CRISPR-Cas9 system is a powerful tool for genome editing, which allows the precise modification of specific DNA sequences. Many efforts are underway to use the CRISPR-Cas9 system to therapeutically correct human genetic diseases1-6. The most widely used orthologs of Cas9 are derived from Staphylococcus aureus and Streptococcus pyogenes5,7. Given that these two bacterial species infect the human population at high frequencies8,9, we hypothesized that humans may harbor preexisting adaptive immune responses to the Cas9 orthologs derived from these bacterial species, SaCas9 (S. aureus) and SpCas9 (S. pyogenes). By probing human serum for the presence of anti-Cas9 antibodies using an enzyme-linked immunosorbent assay, we detected antibodies against both SaCas9 and SpCas9 in 78% and 58% of donors, respectively. We also found anti-SaCas9 T cells in 78% and anti-SpCas9 T cells in 67% of donors, which demonstrates a high prevalence of antigen-specific T cells against both orthologs. We confirmed that these T cells were Cas9-specific by demonstrating a Cas9-specific cytokine response following isolation, expansion, and antigen restimulation. Together, these data demonstrate that there are preexisting humoral and cell-mediated adaptive immune responses to Cas9 in humans, a finding that should be taken into account as the CRISPR-Cas9 system moves toward clinical trials.
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Affiliation(s)
| | | | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | - Liyang Zhang
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Beruh Dejene
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Rosa Romano
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Sruthi Mantri
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
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21
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Järver P, Dondalska A, Poux C, Sandberg A, Bergenstråhle J, Sköld AE, Dereuddre-Bosquet N, Martinon F, Pålsson S, Zaghloul E, Brodin D, Sander B, Lennox KA, Behlke MA, El-Andaloussi S, Lehtiö J, Lundeberg J, LeGrand R, Spetz AL. Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis. Sci Rep 2018; 8:15841. [PMID: 30367171 PMCID: PMC6203749 DOI: 10.1038/s41598-018-33960-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/26/2018] [Indexed: 12/19/2022] Open
Abstract
Recognition of nucleic acids by endosomal Toll-like receptors (TLR) is essential to combat pathogens, but requires strict control to limit inflammatory responses. The mechanisms governing this tight regulation are unclear. We found that single-stranded oligonucleotides (ssON) inhibit endocytic pathways used by cargo destined for TLR3/4/7 signaling endosomes. Both ssDNA and ssRNA conferred the endocytic inhibition, it was concentration dependent, and required a certain ssON length. The ssON-mediated inhibition modulated signaling downstream of TLRs that localized within the affected endosomal pathway. We further show that injection of ssON dampens dsRNA-mediated inflammatory responses in the skin of non-human primates. These studies reveal a regulatory role for extracellular ssON in the endocytic uptake of TLR ligands and provide a mechanistic explanation of their immunomodulation. The identified ssON-mediated interference of endocytosis (SOMIE) is a regulatory process that temporarily dampens TLR3/4/7 signaling, thereby averting excessive immune responses.
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Affiliation(s)
- Peter Järver
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden.
| | - Aleksandra Dondalska
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Candice Poux
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - AnnSofi Sandberg
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joseph Bergenstråhle
- Department of Gene Technology, Science for Life Laboratory, Royal Institute of Technology, 171 65, Solna, Sweden
| | - Annette E Sköld
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Nathalie Dereuddre-Bosquet
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Fréderic Martinon
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Sandra Pålsson
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Eman Zaghloul
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - David Brodin
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - Kim A Lennox
- Integrated DNA Technologies Inc, Coralville, 52241, Iowa, USA
| | - Mark A Behlke
- Integrated DNA Technologies Inc, Coralville, 52241, Iowa, USA
| | - Samir El-Andaloussi
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.,Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3PT, Oxford, UK
| | - Janne Lehtiö
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, Science for Life Laboratory, Royal Institute of Technology, 171 65, Solna, Sweden
| | - Roger LeGrand
- CEA, -Université Paris Sud-Inserm U1184, IDMIT Department, Institut de Biologie Francois Jacob (IBFJ), 922 60, Fontenay-aux-Roses, France
| | - Anna-Lena Spetz
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden.
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22
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Vakulskas CA, Dever DP, Rettig GR, Turk R, Jacobi AM, Collingwood MA, Bode NM, McNeill MS, Yan S, Camarena J, Lee CM, Park SH, Wiebking V, Bak RO, Gomez-Ospina N, Pavel-Dinu M, Sun W, Bao G, Porteus MH, Behlke MA. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nat Med 2018; 24:1216-1224. [PMID: 30082871 PMCID: PMC6107069 DOI: 10.1038/s41591-018-0137-0] [Citation(s) in RCA: 461] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/25/2018] [Indexed: 01/17/2023]
Abstract
Translation of the CRISPR-Cas9 system to human therapeutics holds high promise. However, specificity remains a concern especially when modifying stem cell populations. We show that existing rationally engineered Cas9 high-fidelity variants have reduced on-target activity when using the therapeutically relevant ribonucleoprotein (RNP) delivery method. Therefore, we devised an unbiased bacterial screen to isolate variants that retain activity in the RNP format. Introduction of a single point mutation, p.R691A, in Cas9 (high-fidelity (HiFi) Cas9) retained the high on-target activity of Cas9 while reducing off-target editing. HiFi Cas9 induces robust AAV6-mediated gene targeting at five therapeutically relevant loci (HBB, IL2RG, CCR5, HEXB, and TRAC) in human CD34+ hematopoietic stem and progenitor cells (HSPCs) as well as primary T cells. We also show that HiFi Cas9 mediates high-level correction of the sickle cell disease (SCD)-causing p.E6V mutation in HSPCs derived from patients with SCD. We anticipate that HiFi Cas9 will have wide utility for both basic science and therapeutic genome-editing applications.
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Affiliation(s)
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Shuqi Yan
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Volker Wiebking
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark
| | | | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Wenchao Sun
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA.
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23
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Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. eLife 2018; 7:e35069. [PMID: 29638216 PMCID: PMC5947990 DOI: 10.7554/elife.35069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.
