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Van Goubergen J, Peřina M, Handle F, Morales E, Kremer A, Schmidt O, Kristiansen G, Cronauer MV, Santer FR. Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression. Mol Oncol 2024. [PMID: 39258426 DOI: 10.1002/1878-0261.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/12/2024] Open
Abstract
In advanced prostate cancer (PC), in particular after acquisition of resistance to androgen receptor (AR) signaling inhibitors (ARSI), upregulation of AR splice variants compromises endocrine therapy efficiency. Androgen receptor splice variant-7 (ARV7) is clinically the most relevant and has a distinct 3' untranslated region (3'UTR) compared to the AR full-length variant, suggesting a unique post-transcriptional regulation. Here, we set out to evaluate the applicability of the ARV7 3'UTR as a therapy target. A common single nucleotide polymorphism, rs5918762, was found to affect the splicing rate and thus the expression of ARV7 in cellular models and patient specimens. Serine/arginine-rich splicing factor 9 (SRSF9) was found to bind to and increase the inclusion of the cryptic exon 3 of ARV7 during the splicing process in the alternative C allele of rs5918762. The dual specificity protein kinase CLK2 interferes with the activity of SRSF9 by regulating its expression. Inhibition of the Cdc2-like kinase (CLK) family by the small molecules cirtuvivint or lorecivivint results in the decreased expression of ARV7. Both inhibitors show potent anti-proliferative effects in enzalutamide-treated or -naive PC models. Thus, targeting aberrant alternative splicing at the 3'UTR of ARV7 by disturbing the CLK2/SRSF9 axis might be a valuable therapeutic approach in late stage, ARSI-resistant PC.
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Affiliation(s)
- Jasper Van Goubergen
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
| | - Miroslav Peřina
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Czech Republic
| | - Florian Handle
- Institute of Pathology, Neuropathology & Molecular Pathology, Medical University of Innsbruck, Austria
| | - Elisa Morales
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
| | - Anika Kremer
- Institute of Pathology, University Hospital Bonn, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | | | | | - Frédéric R Santer
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
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2
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Kulkarni A, Mohan V, Tang TT, Post L, Chan YC, Manning M, Thio N, Parker BL, Dawson MA, Rosenbluh J, Vissers JH, Harvey KF. Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription. EMBO Rep 2024; 25:3944-3969. [PMID: 39103676 PMCID: PMC11387499 DOI: 10.1038/s44319-024-00217-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024] Open
Abstract
The Hippo tumor suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs have been reported, with some entering clinical trials for different cancers with Hippo pathway deregulation, most notably, mesothelioma. Using genome-wide CRISPR/Cas9 screens we reveal that mutations in genes from the Hippo, MAPK, and JAK-STAT signaling pathways all modulate the response of mesothelioma cell lines to TEAD palmitoylation inhibitors. By exploring gene expression programs of mutant cells, we find that MAPK pathway hyperactivation confers resistance to TEAD inhibition by reinstating expression of a subset of YAP/TAZ target genes. Consistent with this, combined inhibition of TEAD and the MAPK kinase MEK, synergistically blocks proliferation of multiple mesothelioma and lung cancer cell lines and more potently reduces the growth of patient-derived lung cancer xenografts in vivo. Collectively, we reveal mechanisms by which cells can overcome small-molecule inhibition of TEAD palmitoylation and potential strategies to enhance the anti-tumor activity of emerging Hippo pathway targeted therapies.
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Affiliation(s)
- Aishwarya Kulkarni
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Varshini Mohan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Tracy T Tang
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Leonard Post
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Murray Manning
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Joseph Ha Vissers
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
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3
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Fieni C, Sorrentino C, Ciummo SL, Fontana A, Lotti LV, Scialis S, Calvo Garcia D, Caulo M, Di Carlo E. Immunoliposome-based targeted delivery of the CRISPR/Cas9gRNA-IL30 complex inhibits prostate cancer and prolongs survival. Exp Mol Med 2024; 56:2033-2051. [PMID: 39232121 PMCID: PMC11447253 DOI: 10.1038/s12276-024-01310-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 09/06/2024] Open
Abstract
The development of selective and nontoxic immunotherapy targeting prostate cancer (PC) is challenging. Interleukin (IL)30 plays immunoinhibitory and oncogenic roles in PC, and its tumor-specific suppression may have significant clinical implications. CRISPR/Cas9-mediated IL30 gene deletion in PC xenografts using anti-PSCA antibody-driven lipid nanocomplexes (Cas9gRNA-hIL30-PSCA NxPs) revealed significant genome editing efficiency and circulation stability without off-target effects or organ toxicity. Biweekly intravenous administration of Cas9gRNA-hIL30-PSCA NxPs to PC-bearing mice inhibited tumor growth and metastasis and improved survival. Mechanistically, Cas9gRNA-hIL30-PSCA NxPs suppressed ANGPTL 1/2/4, IL1β, CCL2, CXCL1/6, SERPINE1-F1, EFNB2, PLG, PF4, VEGFA, VEGFD, ANG, TGFβ1, EGF and HGF expression in human PC cells while upregulated CDH1, DKK3 and PTEN expression, leading to low proliferation and extensive ischemic necrosis. In the syngeneic PC model, IL30-targeting immunoliposomes downregulated NFKB1 expression and prevented intratumoral influx of CD11b+Gr-1+MDCs, Foxp3+Tregs, and NKp46+RORγt+ILC3, and prolonged host survival by inhibiting tumor progression. This study serves as a proof of principle that immunoliposome-based targeted delivery of Cas9gRNA-IL30 represent a potentially safe and effective strategy for PC treatment.
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Affiliation(s)
- Cristiano Fieni
- Department of Medicine and Sciences of Aging, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Carlo Sorrentino
- Department of Medicine and Sciences of Aging, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Stefania Livia Ciummo
- Department of Medicine and Sciences of Aging, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Antonella Fontana
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- UDA-TECHLAB Research Center, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | | | - Sofia Scialis
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Darien Calvo Garcia
- Department of Neuroscience, Imaging and Clinical Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Massimo Caulo
- Department of Neuroscience, Imaging and Clinical Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
- Institute for Advanced Biomedical Technologies (ITAB), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy
| | - Emma Di Carlo
- Department of Medicine and Sciences of Aging, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy.
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, Italy.
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Zamolo S, Zakharova E, Boursinhac L, Hollfelder F, Darbre T, Reymond JL. Peptide dendrimers transfecting CRISPR/Cas9 plasmid DNA: optimization and mechanism. RSC Chem Biol 2024; 5:891-900. [PMID: 39211473 PMCID: PMC11352961 DOI: 10.1039/d4cb00116h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Gene editing by CRISPR/Cas9 offers great therapeutic opportunities but requires delivering large plasmid DNA (pDNA) into cells, a task for which transfection reagents are better suited than viral vectors. Here we performed a structure-activity relationship study of Z22, a d-enantiomeric, arginine containing, lipidated peptide dendrimer developed for pDNA transfection of a CRISPR/Cas9 plasmid co-expressing GFP. While all dendrimer analogs tested bound pDNA strongly and internalized their cargo into cells, d-chirality proved essential for transfection by avoiding proteolysis of the dendrimer structure required for endosome escape and possibly crossing of the nuclear envelope. Furthermore, a cysteine residue at the core of Z22 proved non-essential and was removed to yield the more active analog Z34. This dendrimer shows >83% GFP transfection efficiency in HEK cells with no detrimental effect on cell viability and promotes functional CRISPR/Cas9 mediated gene editing. It is accessible by solid-phase peptide synthesis and therefore attractive for further development.
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Affiliation(s)
- Susanna Zamolo
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Elena Zakharova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Lise Boursinhac
- Department of Biochemistry, University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Tamis Darbre
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
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Ramgopal A, Braverman EL, Sun LK, Monlish D, Wittmann C, Kemp F, Qin M, Ramsey MJ, Cattley R, Hawse W, Byersdorfer CA. AMPK drives both glycolytic and oxidative metabolism in murine and human T cells during graft-versus-host disease. Blood Adv 2024; 8:4149-4162. [PMID: 38810258 PMCID: PMC11345362 DOI: 10.1182/bloodadvances.2023010740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/15/2024] [Accepted: 05/19/2024] [Indexed: 05/31/2024] Open
Abstract
ABSTRACT Allogeneic T cells reprogram their metabolism during acute graft-versus-host disease (GVHD) in a process involving the cellular energy sensor adenosine monophosphate (AMP)-activated protein kinase (AMPK). Deletion of AMPK in donor T cells limits GVHD but still preserves homeostatic reconstitution and graft-versus-leukemia effects. In the current studies, murine AMPK knock-out (KO) T cells decreased oxidative metabolism at early time points posttransplant and lacked a compensatory increase in glycolysis after inhibition of the electron transport chain. Immunoprecipitation using an antibody specific to phosphorylated targets of AMPK determined that AMPK modified interactions of several glycolytic enzymes including aldolase, enolase, pyruvate kinase M, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH), with enzyme assays confirming impaired aldolase and GAPDH activity in AMPK KO T cells. Importantly, these changes in glycolysis correlated with both an impaired ability of AMPK KO T cells to produce significant amounts of interferon gamma upon antigenic restimulation and a decrease in the total number of donor CD4 T cells recovered at later times posttransplant. Human T cells lacking AMPK gave similar results, with glycolytic compensation impaired both in vitro and after expansion in vivo. Xenogeneic GVHD results also mirrored those of the murine model, with reduced CD4/CD8 ratios and a significant improvement in disease severity. Together these data highlight a significant role for AMPK in controlling oxidative and glycolytic metabolism in both murine and human T cells and endorse further study of AMPK inhibition as a potential clinical target for future GVHD therapies.
