1
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Perlee S, Ma Y, Hunter MV, Swanson JB, Ming Z, Xia J, Lionnet T, McGrail M, White RM. Identifying in vivo genetic dependencies of melanocyte and melanoma development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586101. [PMID: 38562693 PMCID: PMC10983904 DOI: 10.1101/2024.03.22.586101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The advent of large-scale sequencing in both development and disease has identified large numbers of candidate genes that may be linked to important phenotypes. Validating the function of these candidates in vivo is challenging, due to low efficiency and low throughput of most model systems. We have developed a rapid, scalable system for assessing the role of candidate genes using zebrafish. We generated transgenic zebrafish in which Cas9 was knocked-in to the endogenous mitfa locus, a master transcription factor of the melanocyte lineage. We used this system to identify both cell-autonomous and non-cell autonomous regulators of normal melanocyte development. We then applied this to the melanoma setting to demonstrate that loss of genes required for melanocyte survival can paradoxically promote more aggressive phenotypes, highlighting that in vitro screens can mask in vivo phenotypes. Our high-efficiency genetic approach offers a versatile tool for exploring developmental processes and disease mechanisms that can readily be applied to other cell lineages.
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2
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McKean DM, Zhang Q, Narayan P, Morton SU, Strohmenger V, Tang VT, McAllister S, Sharma A, Quiat D, Reichart D, DeLaughter DM, Wakimoto H, Gorham JM, Brown K, McDonough B, Willcox JA, Jang MY, DePalma SR, Ward T, Kim R, Cleveland JD, Seidman J, Seidman CE. Increased endothelial sclerostin caused by elevated DSCAM mediates multiple trisomy 21 phenotypes. J Clin Invest 2024; 134:e167811. [PMID: 38828726 PMCID: PMC11142749 DOI: 10.1172/jci167811] [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: 12/06/2022] [Accepted: 04/11/2024] [Indexed: 06/05/2024] Open
Abstract
Trisomy 21 (T21), a recurrent aneuploidy occurring in 1:800 births, predisposes to congenital heart disease (CHD) and multiple extracardiac phenotypes. Despite a definitive genetic etiology, the mechanisms by which T21 perturbs development and homeostasis remain poorly understood. We compared the transcriptome of CHD tissues from 49 patients with T21 and 226 with euploid CHD (eCHD). We resolved cell lineages that misexpressed T21 transcripts by cardiac single-nucleus RNA sequencing and RNA in situ hybridization. Compared with eCHD samples, T21 samples had increased chr21 gene expression; 11-fold-greater levels (P = 1.2 × 10-8) of SOST (chr17), encoding the Wnt inhibitor sclerostin; and 1.4-fold-higher levels (P = 8.7 × 10-8) of the SOST transcriptional activator ZNF467 (chr7). Euploid and T21 cardiac endothelial cells coexpressed SOST and ZNF467; however, T21 endothelial cells expressed 6.9-fold more SOST than euploid endothelial cells (P = 2.7 × 10-27). Wnt pathway genes were downregulated in T21 endothelial cells. Expression of DSCAM, residing within the chr21 CHD critical region, correlated with SOST (P = 1.9 × 10-5) and ZNF467 (P = 2.9 × 10-4). Deletion of DSCAM from T21 endothelial cells derived from human induced pluripotent stem cells diminished sclerostin secretion. As Wnt signaling is critical for atrioventricular canal formation, bone health, and pulmonary vascular homeostasis, we concluded that T21-mediated increased sclerostin levels would inappropriately inhibit Wnt activities and promote Down syndrome phenotypes. These findings imply therapeutic potential for anti-sclerostin antibodies in T21.
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Affiliation(s)
- David M. McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Priyanka Narayan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Walter Brendle Centre of Experimental Medicine, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Vi T. Tang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sophie McAllister
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ananya Sharma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Barbara McDonough
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jon A. Willcox
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven R. DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Richard Kim
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - John D. Cleveland
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - J.G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
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3
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Camps G, Maestro S, Torella L, Herrero D, Usai C, Bilbao-Arribas M, Aldaz A, Olagüe C, Vales A, Suárez-Amarán L, Aldabe R, Gonzalez-Aseguinolaza G. Protective role of RIPK1 scaffolding against HDV-induced hepatocyte cell death and the significance of cytokines in mice. PLoS Pathog 2024; 20:e1011749. [PMID: 38739648 PMCID: PMC11115361 DOI: 10.1371/journal.ppat.1011749] [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: 10/15/2023] [Revised: 05/23/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Hepatitis delta virus (HDV) infection represents the most severe form of human viral hepatitis; however, the mechanisms underlying its pathology remain incompletely understood. We recently developed an HDV mouse model by injecting adeno-associated viral vectors (AAV) containing replication-competent HBV and HDV genomes. This model replicates many features of human infection, including liver injury. Notably, the extent of liver damage can be diminished with anti-TNF-α treatment. Here, we found that TNF-α is mainly produced by macrophages. Downstream of the TNF-α receptor (TNFR), the receptor-interacting serine/threonine-protein kinase 1 (RIPK1) serves as a cell fate regulator, playing roles in both cell survival and death pathways. In this study, we explored the function of RIPK1 and other host factors in HDV-induced cell death. We determined that the scaffolding function of RIPK1, and not its kinase activity, offers partial protection against HDV-induced apoptosis. A reduction in RIPK1 expression in hepatocytes through CRISPR-Cas9-mediated gene editing significantly intensifies HDV-induced damage. Contrary to our expectations, the protective effect of RIPK1 was not linked to TNF-α or macrophage activation, as their absence did not alter the extent of damage. Intriguingly, in the absence of RIPK1, macrophages confer a protective role. However, in animals unresponsive to type-I IFNs, RIPK1 downregulation did not exacerbate the damage, suggesting RIPK1's role in shielding hepatocytes from type-I IFN-induced cell death. Interestingly, while the damage extent is similar between IFNα/βR KO and wild type mice in terms of transaminase elevation, their cell death mechanisms differ. In conclusion, our findings reveal that HDV-induced type-I IFN production is central to inducing hepatocyte death, and RIPK1's scaffolding function offers protective benefits. Thus, type-I IFN together with TNF-α, contribute to HDV-induced liver damage. These insights may guide the development of novel therapeutic strategies to mitigate HDV-induced liver damage and halt disease progression.
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Affiliation(s)
- Gracián Camps
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Sheila Maestro
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Laura Torella
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Diego Herrero
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Carla Usai
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Martin Bilbao-Arribas
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Ana Aldaz
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Cristina Olagüe
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Africa Vales
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Lester Suárez-Amarán
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Rafael Aldabe
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
| | - Gloria Gonzalez-Aseguinolaza
- DNA & RNA Medicine Division, CIMA, University of Navarra, Instituto de Investigación Sanitaria de Navarra, IdisNA, Pamplona, Spain
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4
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Gupta P, Goswami SG, Kumari G, Saravanakumar V, Bhargava N, Rai AB, Singh P, Bhoyar RC, Arvinden VR, Gunda P, Jain S, Narayana VK, Deolankar SC, Prasad TSK, Natarajan VT, Scaria V, Singh S, Ramalingam S. Development of pathophysiologically relevant models of sickle cell disease and β-thalassemia for therapeutic studies. Nat Commun 2024; 15:1794. [PMID: 38413594 PMCID: PMC10899644 DOI: 10.1038/s41467-024-46036-x] [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: 03/12/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Ex vivo cellular system that accurately replicates sickle cell disease and β-thalassemia characteristics is a highly sought-after goal in the field of erythroid biology. In this study, we present the generation of erythroid progenitor lines with sickle cell disease and β-thalassemia mutation using CRISPR/Cas9. The disease cellular models exhibit similar differentiation profiles, globin expression and proteome dynamics as patient-derived hematopoietic stem/progenitor cells. Additionally, these cellular models recapitulate pathological conditions associated with both the diseases. Hydroxyurea and pomalidomide treatment enhanced fetal hemoglobin levels. Notably, we introduce a therapeutic strategy for the above diseases by recapitulating the HPFH3 genotype, which reactivates fetal hemoglobin levels and rescues the disease phenotypes, thus making these lines a valuable platform for studying and developing new therapeutic strategies. Altogether, we demonstrate our disease cellular systems are physiologically relevant and could prove to be indispensable tools for disease modeling, drug screenings and cell and gene therapy-based applications.
