Articles published on RNP Complexes
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- Research Article
- 10.1016/j.ijbiomac.2025.148735
- Dec 1, 2025
- International journal of biological macromolecules
- Karuppannasamy Ashok + 8 more
Differential expression of genes in pre-blastoderm embryos of oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) microinjected with white locus CRISPR/Cas9 ribo nucleo protein (RNP) complex.
- Research Article
3
- 10.3390/ijms262110682
- Nov 2, 2025
- International Journal of Molecular Sciences
- Shahin Amiri + 9 more
The CRISPR-Cas9 system has transformed biomedical research by enabling precise genetic modifications. However, efficient delivery of CRISPR components remains a major hurdle for therapeutic applications. To address this, we employed a new modified cationic hyper-branched cyclodextrin-based polymer (Ppoly) system to deliver an integrating GFP gene using the TILD-CRISPR method, which couples donor DNA linearization with RNP complexes. The physicochemical properties, loading efficiency, and cellular uptake of RNP with Ppoly were studied. After transfection, antibiotic selection and single-cell cloning were performed. Junction PCR was then performed on the isolated clones, and we compared the knock-in efficiency of Ppoly with that of the commercial CRISPRMAX™ reagent (Thermo Fisher, Invitrogen™, Waltham, MA, USA). The results demonstrate the encapsulation efficiency of over 90% for RNP and Ppoly, and cell viability remaining above 80%, reflecting the minimal toxicity of this approach. These attributes facilitated successful GFP gene integration using the TILD-CRISPR with RNP delivered via cyclodextrin-based nanosponges. The present method achieved a remarkable 50% integration efficiency in CHO-K1 cells, significantly outperforming the 14% observed with CRISPRMAX™ while maintaining lower cytotoxicity. This study highlights a promising platform for precise and efficient genome editing, with strong potential for therapeutic and regenerative medicine applications.
- Research Article
- 10.1016/j.jmb.2025.169410
- Nov 1, 2025
- Journal of molecular biology
- Harshita Dutta + 2 more
Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly.
- Research Article
- 10.1093/neuonc/noaf193.252
- Oct 3, 2025
- Neuro-Oncology
- J Q Cai
Abstract BACKGROUND Glioblastoma (GBM) is the most lethal central nervous system cancer, with poor prognosis and high resistance to therapies like temozolomide (TMZ). The upregulation of midkine (MDK) in GBM cells accelerates DNA repair, limiting TMZ’s effectiveness. RNAi and CRISPR-Cas9 offer potential solutions by targeting MDK, but delivering these biologics across the blood-brain barrier (BBB) and into GBM cells is challenging. Existing methods struggle with low endo-lysosomal escape rates and BBB penetration. To address this, we developed polymer-locking fusogenic liposomes (Plofsomes) that can cross the BBB and deliver siRNA or CRISPR-Cas9 complexes specifically to GBM cells, enhancing therapeutic efficacy and safety. RESULTS 结果: 1. In Vitro and In Vivo Delivery: Plofsomes effectively delivered siRNA and CRISPR-Cas9 RNP complexes into GBM cells, with higher delivery efficiency in high ROS environments.2.Suppression: Plofsome@siMDK significantly reduced MDK expression (P < 0.0001) in GBM cells and tumors.3. Antitumor Efficacy: Plofsome@siMDK + TMZ treatment inhibited tumor growth by 40% and increased survival rate to 40.0% in mouse models.4. Safety and Specificity: Plofsomes were non-toxic and did not affect MDK expression in normal tissues.5. Mechanistic Insight: MDK interacts with CD109 to enhance TMZ resistance; Plofsome@siMDK disrupted this interaction, reducing DNA repair and tumor proliferation. CONCLUSION We developed Plofsomes, a nanotechnology platform that delivers siRNA and CRISPR-Cas9 RNP complexes across the BBB and into GBM cells. By integrating a ROS-cleavable ‘lock’, Plofsomes ensure targeted fusion and cargo release in high ROS tumor environments. Our findings show Plofsomes effectively suppress MDK expression, reducing TMZ resistance and inhibiting GBM growth in models. This enhances the efficacy and safety of RNAi and CRISPR-Cas9 therapeutics. The study provides insights into TMZ resistance mechanisms and the role of MDK in GBM progression. Plofsomes offer a promising strategy for improving GBM treatment outcomes and could impact future research and patient care.