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Affiliation(s)
- Archana Ramgopal
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Erica L. Braverman
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Lee-Kai Sun
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Darlene Monlish
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Christopher Wittmann
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Felicia Kemp
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Mengtao Qin
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
- School of Medicine, Tsinghua University, Beijing, China
| | - Manda J. Ramsey
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Richard Cattley
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - William Hawse
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Craig A. Byersdorfer
- Division of Blood and Marrow Transplant and Cellular Therapies, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh PA
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Allemailem KS, Almatroudi A, Rahmani AH, Alrumaihi F, Alradhi AE, Alsubaiyel AM, Algahtani M, Almousa RM, Mahzari A, Sindi AAA, Dobie G, Khan AA. Recent Updates of the CRISPR/Cas9 Genome Editing System: Novel Approaches to Regulate Its Spatiotemporal Control by Genetic and Physicochemical Strategies. Int J Nanomedicine 2024; 19:5335-5363. [PMID: 38859956 PMCID: PMC11164216 DOI: 10.2147/ijn.s455574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
The genome editing approach by clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) is a revolutionary advancement in genetic engineering. Owing to its simple design and powerful genome-editing capability, it offers a promising strategy for the treatment of different infectious, metabolic, and genetic diseases. The crystal structure of Streptococcus pyogenes Cas9 (SpCas9) in complex with sgRNA and its target DNA at 2.5 Å resolution reveals a groove accommodating sgRNA:DNA heteroduplex within a bilobate architecture with target recognition (REC) and nuclease (NUC) domains. The presence of a PAM is significantly required for target recognition, R-loop formation, and strand scission. Recently, the spatiotemporal control of CRISPR/Cas9 genome editing has been considerably improved by genetic, chemical, and physical regulatory strategies. The use of genetic modifiers anti-CRISPR proteins, cell-specific promoters, and histone acetyl transferases has uplifted the application of CRISPR/Cas9 as a future-generation genome editing tool. In addition, interventions by chemical control, small-molecule activators, oligonucleotide conjugates and bioresponsive delivery carriers have improved its application in other areas of biological fields. Furthermore, the intermediation of physical control by using heat-, light-, magnetism-, and ultrasound-responsive elements attached to this molecular tool has revolutionized genome editing further. These strategies significantly reduce CRISPR/Cas9's undesirable off-target effects. However, other undesirable effects still offer some challenges for comprehensive clinical translation using this genome-editing approach. In this review, we summarize recent advances in CRISPR/Cas9 structure, mechanistic action, and the role of small-molecule activators, inhibitors, promoters, and physical approaches. Finally, off-target measurement approaches, challenges, future prospects, and clinical applications are discussed.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arwa Essa Alradhi
- General Administration for Infectious Disease Control, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca 21955, Saudi Arabia
| | - Rand Mohammad Almousa
- Department of Education, General Directorate of Education, Qassim 52361, Saudi Arabia
| | - Ali Mahzari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Gasim Dobie
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Gizan 82911, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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Caetano BFR, Rocha VL, Rossini BC, Dos Santos LD, Elgui De Oliveira D. Epstein-Barr Virus miR-BARTs 7 and 9 modulate viral cycle, cell proliferation, and proteomic profiles in Burkitt lymphoma. Tumour Virus Res 2024; 17:200276. [PMID: 38159643 PMCID: PMC11000110 DOI: 10.1016/j.tvr.2023.200276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024] Open
Abstract
The Epstein-Barr Virus (EBV) encodes viral microRNAs (miRs) that have been implicated in the pathogenesis of nasopharyngeal and gastric carcinomas, yet their potential roles in lymphomas remain to be fully elucidated. This study evaluated the impact of CRISPR/Cas9-mediated knockdown of EBV miRs BART-7 and BART-9 in EBV-positive Burkitt lymphoma cells Akata. As anticipated, the Akata cells subjected to CRISPR/Cas9-mediated knockdown of either EBV BART-7 or BART-9 exhibited a significant reduction in the expression of these viral miRs compared to cells with wild-type (wt) EBV genomes. This outcome effectively validates the experimental model employed in this study. Knocking down either BART-7 or BART-9 resulted in a notable reduction in cell viability and proliferation rates, alongside an elevation in the expression of EBV lytic genes. Global proteomic analysis revealed that the knockdown of EBV BART-7 significantly decreased the expression of ubiquitin/proteasome proteins while concurrently increasing RNA binding proteins (RBPs). Conversely, BART-9 knockdown reduced proteins associated with oxidoreductase activity, particularly those involved in fatty acid metabolism. Our findings unveil previously undiscovered EBV miRs BARTs 7 and 9 roles in cellular pathways relevant to both viral biology and lymphomagenesis.
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Affiliation(s)
- Brunno Felipe Ramos Caetano
- São Paulo State University (UNESP), Department of Pathology, Botucatu Medical School, Av. Prof. Dr. Mário Rubens Guimarães Montenegro S/n, CEP 18618-687, Botucatu, São Paulo, Brazil; São Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Alameda Das Tecomarias S/n, CEP 18607-440, Botucatu, São Paulo, Brazil.
| | - Viviana Loureiro Rocha
- São Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Alameda Das Tecomarias S/n, CEP 18607-440, Botucatu, São Paulo, Brazil; São Paulo State University (UNESP), Institute of Biosciences (IBB). R. Prof. Dr. Antônio Celso Wagner Zanin, 250, CEP 18618-689, Botucatu, São Paulo, Brazil.
| | - Bruno Cesar Rossini
- São Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Alameda Das Tecomarias S/n, CEP 18607-440, Botucatu, São Paulo, Brazil.
| | - Lucilene Delazari Dos Santos
- São Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Alameda Das Tecomarias S/n, CEP 18607-440, Botucatu, São Paulo, Brazil.
| | - Deilson Elgui De Oliveira
- São Paulo State University (UNESP), Department of Pathology, Botucatu Medical School, Av. Prof. Dr. Mário Rubens Guimarães Montenegro S/n, CEP 18618-687, Botucatu, São Paulo, Brazil; São Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Alameda Das Tecomarias S/n, CEP 18607-440, Botucatu, São Paulo, Brazil.
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8
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Sharrar A, Meacham Z, Staples-Ager J, Arake de Tacca L, Rabuka D, Collingwood T, Schelle M. Viral Delivery of Compact CRISPR-Cas12f for Gene Editing Applications. CRISPR J 2024; 7:150-155. [PMID: 38695159 DOI: 10.1089/crispr.2024.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024] Open
Abstract
Treating human genetic conditions in vivo requires efficient delivery of the CRISPR gene editing machinery to the affected cells and organs. The gene editing field has seen clinical advances with ex vivo therapies and with in vivo delivery to the liver using lipid nanoparticle technology. Adeno-associated virus (AAV) serotypes have been discovered and engineered to deliver genetic material to nearly every organ in the body. However, the large size of most CRISPR-Cas systems limits packaging into the viral genome and reduces drug development flexibility and manufacturing efficiency. Here, we demonstrate efficient CRISPR gene editing using a miniature CRISPR-Cas12f system with expanded genome targeting packaged into AAV particles. We identified efficient guides for four therapeutic gene targets and encoded the guides and the Cas12f nuclease into a single AAV. We then demonstrate editing in multiple cell lines, patient fibroblasts, and primary hepatocytes. We then screened the cells for off-target editing, demonstrating the safety of the therapeutics. These results represent an important step in applying CRISPR editing to diverse genetic sequences and organs in the body.
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Affiliation(s)
| | | | | | | | - David Rabuka
- Acrigen Biosciences Inc., Berkeley, California, USA
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9
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Masani MYA, Norfaezah J, Bahariah B, Fizree MDPMAA, Sulaiman WNSW, Shaharuddin NA, Rasid OA, Parveez GKA. Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement. 3 Biotech 2024; 14:166. [PMID: 38817736 PMCID: PMC11133284 DOI: 10.1007/s13205-024-04010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.
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Affiliation(s)
- Mat Yunus Abdul Masani
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Jamaludin Norfaezah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Bohari Bahariah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Malaysia
| | - Omar Abdul Rasid
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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10
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Sharrar A, Arake de Tacca L, Meacham Z, Staples-Ager J, Collingwood T, Rabuka D, Schelle M. Discovery and engineering of AiEvo2, a novel Cas12a nuclease for human gene editing applications. J Biol Chem 2024; 300:105685. [PMID: 38272227 PMCID: PMC10877636 DOI: 10.1016/j.jbc.2024.105685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The precision of gene editing technology is critical to creating safe and effective therapies for treating human disease. While the programmability of CRISPR-Cas systems has allowed for rapid innovation of new gene editing techniques, the off-target activity of these enzymes has hampered clinical development for novel therapeutics. Here, we report the identification and characterization of a novel CRISPR-Cas12a enzyme from Acinetobacter indicus (AiCas12a). We engineer the nuclease (termed AiEvo2) for increased specificity, protospacer adjacent motif recognition, and efficacy on a variety of human clinical targets. AiEvo2 is highly precise and able to efficiently discriminate between normal and disease-causing alleles in Huntington's patient-derived cells by taking advantage of a single nucleotide polymorphism on the disease-associated allele. AiEvo2 efficiently edits several liver-associated target genes including PCSK9 and TTR when delivered to primary hepatocytes as mRNA encapsulated in a lipid nanoparticle. The enzyme also engineers an effective CD19 chimeric antigen receptor-T-cell therapy from primary human T cells using multiplexed simultaneous editing and chimeric antigen receptor insertion. To further ensure precise editing, we engineered an anti-CRISPR protein to selectively inhibit off-target gene editing while retaining therapeutic on-target editing. The engineered AiEvo2 nuclease coupled with a novel engineered anti-CRISPR protein represents a new way to control the fidelity of editing and improve the safety and efficacy of gene editing therapies.
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Affiliation(s)
| | | | | | | | | | - David Rabuka
- Acrigen Biosciences, Inc, Berkeley, California, USA
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11
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Bourmoum M, Radulovich N, Sharma A, Tkach JM, Tsao MS, Pelletier L. β-catenin mediates growth defects induced by centrosome loss in a subset of APC mutant colorectal cancer independently of p53. PLoS One 2024; 19:e0295030. [PMID: 38324534 PMCID: PMC10849215 DOI: 10.1371/journal.pone.0295030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024] Open
Abstract
Colorectal cancer is the third most common cancer and the second leading cause of cancer-related deaths worldwide. The centrosome is the main microtubule-organizing center in animal cells and centrosome amplification is a hallmark of cancer cells. To investigate the importance of centrosomes in colorectal cancer, we induced centrosome loss in normal and cancer human-derived colorectal organoids using centrinone B, a Polo-like kinase 4 (Plk4) inhibitor. We show that centrosome loss represses human normal colorectal organoid growth in a p53-dependent manner in accordance with previous studies in cell models. However, cancer colorectal organoid lines exhibited different sensitivities to centrosome loss independently of p53. Centrinone-induced cancer organoid growth defect/death positively correlated with a loss of function mutation in the APC gene, suggesting a causal role of the hyperactive WNT pathway. Consistent with this notion, β-catenin inhibition using XAV939 or ICG-001 partially prevented centrinone-induced death and rescued the growth two APC-mutant organoid lines tested. Our study reveals a novel role for canonical WNT signaling in regulating centrosome loss-induced growth defect/death in a subset of APC-mutant colorectal cancer independently of the classical p53 pathway.
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Affiliation(s)
- Mohamed Bourmoum
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Nikolina Radulovich
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Amit Sharma
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Johnny M. Tkach
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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12
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Zimmerman JAO, Fang M, Pufall MA. PI3Kδ Inhibition Potentiates Glucocorticoids in B-lymphoblastic Leukemia by Decreasing Receptor Phosphorylation and Enhancing Gene Regulation. Cancers (Basel) 2023; 16:143. [PMID: 38201570 PMCID: PMC10778422 DOI: 10.3390/cancers16010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Glucocorticoids are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency should improve treatment. We previously showed that inhibition of the lymphoid-restricted PI3Kδ with idelalisib enhances glucocorticoid activity in B-ALL cells. Here, we show that idelalisib enhances glucocorticoid potency in 90% of primary B-ALL specimens and is most pronounced at sub-saturating doses of glucocorticoids near the EC50. Potentiation is associated with enhanced regulation of all glucocorticoid-regulated genes, including genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at PI3Kδ/MAPK1 (ERK2) targets S203 and S226. Ablation of these phospho-acceptor sites enhances sensitivity to glucocorticoids with ablation of S226 in particular reducing synergy. We also show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro. We propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. This mechanism and the response of patient specimens suggest that idelalisib will benefit most patients with B-ALL, but particularly patients with less responsive, including high-risk, disease. This combination is also promising for the development of less toxic glucocorticoid-sparing therapies.