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Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geeta Kumari
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vinodh Saravanakumar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Praveen Singh
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rahul C Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
| | - V R Arvinden
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society- Kamala Hospital and Research Centre, Shivarampally, Hyderabad, India
| | - Vanya Kadla Narayana
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Sayali C Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Vivek T Natarajan
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shailja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Prykhozhij SV, Berman JN. Mutation Knock-in Methods Using Single-Stranded DNA and Gene Editing Tools in Zebrafish. Methods Mol Biol 2024; 2707:279-303. [PMID: 37668920 DOI: 10.1007/978-1-0716-3401-1_19] [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] [Indexed: 09/06/2023]
Abstract
Introduction or knock-in of precise genomic modifications remains one of the most important applications of CRISPR/Cas9 in all model systems including zebrafish. The most widely used type of donor template containing the desired modification is single-stranded DNA (ssDNA), either in the form of single-stranded oligodeoxynucleotides (ssODN) (<150 nucleotides (nt)) or as long ssDNA (lssDNA) molecules (up to about 2000 nt). Despite the challenges posed by DNA repair after DNA double-strand breaks, knock-in of precise mutations is relatively straightforward in zebrafish. Knock-in efficiency can be enhanced by careful donor template design, using lssDNA as template or tethering the donor template DNA to the Cas9-guide RNA complex. Other point mutation methods such as base editing and prime editing are starting to be applied in zebrafish and many other model systems. However, these methods may not always be sufficiently accessible or may have limited capacity to perform all desired mutation knock-ins which are possible with ssDNA-based knock-in methods. Thus, it is likely that there will be complementarity in the technologies used for generating precise mutants. Here, we review and describe a suite of CRISPR/Cas9 knock-in procedures utilizing ssDNA as the donor template in zebrafish, point out the potential challenges and suggest possible approaches for their solution ultimately leading to successful generation of precise mutant lines.
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Affiliation(s)
- Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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6
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Torella L, Klermund J, Bilbao-Arribas M, Tamayo I, Andrieux G, Chmielewski KO, Vales A, Olagüe C, Moreno-Luqui D, Raimondi I, Abad A, Torrens-Baile J, Salido E, Huarte M, Hernaez M, Boerries M, Cathomen T, Zabaleta N, Gonzalez-Aseguinolaza G. Efficient and safe therapeutic use of paired Cas9-nickases for primary hyperoxaluria type 1. EMBO Mol Med 2024; 16:112-131. [PMID: 38182795 PMCID: PMC10897483 DOI: 10.1038/s44321-023-00008-8] [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: 06/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/07/2024] Open
Abstract
The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored the use of AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target the Hao1 gene for the treatment of primary hyperoxaluria type 1 (PH1). Our study demonstrated effective Hao1 gene disruption, a significant decrease in glycolate oxidase expression, and a therapeutic effect in PH1 mice. The assessment of undesired genetic modifications through CIRCLE-seq and CAST-Seq analyses revealed neither off-target activity nor chromosomal translocations. Importantly, the use of paired-D10ASaCas9 resulted in a significant reduction in AAV integration at the target site compared to SaCas9 nuclease. In addition, our study highlights the limitations of current analytical tools in characterizing modifications introduced by paired D10ASaCas9, necessitating the development of a custom pipeline for more accurate characterization. These results describe a positive advance towards a safe and effective potential long-term treatment for PH1 patients.
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Affiliation(s)
- Laura Torella
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Martin Bilbao-Arribas
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Ibon Tamayo
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
- Bioinformatics Core, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Africa Vales
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Cristina Olagüe
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Daniel Moreno-Luqui
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Ivan Raimondi
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Amaya Abad
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Julen Torrens-Baile
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, CIBERER, 38320, Tenerife, Spain
| | - Maite Huarte
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Mikel Hernaez
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
- Bioinformatics Core, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106, Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany.
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany.
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Harvard Medical School, 02114, Boston, MA, USA.
| | - Gloria Gonzalez-Aseguinolaza
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain.
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7
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Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F, Kappei D. ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun 2023; 14:8252. [PMID: 38086788 PMCID: PMC10716145 DOI: 10.1038/s41467-023-43397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist of TTAGGG repeats, which are bound by dedicated proteins such as the shelterin complex. This complex blocks unwanted DNA damage repair at telomeres, e.g. by suppressing nonhomologous end joining (NHEJ) through its subunit TRF2. Here, we describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity, and reveal base-specific sequence recognition by cocrystallization with telomeric DNA. ZNF524 localizes to telomeres and specifically maintains the presence of the TRF2/RAP1 subcomplex at telomeres without affecting other shelterin members. Loss of ZNF524 concomitantly results in an increase in DNA damage signaling and recombination events. Overall, ZNF524 is a direct telomere-binding protein involved in the maintenance of telomere integrity.
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Affiliation(s)
- Hanna Braun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Ziyan Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fiona Chang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Grishma Rane
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Michal Levin
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | | | - Franziska Roth
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Alexia Hillairet
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zi Wayne Sin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wai Khang Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Oliver Dreesen
- Cell Aging Laboratory, A*STAR Skin Research Labs, Singapore, 138648, Singapore
| | - Yang Yang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yunyu Shi
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany.
- Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, Greifswald, 17493, Germany.
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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8
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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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9
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Zhang P, Abel L, Casanova JL, Yang R. Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells. CRISPR J 2023; 6:462-472. [PMID: 37824834 PMCID: PMC10611965 DOI: 10.1089/crispr.2023.0021] [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: 04/03/2023] [Accepted: 09/10/2023] [Indexed: 10/14/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) creates double-stranded breaks, the repair of which generates indels around the target sites. These repairs can be mono-/multi-allelic, and the editing is often random and sometimes prolonged, resulting in considerable intercellular heterogeneity. The genotyping of CRISPR-Cas9-edited cells is challenging and the traditional genotyping methods are laborious. We introduce here a streamlined experimental and computational protocol for genotyping CRISPR-Cas9 genome-edited cells including cost-effective multiplexed sequencing and the software Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE). In this approach, CRISPR-Cas9-edited products are sequenced in great depth, then GMUSCLE quantitatively and qualitatively identifies the genotypes, which enable the selection and investigation of cell clones with genotypes of interest. We validate the protocol and software by performing CRISPR-Cas9-mediated disruption on interferon-α/β receptor alpha, multiplexed sequencing, and identifying the genotypes simultaneously for 20 cell clones. Besides the multiplexed sequencing ability of this protocol, GMUSCLE is also applicable for the sequencing data from bulk cell populations. GMUSCLE is publicly available at our HGIDSOFT server and GitHub.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA; and Necker Hospital for Sick Children, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
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10
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Neldeborg S, Soerensen JF, Møller CT, Bill M, Gao Z, Bak RO, Holm K, Sorensen B, Nyegaard M, Luo Y, Hokland P, Stougaard M, Ludvigsen M, Holm CK. Dual intron-targeted CRISPR-Cas9-mediated disruption of the AML RUNX1-RUNX1T1 fusion gene effectively inhibits proliferation and decreases tumor volume in vitro and in vivo. Leukemia 2023; 37:1792-1801. [PMID: 37464068 PMCID: PMC10457201 DOI: 10.1038/s41375-023-01950-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023]
Abstract
Oncogenic fusion drivers are common in hematological cancers and are thus relevant targets of future CRISPR-Cas9-based treatment strategies. However, breakpoint-location variation in patients pose a challenge to traditional breakpoint-targeting CRISPR-Cas9-mediated disruption strategies. Here we present a new dual intron-targeting CRISPR-Cas9 treatment strategy, for targeting t(8;21) found in 5-10% of de novo acute myeloid leukemia (AML), which efficiently disrupts fusion genes without prior identification of breakpoint location. We show in vitro growth rate and proliferation reduction by 69 and 94% in AML t(8;21) Kasumi-1 cells, following dual intron-targeted disruption of RUNX1-RUNX1T1 compared to a non t(8;21) AML control. Furthermore, mice injected with RUNX1-RUNX1T1-disrupted Kasumi-1 cells had in vivo tumor growth reduction by 69 and 91% compared to controls. Demonstrating the feasibility of RUNX1-RUNX1T1 disruption, these findings were substantiated in isolated primary cells from a patient diagnosed with AML t(8;21). In conclusion, we demonstrate proof-of-principle of a dual intron-targeting CRISPR-Cas9 treatment strategy in AML t(8;21) without need for precise knowledge of the breakpoint location.
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Affiliation(s)
- Signe Neldeborg
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Johannes Frasez Soerensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Zongliang Gao
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Boe Sorensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Hokland
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Danish Life Science Cluster, Copenhagen, Denmark
| | - Maja Ludvigsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.
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11
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Lumaquin-Yin D, Montal E, Johns E, Baggiolini A, Huang TH, Ma Y, LaPlante C, Suresh S, Studer L, White RM. Lipid droplets are a metabolic vulnerability in melanoma. Nat Commun 2023; 14:3192. [PMID: 37268606 PMCID: PMC10238408 DOI: 10.1038/s41467-023-38831-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/17/2023] [Indexed: 06/04/2023] Open
Abstract
Melanoma exhibits numerous transcriptional cell states including neural crest-like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here, we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets, the specialized organelle responsible for lipid storage. Single-cell RNA-sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake, an increased number of lipid droplets, and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients, these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle.