- Research Article
- 10.1101/2025.09.08.674920
- Sep 8, 2025
- bioRxiv : the preprint server for biology
- Mohamed T Elaswad + 4 more
The ability of oocytes to maintain their quality is essential for successful reproduction. One critical aspect of oocyte quality and successful embryogenesis after fertilization is the proper regulation of the stores of maternal mRNA by RNA-binding proteins. Many RNA-binding proteins undergo regulated phase transitions during oogenesis, and alterations of the protein phase can disrupt its ability to regulate mRNA stability and translation. In C. elegans , genetic screens have identified regulators of RNA-binding protein condensation in arrested oocytes of females and in embryos, but less attention has focused on phase transitions in maturing oocytes of young adult hermaphrodites. Interestingly, of the relatively few regulators of RNA-binding protein phase transitions identified to date in maturing oocytes, several genes overlap with those required for clearance of protein aggregates in maturing oocytes. To determine the extent to which the temporally linked processes of clearance of damaged proteins and maintenance of RNP complexes are coordinated at a molecular level, we conducted a targeted RNAi screen of genes required for removal of protein aggregates in maturing oocytes. We identified six novel regulators of phase transitions of the KH-domain protein MEX-3 and obtained strong evidence that the regulatory network of protein aggregate clearance overlaps with, but is distinct from, the regulation of MEX-3 phase transitions in the oocyte.
- Preprint Article
- 10.21203/rs.3.rs-7012598/v1
- Jul 23, 2025
- Research Square
- M Cortijo-Gutiérrez¹ + 13 more
Abstract BackgroundAdoptive cell therapy (ACT) with genetically engineered T cells expressing chimeric antigen receptors (CARs) has emerged as a promising treatment option for patients with refractory leukaemia or lymphoma. Despite its success in type B malignancies, CAR-T cell therapy still faces some challenges such as toxicity, functional suppression by the tumour microenvironment (TME), and poor persistence in treated patients.MethodsThis study employed a second-generation CD19-targeting CAR construct to generate engineered CAR-T cells with enhanced functionality through precise genome editing. Using CRISPR/Cas9 technology, the PDCD1 gene was to mitigate T cell exhaustion, and in a parallel knock-in strategy, an IL-15 transgene was inserted at the PDCD1 locus. Gene editing was performed via electroporation of RNP complexes, with AAV6 vectors used for homology-directed IL-15 integration. Editing efficiency and off-target activity were assessed by flow cytometry, Sanger sequencing, ICE, and CAST-Seq. Functional characterization included bulk RNA sequencing, metabolic profiling using Seahorse technology, and cytotoxicity assays against CD19+ target cells.ResultsWe initially demonstrated that αCD19 CAR-T cells lacking PD-1 expression (PD-1 KO) exhibited reduced expansion capacity and overall fitness compared to control CAR-T cells but showed a superior cytotoxicity against PDL1+ target cells. To address the impaired fitness of PD-1 KO CAR-T cells, we generated PD-1KIL-15 CAR-T cells, which combine PD-1 KO with the expression of IL-15 under the control of the PD-1 endogenous promoter. Compared to CAR T PD-1 KO cells, PD-1KIL-15 CAR-T cells displayed improved phenotype, viability, and metabolism. More importantly, they also demonstrated enhanced cytolytic capacity of PDL1+ CD19 + target cells, which correlated with increased resistance to apoptosis and improved cell fitness.ConclusionsIn summary, we present a next 4th generation CAR-T cells platform (TRUCKs) that integrates PD-1 deletion with the inducible expression of IL-15 upon T cell activation and/or exhaustion. This strategy addresses the limitations associated with knocking-out PD-1 and those associated with sustained IL-15 cytokine expression. The same platform can be used to generate PD-1 KO TRUCKs targeting different antigens and expressing different cytokines under the control of the PD-1 locus.