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Affiliation(s)
- Jessica A. O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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13
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Meacham Z, de Tacca LA, Bondy-Denomy J, Rabuka D, Schelle M. Cas9 degradation in human cells using phage anti-CRISPR proteins. PLoS Biol 2023; 21:e3002431. [PMID: 38064533 PMCID: PMC10732428 DOI: 10.1371/journal.pbio.3002431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 12/20/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Bacteriophages encode anti-CRISPR (Acr) proteins that inactivate CRISPR-Cas bacterial immune systems, allowing successful invasion, replication, and prophage integration. Acr proteins inhibit CRISPR-Cas systems using a wide variety of mechanisms. AcrIIA1 is encoded by numerous phages and plasmids, binds specifically to the Cas9 HNH domain, and was the first Acr discovered to inhibit SpyCas9. Here, we report the observation of AcrIIA1-induced degradation of SpyCas9 and SauCas9 in human cell culture, the first example of Acr-induced degradation of CRISPR-Cas nucleases in human cells. AcrIIA1-induced degradation of SpyCas9 is abolished by mutations in AcrIIA1 that break a direct physical interaction between the 2 proteins. Targeted Cas9 protein degradation by AcrIIA1 could modulate Cas9 nuclease activity in human therapies. The small size and specificity of AcrIIA1 could be used in a CRISPR-Cas proteolysis-targeting chimera (PROTAC), providing a tool for developing safe and precise gene editing applications.
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Affiliation(s)
- Zuriah Meacham
- Acrigen Biosciences, Inc., Alameda, California, United States of America
| | | | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - David Rabuka
- Acrigen Biosciences, Inc., Alameda, California, United States of America
| | - Michael Schelle
- Acrigen Biosciences, Inc., Alameda, California, United States of America
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14
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Watanabe T, Ochi Y, Kajihara R, Ichikawa K, Ezaki R, Matsuzaki M, Horiuchi H. Lipofection with Lipofectamine™ 2000 in a heparin-free growth medium results in high transfection efficiency in chicken primordial germ cells. Biotechnol J 2023; 18:e2300328. [PMID: 37559489 DOI: 10.1002/biot.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
Primordial germ cells (PGCs) that can differentiate into gametes are used to produce genome-edited chickens. However, the transfection efficiency into PGCs is low in chickens; therefore, the yield efficiency of PGCs modified via genome editing is problematic. In this study, we improved transfection efficiency and achieved highly efficient genome editing in chicken PGCs. For transfection, we used lipofection, which is convenient for gene transfer. Chicken PGC cultures require adding heparin to support growth; however, heparin significantly reduces lipofection efficiency (p < 0.01). Heparin-induced lipofection efficiency was restored by adding protamine. Based on these results, we optimized gene transfer into chicken PGCs. Lipofectamine 2000 and our PGC medium were the most efficient transfection reagent and medium, respectively. Finally, based on established conditions, we compared the gene knock-out efficiencies of ovomucoid, a major egg allergen, and gene knock-in efficiencies at the ACTB locus. These results indicate that optimized lipofection is useful for CRISPR/Cas9-mediated knock-out and knock-in. Our findings may contribute to the generation of genome-edited chickens and stimulate research in various applications involving them.
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Affiliation(s)
- Tenkai Watanabe
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuta Ochi
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ryota Kajihara
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kennosuke Ichikawa
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Japan
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Ryo Ezaki
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Mei Matsuzaki
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroyuki Horiuchi
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Japan
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15
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Çakmak A, Fuerkaiti S, Karagüzel D, Karaaslan Ç, Gümüşderelioğlu M. Enhanced Osteogenic Potential of Noggin Knockout C2C12 Cells on BMP-2 Releasing Silk Scaffolds. ACS Biomater Sci Eng 2023; 9:6175-6185. [PMID: 37796024 PMCID: PMC10646847 DOI: 10.1021/acsbiomaterials.3c00506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023]
Abstract
The CRISPR/Cas9 mechanism offers promising therapeutic approaches for bone regeneration by stimulating or suppressing critical signaling pathways. In this study, we aimed to increase the activity of BMP-2 signaling through knockout of Noggin, thereby establishing a synergistic effect on the osteogenic activity of cells in the presence of BMP-2. Since Noggin is an antagonist expressed in skeletal tissues and binds to subunits of bone morphogenetic proteins (BMPs) to inhibit osteogenic differentiation, here Noggin expression was knocked out using the CRISPR/Cas9 system. In accordance with this purpose, C2C12 (mouse myoblast) cells were transfected with CRISPR/Cas9 plasmids. Transfection was achieved with Lipofectamine and confirmed with intense fluorescent signals in microscopic images and deletion in target sequence in Sanger sequencing analysis. Thus, Noggin knockout cells were identified as a new cell source for tissue engineering studies. Then, the transfected cells were seeded on highly porous silk scaffolds bearing BMP-2-loaded silk nanoparticles (30 ng BMP-2/mg silk nanoparticle) in the size of 288 ± 62 nm. BMP-2 is released from the scaffolds in a controlled manner for up to 60 days. The knockout of Noggin by CRISPR/Cas9 was found to synergistically promote osteogenic differentiation in the presence of BMP-2 through increased Coll1A1 and Ocn expression and mineralization. Gene editing of Noggin and BMP-2 increased almost 2-fold Col1A1 expression and almost 3-fold Ocn expression compared to the control group. Moreover, transfected cells produced extracellular matrix (ECM) containing collagen fibers on the scaffolds and mineral-like structures were formed on the fibers. In addition, mineralization characterized by intense Alizarin red staining was detected in transfected cells cultured in the presence of BMP-2, while the other groups did not exhibit any mineralized areas. As has been demonstrated in this study, the CRISPR/Cas9 mechanism has great potential for obtaining new cell sources to be used in tissue engineering studies.
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Affiliation(s)
- Anıl
Sera Çakmak
- Department
of Chemical Engineering, Hacettepe University, 06800 Ankara, Turkey
| | - Sümeyra Fuerkaiti
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
| | - Dilara Karagüzel
- Department
of Biology, Molecular Biology Section, Hacettepe
University, 06800 Ankara, Turkey
| | - Çağatay Karaaslan
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
- Department
of Biology, Molecular Biology Section, Hacettepe
University, 06800 Ankara, Turkey
| | - Menemşe Gümüşderelioğlu
- Department
of Chemical Engineering, Hacettepe University, 06800 Ankara, Turkey
- Division
of Bioengineering, Graduate School of Science and Engineering, Hacettepe University, 06800 Ankara, Turkey
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16
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Zhao L, Koseki SRT, Silverstein RA, Amrani N, Peng C, Kramme C, Savic N, Pacesa M, Rodríguez TC, Stan T, Tysinger E, Hong L, Yudistyra V, Ponnapati MR, Jacobson JM, Church GM, Jakimo N, Truant R, Jinek M, Kleinstiver BP, Sontheimer EJ, Chatterjee P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 2023; 14:6175. [PMID: 37794046 PMCID: PMC10550912 DOI: 10.1038/s41467-023-41829-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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Affiliation(s)
- Lin Zhao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Christina Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christian Kramme
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Natasha Savic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Teodora Stan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emma Tysinger
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lauren Hong
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Vivian Yudistyra
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Joseph M Jacobson
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Noah Jakimo
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Pranam Chatterjee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
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17
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Delaveris CS, Wang CL, Riley NM, Li S, Kulkarni RU, Bertozzi CR. Microglia mediate contact-independent neuronal pruning via secreted Neuraminidase-3 associated with extracellular vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554214. [PMID: 37662421 PMCID: PMC10473657 DOI: 10.1101/2023.08.21.554214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Neurons communicate with each other through electrochemical transmission at synapses. Microglia, the resident immune cells of the central nervous system, can prune these synapses through a variety of contact-dependent and -independent means. Microglial secretion of active sialidase enzymes upon exposure to inflammatory stimuli is one unexplored mechanism of pruning. Recent work from our lab showed that treatment of neurons with bacterial sialidases disrupts neuronal network connectivity. Here, we find that activated microglia secrete Neuraminidase-3 (Neu3) associated with fusogenic extracellular vesicles. Furthermore, we show Neu3 mediates contact-independent pruning of neurons and subsequent disruption of neuronal networks through neuronal glycocalyx remodeling. We observe that NEU3 is transcriptionally upregulated upon exposure to inflammatory stimuli, and that a genetic knock-out of NEU3 abrogates the sialidase activity of inflammatory microglial secretions. Moreover, we demonstrate that Neu3 is associated with a subpopulation of extracellular vesicles, possibly exosomes, that are secreted by microglia upon inflammatory insult. Finally, we demonstrate that Neu3 is both necessary and sufficient to both desialylate neurons and decrease neuronal network connectivity. These results implicate Neu3 in remodeling of the glycocalyx leading to aberrant network-level activity of neurons, with implications in neuroinflammatory diseases such as Parkinson's disease and Alzheimer's disease.
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Affiliation(s)
- Corleone S. Delaveris
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
| | - Catherine L. Wang
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
| | - Nicholas M. Riley
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
| | - Sherry Li
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
| | - Rishikesh U. Kulkarni
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
| | - Carolyn R. Bertozzi
- Stanford University, Department of Chemistry and Sarafan ChEM-H, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305 USA
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18
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Wimberger S, Akrap N, Firth M, Brengdahl J, Engberg S, Schwinn MK, Slater MR, Lundin A, Hsieh PP, Li S, Cerboni S, Sumner J, Bestas B, Schiffthaler B, Magnusson B, Di Castro S, Iyer P, Bohlooly-Y M, Machleidt T, Rees S, Engkvist O, Norris T, Cadogan EB, Forment JV, Šviković S, Akcakaya P, Taheri-Ghahfarokhi A, Maresca M. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing. Nat Commun 2023; 14:4761. [PMID: 37580318 PMCID: PMC10425386 DOI: 10.1038/s41467-023-40344-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing.