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Affiliation(s)
- Pooran Singh Dewari
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Benjamin Southgate
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Katrina Mccarten
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - German Monogarov
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Eoghan O'Duibhir
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Niall Quinn
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Ashley Tyrer
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Marie-Christin Leitner
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Colin Plumb
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Maria Kalantzaki
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Carla Blin
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rebecca Finch
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Raul Bardini Bressan
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Gillian Morrison
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc.CoralvilleUnited States
| | - Alex von Kriegsheim
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Simon Tomlinson
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jeroen Krijgsveld
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Steven M Pollard
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
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24
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Ferrand J, Croft NP, Pépin G, Diener KR, Wu D, Mangan NE, Pedersen J, Behlke MA, Hayball JD, Purcell AW, Ferrero RL, Gantier MP. The Use of CRISPR/Cas9 Gene Editing to Confirm Congenic Contaminations in Host-Pathogen Interaction Studies. Front Cell Infect Microbiol 2018; 8:87. [PMID: 29616197 PMCID: PMC5867302 DOI: 10.3389/fcimb.2018.00087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/02/2018] [Indexed: 01/08/2023] Open
Abstract
Murine models of Salmonella enterica serovar Typhimurium infection are one of the commonest tools to study host-pathogen interactions during bacterial infections. Critically, the outcome of S. Typhimurium infection is impacted by the genetic background of the mouse strain used, with macrophages from C57BL/6 and BALB/c mice lacking the capacity to control intracellular bacterial replication. For this reason, the use of congenic strains, which mix the genetic backgrounds of naturally protected mouse strains with those of susceptible strains, has the capacity to significantly alter results and interpretation of S. Typhimurium infection studies. Here, we describe how macrophage knockout cell lines generated by CRISPR/Cas9 gene editing can help determine the contribution of background contaminations in the phenotypes of primary macrophages from congenic mice, on the outcome of S. Typhimurium infection studies. Our own experience illustrates how the CRISPR/Cas9 technology can be used to complement pre-existing knockout models, and shows that there is great merit in performing concurrent studies with both genetic models, to exclude unanticipated side-effects on host-pathogen interactions.
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Affiliation(s)
- Jonathan Ferrand
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Kerrilyn R Diener
- Experimental Therapeutics Laboratory, School of Pharmacy and Medical Science, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia.,Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Di Wu
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Niamh E Mangan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - John Pedersen
- TissuPath Specialist Pathology, Mount Waverley, VIC, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, United States
| | - John D Hayball
- Experimental Therapeutics Laboratory, School of Pharmacy and Medical Science, Sansom Institute for Health Research, University of South Australia, Adelaide, SA, Australia.,Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Richard L Ferrero
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.,Department of Microbiology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
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25
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Schubert MS, Cedrone E, Neun B, Behlke MA, Dobrovolskaia MA. Chemical Modification of CRISPR gRNAs Eliminate type I Interferon Responses in Human Peripheral Blood Mononuclear Cells. J Cytokine Biol 2018; 3:121. [PMID: 30225466 PMCID: PMC6138052 DOI: 10.4172/2576-3881.1000121] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES CRISPR/Cas9 is currently the primary tool used for genome editing in mammalian cells. To cleave and alter genomic DNA, both the Cas9 nuclease and a guide RNA (gRNA) must be present in the nucleus. One preferred method of introducing these reagents is direct transfection of a recombinant Cas9 protein complexed with a synthetic gRNA as a ribonucleoprotein (RNP) complex. It is well established from prior work in RNA interference that synthetic RNAs can induce a type I interferon (IFN) response that can limit the application of such methods both in vitro and in vivo. While the immunological properties of short siRNAs are well understood, little is known about the immune recognition of longer CRISPR gRNAs. The objective of our in vitro study was to investigate how the composition of the gRNA influences its recognition by human immune cells. METHODS The study was performed in vitro in human peripheral blood mononuclear cells (PBMCs). The PBMCs from healthy donor volunteers were treated with gRNA for 24 h, and the levels of type I IFNs in culture supernatants were measured by a multiplex enzyme-linked immunosorbent chemiluminescent assay. Prior to the analysis in PBMCs, the physicochemical parameters and functionality of all nucleic acid constructs were confirmed by electrospray-ionization mass spectrometry and CRISPR/Cas9 gene editing assessment in HEK293-Cas9 cells, respectively. RESULTS We found that unmodified synthetic CRISPR gRNAs triggered a strong IFN response in PBMC cultures in vitro that could be prevented with chemical modification. Likewise, in vitro-transcribed single-guide RNAs (sgRNAs) also triggered a strong IFN response that could only be partially suppressed by phosphatase removal of the 5'-triphosphate group. However, the process by which the gRNA is prepared (i.e., chemically synthesized as a two-part crRNA:tracrRNA complex or in vitro-transcribed as an sgRNA) does not directly influence the immune response to an unmodified gRNA. When experiments were performed in the HEK293 cells, only in vitro-transcribed sgRNA containing 5'-triphosphate induced IFN secretion. CONCLUSION The results of our structure-activity relationship study, therefore, suggest that chemical modifications commonly used to reduce the immunostimulation of traditional RNA therapeutics can also be used as effective tools to eliminate undesirable IFN responses to gRNAs.
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Affiliation(s)
- Mollie S. Schubert
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barry Neun
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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26
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Nejad C, Pépin G, Behlke MA, Gantier MP. Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3'-MicroRNA Isoforms. Front Genet 2018; 9:11. [PMID: 29416548 PMCID: PMC5787544 DOI: 10.3389/fgene.2018.00011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/09/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA) detection by reverse transcription (RT) quantitative real-time PCR (RT-qPCR) is the most popular method currently used to measure miRNA expression. Although the majority of miRNA families are constituted of several 3′-end length variants (“isomiRs”), little attention has been paid to their differential detection by RT-qPCR. However, recent evidence indicates that 3′-end miRNA isoforms can exhibit 3′-length specific regulatory functions, underlining the need to develop strategies to differentiate 3′-isomiRs by RT-qPCR approaches. We demonstrate here that polyadenylation-based RT-qPCR strategies targeted to 20–21 nt isoforms amplify entire miRNA families, but that primers targeted to >22 nt isoforms were specific to >21 nt isoforms. Based on this observation, we developed a simple method to increase selectivity of polyadenylation-based RT-qPCR assays toward shorter isoforms, and demonstrate its capacity to help distinguish short RNAs from longer ones, using synthetic RNAs and biological samples with altered isomiR stoichiometry. Our approach can be adapted to many polyadenylation-based RT-qPCR technologies already exiting, providing a convenient way to distinguish long and short 3′-isomiRs.