- Research Article
6
- 10.3389/fgeed.2025.1582097
- Jun 4, 2025
- Frontiers in Genome Editing
- Muhammad W Luqman + 8 more
Over the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations that may be detrimental or otherwise unintended. These bystander mutations are often undetected using conventional genotyping methods. The use of Adeno-Associated Viruses (AAVs) to bring donor templates in zygotes is currently being deployed by transgenic cores around the world to generate knock-ins with large transgenes (i.e., 1–4 kb payloads). Thanks to a high level of efficiency and the relative ease to establish this technique, it recently became a method of choice for transgenic laboratories. However, a thorough analysis of the editing outcomes following this method is yet to be developed. To this end, we generated three different types of integration using AAVs in two different murine genes (i.e., Ace2 and Foxg1) and employed Oxford Nanopore Technologies long read sequencing to analyze the outcomes. Using a workflow that includes Cas9 enrichment and adaptive sampling, we showed that unintended on-target mutations, including duplication events and integration of viral sequences (sometimes reported using other workflows) can occur when using AAVs. This work highlights the importance of in-depth validation of the mutant lines generated and informs the uptake of this new method.
- Research Article
6
- 10.1007/s11248-025-00446-9
- Jun 3, 2025
- Transgenic research
- Hiralben Lakhani + 5 more
The advancement in the CRISPR/Cas system has significantly streamlined genome editing in plants, rendering it simple, reliable, and efficient. However, the development of transgene-free crops is a challenging task for vegetatively propagated plants like banana. In the present study, we established banana protoplasts-based versatile and efficient platform for genome editing to overcome this limitation. Herein, a protocol has been optimized for protoplast isolation by considering leaf and embryogenic cell suspension (ECS) of banana cultivar Grand Naine. Freshly prepared ECS was identified as the best source for protoplast isolation. The protoplast viability and competency were checked by transfection with plasmid and RNP complex. Polyethylene glycol (PEG)-mediated protoplast transfection using pCAMBIA1302 and pJL50TRBO vectors showed GFP expression with 30 and 70% efficiency, respectively, eventually proving the protocol's efficacy. Further, gRNAs targeting banana β-carotene hydroxylase gene are validated by in-vitro cleavage test and subsequently used for RNP complex formation with varied ratios (1:1, 1:2, 1:5, and 1:10) of SpCas9 to gRNA1. Among these, a 1:2 molar ratio proved best to generate indel frequency with 7%. Sequencing analysis of the target amplicon revealed mutations upstream of the PAM region, specifically with gRNA1, among the three in-vitro validated gRNAs. This study evaluated the effectiveness of gRNAs in-vitro and in-vivo, yielding inconsistent results that highlight the need for comprehensive in-vivo validation of their functionality. Conclusively, the optimized protocol for banana transfection has the potential to be harnessed for the generation of transgene-free genetically improved banana.