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Affiliation(s)
- Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Nina Akrap
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Brengdahl
- Cell Assay Development, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Susanna Engberg
- Cell Engineering Sweden, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | | | - Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pei-Pei Hsieh
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan Sumner
- Cell Immunology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bastian Schiffthaler
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Björn Magnusson
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvio Di Castro
- Compound Synthesis & Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Preeti Iyer
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Steve Rees
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tyrell Norris
- Cell Engineering Sweden, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | | | - Saša Šviković
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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19
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Zimmerman JA, Fang M, Pufall MA. PI3Kδ inhibition potentiates glucocorticoids in B-lymphoblastic leukemia by decreasing receptor phosphorylation and enhancing gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527869. [PMID: 36798391 PMCID: PMC9934697 DOI: 10.1101/2023.02.10.527869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Glucocorticoids, including dexamethasone and prednisone, are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency is a route to improving outcomes. However, systematic toxicities prevent the use of higher dose and more potent glucocorticoids. We therefore took a functional genomic approach to identify targets to enhance glucocorticoid activity specifically in B-ALL cells. Here we show that inhibition of the lymphoid-restricted PI3Kδ, signaling through the RAS/MAPK pathway, enhances both prednisone and dexamethasone activity in almost all ex vivo B-ALL specimens tested. This potentiation is most synergistic at sub-saturating doses of glucocorticoids, approaching the EC50. Potentiation correlates with global enhancement of glucocorticoid-induced gene regulation, including regulation of effector genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at MAPK1/ERK2 targets S203 and S226, and ablation of these phospho-acceptor sites enhances glucocorticoid potency. We further show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro, which impairs DNA binding. We therefore propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. The overall enhancement of GR function suggests that idelalisib will provide benefit to most patients with B-ALL by improving outcomes for patients whose disease is less responsive to glucocorticoid-based therapy, including high-risk disease, and allowing less toxic glucocorticoid-sparing strategies for patients with standard-risk disease.
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Affiliation(s)
- Jessica A.O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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20
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Ashraf S, Ahmad A, Khan SH, Jamil A, Sadia B, Brown JK. LbCas12a mediated suppression of Cotton leaf curl Multan virus. FRONTIERS IN PLANT SCIENCE 2023; 14:1233295. [PMID: 37636103 PMCID: PMC10456881 DOI: 10.3389/fpls.2023.1233295] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023]
Abstract
Begomoviruses are contagious and severely affect commercially important fiber and food crops. Cotton leaf curl Multan virus (CLCuMuV) is one of the most dominant specie of Begomovirus and a major constraint on cotton yield in Pakistan. Currently, the field of plant genome editing is being revolutionized by the CRISPR/Cas system applications such as base editing, prime editing and CRISPR based gene drives. CRISPR/Cas9 system has successfully been used against biotic and abiotic plant stresses with proof-of-concept studies in both model and crop plants. CRISPR/Cas12 and CRISPR/Cas13 have recently been applied in plant sciences for basic and applied research. In this study, we used a novel approach, multiplexed crRNA-based Cas12a toolbox to target the different ORFs of the CLCuMuV genome at multiple sites simultaneously. This method successfully eliminated the symptoms of CLCuMuV in Nicotiana benthamiana and Nicotiana tabacum. Three individual crRNAs were designed from the CLCuMuV genome, targeting the specific sites of four different ORFs (C1, V1 and overlapping region of C2 and C3). The Cas12a-based construct Cas12a-MV was designed through Golden Gate three-way cloning for precise editing of CLCuMuV genome. Cas12a-MV construct was confirmed through whole genome sequencing using the primers Ubi-intron-F1 and M13-R1. Transient assays were performed in 4 weeks old Nicotiana benthamiana plants, through the agroinfiltration method. Sanger sequencing indicated that the Cas12a-MV constructs made a considerable mutations at the target sites of the viral genome. In addition, TIDE analysis of Sanger sequencing results showed the editing efficiency of crRNA1 (21.7%), crRNA2 (24.9%) and crRNA3 (55.6%). Furthermore, the Cas12a-MV construct was stably transformed into Nicotiana tabacum through the leaf disc method to evaluate the potential of transgenic plants against CLCuMuV. For transgene analysis, the DNA of transgenic plants of Nicotiana tabacum was subjected to PCR to amplify Cas12a genes with specific primers. Infectious clones were agro-inoculated in transgenic and non-transgenic plants (control) for the infectivity assay. The transgenic plants containing Cas12a-MV showed rare symptoms and remained healthy compared to control plants with severe symptoms. The transgenic plants containing Cas12a-MV showed a significant reduction in virus accumulation (0.05) as compared to control plants (1.0). The results demonstrated the potential use of the multiplex LbCas12a system to develop virus resistance in model and crop plants against begomoviruses.
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Affiliation(s)
- Sidra Ashraf
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
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21
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Ahn E, Botkin J, Curtin SJ, Zsögön A. Ideotype breeding and genome engineering for legume crop improvement. Curr Opin Biotechnol 2023; 82:102961. [PMID: 37331239 DOI: 10.1016/j.copbio.2023.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/20/2022] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Ideotype breeding is a strategy whereby traits are modeled a priori and then introduced into a model or crop species to assess their impact on yield. Thus, knowledge about the connection between genotype and phenotype is required for ideotype breeding to be deployed successfully. The growing understanding of the genetic basis of yield-related traits, combined with increasingly efficient genome engineering tools, improved transformation efficiency, and high-throughput genotyping of regenerants paves the way for the widespread adoption of ideotype breeding as a complement to conventional breeding. We briefly discuss how ideotype breeding, coupled with such state-of-the-art biotechnological tools, could contribute to knowledge-based legume breeding and accelerate yield gains to ensure food security in the coming decades.
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Affiliation(s)
- Ezekiel Ahn
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA; Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil.
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22
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Sharrar A, Arake de Tacca L, Collingwood T, Meacham Z, Rabuka D, Staples-Ager J, Schelle M. Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences. CRISPR J 2023; 6:350-358. [PMID: 37267210 DOI: 10.1089/crispr.2023.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Small Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) effectors are key to developing gene editing therapies due to the packaging constraints of viral vectors. While Cas9 and Cas12a CRISPR-Cas effectors have advanced into select clinical applications, their size is prohibitive for efficient delivery of both nuclease and guide RNA in a single viral vector. Type V Cas12f effectors present a solution given their small size. In this study, we describe a novel set of miniature (<490AA) Cas12f nucleases that cleave double-stranded DNA in human cells. We determined their optimal trans-activating RNA empirically through rational modifications, which resulted in an optimal single guide RNA. We show that these nucleases have broad protospacer adjacent motif (PAM) preferences, allowing for expanded genome targeting. The unique characteristics of these novel nucleases add to the diversity of the miniature CRISPR-Cas toolbox while the expanded PAM allows for the editing of genomic locations that could not be accessed with existing Cas12f nucleases.
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Affiliation(s)
| | | | | | | | - David Rabuka
- Acrigen Biosciences, Inc., Alameda, California, USA
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23
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Kang M, Lee K, Ji Q, Grosic S, Wang K. Enhancing Maize Transformation and Targeted Mutagenesis through the Assistance of Non-Integrating Wus2 Vector. PLANTS (BASEL, SWITZERLAND) 2023; 12:2799. [PMID: 37570953 PMCID: PMC10420852 DOI: 10.3390/plants12152799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
Efficient genetic transformation is a prerequisite for rapid gene functional analyses and crop trait improvements. We recently demonstrated that new T-DNA binary vectors with NptII/G418 selection and a compatible helper plasmid can efficiently transform maize inbred B104 using our rapid Agrobacterium-mediated transformation method. In this work, we implemented the non-integrating Wuschel2 (Wus2) T-DNA vector method for Agrobacterium-mediated B104 transformation and tested its potential for recalcitrant inbred B73 transformation and gene editing. The non-integrating Wus2 (NIW) T-DNA vector-assisted transformation method uses two Agrobacterium strains: one carrying a gene-of-interest (GOI) construct and the other providing an NIW construct. To monitor Wus2 co-integration into the maize genome, we combined the maize Wus2 expression cassette driven by a strong constitutive promoter with a new visible marker RUBY, which produces the purple pigment betalain. As a GOI construct, we used a previously tested CRISPR-Cas9 construct pKL2359 for Glossy2 gene mutagenesis. When both GOI and NIW constructs were delivered by LBA4404Thy- strain, B104 transformation frequency was significantly enhanced by about two-fold (10% vs. 18.8%). Importantly, we were able to transform a recalcitrant inbred B73 using the NIW-assisted transformation method and obtained three transgene-free edited plants by omitting the selection agent G418. These results suggest that NIW-assisted transformation can improve maize B104 transformation frequency and provide a novel option for CRISPR technology for transgene-free genome editing.
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Affiliation(s)
- Minjeong Kang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (M.K.); (K.L.)
- Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA; (Q.J.); (S.G.)
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA 50011, USA
| | - Keunsub Lee
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (M.K.); (K.L.)
- Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA; (Q.J.); (S.G.)
| | - Qing Ji
- Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA; (Q.J.); (S.G.)
| | - Sehiza Grosic
- Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA; (Q.J.); (S.G.)
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (M.K.); (K.L.)
- Crop Bioengineering Center, Iowa State University, Ames, IA 50011, USA; (Q.J.); (S.G.)
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24
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Essien SA, Ahuja I, Eisenhoffer GT. Macrophage Migration Inhibitory Factor on Apoptotic Extracellular Vesicles Regulates Compensatory Proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544889. [PMID: 37398303 PMCID: PMC10312732 DOI: 10.1101/2023.06.14.544889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Apoptotic cells can signal to neighboring cells to stimulate proliferation and compensate for cell loss to maintain tissue homeostasis. While apoptotic cell-derived extracellular vesicles (AEVs) can transmit instructional cues to mediate communication with neighboring cells, the molecular mechanisms that induce cell division are not well understood. Here we show that macrophage migration inhibitory factor (MIF)-containing AEVs regulate compensatory proliferation via ERK signaling in epithelial stem cells of larval zebrafish. Time-lapse imaging showed efferocytosis of AEVs from dying epithelial stem cells by healthy neighboring stem cells. Proteomic and ultrastructure analysis of purified AEVs identified MIF localization on the AEV surface. Pharmacological inhibition or genetic mutation of MIF, or its cognate receptor CD74, decreased levels of phosphorylated ERK and compensatory proliferation in the neighboring epithelial stem cells. Disruption of MIF activity also caused decreased numbers of macrophages patrolling near AEVs, while depletion of the macrophage lineage resulted in a reduced proliferative response by the epithelial stem cells. We propose that AEVs carrying MIF directly stimulate epithelial stem cell repopulation and guide macrophages to cell non-autonomously induce localized proliferation to sustain overall cell numbers during tissue maintenance.
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Affiliation(s)
- Safia A. Essien
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, TX
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ivanshi Ahuja
- Department of Biosciences, Rice University, Houston TX
| | - George T. Eisenhoffer
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, TX
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX
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25
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Ramgopal A, Braverman EL, Sun LK, Monlish D, Wittmann C, Ramsey MJ, Caitley R, Hawse W, Byersdorfer CA. AMPK Drives Both Glycolytic and Oxidative Metabolism in T Cells During Graft-versus-host Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544686. [PMID: 37398326 PMCID: PMC10312647 DOI: 10.1101/2023.06.12.544686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Allogeneic T cells reprogram their metabolism during acute graft-versus-host disease (GVHD) in a process reliant on the cellular energy sensor AMP-activated protein kinase (AMPK). Deletion of AMPK in donor T cells limits GVHD but still preserves homeostatic reconstitution and graft-versus-leukemia (GVL) effects. In the current studies, murine T cells lacking AMPK decreased oxidative metabolism at early timepoints post-transplant and were also unable to mediate a compensatory increase in glycolysis following inhibition of the electron transport chain. Human T cells lacking AMPK gave similar results, with glycolytic compensation impaired both in vitro and following expansion in vivo in a modified model of GVHD. Immunoprecipitation of proteins from day 7 allogeneic T cells, using an antibody specific to phosphorylated AMPK targets, recovered lower levels of multiple glycolysis-related proteins including the glycolytic enzymes aldolase, enolase, pyruvate kinase M (PKM), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Functionally, murine T cells lacking AMPK exhibited impaired aldolase activity following anti-CD3/CD28 stimulation and a decrease in GAPDH activity on day 7 post-transplant. Importantly, these changes in glycolysis correlated with an impaired ability of AMPK KO T cells to produce significant amounts of interferon gamma (IFNγ) upon antigenic re-stimulation. Together these data highlight a significant role for AMPK in controlling oxidative and glycolytic metabolism in both murine and human T cells during GVHD and endorse further study of AMPK inhibition as a potential target for future clinical therapies. KEY POINTS AMPK plays a key role in driving both and oxidative and glycolytic metabolism in T cells during graft-versus-host disease (GVHD)Absence of AMPK simultaneously impairs both glycolytic enzyme activity, most notably by aldolase, and interferon gamma (IFNγ) production.