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Affiliation(s)
- Charlotte Nejad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, United States
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
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27
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Abstract
MicroRNAs (miRNAs) are important modulators of gene expression. Synthetic anti-microRNA oligonucleotides (AMOs, or anti-miRs) are a form of steric-blocking antisense oligonucleotides (ASOs) that inhibit miRNA function through high-affinity binding and subsequent inactivation and/or degradation of the targeted miRNA. AMOs are a primary tool used to empirically determine the biological targets of a miRNA and can also be used therapeutically when overexpression of a miRNA contributes to a disease state. Chemical modification of synthetic AMOs enhance potency by protecting the oligonucleotide from nuclease degradation and by increasing binding affinity to the target miRNA. A new steric-blocking ASO modification strategy with favorable properties for use in AMOs was recently developed that combines use of high-affinity 2'-O-methyl RNA with terminally positioned non-nucleotide "ZEN" modifiers. This protocol describes use of ZEN AMOs in a dual-luciferase reporter assay as a simplified means to validate AMO performance or to quickly test putative miRNA binding sites in target sequences. This protocol also describes a method using Western blot analysis for quantifying the level of upregulation of proteins made from an mRNA that is thought to be under miRNA regulation, following inhibition of that miRNA by ZEN AMO treatment.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA.
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28
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Quadros RM, Miura H, Harms DW, Akatsuka H, Sato T, Aida T, Redder R, Richardson GP, Inagaki Y, Sakai D, Buckley SM, Seshacharyulu P, Batra SK, Behlke MA, Zeiner SA, Jacobi AM, Izu Y, Thoreson WB, Urness LD, Mansour SL, Ohtsuka M, Gurumurthy CB. Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol 2017; 18:92. [PMID: 28511701 PMCID: PMC5434640 DOI: 10.1186/s13059-017-1220-4] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/24/2017] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes. Transgenic mice generated by random genomic insertion approaches pose problems of unreliable expression, and thus there is a need for targeted-insertion models. Although CRISPR-based strategies were reported to create conditional and targeted-insertion alleles via one-step delivery of targeting components directly to zygotes, these strategies are quite inefficient. RESULTS Here we describe Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR), a targeting strategy in which long single-stranded DNA donors are injected with pre-assembled crRNA + tracrRNA + Cas9 ribonucleoprotein (ctRNP) complexes into mouse zygotes. We show for over a dozen loci that Easi-CRISPR generates correctly targeted conditional and insertion alleles in 8.5-100% of the resulting live offspring. CONCLUSIONS Easi-CRISPR solves the major problem of animal genome engineering, namely the inefficiency of targeted DNA cassette insertion. The approach is robust, succeeding for all tested loci. It is versatile, generating both conditional and targeted insertion alleles. Finally, it is highly efficient, as treating an average of only 50 zygotes is sufficient to produce a correctly targeted allele in up to 100% of live offspring. Thus, Easi-CRISPR offers a comprehensive means of building large-scale Cre-LoxP animal resources.
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MESH Headings
- Animals
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Founder Effect
- Gene Editing/methods
- Genes, Reporter
- Genetic Loci
- Integrases/genetics
- Integrases/metabolism
- Mice
- Mice, Transgenic/genetics
- Mice, Transgenic/growth & development
- Microinjections
- Mutagenesis, Insertional/methods
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Recombinational DNA Repair
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Zygote/growth & development
- Zygote/metabolism
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Affiliation(s)
- Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Hisako Akatsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Host Defense Mechanism, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Takehito Sato
- Department of Host Defense Mechanism, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Tomomi Aida
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan
- Laboratory of Recombinant Animals, MRI, TMDU, 2-3-10, 2-3-10, Surugadai, Kanda, Chiyoda, Tokyo, 101-0062, Japan
- Present address: McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ronald Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Guy P Richardson
- Sussex Neuroscience, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Yutaka Inagaki
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Regenerative Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Daisuke Sakai
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Orthopaedic Surgery, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Shannon M Buckley
- Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Sarah A Zeiner
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Ashley M Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA, 52241, USA
| | - Yayoi Izu
- Department of Animal Risk Management, Chiba Institute of Science, 3 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Wallace B Thoreson
- Truhlsen Eye Institute and Department of Ophthalmology & Visual Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lisa D Urness
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Suzanne L Mansour
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA.
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29
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Jacobi AM, Rettig GR, Turk R, Collingwood MA, Zeiner SA, Quadros RM, Harms DW, Bonthuis PJ, Gregg C, Ohtsuka M, Gurumurthy CB, Behlke MA. Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes. Methods 2017; 121-122:16-28. [PMID: 28351759 PMCID: PMC5761324 DOI: 10.1016/j.ymeth.2017.03.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/09/2017] [Accepted: 03/23/2017] [Indexed: 01/14/2023] Open
Abstract
Genome editing using the CRISPR/Cas9 system requires the presence of guide RNAs bound to the Cas9 endonuclease as a ribonucleoprotein (RNP) complex in cells, which cleaves the host cell genome at sites specified by the guide RNAs. New genetic material may be introduced during repair of the double-stranded break via homology dependent repair (HDR) if suitable DNA templates are delivered with the CRISPR components. Early methods used plasmid or viral vectors to make these components in the host cell, however newer approaches using recombinant Cas9 protein with synthetic guide RNAs introduced directly as an RNP complex into cells shows faster onset of action with fewer off-target effects. This approach also enables use of chemically modified synthetic guide RNAs that have improved nuclease stability and reduces the risk of triggering an innate immune response in the host cell. This article provides detailed methods for genome editing using the RNP approach with synthetic guide RNAs using lipofection or electroporation in mammalian cells or using microinjection in murine zygotes, with or without addition of a single-stranded HDR template DNA.
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Affiliation(s)
- Ashley M Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Sarah A Zeiner
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul J Bonthuis
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa 259-1193, Japan; Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193, Japan; The Institute of Medical Sciences, Tokai University, Kanagawa 259-1193, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA; Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA.
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30
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Flenker KS, Burghardt EL, Dutta N, Burns WJ, Grover JM, Kenkel EJ, Weaver TM, Mills J, Kim H, Huang L, Owczarzy R, Musselman CA, Behlke MA, Ford B, McNamara JO. Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity. Mol Ther 2017; 25:1353-1362. [PMID: 28391960 DOI: 10.1016/j.ymthe.2017.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022] Open
Abstract
Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, and food testing applications. The wide diversity of bacterial nucleases provides a rich source of enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective detection of bacterial species. With the exception of the use of micrococcal nuclease activity to detect Staphylococcus aureus, rapid methods that detect bacterial pathogens via their nuclease activities have not been developed. Here, we identify endonuclease I as a robust biomarker for E. coli and develop a rapid ultrasensitive assay that detects its activity. Comparison of nuclease activities of wild-type and nuclease-knockout E. coli clones revealed that endonuclease I is the predominant DNase in E. coli lysates. Endonuclease I is detectable by immunoblot and activity assays in uropathogenic E. coli strains. A rapid assay that detects endonuclease I activity in patient urine with an oligonucleotide probe exhibited substantially higher sensitivity for urinary tract infections than that reported for rapid urinalysis methods. The 3 hr turnaround time is much shorter than that of culture-based methods, thereby providing a means for expedited administration of appropriate antimicrobial therapy. We suggest this approach could address various unmet needs for rapid detection of E. coli.