- Research Article
4
- 10.1093/nar/gkaf318
- Apr 22, 2025
- Nucleic Acids Research
- Kaylee E Dillard + 8 more
Mobile genetic elements evade CRISPR–Cas adaptive immunity by encoding anti-CRISPR proteins (Acrs). Acrs inactivate CRISPR–Cas systems via diverse mechanisms but generally coevolve with a narrow subset of Cas effectors that share high sequence similarity. Here, we demonstrate that AcrIIA11 inhibits Streptococcus pyogenes (Sp), Staphylococcus aureus (Sa), and Francisella novicida (Fn) Cas9s in vitro and in human cells. Single-molecule imaging reveals that AcrIIA11 hinders SaCas9 target search by reducing its diffusion on nonspecific DNA. DNA cleavage is inhibited because the AcrIIA11:SaCas9 complex binds to protospacer adjacent motif (PAM)-rich off-target sites, preventing SaCas9 from reaching its target. AcrIIA11 also greatly slows down DNA cleavage after SaCas9 reaches its target site. A negative-stain electron microscopy reconstruction of an AcrIIA11:SaCas9 RNP complex reveals that the heterodimer assembles with a 1:1 stoichiometry. Physical AcrIIA11–Cas9 interactions across type IIA and IIB Cas9s correlate with nuclease inhibition and support its broad-spectrum activity. These results add a kinetic inhibition mechanism to the phage-CRISPR arms race.
- Research Article
4
- 10.1371/journal.pone.0312722
- Mar 27, 2025
- PloS one
- Dawid Winiarczyk + 3 more
Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) is a genome engineering method for generating site-specific editing in target genes in a variety of species. It is a common tool for generating mouse models of different diseases. However, detecting target modifications in mouse embryos can be time-consuming and expensive. Accordingly, developing a screening method to confirm gene modification may be useful. We propose herein an evaluation method (cleavage assay - CA) for CRISPR/Cas9-mediated gene editing in preimplantation mouse embryos that allows us to detect mutants efficiently and later on initiate in vivo production without the extensive number of samples needing to be sent for Sanger sequencing and animal usage. Our method is based on the inability of the RNP complex to recognize the target sequence after CRISPR-mediated genome editing due to modification of the target locus. It allows us to establish gene edited mice in a user-friendly fashion with a limited number of mice usage by confirming each step of CRISPR-mediated gene editing of mouse embryos and, therefore, can be considered as a supportive tool to existing procedures for verification of successful CRISPR/Cas9-mediated gene alterations in mouse embryos and further mutant production.
- Research Article
2
- 10.1093/nar/gkaf212
- Mar 20, 2025
- Nucleic Acids Research
- Keisuke Fukunaga + 7 more
CS1–LS4 and CS2–LS12 are ultra-high affinity and orthogonal RNA–protein pairs that were identified by PD-SELEX (Phage Display coupled with Systematic Evolution of Ligands by EXponential enrichment). To investigate the molecular basis of the lab-coevolved RNA–RBP pairs, we determined the structures of the CS1–LS4 and CS2–LS12 complexes and the LS12 homodimer in an RNA-free state by X-ray crystallography. The structural analyses revealed that the lab-coevolved RNA–RBPs have acquired unique molecular recognition mechanisms, whereas the overall structures of the RNP complexes were similar to the typical kink-turn RNA-L7Ae complex. The orthogonal RNA–RBP pairs were applied to construct high-performance cell-free riboswitches that regulate translation in response to LS4 or LS12. In addition, by using the orthogonal protein-responsive switches, we generated an AND logic gate that outputs staphylococcal γ-hemolysin in cell-free system and carried out hemolysis assay and calcein leakage assay using rabbit red blood cells and artificial cells, respectively.