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Affiliation(s)
- Dianne Lumaquin-Yin
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Emily Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Eleanor Johns
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yilun Ma
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Charlotte LaPlante
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lorenz Studer
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- University of Oxford, Ludwig Cancer Research, Nuffield Department of Medicine, Oxford, UK.
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12
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Lee A, Park HJ, Jo SH, Jung H, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The spliceophilin CYP18-2 is mainly involved in the splicing of retained introns under heat stress in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1113-1133. [PMID: 36636802 DOI: 10.1111/jipb.13450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/12/2023] [Indexed: 05/13/2023]
Abstract
Peptidyl-prolyl isomerase-like 1 (PPIL1) is associated with the human spliceosome complex. However, its function in pre-mRNA splicing remains unclear. In this study, we show that Arabidopsis thaliana CYCLOPHILIN 18-2 (AtCYP18-2), a PPIL1 homolog, plays an essential role in heat tolerance by regulating pre-mRNA splicing. Under heat stress conditions, AtCYP18-2 expression was upregulated in mature plants and GFP-tagged AtCYP18-2 redistributed to nuclear and cytoplasmic puncta. We determined that AtCYP18-2 interacts with several spliceosome complex BACT components in nuclear puncta and is primarily associated with the small nuclear RNAs U5 and U6 in response to heat stress. The AtCYP18-2 loss-of-function allele cyp18-2 engineered by CRISPR/Cas9-mediated gene editing exhibited a hypersensitive phenotype to heat stress relative to the wild type. Moreover, global transcriptome profiling showed that the cyp18-2 mutation affects alternative splicing of heat stress-responsive genes under heat stress conditions, particularly intron retention (IR). The abundance of most intron-containing transcripts of a subset of genes essential for thermotolerance decreased in cyp18-2 compared to the wild type. Furthermore, the intron-containing transcripts of two heat stress-related genes, HEAT SHOCK PROTEIN 101 (HSP101) and HEAT SHOCK FACTOR A2 (HSFA2), produced functional proteins. HSP101-IR-GFP localization was responsive to heat stress, and HSFA2-III-IR interacted with HSF1 and HSP90.1 in plant cells. Our findings reveal that CYP18-2 functions as a splicing factor within the BACT spliceosome complex and is crucial for ensuring the production of adequate levels of alternatively spliced transcripts to enhance thermotolerance.
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Affiliation(s)
- Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, UST, Daejeon, 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo Bio, Anseong, 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Korea
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13
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Esquerra-Ruvira B, Baquedano I, Ruiz R, Fernandez A, Montoliu L, Mojica FJM. Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering. Microb Biotechnol 2023. [PMID: 37097160 DOI: 10.1111/1751-7915.14266] [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: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins of the prokaryotic CRISPR-Cas systems form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools for in vivo and in vitro modification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of the Streptococcus pyogenes SpCas9 are the most widely used for genome engineering, at least in part due to their catalytic robustness and the requirement of an exceptionally short motif (5'-NGG-3' PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are desirable. Here, we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5'-NGG-3' PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.
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Affiliation(s)
- Belen Esquerra-Ruvira
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ignacio Baquedano
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Raul Ruiz
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Francisco J M Mojica
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
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14
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Naeem M, Alkhnbashi OS. Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects. Int J Mol Sci 2023; 24:ijms24076261. [PMID: 37047235 PMCID: PMC10094584 DOI: 10.3390/ijms24076261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
The CRISPR-Cas system has evolved into a cutting-edge technology that has transformed the field of biological sciences through precise genetic manipulation. CRISPR/Cas9 nuclease is evolving into a revolutionizing method to edit any gene of any species with desirable outcomes. The swift advancement of CRISPR-Cas technology is reflected in an ever-expanding ecosystem of bioinformatics tools designed to make CRISPR/Cas9 experiments easier. To assist researchers with efficient guide RNA designs with fewer off-target effects, nuclease target site selection, and experimental validation, bioinformaticians have built and developed a comprehensive set of tools. In this article, we will review the various computational tools available for the assessment of off-target effects, as well as the quantification of nuclease activity and specificity, including web-based search tools and experimental methods, and we will describe how these tools can be optimized for gene knock-out (KO) and gene knock-in (KI) for model organisms. We also discuss future directions in precision genome editing and its applications, as well as challenges in target selection, particularly in predicting off-target effects.
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15
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Suzuki M, Iida M, Hayashi T, Suzuki KIT. CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. Methods Mol Biol 2023; 2637:341-357. [PMID: 36773159 DOI: 10.1007/978-1-0716-3016-7_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Amphibians have made many fundamental contributions to our knowledge, from basic biology to biomedical research on human diseases. Current genome editing tools based on the CRISPR-Cas system enable us to perform gene functional analysis in vivo, even in non-model organisms. We introduce here a highly efficient and easy protocol for gene knockout, which can be used in three different amphibians seamlessly: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. As it utilizes Cas9 ribonucleoprotein complex (RNP) for injection, this cloning-free method enables researchers to obtain founder embryos with a nearly complete knockout phenotype within a week. To evaluate somatic mutation rate and its correlation to the phenotype of a Cas9 RNP-injected embryo (crispant), we also present accurate and cost-effective genotyping methods using pooled amplicon-sequencing and a user-friendly web-based tool.
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Affiliation(s)
- Miyuki Suzuki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Midori Iida
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Fukuoka, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, Okazaki, Aichi, Japan.
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16
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Suresh S, Rabbie R, Garg M, Lumaquin D, Huang TH, Montal E, Ma Y, Cruz NM, Tang X, Nsengimana J, Newton-Bishop J, Hunter MV, Zhu Y, Chen K, de Stanchina E, Adams DJ, White RM. Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma. Cancer Discov 2023; 13:194-215. [PMID: 36259947 PMCID: PMC9827116 DOI: 10.1158/2159-8290.cd-22-0427] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/25/2022] [Accepted: 10/14/2022] [Indexed: 01/16/2023]
Abstract
In melanoma, predicting which tumors will ultimately metastasize guides treatment decisions. Transcriptional signatures of primary tumors have been utilized to predict metastasis, but which among these are driver or passenger events remains unclear. We used data from the adjuvant AVAST-M trial to identify a predictive gene signature in localized tumors that ultimately metastasized. Using a zebrafish model of primary melanoma, we interrogated the top genes from the AVAST-M signature in vivo. This identified GRAMD1B, a cholesterol transfer protein, as a bona fide metastasis suppressor, with a majority of knockout animals rapidly developing metastasis. Mechanistically, excess free cholesterol or its metabolite 27-hydroxycholesterol promotes invasiveness via activation of an AP-1 program, which is associated with increased metastasis in humans. Our data demonstrate that the transcriptional seeds of metastasis are embedded within localized tumors, suggesting that early targeting of these programs can be used to prevent metastatic relapse. SIGNIFICANCE We analyzed human melanoma transcriptomics data to identify a gene signature predictive of metastasis. To rapidly test clinical signatures, we built a genetic metastasis platform in adult zebrafish and identified GRAMD1B as a suppressor of melanoma metastasis. GRAMD1B-associated cholesterol overload activates an AP-1 program to promote melanoma invasion. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roy Rabbie
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Manik Garg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Dianne Lumaquin
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yilun Ma
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York
| | - Nelly M Cruz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xinran Tang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Biochemistry and Structural Biology, Cellular and Developmental Biology and Molecular Biology Ph.D. Program, Weill Cornell Graduate School of Medical Sciences, New York, New York
| | - Jérémie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Miranda V. Hunter
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuxin Zhu
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kevin Chen
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Richard M. White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
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17
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Dorison A, Ghobrial I, Graham A, Peiris T, Forbes TA, See M, Das M, Saleem MA, Quinlan C, Lawlor KT, Ramialison M, Howden SE, Little MH. Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking. J Am Soc Nephrol 2023; 34:88-109. [PMID: 36167728 PMCID: PMC10101587 DOI: 10.1681/asn.2022060707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND NPHS2 variants are the most common cause of steroid-resistant nephrotic syndrome in children >1 month old. Missense NPHS2 variants were reported to cause mistrafficking of the encoded protein, PODOCIN, but this conclusion was on the basis of overexpression in some nonpodocyte cell lines. METHODS We generated a series of human induced pluripotent stem cell (iPSC) lines bearing pathogenic missense variants of NPHS2 , encoding the protein changes p.G92C, p.P118L, p.R138Q, p.R168H, and p.R291W, and control lines. iPSC lines were also generated from a patient with steroid-resistant nephrotic syndrome (p.R168H homozygote) and a healthy heterozygous parent. All lines were differentiated into kidney organoids. Immunofluorescence assessed PODOCIN expression and subcellular localization. Podocytes were transcriptionally profiled and PODOCIN-NEPHRIN interaction interrogated. RESULTS All variant lines revealed reduced levels of PODOCIN protein in the absence of reduced transcription. Although wild-type PODOCIN localized to the membrane, distinct variant proteins displayed unique patterns of subcellular protein trafficking, some unreported. P118L and R138Q were preferentially retained in the endoplasmic reticulum (ER); R168H and R291W accumulated in the Golgi. Podocyte profiling demonstrated minimal disease-associated transcriptional change. All variants displayed podocyte-specific apoptosis, which was not linked to ER stress. NEPHRIN-PODOCIN colocalization elucidated the variant-specific effect on NEPHRIN association and hence NEPHRIN trafficking. CONCLUSIONS Specific variants of endogenous NPHS2 result in distinct subcellular PODOCIN localization within organoid podocytes. Understanding the effect of each variant on protein levels and localization and the effect on NEPHRIN provides additional insight into the pathobiology of NPHS2 variants. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/JASN/2023_01_05_JASN2022060707.mp3.