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Affiliation(s)
- Katie S Flenker
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Elliot L Burghardt
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nirmal Dutta
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William J Burns
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Julia M Grover
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth J Kenkel
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler M Weaver
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - James Mills
- Department of Psychiatry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hyeon Kim
- University of Iowa Research Foundation, University of Iowa, Iowa City, IA 52242, USA
| | - Lingyan Huang
- Integrated DNA Technologies (IDT), Coralville, IA 52241, USA
| | | | - Catherine A Musselman
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Behlke
- Integrated DNA Technologies (IDT), Coralville, IA 52241, USA
| | - Bradley Ford
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - James O McNamara
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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31
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Ramachandran S, Osterhaus SR, Parekh KR, Jacobi AM, Behlke MA, McCray PB. SYVN1, NEDD8, and FBXO2 Proteins Regulate ΔF508 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Ubiquitin-mediated Proteasomal Degradation. J Biol Chem 2016; 291:25489-25504. [PMID: 27756846 DOI: 10.1074/jbc.m116.754283] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/07/2016] [Indexed: 11/06/2022] Open
Abstract
We previously reported that delivery of a microRNA-138 mimic or siRNA against SIN3A to cultured cystic fibrosis (ΔF508/ΔF508) airway epithelia partially restored ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR)-mediated cAMP-stimulated Cl- conductance. We hypothesized that dissecting this microRNA-138/SIN3A-regulated gene network would identify individual proteins contributing to the rescue of ΔF508-CFTR function. Among the genes in the network, we rigorously validated candidates using functional CFTR maturation and electrolyte transport assays in polarized airway epithelia. We found that depletion of the ubiquitin ligase SYVN1, the ubiquitin/proteasome system regulator NEDD8, or the F-box protein FBXO2 partially restored ΔF508-CFTR-mediated Cl- transport in primary cultures of human cystic fibrosis airway epithelia. Moreover, knockdown of SYVN1, NEDD8, or FBXO2 in combination with corrector compound 18 further potentiated rescue of ΔF508-CFTR-mediated Cl- conductance. This study provides new knowledge of the CFTR biosynthetic pathway. It suggests that SYVN1 and FBXO2 represent two distinct multiprotein complexes that may degrade ΔF508-CFTR in airway epithelia and identifies a new role for NEDD8 in regulating ΔF508-CFTR ubiquitination.
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Affiliation(s)
- Shyam Ramachandran
- From the Department of Pediatrics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 and
| | - Samantha R Osterhaus
- From the Department of Pediatrics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 and
| | - Kalpaj R Parekh
- From the Department of Pediatrics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 and
| | | | | | - Paul B McCray
- From the Department of Pediatrics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242 and
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Rocha CSJ, Lundin KE, Behlke MA, Zain R, El Andaloussi S, Smith CIE. Four Novel Splice-Switch Reporter Cell Lines: Distinct Impact of Oligonucleotide Chemistry and Delivery Vector on Biological Activity. Nucleic Acid Ther 2016; 26:381-391. [PMID: 27629437 DOI: 10.1089/nat.2016.0631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New advances in oligonucleotide (ON) chemistry emerge continuously, and over the last few years, several aspects of ON delivery have been improved. However, clear knowledge regarding how certain chemistries behave alone, or in combination with various delivery vectors, is limited. Moreover, characterization is frequently limited to a single reporter cell line and, when different cell types are studied, experiments are commonly not carried out under similar conditions, hampering comparative analysis. To address this, we have developed a small "tissue" library of new, stable, pLuc/705 splice-switching reporter cell lines (named HuH7_705, U-2 OS_705, C2C12_705, and Neuro-2a_705). Our data show that, indeed, the cell type used in activity screenings influences the efficiency of ONs of different chemistry (phosphorothioate with locked nucleic acid or 2'-O-methyl with or without N,N-diethyl-4-(4-nitronaphthalen-1-ylazo)-phenylamine). Likewise, the delivery method, Lipofectamine® 2000, PepFect14 nanoparticles, or "naked" uptake, also demonstrates cell-type-dependent outcomes. Taken together, these cell lines can potentially become useful tools for future in vitro evaluation of new nucleic acid-based oligomers as well as delivery compounds for splice-switching approaches and cell-specific therapies.
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Affiliation(s)
- Cristina S J Rocha
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Karin E Lundin
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
| | - Mark A Behlke
- 2 Integrated DNA Technologies, Inc. , Coralville, Iowa
| | - Rula Zain
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,3 Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital , Stockholm, Sweden
| | - Samir El Andaloussi
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden .,4 Department of Physiology, Anatomy and Genetics, University of Oxford , Oxford, United Kingdom
| | - C I Edvard Smith
- 1 Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital , Huddinge, Sweden
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Bégin-Lavallée V, Midavaine É, Dansereau MA, Tétreault P, Longpré JM, Jacobi AM, Rose SD, Behlke MA, Beaudet N, Sarret P. Functional inhibition of chemokine receptor CCR2 by dicer-substrate-siRNA prevents pain development. Mol Pain 2016; 12:12/0/1744806916653969. [PMID: 27306408 PMCID: PMC4956154 DOI: 10.1177/1744806916653969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/16/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that the C-C chemokine ligand 2 (CCL2, or monocyte chemoattractant protein 1) acts as a neuromodulator in the central nervous system through its binding to the C-C chemokine receptor 2 (CCR2). Notably, it is well established that the CCL2/CCR2 axis plays a key role in neuron-glia communication as well as in spinal nociceptive transmission. Gene silencing through RNA interference has recently emerged as a promising avenue in research and drug development, including therapeutic management of chronic pain. In the present study, we used 27-mer Dicer-substrate small interfering RNA (DsiRNA) targeting CCR2 and assessed their ability to reverse the nociceptive behaviors induced by spinal CCL2 injection or following intraplantar injection of complete Freund's adjuvant. RESULTS To this end, we first developed high-potency DsiRNAs designed to target different sequences distributed across the rat CCR2 (rCCR2) messenger RNA. For optimization, methyl groups were added to the two most potent DsiRNA candidates (Evader and M7 2'-O-methyl modified duplexes) in order to improve in vivo duplex stability and to reduce potential immunostimulatory activity. Our results demonstrated that all modified candidates formulated with the cell-penetrating peptide reagent Transductin showed strong RNAi activity following intrathecal delivery, exhibiting >50% rCCR2 knockdown in lumbar dorsal root ganglia. Accordingly, we found that these DsiRNA duplexes were able to reduce spinal microglia activation and were effective at blocking CCL2-induced mechanical hypersensitivity. Along with similar reductions of rCCR2 messenger RNA, both sequences and methylation patterns were similarly effective in inhibiting the CCL2 nociceptive action for the whole seven days testing period, compared to mismatch DsiRNA. DsiRNAs against CCR2 also reversed the hypernociceptive responses observed in the complete Freund's adjuvant-induced inflammatory chronic pain model. CONCLUSION Altogether, these results validate CCR2 as a an appropriate molecular target for pain control and demonstrate that RNAi-based gene therapy represent an highly specific alternative to classical pharmacological approaches to treat central pathologies such as chronic pain.
