scholarly journals CRISPR/Cas9-mediated gene knockin in the hydroid Hydractinia symbiolongicarpus

2018 ◽  
Author(s):  
Steven M. Sanders ◽  
Zhiwei Ma ◽  
Julia M. Hughes ◽  
Brooke M. Riscoe ◽  
Gregory A. Gibson ◽  
...  
Keyword(s):  
Genome Editing ◽  
Ex Vivo ◽  
Elongation Factor ◽  
Exogenous Dna ◽  
Hydractinia Symbiolongicarpus ◽  
Eukaryotic Elongation Factor ◽  
Two Generations ◽  
Genomics Tools ◽  
Endogenous Proteins

AbstractBackgroundHydractinia symbiolongicarpus, a colonial cnidarian, is a tractable model system for many cnidarian-specific and general biological questions. Until recently, tests of gene function in Hydractinia have relied on laborious forward genetic approaches, randomly integrated transgenes, or transient knockdown of mRNAs.ResultsHere, we report the use of CRISPR/Cas9 genome editing to generate targeted genomic insertions in H. symbiolonigcarpus. We used CRISPR/Cas9 to promote homologous recombination of two fluorescent reporters, eGFP and tdTomato, into the Eukaryotic elongation factor 1 alpha (Eef1a) locus. We demonstrate that the transgenes are expressed ubiquitously and are stable over two generations of breeding. We further demonstrate that CRISPR/Cas9 genome editing can be used to mark endogenous proteins with FLAG or StrepII-FLAG affinity tags to enable in vivo and ex vivo protein studies.ConclusionsThis is the first account of CRISPR/Cas9 mediated knockins in Hydractinia and the first example of the germline transmission of a CRISPR/Cas9 inserted transgene in a cnidarian. The ability to precisely insert exogenous DNA into the Hydractinia genome will enable sophisticated genetic studies and further development of functional genomics tools in this understudied cnidarian model.

scholarly journals Retron Editing for Precise Genome Editing without Exogenous Donor DNA in Human Cells

2021 ◽  
Author(s):  
Xiangfeng Kong ◽  
Zikang Wang ◽  
Yingsi Zhou ◽  
Xing Wang ◽  
Linyu Shi ◽  
...  
Keyword(s):  
Genome Editing ◽  
Ex Vivo ◽  
Human Cells ◽  
Exogenous Dna ◽  
Guide Rna ◽  
Homology Directed Repair ◽  
Non Coding Rna ◽  
Bacterial Genetic ◽  
Low Efficiency

CRISPR-Cas9 mediated seamless genome editing can be achieved by incorporating donor DNA into the CRISPR-Cas9 target loci via homology-directed repair (HDR), albeit with relative low efficiency due to the inefficient delivery of exogenous DNA. Retrons are bacterial genetic element composed of a non-coding RNA (ncRNA) and reverse transcriptase (RT). Retrons coupled with CRISPR-Cas9 have been shown to enhance precise genome editing via HDR in yeast through fusing guide RNA (gRNA) to the 3′ end of retron ncRNA, producing multicopy single-stranded DNA (msDNA) covalently tethered to gRNA. Here, we further engineered retrons by fusing Cas9 with E.coli RT from different clades and joining gRNA at the 5′ end of retron ncRNA, and found that retron editing can achieve precise genome editing efficiently in human cells. By co- expression of Cas9-RT fusions and retron-ncRNA gRNA (rgRNA) in HEK293T cells, we demonstrated the rates of retron editing at endogenous genomic loci was up to 10 %. We expect our retron editing system could aid in advancing the ex vivo and in vivo therapeutic applications of retron.

scholarly journals Μελέτη μορίων του πρωτόζωου Leishmania που εμπλέκονται στην πρόοδο του κυτταρικού κύκλου

2014 ◽  
Author(s):  
Αλέξανδρος Αλεξανδράτος
Keyword(s):  
Heat Shock ◽  
Elongation Factor ◽  
Alpha Subunit ◽  
Elongation Factor 2 ◽  
Mitochondrial Processing Peptidase ◽  
Eukaryotic Elongation Factor 2 ◽  
Eukaryotic Elongation Factor ◽  
Processing Peptidase