- Research Article
1
- 10.18699/vjgb-25-04
- Mar 3, 2025
- Vavilovskii zhurnal genetiki i selektsii
- A V Smirnov + 6 more
In pronuclear microinjection, the Cas9 endonuclease is employed to introduce in vivo DNA double-strand breaks at the genomic target locus or within the donor vector, thereby enhancing transgene integration. The manner by which Cas9 interacts with DNA repair factors during transgene end processing and integration is a topic of considerable interest and debate. In a previous study, we developed a barcode-based genetic system for the analysis of transgene recombination following pronuclear microinjection in mice. In this approach, the plasmid library is linearized with a restriction enzyme or a Cas9 RNP complex at the site between a pair of barcodes. A pool of barcoded molecules is injected into the pronucleus, resulting in the generation of multicopy concatemers. In the present report, we compared the effects of in vivo Cas9 cleavage (RNP+ experiment) and in vitro production of Cas9- linearized transgenes (RNP- experiment) on concatenation. In the RNP+ experiment, two transgenic single-copy embryos were identified. In the RNP- experiment, six positive embryos were identified, four of which exhibited lowcopy concatemers. Next-generation sequencing (NGS) analysis of the barcodes revealed that 53 % of the barcoded ends had switched their initial library pairs, indicating the involvement of the homologous recombination pathway. Out of the 20 transgene-transgene junctions examined, 11 exhibited no mutations and were presumably generated through re-ligation of Cas9-induced blunt ends. The majority of mutated junctions harbored asymmetrical deletions of 2-4 nucleotides, which were attributed to Cas9 end trimming. These findings suggest that Cas9-bound DNA may present obstacles to concatenation. Conversely, clean DNA ends were observed to be joined in a manner similar to restriction-digested ends, albeit with distinctive asymmetry. Future experiments utilizing in vivo CRISPR/ Cas cleavage will facilitate a deeper understanding of how CRISPR-endonucleases influence DNA repair processes.
- Research Article
- 10.1063/4.0000632
- Mar 1, 2025
- Structural Dynamics
- Hasan Al Banna + 1 more
Human immunodeficiency virus (HIV) remains a major global public health threat that infects the human body's immune system and causes acquired immunodeficiency syndrome (AIDS) in the final stage of the disease. Retroviruses such as HIV usually have an RNA genome released into the host cell, which is then used to generate proviral DNA through reverse transcription. Thus, the double-stranded proviral DNA is integrated into the human genome and undergoes transcription to produce the viral RNA in the nucleus. To translate structural proteins and package the genomic RNA into new virions, the unspliced viral RNAs are required to export out of the nucleus after transcription. The nuclear export of such intron-retaining HIV RNA is promoted by a specific RNA scaffold called Rev Response Element (RRE) within the viral genome. The RRE RNA cooperatively binds multiple copies of Rev proteins to form an RNP complex recognized by the nuclear export machinery. The secondary structure of RRE is proposed to form either four- or five-stem-loop conformation that differs in regions outside the predicted primary Rev binding sites. However, the structural basis of RRE-rev interactions remains largely unknown. To understand the tertiary structure of the RRE, we designed an RNA construct with four-stem-loop conformation stabilizing mutations with a Fab BL3-6 binding sequence by replacing one of the loops outside the Rev binding site. As these constructs bind with the Fab as expected, we set up crystallization trials for the Fab-RNA complex. Interestingly, one of the Fab-RNA complexes was crystallized robustly, producing large hexagonal crystals. After further optimization of crystallization conditions for precipitant and pH, the crystals diffracted to 2.85 Å resolution. The structure-solving process is underway. Upon solving this RRE four-stem-loop core structure, we will be able to define how RRE folds to organize the rev-binding sites, setting up a stage for further investigation of RRE-rev interactions and how this RNP complex promotes the nuclear export of HIV RNA.