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Affiliation(s)
- Aude Dorison
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Irene Ghobrial
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - Alison Graham
- Murdoch Children’s Research Institute, Melbourne, Australia
| | | | - Thomas A. Forbes
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Royal Children’s Hospital, Melbourne, Australia
| | - Michael See
- Murdoch Children’s Research Institute, Melbourne, Australia
- Monash Bioinformatics Platform, Monash University, Clayton, Australia
| | - Mithun Das
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - Moin A. Saleem
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Catherine Quinlan
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Royal Children’s Hospital, Melbourne, Australia
| | - Kynan T. Lawlor
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mirana Ramialison
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
- Australian Regenerative Medicine Institute, Clayton, Australia
| | - Sara E. Howden
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Melissa H. Little
- Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Novo Nordisk Foundation Centre for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
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18
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Alonso-Lerma B, Jabalera Y, Samperio S, Morin M, Fernandez A, Hille LT, Silverstein RA, Quesada-Ganuza A, Reifs A, Fernández-Peñalver S, Benitez Y, Soletto L, Gavira JA, Diaz A, Vranken W, Sanchez-Mejias A, Güell M, Mojica FJM, Kleinstiver BP, Moreno-Pelayo MA, Montoliu L, Perez-Jimenez R. Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins. Nat Microbiol 2023; 8:77-90. [PMID: 36593295 DOI: 10.1038/s41564-022-01265-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/07/2022] [Indexed: 01/03/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 is an effector protein that targets invading DNA and plays a major role in the prokaryotic adaptive immune system. Although Streptococcus pyogenes CRISPR-Cas9 has been widely studied and repurposed for applications including genome editing, its origin and evolution are poorly understood. Here, we investigate the evolution of Cas9 from resurrected ancient nucleases (anCas) in extinct firmicutes species that last lived 2.6 billion years before the present. We demonstrate that these ancient forms were much more flexible in their guide RNA and protospacer-adjacent motif requirements compared with modern-day Cas9 enzymes. Furthermore, anCas portrays a gradual palaeoenzymatic adaptation from nickase to double-strand break activity, exhibits high levels of activity with both single-stranded DNA and single-stranded RNA targets and is capable of editing activity in human cells. Prediction and characterization of anCas with a resurrected protein approach uncovers an evolutionary trajectory leading to functionally flexible ancient enzymes.
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Affiliation(s)
| | | | | | - Matias Morin
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Logan T Hille
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,PhD Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel A Silverstein
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,PhD Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | | | | | - Sergio Fernández-Peñalver
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Yolanda Benitez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain.,INGEMM, Hospital Universitario La Paz, Madrid, Spain
| | - Lucia Soletto
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, Armilla, Spain
| | - Adrian Diaz
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Centre, VIB, Brussels, Belgium
| | | | - Marc Güell
- Integra Therapeutics S.L., Barcelona, Spain.,Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología and Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, Madrid, Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology and Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Raul Perez-Jimenez
- CIC nanoGUNE BRTA, San Sebastian, Spain. .,Ikerbasque Foundation for Science, Bilbao, Spain.
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19
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Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun 2022; 13:6568. [PMID: 36323688 PMCID: PMC9630310 DOI: 10.1038/s41467-022-34320-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi), CRISPR base editing (CRISPRbe) and CRISPR knockdown (CRISPRkd). The core package, crisprDesign, offers a user-friendly and unified interface to add off-target annotations, rich gene and SNP annotations, and on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. The crisprVerse ecosystem is open-source and deployed through the Bioconductor project ( https://github.com/crisprVerse ).
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Affiliation(s)
- Luke Hoberecht
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Aaron Lun
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jean-Philippe Fortin
- Genentech Research and Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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20
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van Schendel R, Schimmel J, Tijsterman M. SIQ: easy quantitative measurement of mutation profiles in sequencing data. NAR Genom Bioinform 2022; 4:lqac063. [PMID: 36071722 PMCID: PMC9442499 DOI: 10.1093/nargab/lqac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-mine and visualize complex sets of targeted sequencing data. SIQ can analyse Sanger sequences but specifically benefit the processing of short- and long-read next-generation sequencing data (e.g. Illumina and PacBio). SIQ facilitates their interpretation by establishing mutational profiles, with a focus on event classification such as deletions, single-nucleotide variations, (templated) insertions and tandem duplications. SIQ results can be directly analysed and visualized via SIQPlotteR, an interactive web tool that we made freely available. Using insightful tornado plot visualizations as outputs, we illustrate that SIQ readily identifies sequence- and repair pathway-specific mutational signatures in a variety of model systems, such as nematodes, plants and mammalian cell culture.
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Affiliation(s)
- Robin van Schendel
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joost Schimmel
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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21
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Vergara X, Schep R, Medema RH, van Steensel B. From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies. DNA Repair (Amst) 2022; 118:103388. [PMID: 36037787 DOI: 10.1016/j.dnarep.2022.103388] [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: 06/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
Technologies to study DNA double-strand break (DSB) repair have traditionally mostly relied on fluorescence read-outs, either by microscopy or flow cytometry. The advent of high throughput sequencing (HTS) has created fundamentally new opportunities to study the mechanisms underlying DSB repair. Here, we review the suite of HTS-based assays that are used to study three different aspects of DNA repair: detection of broken ends, protein recruitment and pathway usage. We highlight new opportunities that HTS technology offers towards a better understanding of the DSB repair process.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, the Netherlands.
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22
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Moya-Jódar M, Coppiello G, Rodríguez-Madoz JR, Abizanda G, Barlabé P, Vilas-Zornoza A, Ullate-Agote A, Luongo C, Rodríguez-Tobón E, Navarro-Serna S, París-Oller E, Oficialdegui M, Carvajal-Vergara X, Ordovás L, Prósper F, García-Vázquez FA, Aranguren XL. One-Step In Vitro Generation of ETV2-Null Pig Embryos. Animals (Basel) 2022; 12:ani12141829. [PMID: 35883376 PMCID: PMC9311767 DOI: 10.3390/ani12141829] [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: 04/27/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary One of the latest goals in regenerative medicine is to use pluripotent stem cells to generate whole organs in vivo through the blastocyst complementation technique. This method consists of the microinjection of pluripotent stem cells into preimplantation embryos that have been genetically modified to ablate the development of a target organ. By taking advantage of the spatiotemporal clues present in the developing embryo, pluripotent stem cells are able to colonize the empty developmental niche and create the missing organ. Combining human pluripotent stem cells with genetically engineered pig embryos, it would be possible to obtain humanized organs that could be used for transplantation, and, therefore, solve the worldwide issue of insufficient availability of transplantable organs. As endothelial cells play a critical role in xenotransplantation rejection in all organs, in this study, we optimized a protocol to generate a vascular-disabled preimplantation pig embryo using the CRISPR/Cas9 system. This protocol could be used to generate avascular embryos for blastocyst complementation experiments and work towards the generation of rejection-free humanized organs in pigs. Abstract Each year, tens of thousands of people worldwide die of end-stage organ failure due to the limited availability of organs for use in transplantation. To meet this clinical demand, one of the last frontiers of regenerative medicine is the generation of humanized organs in pigs from pluripotent stem cells (PSCs) via blastocyst complementation. For this, organ-disabled pig models are needed. As endothelial cells (ECs) play a critical role in xenotransplantation rejection in every organ, we aimed to produce hematoendothelial-disabled pig embryos targeting the master transcription factor ETV2 via CRISPR-Cas9-mediated genome modification. In this study, we designed five different guide RNAs (gRNAs) against the DNA-binding domain of the porcine ETV2 gene, which were tested on porcine fibroblasts in vitro. Four out of five guides showed cleavage capacity and, subsequently, these four guides were microinjected individually as ribonucleoprotein complexes (RNPs) into one-cell-stage porcine embryos. Next, we combined the two gRNAs that showed the highest targeting efficiency and microinjected them at higher concentrations. Under these conditions, we significantly improved the rate of biallelic mutation. Hence, here, we describe an efficient one-step method for the generation of hematoendothelial-disabled pig embryos via CRISPR-Cas9 microinjection in zygotes. This model could be used in experimentation related to the in vivo generation of humanized organs.