Τα είδη του γένους Leishmania αποτελούν υποχρεωτικά ενδοκυττάρια πρωτοζωικά παράσιτα που προκαλούν ένα ευρύ φάσμα ασθενειών, τις λεισμανιάσεις. Η λεϊσμανίαση θεωρείται νόσος εξέχουσας σπουδαιότητας, με 2 εκατομμύρια νέα κρούσματα το χρόνο, χρήζουσας μεγάλης κοινωνικής και οικονομικής σημασίας. Για τον έλεγχο των συνεχώς αυξανόμενων κρουσμάτων, είναι επιτακτική ανάγκη η ανάπτυξη νέων μη-τοξικών φαρμάκων που θα στοχεύουν σε μόρια-στόχους σημαντικά για την ολοκλήρωση του παρασιτικού κύκλου ζωής. Κατ’ αυτόν τον τρόπο κρίνεται απαραίτητη η μελέτη μηχανισμών και παραγόντων μολυσματικότητας του παρασίτου, που ελέγχουν τον κυτταρικό κύκλο και τη διαφοροποίηση του παρασίτου. Στα πλαίσια αυτά, έχει δειχθεί ότι η επισωμική υπερέκφραση της συνδετικής ιστόνης Η1 του παρασίτου Leishmania (LeishH1) οδηγεί στην καθυστέρηση της ολοκλήρωσης του κυτταρικού κύκλου, αλλά παράλληλα και στη μείωση του ρυθμού διαφοροποίησης των παρασίτων από προμαστιγωτές σε αμαστιγωτές μορφές, έχοντας σαν αποτέλεσμα τη μείωση της μολυσματικότητας του παρασίτου τόσο in vitro όσο και in vivo. Στόχος αυτής της διατριβής ήταν η ανάδειξη μορίων που επηρεάζουν τη μολυσματικότητα του παρασίτου, μελετώντας το προτέωμα των μη μολυσματικών παρασίτων που υπερεκφράζουν την LeishH1. Η συγκριτική μελέτη των παρασίτων που υπερεκφράζουν τη LeishH1 σε σχέση με τα παράσιτα ελέγχου, είχε επίσης ως σκοπό την περαιτέρω μελέτη του βιολογικού ρόλου της LeishH1 στα παράσιτα και τη διερεύνηση του ρόλου της στη γονιδιακή ρύθμιση του παρασίτου. Η συγκριτική πρωτεομική ανάλυση με ηλεκτροφόρηση δυο-διαστάσεων, των παρασίτων που υπερεκφράζουν την LeishH1 σε σχέση με τα παράσιτα ελέγχου, κατέδειξε πως μόνο μια μικρή ομάδα πρωτεϊνών παρουσιάζει διαφορική έκφραση. Συγκεκριμένα, τρεις πρωτεΐνες [heat shock protein 83 (HSP83), eukaryotic elongation factor 2(eEF-2), alpha subunit of the mitochondrial processing peptidase (α-MPP)] παρουσιάζουν χαμηλότερα επίπεδα έκφρασης ενώ άλλες δυο (α/β τουμπουλίνη, ΜΑΡ) παρουσιάζουν μεγαλύτερη κατανομή έκφρασης. Πειράματα αλυσιδωτής αντίδρασης πολυμεράσης αντίστροφης μεταγραφάσης πραγματικού χρόνου, επιβεβαίωσαν το αποτέλεσμα αυτό, υποδηλώνοντας ότι η LeishH1 δεν είναι γενικός καταστολέας της μεταγραφής αλλά επηρεάζει ένα ειδικό υποσύνολο πρωτεϊνών, σε προ- ή μετα-μεταγραφικό επίπεδο. Ανάμεσα στις πρωτεΐνες με διαφορική έκφραση ήταν και η τουμπουλίνη. Η διαφορική έκφραση της πρωτεΐνης αντικατοπτρίζεται άμεσα στη μορφολογία των παρασίτων που υπερεκφράζουν την LeishH1, καθώς τα παράσιτα αυτά παρουσιάζουν μικρότερο και πιο στρογγυλό σχήμα και μεγαλύτερη μορφολογική ετερογένεια. Μια ακόμα πρωτεΐνη με διαφορική έκφραση, ήταν και η HSP83, η οποία παρουσίασε χαμηλότερα επίπεδα. Θέλοντας να εξακριβώσουμε σε ποιο επίπεδο παρεμβαίνει η LeishH1 στο μηχανισμό έκφρασης της HSP83, συγκρίναμε τα επίπεδα του mRNA και η ανάλυση κατέδειξε ότι δεν υπάρχουν διαφορές στα επίπεδα αυτά. Επίσης, μελετήθηκε ο ρυθμός έκφρασης της πρωτεΐνης μέσω της μεταβολικής σήμανσης των πρωτεϊνών και αποκαλύφθηκε πως σε αυτό το στάδιο εντοπίζεται η παρεμβολή της LeishH1, καθώς τα παράσιτα που την υπερεκφράζουν παρουσιάζουν χαμηλότερο ρυθμό έκφρασης της HSP83. Συμπερασματικά διαφαίνεται πως υπάρχει μια συσχέτιση μεταξύ μονοπατιών που εμπλέκονται στην αντίσταση έναντι φαρμακευτικών ουσιών, στην απόπτωση και τη μολυσματικότητα. Κατ’ αυτόν τον τρόπο, τα ειδικά σήματα και οι μηχανισμοί που ρυθμίζουν τη διαφοροποίηση/μολυσματικότητα του παρασίτου και την απόπτωση/απόκριση στο στρες, χρήζουν περαιτέρω διερεύνησης καθώς φαίνεται να αποτελούν τις δυο όψεις του ίδιου νομίσματος.