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26
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Afanasyeva TA, Athanasiou D, Perdigao PR, Whiting KR, Duijkers L, Astuti GD, Bennett J, Garanto A, van der Spuy J, Roepman R, Cheetham ME, Collin RW. CRISPR-Cas9 correction of a nonsense mutation in LCA5 rescues lebercilin expression and localization in human retinal organoids. Mol Ther Methods Clin Dev 2023; 29:522-531. [PMID: 37305852 PMCID: PMC10250556 DOI: 10.1016/j.omtm.2023.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/12/2023] [Indexed: 06/13/2023]
Abstract
Mutations in the lebercilin-encoding gene LCA5 cause one of the most severe forms of Leber congenital amaurosis, an early-onset retinal disease that results in severe visual impairment. Here, we report on the generation of a patient-specific cellular model to study LCA5-associated retinal disease. CRISPR-Cas9 technology was used to correct a homozygous nonsense variant in LCA5 (c.835C>T; p.Q279∗) in patient-derived induced pluripotent stem cells (iPSCs). The absence of off-target editing in gene-corrected (isogenic) control iPSCs was demonstrated by whole-genome sequencing. We differentiated the patient, gene-corrected, and unrelated control iPSCs into three-dimensional retina-like cells, so-called retinal organoids. We observed opsin and rhodopsin mislocalization to the outer nuclear layer in patient-derived but not in the gene-corrected or unrelated control organoids. We also confirmed the rescue of lebercilin expression and localization along the ciliary axoneme within the gene-corrected organoids. Here, we show the potential of combining precise single-nucleotide gene editing with the iPSC-derived retinal organoid system for the generation of a cellular model of early-onset retinal disease.
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Affiliation(s)
- Tess A.V. Afanasyeva
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GD Nijmegen, the Netherlands
| | | | | | - Kae R. Whiting
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Galuh D.N. Astuti
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jean Bennett
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Paediatrics, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GD Nijmegen, the Netherlands
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27
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Ahn E, Fall C, Botkin J, Curtin S, Prom LK, Magill C. Inoculation and Screening Methods for Major Sorghum Diseases Caused by Fungal Pathogens: Claviceps africana, Colletotrichum sublineola, Sporisorium reilianum, Peronosclerospora sorghi and Macrophomina phaseolina. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091906. [PMID: 37176964 PMCID: PMC10180756 DOI: 10.3390/plants12091906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Sorghum is the fifth most important crop globally. Researching interactions between sorghum and fungal pathogens is essential to further elucidate plant defense mechanisms to biotic stress, which allows breeders to employ genetic resistance to disease. A variety of creative and useful inoculation and screening methods have been developed by sorghum pathologists to study major fungal diseases. As inoculation and screening methods can be keys for successfully conducting experiments, it is necessary to summarize the techniques developed by this research community. Among many fungal pathogens of sorghum, here we summarize inoculation and screening methods for five important fungal pathogens of sorghum: Claviceps africana, Colletotrichum sublineola, Sporisorium reilianum, Peronosclerospora sorghi and Macrophomina phaseolina. The methods described within will be useful for researchers who are interested in exploring sorghum-fungal pathogen interactions. Finally, we discuss the latest biotechnologies and methods for studying plant-fungal pathogen interactions and their applicability to sorghum pathology.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Coumba Fall
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun Curtin
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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28
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Ding Y, Wang M, Bu H, Li J, Lin X, Xu X. Application of an F0-based genetic assay in adult zebrafish to identify modifier genes of an inherited cardiomyopathy. Dis Model Mech 2023; 16:dmm049427. [PMID: 35481478 PMCID: PMC9239171 DOI: 10.1242/dmm.049427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Modifier genes contribute significantly to our understanding of pathophysiology in human diseases; however, effective approaches to identify modifier genes are still lacking. Here, we aim to develop a rapid F0-based genetic assay in adult zebrafish using the bag3 gene knockout (bag3e2/e2) cardiomyopathy model as a paradigm. First, by utilizing a classic genetic breeding approach, we identified dnajb6b as a deleterious modifier gene for bag3 cardiomyopathy. Next, we established an F0-based genetic assay in adult zebrafish through injection of predicted microhomology-mediated end joining (MMEJ)-inducing single guide RNA/Cas9 protein complex. We showed that effective gene knockdown is maintained in F0 adult fish, enabling recapitulation of both salutary modifying effects of the mtor haploinsufficiency and deleterious modifying effects of the dnajb6b gene on bag3 cardiomyopathy. We finally deployed the F0-based genetic assay to screen differentially expressed genes in the bag3 cardiomyopathy model. As a result, myh9b was identified as a novel modifier gene for bag3 cardiomyopathy. Together, these data prove the feasibility of an F0 adult zebrafish-based genetic assay that can be effectively used to discover modifier genes for inherited cardiomyopathy.
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Affiliation(s)
- Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Mingmin Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Haisong Bu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiothoracic Surgery, Xiangfan Hospital, Central South University, Changsha 410008, China
| | - Jiarong Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Surgery, The Second Xiangfan Hospital of Central South University, Changsha 410011, China
| | - Xueying Lin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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29
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Matsushita Y, Liu J, Chu AKY, Tsutsumi-Arai C, Nagata M, Arai Y, Ono W, Yamamoto K, Saunders TL, Welch JD, Ono N. Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis. Nat Commun 2023; 14:2383. [PMID: 37185464 PMCID: PMC10130060 DOI: 10.1038/s41467-023-38034-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The bone marrow contains various populations of skeletal stem cells (SSCs) in the stromal compartment, which are important regulators of bone formation. It is well-described that leptin receptor (LepR)+ perivascular stromal cells provide a major source of bone-forming osteoblasts in adult and aged bone marrow. However, the identity of SSCs in young bone marrow and how they coordinate active bone formation remains unclear. Here we show that bone marrow endosteal SSCs are defined by fibroblast growth factor receptor 3 (Fgfr3) and osteoblast-chondrocyte transitional (OCT) identities with some characteristics of bone osteoblasts and chondrocytes. These Fgfr3-creER-marked endosteal stromal cells contribute to a stem cell fraction in young stages, which is later replaced by Lepr-cre-marked stromal cells in adult stages. Further, Fgfr3+ endosteal stromal cells give rise to aggressive osteosarcoma-like lesions upon loss of p53 tumor suppressor through unregulated self-renewal and aberrant osteogenic fates. Therefore, Fgfr3+ endosteal SSCs are abundant in young bone marrow and provide a robust source of osteoblasts, contributing to both normal and aberrant osteogenesis.
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Affiliation(s)
- Yuki Matsushita
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Jialin Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Angel Ka Yan Chu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chiaki Tsutsumi-Arai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Mizuki Nagata
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Yuki Arai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Wanida Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA.
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30
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She K, Liu Y, Zhao Q, Jin X, Yang Y, Su J, Li R, Song L, Xiao J, Yao S, Lu F, Wei Y, Yang Y. Dual-AAV split prime editor corrects the mutation and phenotype in mice with inherited retinal degeneration. Signal Transduct Target Ther 2023; 8:57. [PMID: 36740702 PMCID: PMC9899767 DOI: 10.1038/s41392-022-01234-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/07/2022] [Accepted: 10/17/2022] [Indexed: 02/07/2023] Open
Abstract
The prime editor (PE) can edit genomes with almost any intended changes, including all 12 possible types of base substitutions, small insertions and deletions, and their combinations, without the requirement for double strand breaks or exogenous donor templates. PE demonstrates the possibility of correcting a variety of disease-causing mutations and might expand the therapeutic application of gene editing. In this study, PE was optimized based on a dual-adeno-associated virus (AAV) split-intein system in vitro by screening different split sites and split inteins. We found that splitting PE before amino acid 1105(Ser) of SpCas9 with Rma intein resulted in the highest on-target editing. The orientations of pegRNA and nicking sgRNA in the AAV vector were further optimized. To test the in vivo performance of the optimized dual-AAV split-PE3, it was delivered by subretinal injection in rd12 mice with inherited retinal disease Leber congenital amaurosis. The prime editors corrected the pathogenic mutation with up to 16% efficiency in a precise way, with no detectable off-target edits, restored RPE65 expression, rescued retinal and visual function, and preserved photoceptors. Our findings establish a framework for the preclinical development of PE and motivate further testing of PE for the treatment of inherited retinal diseases caused by various mutations.
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Affiliation(s)
- Kaiqin She
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Qinyu Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Xiu Jin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yiliu Yang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Ruiting Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Li Song
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jianlu Xiao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shaohua Yao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Fang Lu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yang Yang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China.
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31
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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32
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Ferreira DA, Idris A, McMillan NAJ. Analysis of a hit-and-run tumor model by HPV in oropharyngeal cancers. J Med Virol 2023; 95:e28260. [PMID: 36305515 PMCID: PMC9828080 DOI: 10.1002/jmv.28260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 01/12/2023]
Abstract
Several viruses are known to be associated with the development of certain cancers, including human papilloma virus (HPV), an established causative agent for a range of anogenital and head and neck cancers. However, the causality has been based on the presence of the virus, or its genetic material, in the sampled tumors. We have long wondered if viruses cause cancer via a "hit and run" mechanism such that they are no longer present in the resulting tumors. Here, we hypothesize that the absence of viral genes from the tumor does not necessarily exclude the viral aetiology. To test this, we used an HPV-driven oropharyngeal cancer (OPC) tumor model and CRISPR to delete the viral oncogene, E7. Indeed, the genetic removal of HPV E7 oncogene eliminates tumors in vivo. Remarkably, E7 deleted tumors recurred over time and develop new mutations not previously seen in HPV+ OPC tumors. Importantly, a number of these new mutations are found to be already present in HPV- OPC tumors.