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Affiliation(s)
- Valérie Bégin-Lavallée
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Philippe Sarret, Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, Canada.
| | - Élora Midavaine
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Marc-André Dansereau
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pascal Tétreault
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Michel Longpré
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Scott D Rose
- Integrated DNA Technologies Inc, Coralville, IA, USA
| | - Mark A Behlke
- Integrated DNA Technologies Inc, Coralville, IA, USA
| | - Nicolas Beaudet
- Department of Anesthesiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Sarret
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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Zhao D, Yang Y, Qu N, Chen M, Ma Z, Krueger CJ, Behlke MA, Chen AK. Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons. Biomaterials 2016; 100:172-83. [PMID: 27261815 DOI: 10.1016/j.biomaterials.2016.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Molecular Beacons (MBs) composed of 2'-O-methyl RNA (2Me) and phosphorothioate (PS) linkages throughout the backbone (2Me/PSFULL MBs) have enabled long-term imaging of RNA in living cells, but excess PS modification can induce nonspecific binding, causing false-positive signals. In this study, we evaluate the intracellular stability of MBs composed of 2Me with various PS modifications, and found that false-positive signals could be reduced to marginal levels when the MBs possess a fully PS-modified loop domain and a phosphodiester stem (2Me/PSLOOP MB). Additionally, 2Me/PSLOOP MBs exhibited uncompromised hybridization kinetics, prolonged functionality and >88% detection accuracy for single RNA transcripts, and could do so without interfering with gene expression or cell growth. Finally, 2Me/PSLOOP MBs could image the dynamics of single mRNA transcripts in the nucleus and the cytoplasm simultaneously, regardless of whether the MBs targeted the 5'- or the 3'-UTR. Together, these findings demonstrate the effectiveness of loop-domain PS modification in reducing nonspecific signals and the potential for sensitive and accurate imaging of individual RNAs at the single-molecule level. With the growing interest in the role of RNA localization and dynamics in health and disease, 2Me/PSLOOP MBs could enable new discoveries in RNA research.
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Affiliation(s)
- Dan Zhao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Na Qu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, 52241, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
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35
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Pépin G, Ferrand J, Höning K, Jayasekara WSN, Cain JE, Behlke MA, Gough DJ, G Williams BR, Hornung V, Gantier MP. Cre-dependent DNA recombination activates a STING-dependent innate immune response. Nucleic Acids Res 2016; 44:5356-64. [PMID: 27166376 PMCID: PMC4914124 DOI: 10.1093/nar/gkw405] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023] Open
Abstract
Gene-recombinase technologies, such as Cre/loxP-mediated DNA recombination, are important tools in the study of gene function, but have potential side effects due to damaging activity on DNA. Here we show that DNA recombination by Cre instigates a robust antiviral response in mammalian cells, independent of legitimate loxP recombination. This is due to the recruitment of the cytosolic DNA sensor STING, concurrent with Cre-dependent DNA damage and the accumulation of cytoplasmic DNA. Importantly, we establish a direct interplay between this antiviral response and cell–cell interactions, indicating that low cell densities in vitro could be useful to help mitigate these effects of Cre. Taking into account the wide range of interferon stimulated genes that may be induced by the STING pathway, these results have broad implications in fields such as immunology, cancer biology, metabolism and stem cell research. Further, this study sets a precedent in the field of gene-engineering, possibly applicable to other enzymatic-based genome editing technologies.
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Affiliation(s)
- Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Jonathan Ferrand
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Klara Höning
- Institute of Molecular Medicine, University Hospital University of Bonn, 53127 Bonn, Germany
| | - W Samantha N Jayasekara
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Jason E Cain
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Daniel J Gough
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Bryan R G Williams
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Veit Hornung
- Institute of Molecular Medicine, University Hospital University of Bonn, 53127 Bonn, Germany Gene Centre and Department of Biochemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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Lennox KA, Behlke MA. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res 2015; 44:863-77. [PMID: 26578588 PMCID: PMC4737147 DOI: 10.1093/nar/gkv1206] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammalian cells. Some have important functions and their dysregulation can contribute to a variety of disease states. However, most lncRNAs have not been functionally characterized. Complicating their study, lncRNAs have widely varying subcellular distributions: some reside predominantly in the nucleus, the cytoplasm or in both compartments. One method to query function is to suppress expression and examine the resulting phenotype. Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and RNAi-based gene-knockdown methods vary in efficacy between different cellular compartments. It is not known if this affects their ability to suppress lncRNAs. To address whether localization of the lncRNA influences susceptibility to degradation by either ASOs or RNAi, nuclear lncRNAs (MALAT1 and NEAT1), cytoplasmic lncRNAs (DANCR and OIP5-AS1) and dual-localized lncRNAs (TUG1, CasC7 and HOTAIR) were compared for knockdown efficiency. We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. A mixed-modality approach combining ASOs and RNAi reagents improved knockdown efficacy, particularly for those lncRNAs that localize to both nuclear and cytoplasmic compartments.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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37
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Pauli A, Montague TG, Lennox KA, Behlke MA, Schier AF. Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One 2015; 10:e0139504. [PMID: 26436892 PMCID: PMC4593562 DOI: 10.1371/journal.pone.0139504] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/12/2015] [Indexed: 01/04/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are synthetic, single-strand RNA-DNA hybrids that induce catalytic degradation of complementary cellular RNAs via RNase H. ASOs are widely used as gene knockdown reagents in tissue culture and in Xenopus and mouse model systems. To test their effectiveness in zebrafish, we targeted 20 developmental genes and compared the morphological changes with mutant and morpholino (MO)-induced phenotypes. ASO-mediated transcript knockdown reproduced the published loss-of-function phenotypes for oep, chordin, dnd, ctnnb2, bmp7a, alk8, smad2 and smad5 in a dosage-sensitive manner. ASOs knocked down both maternal and zygotic transcripts, as well as the long noncoding RNA (lncRNA) MALAT1. ASOs were only effective within a narrow concentration range and were toxic at higher concentrations. Despite this drawback, quantitation of knockdown efficiency and the ability to degrade lncRNAs make ASOs a useful knockdown reagent in zebrafish.