scholarly journals Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing

Blood ◽  
2018 ◽  
Vol 131 (26) ◽  
pp. 2915-2928 ◽  
Author(s):  
Chang Li ◽  
Nikoletta Psatha ◽  
Pavel Sova ◽  
Sucheol Gil ◽  
Hongjie Wang ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Stem Cell ◽  
Binding Site ◽  
Genome Editing ◽  
Ex Vivo ◽  
Hematopoietic Stem ◽  
Key Points ◽  
Cell Genome ◽  
Hsc Transplantation

Key Points CRISPR/Cas9-mediated disruption of a BCL11A binding site in HSCs of β-YAC mice results in the reactivation of γ-globin in erythrocytes. Our approach for in vivo HSC genome editing that does not require HSC transplantation and myeloablation should simplify HSC gene therapy.

scholarly journals In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations

2018 ◽  
Author(s):  
Pinar Akcakaya ◽  
Maggie L. Bobbin ◽  
Jimmy A. Guo ◽  
Jose M. Lopez ◽  
M. Kendell Clement ◽  
...  
Keyword(s):  
Genome Editing ◽  
Ex Vivo ◽  
Strong Support ◽  
Guide Rna ◽  
Genome Wide ◽  
Highly Sensitive ◽  
Further Development ◽  
Target Effects ◽  
Cas Gene

CRISPR-Cas genome-editing nucleases hold substantial promise for human therapeutics1–5 but identifying unwanted off-target mutations remains an important requirement for clinical translation6, 7. For ex vivo therapeutic applications, previously published cell-based genome-wide methods provide potentially useful strategies to identify and quantify these off-target mutation sites8–12. However, a well-validated method that can reliably identify off-targets in vivo has not been described to date, leaving the question of whether and how frequently these types of mutations occur. Here we describe Verification of In Vivo Off-targets (VIVO), a highly sensitive, unbiased, and generalizable strategy that we show can robustly identify genome-wide CRISPR-Cas nuclease off-target effects in vivo. To our knowledge, these studies provide the first demonstration that CRISPR-Cas nucleases can induce substantial off-target mutations in vivo, a result we obtained using a deliberately promiscuous guide RNA (gRNA). More importantly, we used VIVO to show that appropriately designed gRNAs can direct efficient in vivo editing without inducing detectable off-target mutations. Our findings provide strong support for and should encourage further development of in vivo genome editing therapeutic strategies.