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Affiliation(s)
- Marta Moya-Jódar
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Giulia Coppiello
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Juan Roberto Rodríguez-Madoz
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Gloria Abizanda
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Paula Barlabé
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Amaia Vilas-Zornoza
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - Asier Ullate-Agote
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - Chiara Luongo
- Department of Physiology, Veterinary School, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, 30100 Murcia, Spain; (C.L.); (E.R.-T.); (S.N.-S.); (E.P.-O.)
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Ernesto Rodríguez-Tobón
- Department of Physiology, Veterinary School, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, 30100 Murcia, Spain; (C.L.); (E.R.-T.); (S.N.-S.); (E.P.-O.)
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Sergio Navarro-Serna
- Department of Physiology, Veterinary School, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, 30100 Murcia, Spain; (C.L.); (E.R.-T.); (S.N.-S.); (E.P.-O.)
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | - Evelyne París-Oller
- Department of Physiology, Veterinary School, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, 30100 Murcia, Spain; (C.L.); (E.R.-T.); (S.N.-S.); (E.P.-O.)
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
| | | | - Xonia Carvajal-Vergara
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
| | - Laura Ordovás
- Aragon Agency for Research and Development (ARAID), 50018 Zaragoza, Spain;
- Biomedical Signal Interpretation and Computational Simulation (BSICoS), Institute of Engineering Research (I3A), University of Zaragoza & Instituto de Investigación Sanitaria (IIS), 50018 Zaragoza, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain
- Department of Hematology and Cell Therapy, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Francisco Alberto García-Vázquez
- Department of Physiology, Veterinary School, International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), University of Murcia, 30100 Murcia, Spain; (C.L.); (E.R.-T.); (S.N.-S.); (E.P.-O.)
- Institute for Biomedical Research of Murcia, IMIB-Arrixaca, 30100 Murcia, Spain
- Correspondence: (F.A.G.-V.); (X.L.A.)
| | - Xabier L. Aranguren
- Program of Regenerative Medicine, Centre for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), University of Navarra, 31008 Pamplona, Spain; (M.M.-J.); (G.C.); (J.R.R.-M.); (G.A.); (P.B.); (A.U.-A.); (X.C.-V.); (F.P.)
- Correspondence: (F.A.G.-V.); (X.L.A.)
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23
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In vivo CRISPR-Cas9 inhibition of hepatic LDH as treatment of primary hyperoxaluria. Mol Ther Methods Clin Dev 2022; 25:137-146. [PMID: 35402636 PMCID: PMC8971349 DOI: 10.1016/j.omtm.2022.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 03/14/2022] [Indexed: 12/26/2022]
Abstract
Genome-editing strategies, especially CRISPR-Cas9 systems, have substantially increased the efficiency of innovative therapeutic approaches for monogenic diseases such as primary hyperoxalurias (PHs). We have previously demonstrated that inhibition of glycolate oxidase using CRISPR-Cas9 systems represents a promising therapeutic option for PH type I (PH1). Here, we extended our work evaluating the efficacy of liver-specific inhibition of lactate dehydrogenase (LDH), a key enzyme responsible for converting glyoxylate to oxalate; this strategy would not be limited to PH1, being applicable to other PH subtypes. In this work, we demonstrate a liver-specific inhibition of LDH that resulted in a drastic reduction of LDH levels in the liver of PH1 and PH3 mice after a single-dose delivery of AAV8 vectors expressing the CRISPR-Cas9 system, resulting in reduced urine oxalate levels and kidney damage without signs of toxicity. Deep sequencing analysis revealed that this approach was safe and specific, with no off-targets detected in the liver of treated animals and no on-target/off-tissue events. Altogether, our data provide evidence that in vivo genome editing using CRISPR-Cas9 systems would represent a valuable tool for improved therapeutic approaches for PH.
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24
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A functional map of HIV-host interactions in primary human T cells. Nat Commun 2022; 13:1752. [PMID: 35365639 PMCID: PMC8976027 DOI: 10.1038/s41467-022-29346-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.
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25
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Weiss JM, Hunter MV, Cruz NM, Baggiolini A, Tagore M, Ma Y, Misale S, Marasco M, Simon-Vermot T, Campbell NR, Newell F, Wilmott JS, Johansson PA, Thompson JF, Long GV, Pearson JV, Mann GJ, Scolyer RA, Waddell N, Montal ED, Huang TH, Jonsson P, Donoghue MTA, Harris CC, Taylor BS, Xu T, Chaligné R, Shliaha PV, Hendrickson R, Jungbluth AA, Lezcano C, Koche R, Studer L, Ariyan CE, Solit DB, Wolchok JD, Merghoub T, Rosen N, Hayward NK, White RM. Anatomic position determines oncogenic specificity in melanoma. Nature 2022; 604:354-361. [PMID: 35355015 PMCID: PMC9355078 DOI: 10.1038/s41586-022-04584-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/25/2022] [Indexed: 12/19/2022]
Abstract
Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programmes in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma and enrichment for CRKL amplifications in acral melanoma. We modelled these changes in transgenic zebrafish models and found that CRKL-driven tumours formed predominantly in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin and limb melanocytes, when compared with body melanocytes, revealed a positional identity gene programme typified by posterior HOX13 genes. This positional gene programme synergized with CRKL to amplify insulin-like growth factor (IGF) signalling and drive tumours at acral sites. Abrogation of this CRKL-driven programme eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.
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Affiliation(s)
- Joshua M Weiss
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Miranda V Hunter
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nelly M Cruz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arianna Baggiolini
- Developmental Biology, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohita Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yilun Ma
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Sandra Misale
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theresa Simon-Vermot
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nathaniel R Campbell
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Emily D Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher C Harris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianhao Xu
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligné
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pavel V Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald Hendrickson
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cecilia Lezcano
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- Developmental Biology, The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte E Ariyan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Weill Cornell Medicine, New York, NY, USA
| | | | - Neal Rosen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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27
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Computational tools and resources for CRISPR/Cas genome editing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00027-4. [PMID: 35341983 PMCID: PMC10372911 DOI: 10.1016/j.gpb.2022.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 12/21/2022]
Abstract
The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) nucleases and their functional variants as well as in developing precise CRISPR/Cas-derived genome editors. The programmable and robust features of the genomic editors provide an effective RNA-guided platform for fundamental life science research and subsequent applications in diverse scenarios, including biomedical innovation and targeted crop improvement. One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts, which strongly depends on the efficiency and specificity of single guide RNA (sgRNA)-directed recognition of targeted DNA sequences. Recent advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target prediction. In this review, we first briefly introduced the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes. Secondly, we focused on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on- and off-target mutations. Thirdly, we provide insights on the limitations of available computational tools that surely help researchers of this field for further optimization. Lastly, we suggested a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.
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28
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Uribe-Salazar JM, Kaya G, Sekar A, Weyenberg K, Ingamells C, Dennis MY. Evaluation of CRISPR gene-editing tools in zebrafish. BMC Genomics 2022; 23:12. [PMID: 34986794 PMCID: PMC8734261 DOI: 10.1186/s12864-021-08238-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/04/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Zebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. In particular, the use of G0 mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies. METHODS To systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G0-based CRISPR screens by assaying control embryos for spurious mutations and altered gene expression. RESULTS We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (< 1%). To characterize if commonly used 'mock' CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation. CONCLUSION Overall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.
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Affiliation(s)
- José M Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Gulhan Kaya
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Aadithya Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - KaeChandra Weyenberg
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Cole Ingamells
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, USA.
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29
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Kwanten B, Neggers JE, Daelemans D. Target Identification of Small Molecules Using Large-Scale CRISPR-Cas Mutagenesis Scanning of Essential Genes. Methods Mol Biol 2022; 2377:43-67. [PMID: 34709610 DOI: 10.1007/978-1-0716-1720-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Target deconvolution of new bioactive agents identified from phenotypic screens remains a challenging task. The discovery of mutations that confer resistance to such agents is regarded as the gold standard proof of target identification. Here, we describe a method that exploits the error-prone repair of CRISPR-induced DNA double-strand breaks to enhance mutagenesis and increase the incidence of drug resistance mutations in essential genes. As each DNA double-strand break is introduced at a targeted genomic site predefined by the presence of a protospacer adjacent motif (PAM) and a particular CRISPR single guide RNA (sgRNA), the genetic location of drug resistance mutations can be easily uncovered through targeted sequencing of CRISPR sgRNAs. Moreover, the method allows for the identification of not only the drug target gene, but also the drug-binding domain within the target gene.
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Affiliation(s)
- Bert Kwanten
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
| | - Jasper Edgar Neggers
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
- Promakhos Therapeutics, Pagliuca Harvard Life Lab, Allston, Massachusetts, USA
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium.