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Affiliation(s)
- Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Masschusetts, United States of America
- * E-mail: (AP); (AFS)
| | - Tessa G. Montague
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Masschusetts, United States of America
| | - Kim A. Lennox
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Alexander F. Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Masschusetts, United States of America
- * E-mail: (AP); (AFS)
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38
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Khan SM, Min A, Gora S, Houranieh GM, Campden R, Robitaille M, Trieu P, Pétrin D, Jacobi AM, Behlke MA, Angers S, Hébert TE. Gβ 4 γ 1 as a modulator of M3 muscarinic receptor signalling and novel roles of Gβ 1 subunits in the modulation of cellular signalling. Cell Signal 2015; 27:1597-608. [DOI: 10.1016/j.cellsig.2015.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/01/2023]
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39
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Sarvestani ST, Stunden HJ, Behlke MA, Forster SC, McCoy CE, Tate MD, Ferrand J, Lennox KA, Latz E, Williams BRG, Gantier MP. Sequence-dependent off-target inhibition of TLR7/8 sensing by synthetic microRNA inhibitors. Nucleic Acids Res 2014; 43:1177-88. [PMID: 25539920 PMCID: PMC4333393 DOI: 10.1093/nar/gku1343] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immunostimulatory RNA, independent of their miRNA-targeting function. Through a screen of 29 AMOs targeting common miRNAs, we found a subset of sequences highly inhibitory to TLR7 sensing in mouse macrophages. Interspecies conservation of this inhibitory activity was confirmed on TLR7/8 activity in human peripheral blood mononuclear cells. Significantly, we identified a core motif governing the inhibitory activity of these AMOs, which is present in more than 50 AMOs targeted to human miRNAs in miRBaseV20. DNA/locked nucleic acids (LNA) AMOs synthesized with a phosphorothioate backbone also inhibited TLR7 sensing in a sequence-dependent manner, demonstrating that the off-target effects of AMOs are not restricted to 2'OMe modification. Taken together, our work establishes the potential for off-target effects of AMOs on TLR7/8 function, which should be taken into account in their therapeutic development and in vivo application.
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Affiliation(s)
- Soroush T Sarvestani
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - H James Stunden
- Institute of Innate Immunity, Biomedical Center, University Hospitals Bonn, Bonn 53127, Germany
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Claire E McCoy
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Michelle D Tate
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Jonathan Ferrand
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Kim A Lennox
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Eicke Latz
- Institute of Innate Immunity, Biomedical Center, University Hospitals Bonn, Bonn 53127, Germany Division of Infectious Diseases & Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA Deutsches Zentrum für Neurodegenerative Erkrankungen, Bonn 53127, Germany
| | - Bryan R G Williams
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Michael P Gantier
- Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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Bestas B, Moreno PMD, Blomberg KEM, Mohammad DK, Saleh AF, Sutlu T, Nordin JZ, Guterstam P, Gustafsson MO, Kharazi S, Piątosa B, Roberts TC, Behlke MA, Wood MJA, Gait MJ, Lundin KE, El Andaloussi S, Månsson R, Berglöf A, Wengel J, Smith CIE. Splice-correcting oligonucleotides restore BTK function in X-linked agammaglobulinemia model. J Clin Invest 2014; 124:4067-81. [PMID: 25105368 DOI: 10.1172/jci76175] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/03/2014] [Indexed: 11/17/2022] Open
Abstract
X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency that results from mutations within the gene encoding Bruton's tyrosine kinase (BTK). Many XLA-associated mutations affect splicing of BTK pre-mRNA and severely impair B cell development. Here, we assessed the potential of antisense, splice-correcting oligonucleotides (SCOs) targeting mutated BTK transcripts for treating XLA. Both the SCO structural design and chemical properties were optimized using 2'-O-methyl, locked nucleic acid, or phosphorodiamidate morpholino backbones. In order to have access to an animal model of XLA, we engineered a transgenic mouse that harbors a BAC with an authentic, mutated, splice-defective human BTK gene. BTK transgenic mice were bred onto a Btk knockout background to avoid interference of the orthologous mouse protein. Using this model, we determined that BTK-specific SCOs are able to correct aberrantly spliced BTK in B lymphocytes, including pro-B cells. Correction of BTK mRNA restored expression of functional protein, as shown both by enhanced lymphocyte survival and reestablished BTK activation upon B cell receptor stimulation. Furthermore, SCO treatment corrected splicing and restored BTK expression in primary cells from patients with XLA. Together, our data demonstrate that SCOs can restore BTK function and that BTK-targeting SCOs have potential as personalized medicine in patients with XLA.
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Song Y, Zhang X, Huang L, Behlke MA, Tsourkas A. Real-time imaging of single engineered RNA transcripts in living cells using ratiometric bimolecular beacons. J Vis Exp 2014:e51544. [PMID: 25146531 DOI: 10.3791/51544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3'-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of Pennsylvania
| | - Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania
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Ramachandran S, Karp PH, Osterhaus SR, Jiang P, Wohlford-Lenane C, Lennox KA, Jacobi AM, Praekh K, Rose SD, Behlke MA, Xing Y, Welsh MJ, McCray PB. Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs. Am J Respir Cell Mol Biol 2014; 49:544-51. [PMID: 23646886 DOI: 10.1165/rcmb.2012-0430oc] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are increasingly recognized as important posttranscriptional regulators of gene expression, and changes in their actions can contribute to disease states. Little is understood regarding miRNA functions in the airway epithelium under normal or diseased conditions. We profiled miRNA expression in well-differentiated primary cultures of human cystic fibrosis (CF) and non-CF airway epithelia, and discovered that miR-509-3p and miR-494 concentrations were increased in CF epithelia. Human non-CF airway epithelia, transfected with the mimics of miR-509-3p or miR-494, showed decreased cystic fibrosis transmembrane conductance regulator (CFTR) expression, whereas their respective anti-miRs exerted the opposite effect. Interestingly, the two miRNAs acted cooperatively in regulating CFTR expression. Upon infecting non-CF airway epithelial cells with Staphylococcus aureus, or upon stimulating them with the proinflammatory cytokines TNF-α or IL-1β, we observed an increased expression of both miRNAs and a concurrent decrease in CFTR expression and function, suggesting that inflammatory mediators may regulate these miRNAs. Transfecting epithelia with anti-miRs for miR-509-3p and miR-494, or inhibiting NF-κB signaling before stimulating cells with TNFα or IL-1β, suppressed these responses, suggesting that the expression of both miRNAs was responsive to NF-κB signaling. Thus, miR-509-3p and miR-494 are dynamic regulators of CFTR abundance and function in normal, non-CF airway epithelia.