scholarly journals eEF3 promotes late stages of tRNA translocation on the ribosome

2020 ◽  
Author(s):  
Namit Ranjan ◽  
Agnieszka A. Pochopien ◽  
Colin Chih-Chien Wu ◽  
Bertrand Beckert ◽  
Sandra Blanchet ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Elongation Factor ◽  
Translation Elongation ◽  
Elongation Cycle ◽  
Trna Translocation ◽  
A Site ◽  
Late Stages ◽  
Structural Insights ◽  
Trna Binding

SummaryIn addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the A and E sites, its exact mechanism of action is unclear. Here we show that eEF3 acts at the mRNA–tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. Depletion of eEF3 in vivo leads to a general slow-down in translation elongation due to accumulation of ribosomes with an occupied A site. Cryo-EM analysis of ex vivo eEF3-ribosome complexes shows that eEF3 facilitates late steps of translocation by favoring non-rotated ribosomal states as well as by opening the L1 stalk to release the E-site tRNA. Additionally, our analysis provides structural insights into novel translation elongation states, enabling presentation of a revised yeast translation elongation cycle.

scholarly journals Translation Elongation Factor 2 Anticodon Mimicry Domain Mutants Affect Fidelity and Diphtheria Toxin Resistance

2006 ◽  
Vol 281 (43) ◽  
pp. 32639-32648 ◽  
Author(s):  
Pedro A. Ortiz ◽  
Rory Ulloque ◽  
George K. Kihara ◽  
Haiyan Zheng ◽  
Terri Goss Kinzy
Keyword(s):  
Diphtheria Toxin ◽  
Molecular Mimicry ◽  
Elongation Factor ◽  
Lethal Effect ◽  
Translational Machinery ◽  
Toxin Resistance ◽  
Protein Levels ◽  
Elongation Factor 2 ◽  
Eukaryotic Elongation Factor

Eukaryotic elongation factor 2 (eEF2) mediates translocation in protein synthesis. The molecular mimicry model proposes that the tip of domain IV mimics the anticodon loop of tRNA. His-699 in this region is post-translationally modified to diphthamide, the target for Corynebacterium diphtheriae and Pseudomonas aeruginosa toxins. ADP-ribosylation by these toxins inhibits eEF2 function causing cell death. Mutagenesis of the tip of domain IV was used to assess both functions. A H694A mutant strain was non-functional, whereas D696A, I698A, and H699N strains conferred conditional growth defects, sensitivity to translation inhibitors, and decreased total translation in vivo. These mutant strains and those lacking diphthamide modification enzymes showed increased -1 frameshifting. The effects are not due to reduced protein levels, ribosome binding, or GTP hydrolysis. Functional eEF2 forms substituted in domain IV confer dominant diphtheria toxin resistance, which correlates with an in vivo effect on translation-linked phenotypes. These results provide a new mechanism in which the translational machinery maintains the accurate production of proteins, establishes a role for the diphthamide modification, and provides evidence of the ability to suppress the lethal effect of a toxin targeted to eEF2.

scholarly journals Gene editing and CRISPR in the clinic: current and future perspectives

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Matthew P. Hirakawa ◽  
Raga Krishnakumar ◽  
Jerilyn A. Timlin ◽  
James P. Carney ◽  
Kimberly S. Butler
Keyword(s):  
Clinical Trials ◽  
Genome Editing ◽  
Dna Sequences ◽  
Gene Editing ◽  
Ex Vivo ◽  
Scientific Basis ◽  
Current Status ◽  
Zinc Finger Nucleases ◽  
Transcription Activator

Abstract Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.