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30
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Abstract
:
Clustered regularly interspaced short palindromic repeats along with CRISPR-associated protein
mechanisms preserve the memory of previous experiences with DNA invaders, in particular spacers
that are embedded in CRISPR arrays between coordinate repeats. There has been a fast progression in
the comprehension of this immune system and its implementations; however, there are numerous points
of view that anticipate explanations to make the field an energetic research zone. The efficiency of
CRISPR-Cas depends upon well-considered single guide RNA; for this purpose, many bioinformatics
methods and tools are created to support the design of greatly active and precise single guide RNA. Insilico
single guide RNA architecture is a crucial point for effective gene editing by means of the
CRISPR technique. Persistent attempts have been made to improve in-silico single guide RNA formulation
having great on-target effectiveness and decreased off-target effects. This review offers a summary
of the CRISPR computational tools to help different researchers pick a specific tool for their work according
to pros and cons, along with new thoughts to make new computational tools to overcome all existing
limitations.
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Affiliation(s)
- Mohsin Ali Nasir
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Samia Nawaz
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
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31
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Douglas C, Maciulyte V, Zohren J, Snell DM, Mahadevaiah SK, Ojarikre OA, Ellis PJI, Turner JMA. CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes. Nat Commun 2021; 12:6926. [PMID: 34862376 PMCID: PMC8642469 DOI: 10.1038/s41467-021-27227-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Animals are essential genetic tools in scientific research and global resources in agriculture. In both arenas, a single sex is often required in surplus. The ethical and financial burden of producing and culling animals of the undesired sex is considerable. Using the mouse as a model, we develop a synthetic lethal, bicomponent CRISPR-Cas9 strategy that produces male- or female-only litters with one hundred percent efficiency. Strikingly, we observe a degree of litter size compensation relative to control matings, indicating that our system has the potential to increase the yield of the desired sex in comparison to standard breeding designs. The bicomponent system can also be repurposed to generate postnatal sex-specific phenotypes. Our approach, harnessing the technological applications of CRISPR-Cas9, may be applicable to other vertebrate species, and provides strides towards ethical improvements for laboratory research and agriculture.
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Affiliation(s)
- Charlotte Douglas
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Valdone Maciulyte
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Obah A Ojarikre
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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32
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Benamozig O, Baudrier L, Billon P. A detection method for the capture of genomic signatures: From disease diagnosis to genome editing. Methods Enzymol 2021; 661:251-282. [PMID: 34776215 DOI: 10.1016/bs.mie.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Variations in the genetic information originate from errors during DNA replication, error-prone repair of DNA damages, or genome editing. The most common approach to detect changes in DNA sequences employs sequencing technologies. However, they remain expensive and time-consuming, limiting their utility for routine laboratory experiments. We recently developed DinucleoTidE Signature CapTure (DTECT). DTECT is a marker-free and versatile detection method that captures targeted dinucleotide signatures resulting from the digestion of genomic amplicons by the type IIS restriction enzyme AcuI. Here, we describe the DTECT protocol to identify mutations introduced by CRISPR-based precision genome editing technologies or resulting from genetic variation. DTECT enables accurate detection of mutations using basic laboratory equipment and off-the-shelf reagents with qualitative or quantitative capture of signatures.
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Affiliation(s)
- Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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33
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Lea RA, McCarthy A, Boeing S, Fallesen T, Elder K, Snell P, Christie L, Adkins S, Shaikly V, Taranissi M, Niakan KK. KLF17 promotes human naïve pluripotency but is not required for its establishment. Development 2021; 148:272511. [PMID: 34661235 PMCID: PMC8645209 DOI: 10.1242/dev.199378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of interspecies conservation observed. Single-cell transcriptomics analysis of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve human embryonic stem cells (hESCs). Here, we show that KLF17 is expressed coincident with the known pluripotency-associated factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisition in vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling pathways following KLF17 loss of function, and possible redundancy with other KLF paralogues. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the given in vitro conditions. Summary: Given that KLF17 was shown to be sufficient, but not necessary, to establish naïve pluripotent hESCs, KLF17 might function as a peripheral regulator of human pluripotent stem cells.
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Affiliation(s)
- Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Todd Fallesen
- Crick Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Sarah Adkins
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | - Valerie Shaikly
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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34
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Avagyan S, Henninger JE, Mannherz WP, Mistry M, Yoon J, Yang S, Weber MC, Moore JL, Zon LI. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis. Science 2021; 374:768-772. [PMID: 34735227 DOI: 10.1126/science.aba9304] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- S Avagyan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - J E Henninger
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - M Mistry
- Harvard Chan Bioinformatics Core, Boston, MA, USA
| | - J Yoon
- Harvard Chan Bioinformatics Core, Boston, MA, USA
| | - S Yang
- Boston Children's Hospital, Boston, MA, USA
| | - M C Weber
- Boston Children's Hospital, Boston, MA, USA
| | - J L Moore
- Boston Children's Hospital, Boston, MA, USA
| | - L I Zon
- Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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35
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Shen Y, Jiang L, Iyer VS, Raposo B, Dubnovitsky A, Boddul SV, Kasza Z, Wermeling F. A rapid CRISPR competitive assay for in vitro and in vivo discovery of potential drug targets affecting the hematopoietic system. Comput Struct Biotechnol J 2021; 19:5360-5370. [PMID: 34745454 PMCID: PMC8531760 DOI: 10.1016/j.csbj.2021.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/29/2021] [Accepted: 09/16/2021] [Indexed: 12/24/2022] Open
Abstract
CRISPR/Cas9 can be used as an experimental tool to inactivate genes in cells. However, a CRISPR-targeted cell population will not show a uniform genotype of the targeted gene. Instead, a mix of genotypes is generated - from wild type to different forms of insertions and deletions. Such mixed genotypes complicate analysis of the role of the targeted gene in the studied cell population. Here, we present a rapid and universal experimental approach to functionally analyze a CRISPR-targeted cell population that does not involve generating clonal lines. As a simple readout, we leverage the CRISPR-induced genetic heterogeneity and use sequencing to identify how different genotypes are enriched or depleted in relation to the studied cellular behavior or phenotype. The approach uses standard PCR, Sanger sequencing, and a simple sequence deconvoluting software, enabling laboratories without specific in-depth experience to perform these experiments. As proof of principle, we present examples studying various aspects related to hematopoietic cells (T cell development in vivo and activation in vitro, differentiation of macrophages and dendritic cells, as well as a leukemia-like phenotype induced by overexpressing a proto-oncogene). In conclusion, we present a rapid experimental approach to identify potential drug targets related to mature immune cells, as well as normal and malignant hematopoiesis.
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Affiliation(s)
- Yunbing Shen
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Long Jiang
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Vaishnavi Srinivasan Iyer
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Bruno Raposo
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Anatoly Dubnovitsky
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Sanjaykumar V. Boddul
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Zsolt Kasza
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Wermeling
- Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
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36
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Bower OJ, McCarthy A, Lea RA, Alanis-Lobato G, Zohren J, Gerri C, Turner JMA, Niakan KK. Generating CRISPR-Cas9-Mediated Null Mutations and Screening Targeting Efficiency in Human Pluripotent Stem Cells. Curr Protoc 2021; 1:e232. [PMID: 34432381 DOI: 10.1002/cpz1.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CRISPR-Cas9 mutagenesis facilitates the investigation of gene function in a number of developmental and cellular contexts. Human pluripotent stem cells (hPSCs), either embryonic or induced, are a tractable cellular model to investigate molecular mechanisms involved in early human development and cell fate decisions. hPSCs also have broad potential in regenerative medicine to model, investigate, and ameliorate diseases. Here, we provide an optimized protocol for efficient CRISPR-Cas9 genome editing of hPSCs to investigate the functional role of genes by engineering null mutations. We emphasize the importance of screening single guide RNAs (sgRNAs) to identify those with high targeting efficiency for generation of clonally derived null mutant hPSC lines. We provide important considerations for targeting genes that may have a role in hPSC maintenance. We also present methods to evaluate the on-target mutation spectrum and unintended karyotypic changes. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Selecting and ligating sgRNAs into expression plasmids Basic Protocol 2: Validation of sgRNA via in vitro transcription and cleavage assay Basic Protocol 3: Nucleofection of primed human embryonic stem cells Basic Protocol 4: MiSeq analysis of indel mutations Basic Protocol 5: Single cell cloning of targeted hPSCs Basic Protocol 6: Karyotyping of targeted hPSCs.