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Affiliation(s)
- Danyelle Assis Ferreira
- Griffith Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, School of Pharmacy and Medical ScienceGriffith UniversitySouthportQueenslandAustralia
| | - Adi Idris
- Griffith Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, School of Pharmacy and Medical ScienceGriffith UniversitySouthportQueenslandAustralia
| | - Nigel A. J. McMillan
- Griffith Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, School of Pharmacy and Medical ScienceGriffith UniversitySouthportQueenslandAustralia
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33
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Wegner J, Hunkler C, Ciupka K, Hartmann G, Schlee M. Increased IKKϵ protein stability ensures efficient type I interferon responses in conditions of TBK1 deficiency. Front Immunol 2023; 14:1073608. [PMID: 36936901 PMCID: PMC10020501 DOI: 10.3389/fimmu.2023.1073608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
TBK1 and IKKϵ are related, crucial kinases in antiviral immune signaling pathways downstream of cytosolic nucleic acid receptors such as cGAS and RIG-I-like receptors. Upon activation, they phosphorylate the transcription factors IRF3 and IRF7 and thereby initiate the expression of type I interferons and antiviral effectors. While point mutation-induced loss of TBK1 kinase activity results in clinical hyper-susceptibility to viral infections, a complete lack of TBK1 expression in humans is unexpectedly not associated with diminished antiviral responses. Here, we provide a mechanistic explanation for these so-far unexplained observations by showing that TBK1 controls the protein expression of its related kinase IKKϵ in human myeloid cells. Mechanistically, TBK1 constitutively diminishes the protein stability of IKKϵ independent of TBK1 kinase activity but dependent on its interaction with the scaffold protein TANK. In consequence, depletion of TBK1 protein but not mutation-induced kinase deficiency induces the upregulation of IKKϵ. Due to the functional redundancy of the kinases in cGAS-STING and RIG-I-like receptor signaling in human myeloid cells, enhanced IKKϵ expression can compensate for the loss of TBK1. We show that IKKϵ upregulation is crucial to ensure unmitigated type I interferon production in conditions of TBK1 deficiency: While the type I interferon response to Listeria monocytogenes infection is maintained upon TBK1 loss, it is strongly diminished in cells harboring a kinase-deficient TBK1 variant, in which IKKϵ is not upregulated. Many pathogens induce TBK1 degradation, suggesting that loss of TBK1-mediated destabilization of IKKϵ is a critical backup mechanism to prevent diminished interferon responses upon TBK1 depletion.
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34
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Inglebert M, Dettwiler M, Hahn K, Letko A, Drogemuller C, Doench J, Brown A, Memari Y, Davies HR, Degasperi A, Nik-Zainal S, Rottenberg S. A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer. Sci Rep 2022; 12:18051. [PMID: 36302863 PMCID: PMC9614008 DOI: 10.1038/s41598-022-21706-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/30/2022] [Indexed: 01/20/2023] Open
Abstract
Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression patterns, prognostic factors, and genetic characteristics as their human counterparts. We aimed to develop in vitro tools that allow functional analysis of canine mammary tumors (CMT), as we have a poor understanding of the underlying biology that drives the growth of these heterogeneous tumors. We established the long-term culture of 24 organoid lines from 16 dogs, including organoids derived from normal mammary epithelium or benign lesions. CMT organoids recapitulated key morphological and immunohistological features of the primary tissue from which they were derived, including hormone receptor status. Furthermore, genetic characteristics (driver gene mutations, DNA copy number variations, and single-nucleotide variants) were conserved within tumor-organoid pairs. We show how CMT organoids are a suitable model for in vitro drug assays and can be used to investigate whether specific mutations predict therapy outcomes. Specifically, certain CMT subtypes, such as PIK3CA mutated, estrogen receptor-positive simple carcinomas, can be valuable in setting up a preclinical model highly relevant to human breast cancer research. In addition, we could genetically modify the CMT organoids and use them to perform pooled CRISPR/Cas9 screening, where library representation was accurately maintained. In summary, we present a robust 3D in vitro preclinical model that can be used in translational research, where organoids from normal, benign as well as malignant mammary tissues can be propagated from the same animal to study tumorigenesis.
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Affiliation(s)
- Marine Inglebert
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Martina Dettwiler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Vetscope Pathologie Dettwiler, Lörracherstrasse 50, 4125, Riehen, Switzerland
| | - Kerstin Hahn
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, COMPATH, University of Bern, Bern, Switzerland
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cord Drogemuller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - John Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Adam Brown
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Yasin Memari
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Helen R Davies
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland.
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Institute of Animal Pathology, COMPATH, University of Bern, Bern, Switzerland.
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35
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Oulhen N, Pieplow C, Perillo M, Gregory P, Wessel GM. Optimizing CRISPR/Cas9-based gene manipulation in echinoderms. Dev Biol 2022; 490:117-124. [PMID: 35917936 DOI: 10.1016/j.ydbio.2022.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/26/2022]
Abstract
The impact of new technology can be appreciated by how broadly it is used. Investigators that previously relied only on pharmacological approaches or the use of morpholino antisense oligonucleotide (MASO) technologies are now able to apply CRISPR-Cas9 to study biological problems in their model organism of choice much more effectively. The transitions to new CRISPR-based approaches could be enhanced, first, by standardized protocols and education in their applications. Here we summarize our results for optimizing the CRISPR-Cas9 technology in a sea urchin and a sea star, and provide advice on how to set up CRISPR-Cas9 experiments and interpret the results in echinoderms. Our goal through these protocols and sharing examples of success by other labs is to lower the activation barrier so that more laboratories can apply CRISPR-Cas9 technologies in these important animals.
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Affiliation(s)
- Nathalie Oulhen
- MCB Department, Brown University, Providence, RI, 02906, USA
| | - Cosmo Pieplow
- MCB Department, Brown University, Providence, RI, 02906, USA
| | | | - Pauline Gregory
- MCB Department, Brown University, Providence, RI, 02906, USA
| | - Gary M Wessel
- MCB Department, Brown University, Providence, RI, 02906, USA.
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36
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The Inflammasome Activity of NLRP3 Is Independent of NEK7 in HEK293 Cells Co-Expressing ASC. Int J Mol Sci 2022; 23:ijms231810269. [PMID: 36142182 PMCID: PMC9499477 DOI: 10.3390/ijms231810269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
The cytosolic immune receptor NLRP3 (nucleotide-binding domain, leucine-rich repeat (LRR), and pyrin domain (PYD)-containing protein 3) oligomerizes into the core of a supramolecular complex termed inflammasome in response to microbes and danger signals. It is thought that NLRP3 has to bind NEK7 (NIMA (never in mitosis gene a)-related kinase 7) to form a functional inflammasome core that induces the polymerization of the adaptor protein ASC (Apoptosis-associated speck-like protein containing a CARD (caspase recruitment domain)), which is a hallmark for NLRP3 activity. We reconstituted the NLRP3 inflammasome activity in modified HEK293 (human embryonic kidney 293) cells and showed that the ASC speck polymerization is independent of NEK7 in the context of this cell system. Probing the interfaces observed in the different, existing structural models of NLRP3 oligomers, we present evidence that the NEK7-independent, constitutively active NLRP3 inflammasome core in HEK293 cells may resemble a stacked-torus-like hexamer seen for NLRP3 lacking its PYD (pyrin domain).
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37
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Dai YY, Gao YP, Chen LX, Liu JS, Zeng C, Zhou JD, Wu HL. Predicting prognosis and immune responses in hepatocellular carcinoma based on N7-methylguanosine-related long noncoding RNAs. Front Genet 2022; 13:930446. [PMID: 36110218 PMCID: PMC9468367 DOI: 10.3389/fgene.2022.930446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC), which has high rates of recurrence and metastasis and is the main reason and the most common tumor for cancer mortality worldwide, has an unfavorable prognosis. N7-methylguanosine (m7G) modification can affect the formation and development of tumors by affecting gene expression and other biological processes. In addition, many previous studies have confirmed the unique function of long noncoding RNAs (lncRNAs) in tumor progression; however, studies exploring the functions of m7G-related lncRNAs in HCC patients has been limited. Methods: Relevant RNA expression information was acquired from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov), and m7G-related lncRNAs were identified via gene coexpression analysis. Afterward, univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and multivariate regression analyses were implemented to construct an ideal risk model whose validity was verified using Kaplan–Meier survival, principal component, receiver operating characteristic (ROC) curve, and nomogram analyses. In addition, the potential functions of lncRNAs in the novel signature were explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analyses and gene set enrichment analysis (GSEA). At last, in both risk groups and subtypes classified based on the expression of the risk-related lncRNAs, we analyzed the immune characteristics and drug sensitivity of patients. Results: After rigorous screening processes, we built a model based on 11 m7G-related lncRNAs for predicting patient overall survival (OS). The results suggested that the survival status of patients with high-risk scores was lower than that of patients with low-risk scores, and a high-risk score was related to malignant clinical features. Cox regression analysis showed that the m7G risk score was an independent prognostic parameter. Moreover, immune cell infiltration and immunotherapy sensitivity differed between the risk groups. Conclusion: The m7G risk score model constructed based on 11 m7G-related lncRNAs can effectively assess the OS of HCC patients and may offer support for making individualized treatment and immunotherapy decisions for HCC patients.
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Affiliation(s)
- Yu-yang Dai
- Department of Radiology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu Province, China
- Department of Radiology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Yi-ping Gao
- Department of Interventional Radiology, Nanfang Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China
| | - Lin-xin Chen
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jin-song Liu
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Cheng Zeng
- Department of Oncology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Jian-dong Zhou
- Department of Nephrology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
- Department of Nephrology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
| | - Hong-lin Wu
- Department of Radiology, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu Province, China
- Department of Radiology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China
- *Correspondence: Hong-lin Wu,
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38
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Lohmüller M, Roeck BF, Szabo TG, Schapfl MA, Pegka F, Herzog S, Villunger A, Schuler F. The SKP2-p27 axis defines susceptibility to cell death upon CHK1 inhibition. Mol Oncol 2022; 16:2771-2787. [PMID: 35673965 PMCID: PMC9348596 DOI: 10.1002/1878-0261.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/05/2022] [Accepted: 06/07/2022] [Indexed: 11/07/2022] Open
Abstract
Checkpoint kinase 1 (CHK1; encoded by CHEK1) is an essential gene that monitors DNA replication fidelity and prevents mitotic entry in the presence of under-replicated DNA or exogenous DNA damage. Cancer cells deficient in p53 tumor suppressor function reportedly develop a strong dependency on CHK1 for proper cell cycle progression and maintenance of genome integrity, sparking interest in developing kinase inhibitors. Pharmacological inhibition of CHK1 triggers B-Cell CLL/Lymphoma 2 (BCL2)-regulated cell death in malignant cells largely independently of p53, and has been suggested to kill p53-deficient cancer cells even more effectively. Next to p53 status, our knowledge about factors predicting cancer cell responsiveness to CHK1 inhibitors is limited. Here, we conducted a genome-wide CRISPR/Cas9-based loss-of-function screen to identify genes defining sensitivity to chemical CHK1 inhibitors. Next to the proapoptotic BCL2 family member, BCL2 Binding Component 3 (BBC3; also known as PUMA), the F-box protein S-phase Kinase-Associated Protein 2 (SKP2) was validated to tune the cellular response to CHK1 inhibition. SKP2 is best known for degradation of the Cyclin-dependent Kinase Inhibitor 1B (CDKN1B; also known as p27), thereby promoting G1-S transition and cell cycle progression in response to mitogens. Loss of SKP2 resulted in the predicted increase in p27 protein levels, coinciding with reduced DNA damage upon CHK1-inhibitor treatment and reduced cell death in S-phase. Conversely, overexpression of SKP2, which consequently results in reduced p27 protein levels, enhanced cell death susceptibility to CHK1 inhibition. We propose that assessing SKP2 and p27 expression levels in human malignancies will help to predict the responsiveness to CHK1-inhibitor treatment.