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Zhang X, Zajac AL, Huang L, Behlke MA, Tsourkas A. Imaging the directed transport of single engineered RNA transcripts in real-time using ratiometric bimolecular beacons. PLoS One 2014; 9:e85813. [PMID: 24454933 PMCID: PMC3893274 DOI: 10.1371/journal.pone.0085813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022] Open
Abstract
The relationship between RNA expression and cell function can often be difficult to decipher due to the presence of both temporal and sub-cellular processing of RNA. These intricacies of RNA regulation can often be overlooked when only acquiring global measurements of RNA expression. This has led to development of several tools that allow for the real-time imaging of individual engineered RNA transcripts in living cells. Here, we describe a new technique that utilizes an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), to image RNA transcripts that were engineered to contain 96-tandem repeats of the RBMB target sequence in the 3′-untranslated region. Binding of RBMBs to the target RNA resulted in discrete bright fluorescent spots, representing individual transcripts, that could be imaged in real-time. Since RBMBs are a synthetic probe, the use of photostable, bright, and red-shifted fluorophores led to a high signal-to-background. RNA motion was readily characterized by both mean squared displacement and moment scaling spectrum analyses. These analyses revealed clear examples of directed, Brownian, and subdiffusive movements.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Allison L. Zajac
- Cell Biology and Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lingyan Huang
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Khairuddin N, Blake SJ, Firdaus F, Steptoe RJ, Behlke MA, Hertzog PJ, McMillan NAJ. In vivo comparison of local versus systemic delivery of immunostimulating siRNA in HPV-driven tumours. Immunol Cell Biol 2013; 92:156-63. [PMID: 24217808 DOI: 10.1038/icb.2013.75] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/16/2013] [Accepted: 10/16/2013] [Indexed: 12/12/2022]
Abstract
Small interfering RNAs (siRNAs) to inhibit oncogene expression and also to activate innate immune responses via Toll-like receptor (TLR) recognition have been shown to be beneficial as anti-cancer therapy in certain cancer models. In this study, we investigated the effects of local versus systemic delivery of such immune-stimulating Dicer-substrate siRNAs (IS-DsiRNAs) on a human papillomavirus (HPV)-driven tumour model. Localized siRNA delivery using intratumour injection of siRNA was able to increase siRNA delivery to the tumour compared with intravenous (IV) delivery and potently activated innate immune responses. However, IV injection remained the more effective delivery route for reducing tumour growth. Although IS-DsiRNAs activated innate immune cells and required interferon-α (IFNα) for full effect on tumour growth, we found that potent silencing siRNA acting independently of IFNα were overall more effective at inhibiting TC-1 tumour growth. Other published work utilising IS-siRNAs have been carried out on tumour models with low levels of major histocompatibility complex (MHC)-class 1, a target of natural killer cells that are potently activated by IS-siRNA. As TC-1 cells used in our study express high levels of MHC-class I, the addition of the immunostimulatory motifs may not be as beneficial in this particular tumour model. Our data suggest that selection of siRNA profile and delivery method based on tumour environment is crucial to developing siRNA-based therapies.
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Affiliation(s)
- Norliana Khairuddin
- 1] The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia [2] Immunotherapeutics Laboratory (ITL) and Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Stephen J Blake
- The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
| | - Farah Firdaus
- The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
| | - Raymond J Steptoe
- The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
| | - Mark A Behlke
- Integrated DNA Technologies (IDT), Coralville, IA, USA
| | - Paul J Hertzog
- Monash Institute of Medical Research (MIMR), Clayton, Victoria, Australia
| | - Nigel A J McMillan
- 1] The University of Queensland Diamantina Institute, Brisbane, Queensland, Australia [2] School of Medical Science and Griffith Health Institute, Griffith University, Southport, Queensland, Australia
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Dahan L, Huang L, Kedmi R, Behlke MA, Peer D. SNP detection in mRNA in living cells using allele specific FRET probes. PLoS One 2013; 8:e72389. [PMID: 24039756 PMCID: PMC3767744 DOI: 10.1371/journal.pone.0072389] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/09/2013] [Indexed: 12/24/2022] Open
Abstract
Live mRNA detection allows real time monitoring of specific transcripts and genetic alterations. The main challenge of live genetic detection is overcoming the high background generated by unbound probes and reaching high level of specificity with minimal off target effects. The use of Fluorescence Resonance Energy Transfer (FRET) probes allows differentiation between bound and unbound probes thus decreasing background. Probe specificity can be optimized by adjusting the length and through use of chemical modifications that alter binding affinity. Herein, we report the use of two oligonucleotide FRET probe system to detect a single nucleotide polymorphism (SNP) in murine Hras mRNA, which is associated with malignant transformations. The FRET oligonucleotides were modified with phosphorothioate (PS) bonds, 2′OMe RNA and LNA residues to enhance nuclease stability and improve SNP discrimination. Our results show that a point mutation in Hras can be detected in endogenous RNA of living cells. As determined by an Acceptor Photobleaching method, FRET levels were higher in cells transfected with perfect match FRET probes whereas a single mismatch showed decreased FRET signal. This approach promotes in vivo molecular imaging methods and could further be applied in cancer diagnosis and theranostic strategies.