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Affiliation(s)
- Oliver J Bower
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gregorio Alanis-Lobato
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Claudia Gerri
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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37
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Jiang X, Ho DBT, Mahe K, Mia J, Sepulveda G, Antkowiak M, Jiang L, Yamada S, Jao LE. Condensation of pericentrin proteins in human cells illuminates phase separation in centrosome assembly. J Cell Sci 2021; 134:jcs258897. [PMID: 34308971 PMCID: PMC8349556 DOI: 10.1242/jcs.258897] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
At the onset of mitosis, centrosomes expand the pericentriolar material (PCM) to maximize their microtubule-organizing activity. This step, termed centrosome maturation, ensures proper spindle organization and faithful chromosome segregation. However, as the centrosome expands, how PCM proteins are recruited and held together without membrane enclosure remains elusive. We found that endogenously expressed pericentrin (PCNT), a conserved PCM scaffold protein, condenses into dynamic granules during late G2/early mitosis before incorporating into mitotic centrosomes. Furthermore, the N-terminal portion of PCNT, enriched with conserved coiled-coils (CCs) and low-complexity regions (LCRs), phase separates into dynamic condensates that selectively recruit PCM proteins and nucleate microtubules in cells. We propose that CCs and LCRs, two prevalent sequence features in the centrosomal proteome, are preserved under evolutionary pressure in part to mediate liquid-liquid phase separation, a process that bestows upon the centrosome distinct properties critical for its assembly and functions.
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Affiliation(s)
- Xueer Jiang
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Dac Bang Tam Ho
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Karan Mahe
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Jennielee Mia
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Guadalupe Sepulveda
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Mark Antkowiak
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Linhao Jiang
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
| | - Soichiro Yamada
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Li-En Jao
- Department of Cell Biology and Human Anatomy, University of California, Davis, School of Medicine, Davis, CA 95616, USA
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38
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Oura S, Noda T, Morimura N, Hitoshi S, Nishimasu H, Nagai Y, Nureki O, Ikawa M. Precise CAG repeat contraction in a Huntington's Disease mouse model is enabled by gene editing with SpCas9-NG. Commun Biol 2021; 4:771. [PMID: 34163001 PMCID: PMC8222283 DOI: 10.1038/s42003-021-02304-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 06/03/2021] [Indexed: 12/22/2022] Open
Abstract
The clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system is a research hotspot in gene therapy. However, the widely used Streptococcus pyogenes Cas9 (WT-SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting targetable disease mutations. To address this issue, we recently reported an engineered SpCas9 nuclease variant (SpCas9-NG) recognizing NGN PAMs. Here, as a feasibility study, we report SpCas9-NG-mediated repair of the abnormally expanded CAG repeat tract in Huntington's disease (HD). By targeting the boundary of CAG repeats with SpCas9-NG, we precisely contracted the repeat tracts in HD-mouse-derived embryonic stem (ES) cells. Further, we confirmed the recovery of phenotypic abnormalities in differentiated neurons and animals produced from repaired ES cells. Our study shows that SpCas9-NG can be a powerful tool for repairing abnormally expanded CAG repeats as well as other disease mutations that are difficult to access with WT-SpCas9.
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Affiliation(s)
- Seiya Oura
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Taichi Noda
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Division of Reproductive Biology, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Naoko Morimura
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Seiji Hitoshi
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Structural Biology, Research center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Neurology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.
- Laboratory of Reproductive Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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39
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Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, Florus K, Behlke MA, Wang Y, McNeill MS. CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing. Mol Ther Methods Clin Dev 2021; 21:478-491. [PMID: 33981780 PMCID: PMC8082044 DOI: 10.1016/j.omtm.2021.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
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Affiliation(s)
- Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | | | - Lauren Tso
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | | | | | | | | | - Yu Wang
- Integrated DNA Technologies, Coralville, IA 52241, USA
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40
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Gaillochet C, Develtere W, Jacobs TB. CRISPR screens in plants: approaches, guidelines, and future prospects. THE PLANT CELL 2021; 33:794-813. [PMID: 33823021 PMCID: PMC8226290 DOI: 10.1093/plcell/koab099] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-associated systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene functions in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.
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Affiliation(s)
- Christophe Gaillochet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
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41
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Amit I, Iancu O, Levy-Jurgenson A, Kurgan G, McNeill MS, Rettig GR, Allen D, Breier D, Ben Haim N, Wang Y, Anavy L, Hendel A, Yakhini Z. CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data. Nat Commun 2021; 12:3042. [PMID: 34031394 PMCID: PMC8144550 DOI: 10.1038/s41467-021-22417-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
Controlling off-target editing activity is one of the central challenges in making CRISPR technology accurate and applicable in medical practice. Current algorithms for analyzing off-target activity do not provide statistical quantification, are not sufficiently sensitive in separating signal from noise in experiments with low editing rates, and do not address the detection of translocations. Here we present CRISPECTOR, a software tool that supports the detection and quantification of on- and off-target genome-editing activity from NGS data using paired treatment/control CRISPR experiments. In particular, CRISPECTOR facilitates the statistical analysis of NGS data from multiplex-PCR comparative experiments to detect and quantify adverse translocation events. We validate the observed results and show independent evidence of the occurrence of translocations in human cell lines, after genome editing. Our methodology is based on a statistical model comparison approach leading to better false-negative rates in sites with weak yet significant off-target activity.
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Affiliation(s)
- Ido Amit
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ortal Iancu
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Levy-Jurgenson
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gavin Kurgan
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | | | | | - Daniel Allen
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Dor Breier
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nimrod Ben Haim
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yu Wang
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | - Leon Anavy
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Zohar Yakhini
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel.
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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42
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Chen Z, Traniello IM, Rana S, Cash-Ahmed AC, Sankey AL, Yang C, Robinson GE. Neurodevelopmental and transcriptomic effects of CRISPR/Cas9-induced somatic orco mutation in honey bees. J Neurogenet 2021; 35:320-332. [PMID: 33666542 DOI: 10.1080/01677063.2021.1887173] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In insects, odorant receptors facilitate olfactory communication and require the functionality of the highly conserved co-receptor gene orco. Genome editing studies in a few species of ants and moths have revealed that orco can also have a neurodevelopmental function, in addition to its canonical role in adult olfaction, discovered first in Drosophila melanogaster. To extend this analysis, we determined whether orco mutations also affect the development of the adult brain of the honey bee Apis mellifera, an important model system for social behavior and chemical communication. We used CRISPR/Cas9 to knock out orco and examined anatomical and molecular consequences. To increase efficiency, we coupled embryo microinjection with a laboratory egg collection and in vitro rearing system. This new workflow advances genomic engineering technologies in honey bees by overcoming restrictions associated with field studies. We used Sanger sequencing to quickly select individuals with complete orco knockout for neuroanatomical analyses and later validated and described the mutations with amplicon sequencing. Mutant bees had significantly fewer glomeruli, smaller total volume of all the glomeruli, and higher mean individual glomerulus volume in the antennal lobe compared to wild-type controls. RNA-Sequencing revealed that orco knockout also caused differential expression of hundreds of genes in the antenna, including genes related to neural development and genes encoding odorant receptors. The expression of other types of chemoreceptor genes was generally unaffected, reflecting specificity of CRISPR activity in this study. These results suggest that neurodevelopmental effects of orco are related to specific insect life histories.
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Affiliation(s)
- Zhenqing Chen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ian M Traniello
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Seema Rana
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amy C Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alison L Sankey
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Che Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Biochemistry Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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43
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Ramadan M, Alariqi M, Ma Y, Li Y, Liu Z, Zhang R, Jin S, Min L, Zhang X. Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton. PLANT METHODS 2021; 17:16. [PMID: 33557889 PMCID: PMC7869495 DOI: 10.1186/s13007-021-00712-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. RESULTS To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. CONCLUSION All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.
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Affiliation(s)
- Mohamed Ramadan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Plant Genetic Resources, Division of Ecology and Dry Land Agriculture, Desert Research Center, Cairo, Egypt
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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44
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Villiger L, Rothgangl T, Witzigmann D, Oka R, Lin PJC, Qi W, Janjuha S, Berk C, Ringnalda F, Beattie MB, Stoffel M, Thöny B, Hall J, Rehrauer H, van Boxtel R, Tam YK, Schwank G. In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA. Nat Biomed Eng 2021; 5:179-189. [PMID: 33495639 PMCID: PMC7610981 DOI: 10.1038/s41551-020-00671-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022]
Abstract
Base editors are RNA-programmable deaminases that enable precise single-base conversions in genomic DNA. However, off-target activity is a concern in the potential use of base editors to treat genetic diseases. Here, we report unbiased analyses of transcriptome-wide and genome-wide off-target modifications effected by cytidine base editors in the liver of mice with phenylketonuria. The intravenous delivery of intein-split cytidine base editors by dual adeno-associated viruses led to the repair of the disease-causing mutation without generating off-target mutations in the RNA and DNA of the hepatocytes. Moreover, the transient expression of a cytidine base editor mRNA and a relevant single-guide RNA intravenously delivered by lipid nanoparticles led to ~21% on-target editing and to the reversal of the disease phenotype; there were also no detectable transcriptome-wide and genome-wide off-target edits. Our findings support the feasibility of therapeutic cytidine base editing to treat genetic liver diseases.