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Affiliation(s)
- Michael Lohmüller
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Bernhard F Roeck
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Tamas G Szabo
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Marina A Schapfl
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Fragka Pegka
- Institute for Medical Biochemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Sebastian Herzog
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Fabian Schuler
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
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Martin CE, Phippen NJ, Keyvani Chahi A, Tilak M, Banerjee SL, Lu P, New LA, Williamson CR, Platt MJ, Simpson JA, Krendel M, Bisson N, Gingras AC, Jones N. Complementary Nck1/2 Signaling in Podocytes Controls α Actinin-4-Mediated Actin Organization, Adhesion, and Basement Membrane Composition. J Am Soc Nephrol 2022; 33:1546-1567. [PMID: 35906089 PMCID: PMC9342632 DOI: 10.1681/asn.2021101343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/26/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Maintenance of the kidney filtration barrier requires coordinated interactions between podocytes and the underlying glomerular basement membrane (GBM). GBM ligands bind podocyte integrins, which triggers actin-based signaling events critical for adhesion. Nck1/2 adaptors have emerged as essential regulators of podocyte cytoskeletal dynamics. However, the precise signaling mechanisms mediated by Nck1/2 adaptors in podocytes remain to be fully elucidated. METHODS We generated podocytes deficient in Nck1 and Nck2 and used transcriptomic approaches to profile expression differences. Proteomic techniques identified specific binding partners for Nck1 and Nck2 in podocytes. We used cultured podocytes and mice deficient in Nck1 and/or Nck2, along with podocyte injury models, to comprehensively verify our findings. RESULTS Compound loss of Nck1/2 altered expression of genes involved in actin binding, cell adhesion, and extracellular matrix composition. Accordingly, Nck1/2-deficient podocytes showed defects in actin organization and cell adhesion in vitro, with podocyte detachment and altered GBM morphology present in vivo. We identified distinct interactomes for Nck1 and Nck2 and uncovered a mechanism by which Nck1 and Nck2 cooperate to regulate actin bundling at focal adhesions via α actinin-4. Furthermore, loss of Nck1 or Nck2 resulted in increased matrix deposition in vivo, with more prominent defects in Nck2-deficient mice, consistent with enhanced susceptibility to podocyte injury. CONCLUSION These findings reveal distinct, yet complementary, roles for Nck proteins in regulating podocyte adhesion, controlling GBM composition, and sustaining filtration barrier integrity.
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Affiliation(s)
- Claire E Martin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Noah J Phippen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ava Keyvani Chahi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Manali Tilak
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sara L Banerjee
- Division of Oncology, Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Laval University, Quebec City, Quebec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, Quebec, Canada
| | - Peihua Lu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura A New
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Casey R Williamson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mathew J Platt
- Department of Human Health and Nutritional Science, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy A Simpson
- Department of Human Health and Nutritional Science, University of Guelph, Guelph, Ontario, Canada
| | - Mira Krendel
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York
| | - Nicolas Bisson
- Division of Oncology, Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Laval University, Quebec City, Quebec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, Quebec, Canada.,PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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40
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Gonzalez-Salinas F, Martinez-Amador C, Trevino V. Characterizing genes associated with cancer using the CRISPR/Cas9 system: A systematic review of genes and methodological approaches. Gene 2022; 833:146595. [PMID: 35598687 DOI: 10.1016/j.gene.2022.146595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022]
Abstract
The CRISPR/Cas9 system enables a versatile set of genomes editing and genetic-based disease modeling tools due to its high specificity, efficiency, and accessible design and implementation. In cancer, the CRISPR/Cas9 system has been used to characterize genes and explore different mechanisms implicated in tumorigenesis. Different experimental strategies have been proposed in recent years, showing dependency on various intrinsic factors such as cancer type, gene function, mutation type, and technical approaches such as cell line, Cas9 expression, and transfection options. However, the successful methodological approaches, genes, and other experimental factors have not been analyzed. We, therefore, initially considered more than 1,300 research articles related to CRISPR/Cas9 in cancer to finally examine more than 400 full-text research publications. We summarize findings regarding target genes, RNA guide designs, cloning, Cas9 delivery systems, cell enrichment, and experimental validations. This analysis provides valuable information and guidance for future cancer gene validation experiments.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Claudia Martinez-Amador
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico; Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada avenue 2501, Monterrey, Nuevo Leon 64849, México.
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41
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Pan X, Qu K, Yuan H, Xiang X, Anthon C, Pashkova L, Liang X, Han P, Corsi GI, Xu F, Liu P, Zhong J, Zhou Y, Ma T, Jiang H, Liu J, Wang J, Jessen N, Bolund L, Yang H, Xu X, Church GM, Gorodkin J, Lin L, Luo Y. Massively targeted evaluation of therapeutic CRISPR off-targets in cells. Nat Commun 2022; 13:4049. [PMID: 35831290 PMCID: PMC9279339 DOI: 10.1038/s41467-022-31543-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously evaluating thousands of therapeutic RGN OTs in cells. SURRO-seq captures RGN-induced indels in cells by pooled lentiviral OTs libraries and deep sequencing, an approach comparable and complementary to OTs detection by T7 endonuclease 1, GUIDE-seq, and CIRCLE-seq. Application of SURRO-seq to 8150 OTs from 110 therapeutic RGNs identifies significantly detectable indels in 783 OTs, of which 37 OTs are found in cancer genes and 23 OTs are further validated in five human cell lines by targeted amplicon sequencing. Finally, SURRO-seq reveals that thermodynamically stable wobble base pair (rG•dT) and free binding energy strongly affect RGN specificity. Our study emphasizes the necessity of thoroughly evaluating therapeutic RGN OTs to minimize inevitable off-target effects.
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Affiliation(s)
- Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Hao Yuan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xi Xiang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Liubov Pashkova
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Giulia I Corsi
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Research, BGI-Shenzhen, Shenzhen, China
| | - Ping Liu
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Jiayan Zhong
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Yan Zhou
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Tao Ma
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Junnian Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jian Wang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Huanming Yang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Xun Xu
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- BGI-Research, BGI-Shenzhen, Shenzhen, China.
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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42
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Uetz P, Melnik S, Grünwald-Gruber C, Strasser R, Stoger E. CRISPR/Cas9-mediated knockout of a prolyl-4-hydroxylase subfamily in Nicotiana benthamiana using DsRed2 for plant selection. Biotechnol J 2022; 17:e2100698. [PMID: 35427441 DOI: 10.1002/biot.202100698] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
The properties of host plants used for molecular farming can be modified by CRISPR/Cas9 genome editing to improve the quality and yield of recombinant proteins. However, it is often necessary to target multiple genes simultaneously, particularly when using host plants with large and complex genomes. This is the case for Nicotiana benthamiana, an allotetraploid relative of tobacco frequently used for transient protein expression. A multiplex genome editing system incorporating the DsRed2 fluorescent marker for the identification and selection of transgenic plants was established. As proof of principle, NbP4H4 was targeted encoding a prolyl-4-hydroxylase involved in protein O-linked glycosylation. Using preselected gRNAs with efficiencies confirmed by transient expression, transgenic plant lines with knockout mutations in all four NbP4H4 genes were obtained. Leaf fluorescence was then used to screen for the absence of the SpCas9 transgene in T1 plants, and transgene-free lines with homozygous or biallelic mutations were identified. The analysis of plant-produced recombinant IgA1 as a reporter protein revealed changes in the number of peptides containing hydroxyproline residues and pentoses in the knockout plants. The selection of efficient gRNAs combined with the DsRed2 marker reduces the effort needed to generate N. benthamiana mutants and simplifies the screening processes to obtain transgene-free progeny.
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Affiliation(s)
- Pia Uetz
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stanislav Melnik
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eva Stoger
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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43
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Liu Z, Jiang M, Liakath-Ali K, Sclip A, Ko J, Zhang RS, Südhof TC. Deletion of Calsyntenin-3, an atypical cadherin, suppresses inhibitory synapses but increases excitatory parallel-fiber synapses in cerebellum. eLife 2022; 11:e70664. [PMID: 35420982 PMCID: PMC9064300 DOI: 10.7554/elife.70664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 04/14/2022] [Indexed: 01/11/2023] Open
Abstract
Cadherins contribute to the organization of nearly all tissues, but the functions of several evolutionarily conserved cadherins, including those of calsyntenins, remain enigmatic. Puzzlingly, two distinct, non-overlapping functions for calsyntenins were proposed: As postsynaptic neurexin ligands in synapse formation, or as presynaptic kinesin adaptors in vesicular transport. Here, we show that, surprisingly, acute CRISPR-mediated deletion of calsyntenin-3 in mouse cerebellum in vivo causes a large decrease in inhibitory synapse, but a robust increase in excitatory parallel-fiber synapses in Purkinje cells. As a result, inhibitory synaptic transmission was suppressed, whereas parallel-fiber synaptic transmission was enhanced in Purkinje cells by the calsyntenin-3 deletion. No changes in the dendritic architecture of Purkinje cells or in climbing-fiber synapses were detected. Sparse selective deletion of calsyntenin-3 only in Purkinje cells recapitulated the synaptic phenotype, indicating that calsyntenin-3 acts by a cell-autonomous postsynaptic mechanism in cerebellum. Thus, by inhibiting formation of excitatory parallel-fiber synapses and promoting formation of inhibitory synapses in the same neuron, calsyntenin-3 functions as a postsynaptic adhesion molecule that regulates the excitatory/inhibitory balance in Purkinje cells.
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Affiliation(s)
- Zhihui Liu
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Man Jiang
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Kif Liakath-Ali
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Alessandra Sclip
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Jaewon Ko
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and TechnologyDaeguRepublic of Korea
| | - Roger Shen Zhang
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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44
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Brackett NF, Davis BW, Adli M, Pomés A, Chapman MD. Evolutionary Biology and Gene Editing of Cat Allergen, Fel d 1. CRISPR J 2022; 5:213-223. [PMID: 35343817 DOI: 10.1089/crispr.2021.0101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Allergy to domestic cat affects up to 15% of the population, and sensitization to cat allergen is associated with asthma. Despite the pervasiveness of cat allergic disease, current treatments have limited impact. Here, we present a bioinformatics analysis of the major cat allergen, Fel d 1, and demonstrate proof of principle for CRISPR gene editing of the allergen. Sequence and structural analyses of Fel d 1 from 50 domestic cats identified conserved coding regions in genes CH1 and CH2 suitable for CRISPR editing. Comparative analyses of Fel d 1 and orthologous sequences from eight exotic felid species determined relatively low-sequence identities for CH1 and CH2, and implied that the allergen may be nonessential for cats, given the apparent lack of evolutionary conservation. In vitro knockouts of domestic cat Fel d 1 using CRISPR-Cas9 yielded editing efficiencies of up to 55% and found no evidence of editing at predicted potential off-target sites. Taken together, our data indicate that Fel d 1 is both a rational and viable candidate for gene deletion, which may profoundly benefit cat allergy sufferers by removing the major allergen at the source.