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Affiliation(s)
- Liya Dahan
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lingyan Huang
- Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Ranit Kedmi
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Mark A. Behlke
- Integrated DNA Technologies, Coralville, Iowa, United States of America
- * E-mail: (MAB); (DP)
| | - Dan Peer
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (MAB); (DP)
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Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, Behlke MA, Tsourkas A. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Res 2013; 41:e152. [PMID: 23814183 PMCID: PMC3753654 DOI: 10.1093/nar/gkt561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recently, we developed an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), which generates a detectable fluorescent signal in living cells that express the target RNA. Here, we show that RBMBs can also be used to image single RNA transcripts in living cells, when the target RNA is engineered to contain as few as four hybridization sites. Moreover, comparison with single-molecule fluorescence in situ hybridization confirmed that RBMBs could be used to accurately quantify the number of RNA transcripts within individual cells. Measurements of gene expression could be acquired within 30 min and using a wide range of RBMB concentrations. The ability to acquire accurate measurements of RNA copy number in both HT-1080 cells and CHO cells also suggests that RBMBs can be used to image and quantify single RNA transcripts in a wide range of cell lines. Overall, these findings highlight the robustness and versatility of RBMBs as a tool for imaging RNA in live cells. We envision that the unique capabilities of RBMBs will open up new avenues for RNA research.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA, Department of Biology, University of Pennsylvania, 433 S. University Ave, 102 Leidy Laboratories, Philadelphia, PA 19104, USA and Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
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Tétreault P, Beaudet N, Perron A, Belleville K, René A, Cavelier F, Martinez J, Stroh T, Jacobi AM, Rose SD, Behlke MA, Sarret P. Spinal NTS2 receptor activation reverses signs of neuropathic pain. FASEB J 2013; 27:3741-52. [DOI: 10.1096/fj.12-225540] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pascal Tétreault
- Department of Physiology and BiophysicsFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuébecCanada
| | - Nicolas Beaudet
- Department of Physiology and BiophysicsFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuébecCanada
| | - Amélie Perron
- Institute for Integrated Cell‐Material SciencesKyoto UniversityKyotoJapan
| | - Karine Belleville
- Department of Physiology and BiophysicsFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuébecCanada
| | - Adeline René
- Institut des Biomolécules Max MousseronUnité Mixte de Recherche‐Centre National de la Recherche Scientifique (UMR‐CNRS)‐5247Universités Montpellier I and IIMontpellierFrance
| | - Florine Cavelier
- Institut des Biomolécules Max MousseronUnité Mixte de Recherche‐Centre National de la Recherche Scientifique (UMR‐CNRS)‐5247Universités Montpellier I and IIMontpellierFrance
| | - Jean Martinez
- Institut des Biomolécules Max MousseronUnité Mixte de Recherche‐Centre National de la Recherche Scientifique (UMR‐CNRS)‐5247Universités Montpellier I and IIMontpellierFrance
| | - Thomas Stroh
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill UniversityMontréalQuébecCanada
| | | | | | | | - Philippe Sarret
- Department of Physiology and BiophysicsFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQuébecCanada
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Ramachandran S, Krishnamurthy S, Jacobi AM, Wohlford-Lenane C, Behlke MA, Davidson BL, McCray PB. Efficient delivery of RNA interference oligonucleotides to polarized airway epithelia in vitro. Am J Physiol Lung Cell Mol Physiol 2013; 305:L23-32. [PMID: 23624792 DOI: 10.1152/ajplung.00426.2012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Polarized and pseudostratified primary airway epithelia present barriers that significantly reduce their transfection efficiency and the efficacy of RNA interference oligonucleotides. This creates an impediment in studies of the airway epithelium, diminishing the utility of loss-of-function as a research tool. Here we outline methods to introduce RNAi oligonucleotides into primary human and porcine airway epithelia grown at an air-liquid interface and difficult-to-transfect transformed epithelial cell lines grown on plastic. At the time of plating, we reverse transfect small-interfering RNA (siRNA), Dicer-substrate siRNA, or microRNA oligonucleotides into cells by use of lipid or peptide transfection reagents. Using this approach we achieve significant knockdown in vitro of hypoxanthine-guanine phosphoribosyltransferase, IL-8, and CFTR expression at the mRNA and protein levels in 1-3 days. We also attain significant reduction of secreted IL-8 in polarized primary pig airway epithelia 3 days posttransfection and inhibition of CFTR-mediated Cl⁻ conductance in polarized air-liquid interface cultures of human airway epithelia 2 wk posttransfection. These results highlight an efficient means to deliver RNA interference reagents to airway epithelial cells and achieve significant knockdown of target gene expression and function. The ability to reliably conduct loss-of-function assays in polarized primary airway epithelia offers benefits to research in studies of epithelial cell homeostasis, candidate gene function, gene-based therapeutics, microRNA biology, and targeting the replication of respiratory viruses.
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Abstract
The physiological barriers of the brain impair drug delivery for treatment of many neurological disorders. One delivery approach that has not been investigated for their ability to penetrate the brain is RNA-based aptamers. These molecules can impart delivery to peripheral tissues and circulating immune cells, where they act as ligand mimics or can be modified to carry payloads. We developed a library of aptamers and an in vivo evolution protocol to determine whether specific aptamers could be identified that would home to the brain after injection into the peripheral vasculature. Unlike biopanning with recombinant bacteriophage libraries, we found that the aptamer library employed here required more than 15 rounds of in vivo selection for convergence to specific sequences. The aptamer species identified through this approach bound to brain capillary endothelia and penetrated into the parenchyma. The methods described may find general utility for targeting various payloads to the brain.Molecular Therapy - Nucleic Acids (2013) 2, e67; doi:10.1038/mtna.2012.59; published online 8 January 2013.
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Affiliation(s)
- Congsheng Cheng
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
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50
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Walk RM, Elliott ST, Blanco FC, Snyder JA, Jacobi AM, Rose SD, Behlke MA, Salem AK, Vukmanovic S, Sandler AD. T-cell activation is enhanced by targeting IL-10 cytokine production in toll-like receptor-stimulated macrophages. Immunotargets Ther 2012; 1:13-23. [PMID: 27471682 PMCID: PMC4934151 DOI: 10.2147/itt.s32615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Toll-like receptor (TLR) agonists represent potentially useful cancer vaccine adjuvants in their ability to stimulate antigen-presenting cells (APCs) and subsequently amplify the cytotoxic T-cell response. The purpose of this study was to characterize APC responses to TLR activation and to determine the subsequent effect on lymphocyte activation. We exposed murine primary bone marrow-derived macrophages to increasing concentrations of agonists to TLRs 2, 3, 4, and 9. This resulted in a dose-dependent increase in production of not only tumor necrosis factor–alpha (TNF-α), a surrogate marker of the proinflammatory response, but also interleukin 10 (IL-10), a well-described inhibitory cytokine. Importantly, IL-10 secretion was not induced by low concentrations of TLR agonists that readily produced TNF-α. We subsequently stimulated lymphocytes with anti-CD3 antibody in the presence of media from macrophages activated with higher doses of TLR agonists and observed suppression of interferon gamma release. Use of both IL-10 knockout macrophages and IL-10 small-interfering RNA (siRNA) ablated this suppressive effect. Finally, IL-10 siRNA was successfully used to suppress CpG-induced IL-10 production in vivo. We conclude that TLR-mediated APC stimulation can induce a paradoxical inhibitory effect on T-cell activation mediated by IL-10.
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Affiliation(s)
- Ryan M Walk
- Department of Surgery, Walter Reed Army Medical Center, Washington, DC, USA; Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
| | - Steven T Elliott
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
| | - Felix C Blanco
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
| | - Jason A Snyder
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
| | | | - Scott D Rose
- Integrated DNA Technologies, Coralville, IA, USA
| | | | - Aliasger K Salem
- Division of Pharmaceutics, University of Iowa, Iowa City, IA, USA
| | - Stanislav Vukmanovic
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
| | - Anthony D Sandler
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC, USA
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