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Affiliation(s)
- Lukas Villiger
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Tanja Rothgangl
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Dominik Witzigmann
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Paulo J C Lin
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Sharan Janjuha
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Christian Berk
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Femke Ringnalda
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Beat Thöny
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
- Division of Metabolism, University Children's Hospital Zurich and Children's Research Centre, Zurich, Switzerland
| | - Jonathan Hall
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ying K Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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45
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Dilshat R, Fock V, Kenny C, Gerritsen I, Lasseur RMJ, Travnickova J, Eichhoff OM, Cerny P, Möller K, Sigurbjörnsdóttir S, Kirty K, Einarsdottir BÓ, Cheng PF, Levesque M, Cornell RA, Patton EE, Larue L, de Tayrac M, Magnúsdóttir E, Ögmundsdóttir MH, Steingrimsson E. MITF reprograms the extracellular matrix and focal adhesion in melanoma. eLife 2021; 10:63093. [PMID: 33438577 PMCID: PMC7857731 DOI: 10.7554/elife.63093] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
The microphthalmia-associated transcription factor (MITF) is a critical regulator of melanocyte development and differentiation. It also plays an important role in melanoma where it has been described as a molecular rheostat that, depending on activity levels, allows reversible switching between different cellular states. Here, we show that MITF directly represses the expression of genes associated with the extracellular matrix (ECM) and focal adhesion pathways in human melanoma cells as well as of regulators of epithelial-to-mesenchymal transition (EMT) such as CDH2, thus affecting cell morphology and cell-matrix interactions. Importantly, we show that these effects of MITF are reversible, as expected from the rheostat model. The number of focal adhesion points increased upon MITF knockdown, a feature observed in drug-resistant melanomas. Cells lacking MITF are similar to the cells of minimal residual disease observed in both human and zebrafish melanomas. Our results suggest that MITF plays a critical role as a repressor of gene expression and is actively involved in shaping the microenvironment of melanoma cells in a cell-autonomous manner.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Valerie Fock
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Colin Kenny
- Department of Anatomy and Cell biology, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Ilse Gerritsen
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Romain Maurice Jacques Lasseur
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jana Travnickova
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Ossia M Eichhoff
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Philipp Cerny
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Katrin Möller
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sara Sigurbjörnsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kritika Kirty
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Berglind Ósk Einarsdottir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Phil F Cheng
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Mitchell Levesque
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Robert A Cornell
- Department of Anatomy and Cell biology, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Lionel Larue
- Institut Curie, CNRS UMR3347, INSERM U1021, Centre Universitaire, Orsay, France
| | - Marie de Tayrac
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France.,Univ Rennes1, CNRS, IGDR (Institut de Génétique et Développement de Rennes), Rennes, France
| | - Erna Magnúsdóttir
- Department of Anatomy, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Margrét Helga Ögmundsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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46
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Hennig SL, Owen JR, Lin JC, Young AE, Ross PJ, Van Eenennaam AL, Murray JD. Evaluation of mutation rates, mosaicism and off target mutations when injecting Cas9 mRNA or protein for genome editing of bovine embryos. Sci Rep 2020; 10:22309. [PMID: 33339870 PMCID: PMC7749171 DOI: 10.1038/s41598-020-78264-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrated that the use of gRNA/Cas9 ribonucleoprotein complex resulted in a high editing efficiency at three different loci in bovine embryos and decreased levels of mosaicism relative to Cas9 mRNA. Additional optimization will be required to further reduce mosaicism to levels that make single-step embryo editing in cattle commercially feasible.
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Affiliation(s)
- Sadie L Hennig
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Joseph R Owen
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Jason C Lin
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Amy E Young
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | | | - James D Murray
- Department of Animal Science, University of California - Davis, Davis, CA, USA.,Department of Population Health and Reproduction, University of California - Davis, Davis, CA, USA
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47
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Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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48
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Colón-Rodríguez A, Uribe-Salazar JM, Weyenberg KB, Sriram A, Quezada A, Kaya G, Jao E, Radke B, Lein PJ, Dennis MY. Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform. Front Cell Dev Biol 2020; 8:586296. [PMID: 33330465 PMCID: PMC7719691 DOI: 10.3389/fcell.2020.586296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022] Open
Abstract
In recent years, zebrafish have become commonly used as a model for studying human traits and disorders. Their small size, high fecundity, and rapid development allow for more high-throughput experiments compared to other vertebrate models. Given that zebrafish share >70% gene homologs with humans and their genomes can be readily edited using highly efficient CRISPR methods, we are now able to rapidly generate mutations impacting practically any gene of interest. Unfortunately, our ability to phenotype mutant larvae has not kept pace. To address this challenge, we have developed a protocol that obtains multiple phenotypic measurements from individual zebrafish larvae in an automated and parallel fashion, including morphological features (i.e., body length, eye area, and head size) and movement/behavior. By assaying wild-type zebrafish in a variety of conditions, we determined optimal parameters that avoid significant developmental defects or physical damage; these include morphological imaging of larvae at two time points [3 days post fertilization (dpf) and 5 dpf] coupled with motion tracking of behavior at 5 dpf. As a proof-of-principle, we tested our approach on two novel CRISPR-generated mutant zebrafish lines carrying predicted null-alleles of syngap1b and slc7a5, orthologs to two human genes implicated in autism-spectrum disorder, intellectual disability, and epilepsy. Using our optimized high-throughput phenotyping protocol, we recapitulated previously published results from mouse and zebrafish models of these candidate genes. In summary, we describe a rapid parallel pipeline to characterize morphological and behavioral features of individual larvae in a robust and consistent fashion, thereby improving our ability to better identify genes important in human traits and disorders.
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Affiliation(s)
- Alexandra Colón-Rodríguez
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - José M Uribe-Salazar
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, United States
| | - KaeChandra B Weyenberg
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Aditya Sriram
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Alejandra Quezada
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Sacramento State RISE Program, California State University, Sacramento, Sacramento, CA, United States
| | - Gulhan Kaya
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Emily Jao
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Brittany Radke
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Pamela J Lein
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Megan Y Dennis
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, United States.,MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
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49
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Zhang Y, Zhao G, Ahmed FYH, Yi T, Hu S, Cai T, Liao Q. In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. Front Oncol 2020; 10:584404. [PMID: 33123486 PMCID: PMC7567020 DOI: 10.3389/fonc.2020.584404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas system has stood in the center of attention in the last few years as a revolutionary gene editing tool with a wide application to investigate gene functions. However, the labor-intensive workflow requires a sophisticated pre-experimental and post-experimental analysis, thus becoming one of the hindrances for the further popularization of practical applications. Recently, the increasing emergence and advancement of the in silico methods play a formidable role to support and boost experimental work. However, various tools based on distinctive design principles and frameworks harbor unique characteristics that are likely to confuse users about how to choose the most appropriate one for their purpose. In this review, we will present a comprehensive overview and comparisons on the in silico methods from the aspects of CRISPR/Cas system identification, guide RNA design, and post-experimental assistance. Furthermore, we establish the hypotheses in light of the new trends around the technical optimization and hope to provide significant clues for future tools development.
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Affiliation(s)
- Yuwei Zhang
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Guofang Zhao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Fatma Yislam Hadi Ahmed
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Tianfei Yi
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Shiyun Hu
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Ting Cai
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Qi Liao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
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50
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Owen JR, Hennig SL, McNabb BR, Lin JC, Young AE, Murray JD, Ross PJ, Van Eenennaam AL. Harnessing endogenous repair mechanisms for targeted gene knock-in of bovine embryos. Sci Rep 2020; 10:16031. [PMID: 32994506 PMCID: PMC7525238 DOI: 10.1038/s41598-020-72902-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/04/2020] [Indexed: 01/06/2023] Open
Abstract
Introducing useful traits into livestock breeding programs through gene knock-ins has proven challenging. Typically, targeted insertions have been performed in cell lines, followed by somatic cell nuclear transfer cloning, which can be inefficient. An alternative is to introduce genome editing reagents and a homologous recombination (HR) donor template into embryos to trigger homology directed repair (HDR). However, the HR pathway is primarily restricted to actively dividing cells (S/G2-phase) and its efficiency for the introduction of large DNA sequences in zygotes is low. The homology-mediated end joining (HMEJ) approach has been shown to improve knock-in efficiency in non-dividing cells and to harness HDR after direct injection of embryos. The knock-in efficiency for a 1.8 kb gene was contrasted when combining microinjection of a gRNA/Cas9 ribonucleoprotein complex with a traditional HR donor template or an HMEJ template in bovine zygotes. The HMEJ template resulted in a significantly higher rate of gene knock-in as compared to the HR template (37.0% and 13.8%; P < 0.05). Additionally, more than a third of the knock-in embryos (36.9%) were non-mosaic. This approach will facilitate the one-step introduction of gene constructs at a specific location of the bovine genome and contribute to the next generation of elite cattle.
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Affiliation(s)
- Joseph R Owen
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
| | - Sadie L Hennig
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of CA - Davis, Davis, CA, USA
| | - Jason C Lin
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
| | - Amy E Young
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
| | - James D Murray
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of CA - Davis, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of CA - Davis, Davis, CA, USA
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