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Affiliation(s)
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Mazhar Adli
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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45
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Schep R, Leemans C, Brinkman EK, van Schaik T, van Steensel B. Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair. Front Genet 2022; 12:785947. [PMID: 35173762 PMCID: PMC8842231 DOI: 10.3389/fgene.2021.785947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired through various pathways. Understanding how these pathways are regulated is of great interest for cancer research and optimization of gene editing. The local chromatin environment can affect the balance between repair pathways, but this is still poorly understood. Here we provide a detailed protocol for DSB-TRIP, a technique that utilizes the specific DNA scars left by DSB repair pathways to study pathway usage throughout the genome. DSB-TRIP randomly integrates a repair reporter into many genomic locations, followed by the induction of DSBs in the reporter. Multiplexed sequencing of the resulting scars at all integration sites then reveals the balance between several repair pathways, which can be linked to the local chromatin state of the integration sites. Here we present a step-by-step protocol to perform DSB-TRIP in K562 cells and to analyse the data by a dedicated computational pipeline. We discuss strengths and limitations of the technique, as well as potential additional applications to study DNA repair.
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Affiliation(s)
- Ruben Schep
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Christ Leemans
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eva K. Brinkman
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tom van Schaik
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bas van Steensel
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Cell Biology, Erasmus University Medical Centre, Rotterdam, Netherlands
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46
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Liang SQ, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, Yang Q, Lee J, Haynes CM, Zhu LJ, Watts JK, Sontheimer EJ, Wolfe SA, Xue W. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat Commun 2022; 13:437. [PMID: 35064134 PMCID: PMC8782884 DOI: 10.1038/s41467-022-28135-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of off-target editing is an important aspect of the development of safe nuclease-based genome editing therapeutics. in vivo assessment of nuclease off-target activity has primarily been indirect (based on discovery in vitro, in cells or via computational prediction) or through ChIP-based detection of double-strand break (DSB) DNA repair factors, which can be cumbersome. Herein we describe GUIDE-tag, which enables one-step, off-target genome editing analysis in mouse liver and lung. The GUIDE-tag system utilizes tethering between the Cas9 nuclease and the DNA donor to increase the capture rate of nuclease-mediated DSBs and UMI incorporation via Tn5 tagmentation to avoid PCR bias. These components can be delivered as SpyCas9-mSA ribonucleoprotein complexes and biotin-dsDNA donor for in vivo editing analysis. GUIDE-tag enables detection of off-target sites where editing rates are ≥ 0.2%. UDiTaS analysis utilizing the same tagmented genomic DNA detects low frequency translocation events with off-target sites and large deletions in vivo. The SpyCas9-mSA and biotin-dsDNA system provides a method to capture DSB loci in vivo in a variety of tissues with a workflow that is amenable to analysis of gross genomic alterations that are associated with genome editing.
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Affiliation(s)
- Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jordan L Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stacy Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xiaolong Dong
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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47
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Brackett NF, Pomés A, Chapman MD. New Frontiers: Precise Editing of Allergen Genes Using CRISPR. FRONTIERS IN ALLERGY 2022; 2:821107. [PMID: 35386981 PMCID: PMC8974684 DOI: 10.3389/falgy.2021.821107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/24/2021] [Indexed: 11/14/2022] Open
Abstract
Genome engineering with clustered regularly interspaced short palindromic repeats (CRISPR) technology offers the unique potential for unequivocally deleting allergen genes at the source. Compared to prior gene editing approaches, CRISPR boasts substantial improvements in editing efficiency, throughput, and precision. CRISPR has demonstrated success in several clinical applications such as sickle cell disease and β-thalassemia, and preliminary knockout studies of allergenic proteins using CRISPR editing show promise. Given the advantages of CRISPR, as well as specific DNA targets in the allergen genes, CRISPR gene editing is a viable approach for tackling allergy, which may lead to significant disease improvement. This review will highlight recent applications of CRISPR editing of allergens, particularly cat allergen Fel d 1, and will discuss the advantages and limitations of this approach compared to existing treatment options.
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48
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Ittiprasert W, Chatupheeraphat C, Mann VH, Li W, Miller A, Ogunbayo T, Tran K, Alrefaei YN, Mentink-Kane M, Brindley PJ. RNA-Guided AsCas12a- and SpCas9-Catalyzed Knockout and Homology Directed Repair of the Omega-1 Locus of the Human Blood Fluke, Schistosoma mansoni. Int J Mol Sci 2022; 23:631. [PMID: 35054816 PMCID: PMC8775552 DOI: 10.3390/ijms23020631] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/17/2022] Open
Abstract
The efficiency of the RNA-guided AsCas12a nuclease of Acidaminococcus sp. was compared with SpCas9 from Streptococcus pyogenes, for functional genomics in Schistosoma mansoni. We deployed optimized conditions for the ratio of guide RNAs to the nuclease, donor templates, and electroporation parameters, to target a key schistosome enzyme termed omega-1. Programmed cleavages catalyzed by Cas12a and Cas9 resulted in staggered- and blunt-ended strand breaks, respectively. AsCas12a was more efficient than SpCas9 for gene knockout, as determined by TIDE analysis. CRISPResso2 analysis confirmed that most mutations were deletions. Knockout efficiency of both nucleases markedly increased in the presence of single-stranded oligodeoxynucleotide (ssODN) template. With AsCas12a, ssODNs representative of both the non-CRISPR target (NT) and target (T) strands were tested, resulting in KO efficiencies of 15.67, 28.71, and 21.43% in the SpCas9 plus ssODN, AsCas12a plus NT-ssODN, and AsCas12a plus T-ssODN groups, respectively. Trans-cleavage against the ssODNs by activated AsCas12a was not apparent in vitro. SpCas9 catalyzed more precise transgene insertion, with knock-in efficiencies of 17.07% for the KI_Cas9 group, 14.58% for KI_Cas12a-NT-ssODN, and 12.37% for KI_Cas12a-T-ssODN. Although AsCas12a induced fewer mutations per genome than SpCas9, the phenotypic impact on transcription and expression of omega-1 was similar for both nucleases.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Chawalit Chatupheeraphat
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Wenhui Li
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Taiwo Ogunbayo
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Kenny Tran
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Yousef N. Alrefaei
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Department of Medical Laboratory Technology, College of Health Sciences, PAEET, Adailiya, Kuwait City 73101, Kuwait
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
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49
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Oikemus SR, Pfister EL, Sapp E, Chase KO, Kennington LA, Hudgens E, Miller R, Zhu LJ, Chaudhary A, Mick EO, Sena-Esteves M, Wolfe SA, DiFiglia M, Aronin N, Brodsky MH. Allele-Specific Knockdown of Mutant Huntingtin Protein via Editing at Coding Region Single Nucleotide Polymorphism Heterozygosities. Hum Gene Ther 2022; 33:25-36. [PMID: 34376056 PMCID: PMC8819514 DOI: 10.1089/hum.2020.323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/26/2021] [Indexed: 01/03/2023] Open
Abstract
Huntington's disease (HD) is a devastating, autosomal dominant neurodegenerative disease caused by a trinucleotide repeat expansion in the huntingtin (HTT) gene. Inactivation of the mutant allele by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 based gene editing offers a possible therapeutic approach for this disease, but permanent disruption of normal HTT function might compromise adult neuronal function. Here, we use a novel HD mouse model to examine allele-specific editing of mutant HTT (mHTT), with a BAC97 transgene expressing mHTT and a YAC18 transgene expressing normal HTT. We achieve allele-specific inactivation of HTT by targeting a protein coding sequence containing a common, heterozygous single nucleotide polymorphism (SNP). The outcome is a marked and allele-selective reduction of mHTT protein in a mouse model of HD. Expression of a single CRISPR-Cas9 nuclease in neurons generated a high frequency of mutations in the targeted HD allele that included both small insertion/deletion (InDel) mutations and viral vector insertions. Thus, allele-specific targeting of InDel and insertion mutations to heterozygous coding region SNPs provides a feasible approach to inactivate autosomal dominant mutations that cause genetic disease.
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Affiliation(s)
- Sarah R. Oikemus
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Edith L. Pfister
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, Massachusetts, USA
| | - Kathryn O. Chase
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lori A. Kennington
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Edward Hudgens
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Rachael Miller
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Akanksh Chaudhary
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Eric O. Mick
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Miguel Sena-Esteves
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Scot A. Wolfe
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, Massachusetts, USA
| | - Neil Aronin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Michael H. Brodsky
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Sladen PE, Perdigão PR, Salsbury G, Novoselova T, van der Spuy J, Chapple JP, Yu-Wai-Man P, Cheetham ME. CRISPR-Cas9 correction of OPA1 c.1334G>A: p.R445H restores mitochondrial homeostasis in dominant optic atrophy patient-derived iPSCs. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:432-443. [PMID: 34589289 PMCID: PMC8455316 DOI: 10.1016/j.omtn.2021.08.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/09/2021] [Indexed: 12/26/2022]
Abstract
Autosomal dominant optic atrophy (DOA) is the most common inherited optic neuropathy in the United Kingdom. DOA has an insidious onset in early childhood, typically presenting with bilateral, central visual loss caused by the preferential loss of retinal ganglion cells. 60%-70% of genetically confirmed DOA cases are associated with variants in OPA1, a ubiquitously expressed GTPase that regulates mitochondrial homeostasis through coordination of inner membrane fusion, maintenance of cristae structure, and regulation of bioenergetic output. Whether genetic correction of OPA1 pathogenic variants can alleviate disease-associated phenotypes remains unknown. Here, we demonstrate generation of patient-derived OPA1 c.1334G>A: p.R445H mutant induced pluripotent stem cells (iPSCs), followed by correction of OPA1 through CRISPR-Cas9-guided homology-directed repair (HDR) and evaluate the effect of OPA1 correction on mitochondrial homeostasis. CRISPR-Cas9 gene editing demonstrated an efficient method of OPA1 correction, with successful gene correction in 57% of isolated iPSCs. Correction of OPA1 restored mitochondrial homeostasis, re-establishing the mitochondrial network and basal respiration and ATP production levels. In addition, correction of OPA1 re-established the levels of wild-type (WT) mitochondrial DNA (mtDNA) and reduced susceptibility to apoptotic stimuli. These data demonstrate that nuclear gene correction can restore mitochondrial homeostasis and improve mtDNA integrity in DOA patient-derived cells carrying an OPA1 variant.
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Affiliation(s)
- Paul E. Sladen
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | | | - Grace Salsbury
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Tatiana Novoselova
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - J. Paul Chapple
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Patrick Yu-Wai-Man
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Cambridge Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, ED Adrian Building, Robinson Way, Cambridge CB2 0PY, UK
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
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