scholarly journals Successful i-GONAD in Brown Norway Rats by Modification of in vivo Electroporation Conditions

2020 ◽  
Vol 4 (4) ◽  
Author(s):  
Shuji Takabayashi ◽  
◽  
Takuya Aoshima ◽  
Yukari Kobayashi ◽  
Hisayoshi Takagi ◽  
...  
Keyword(s):  
Genome Editing ◽  
Ex Vivo ◽  
Preimplantation Embryos ◽  
Brown Norway ◽  
Sprague Dawley ◽  
In Vivo Electroporation ◽  
Nucleic Acids Delivery ◽  
A Current

Improved-Genome editing via Oviductal Nucleic Acids Delivery (i-GONAD) was developed for in situ genome editing of the preimplantation embryos present within the oviductal lumen of mice. This method is based on intra-oviductal instillation of genome editing components and subsequent in vivo electroporation (EP) in the entire oviduct. Therefore, i-GONAD differs from the previous methods (i.e., zygote microinjection and in vitro EP) in producing genome-edited mice, which relied on ex vivo handling of preimplantation embryos and egg transfer to the recipient females. We have previously demonstrated that i-GONAD can be successfully applied to produce genome-edited rats, including albino Sprague-Dawley and albino Lewis rats (however, not pigmented Brown Norway [BN] rats). We observed that the successful i-GONAD was dependent on the mouse strain used; for example, in random-bred mice, such as ICR and C3H/He × C57BL/6, it was successful under relatively stringent electrical conditions but not in the C57BL/6 strain. Under less stringent conditions, i-GONAD was successful in the C57BL/6 strain. We speculated that this would also be true for i-GONAD using BN rats. On applying a current of >500 mA, we failed to obtain rat offspring (fetuses/newborns); however, i-GONAD under a current of 100-300 mA using NEPA21 (NEPA GENE) led to the production of genome-edited BN rats with efficiencies of 75%-100%. Similarly, i-GONAD, under a current of 150-200 mA using CUY21EDIT II (BEX Co.) led to the production of genome-edited BN rats with efficiencies of 24%-55%. These experiments suggest the importance of selecting the appropriate current value, depending on the rat strain used, when performing i-GONAD.

scholarly journals Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growth in vivo

2020 ◽  
Author(s):  
Ferah Comert Onder ◽  
Nermin Kahraman ◽  
Esen Bellur Atici ◽  
Ali Cagir ◽  
Hakan Kandemir ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Kinase Inhibitor ◽  
Elongation Factor ◽  
Binding Pocket ◽  
Clinical Prognosis ◽  
Elongation Factor 2 ◽  
Eukaryotic Elongation Factor ◽  
Breast Cancer Growth

AbstractEukaryotic elongation factor 2 kinase (eEF-2K), an unusual alpha kinase, is involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is indicated as one of the critical drivers of breast cancer and associated with poor clinical prognosis, representing a potential molecular target. The crystal structure of eEF-2K is unknown and there is no potent and effective eEF-2K inhibitor reported for clinical applications. To meet this challenge, we designed and synthesized several generations of potential inhibitor compounds and performed in silico studies. The effect of the inhibitors at the binding pocket of eEF-2K is analyzed after developing a 3D target model by homology modeling approaches using a domain of another α-kinase called myosin heavy-chain kinase A (MHCKA) that is closely resembling eEF-2K. Our results showed that compounds with coumarin-chalcone cores have a high predicted binding affinity for binding to eEF-2K. Following in vitro studies, we identified a compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and inhibited proliferation of various breast cancer cells with different features (BT20, MDA-MB-231, MDA-MB-436 and MCF-7) by induction of apoptosis while sparing normal cells. In vivo systemic administration of the the lead inhibitor encapsulated in single lipid-based nanoparticles twice a week significantly supressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice. In conclusion, our study provides the first in vivo effective small molecule eEF-2K inhibitor that may be used for molecularly targeted precison medicine strategies in breast cancer or other eEF-2K-dependent tumors.

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