- Research Article
2
- 10.1002/cpz1.70109
- Feb 1, 2025
- Current protocols
- Marina Gertsenstein + 2 more
Mice carrying patient-associated base changes are powerful tools to define the causality of single-nucleotide variants to disease states. Epitope tags enable immuno-based studies of genes for which no antibodies are available. These alleles enable detailed and precise developmental, mechanistic, and translational research. The first step in generating these alleles is to identify within the target sequence-the orthologous sequence for base changes or the N or C terminus for epitope tags-appropriate Cas9 protospacer sequences. Subsequent steps include design and acquisition of a single-stranded oligonucleotide repair template, synthesis of a single guide RNA (sgRNA), collection of zygotes, and microinjection or electroporation of zygotes with Cas9 mRNA or protein, sgRNA, and repair template followed by screening born mice for the presence of the desired sequence change. Quality control of mouse lines includes screening for random or multicopy insertions of the repair template and, depending on sgRNA sequence, off-target sequence variation introduced by Cas9. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Single guide RNA design and synthesis Alternate Protocol 1: Single guide RNA synthesis by primer extension and in vitro transcription Basic Protocol 2: Design of oligonucleotide repair template Basic Protocol 3: Preparation of RNA mixture for microinjection Support Protocol 1: Preparation of microinjection buffer Alternate Protocol 2: Preparation of RNP complexes for electroporation Basic Protocol 4: Collection and preparation of mouse zygotes for microinjection or electroporation Basic Protocol 5: Electroporation of Cas9 RNP into zygotes using cuvettes Alternate Protocol 3: Electroporation of Cas9 RNP into zygotes using electrode slides Basic Protocol 6: Screening and quality control of derived mice Support Protocol 2: Deconvoluting multiple sequence chromatograms with DECODR.
- Research Article
8
- 10.1038/s41467-025-56149-6
- Jan 22, 2025
- Nature Communications
- Nicholas M Forino + 7 more
Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-pseudoknot (t/PK) and the three-way junction (CR4/5). These hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are essential for telomerase activity. Here, we probe hTR structure in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features required for hTERT binding. The proportion of hTR CR4/5 folded into the primary functional conformation is independent of hTERT expression levels. Mutations that stabilize the alternative CR4/5 conformation are detrimental to telomerase assembly and activity. Moreover, the alternative CR4/5 conformation is not found in purified telomerase RNP complexes, supporting the hypothesis that only the primary CR4/5 conformer is active. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded, suggesting that kinetic RNA folding traps studied in vitro may also hinder ribonucleoprotein assembly in vivo.
- Research Article
- 10.19746/j.cnki.issn.1009-2137.2024.06.040
- Dec 1, 2024
- Zhongguo shi yan xue ye xue za zhi
- Yan-Min He + 4 more
To establish an efficient gene editing method of HLA-I gene to prepare HLA-I universal hematopoietic stem cells. The easyedit small guide RNA(sgRNA) was designed according to the sequences of β2 microglobulin gene and synthesized by GenScript company. RNP complexes were formed by NLS-Cas9-NLS nuclease and Easyedit sgRNA according to different molar ratios (1∶1~1∶4). Control group and four transfection groups were performed respectively. HEK-293 cells and CD34+ hematopoietic stem cells were nucleotransfected with RNP complex by Lonza 4D Nucleofector system. The expression of HLA-I on the surface of HEK-293 cells was detected by flow cytometry after transfection for 72 hours, the cleavage effect was determined by T7E1 enzyme digestion reaction and the presence of nested peak in the DNA sequence was identified by direct sequencing. The transfection groups had different levels of HLA-I negative expression cell populations by flow cytometry after transient transfection of HEK-293 cells and CD34+ hematopoietic stem cells with different molar concentrations of RNP complex for 72 hours. There were nested peaks proximal to the sgRNA PAM sequence in the transfection groups by direct DNA sequencing, indicating that sgRNA had obvious editing effect. In the transfection of HEK-293 cells, the highest proportion of HLA-I negative expression cells was (87.69±0.83)% when the molar ratio of NLS-Cas9-NLS nuclease to Easyedit sgRNA was 1∶4. The cutting efficiency of T7E1 was the highest up to (38±2.0)% when the molar ratio was 1∶3. In the transfection of CD34+ hematopoietic stem cells, the proportion of HLA-I negative expression cells was (91.56±3.39)% when the molar ratio was 1∶2, and the cutting efficiency of T7E1 was (64±8.45)% when the molar ratio was 1∶1. This study provides an efficient gene editing method for classical HLA-I molecules, which can effectively silence the expression of class HLA-I molecules on the cell surface, and is suitable for stem cell system with difficult transfection.
- Research Article
16
- 10.1093/plphys/kiae491
- Sep 23, 2024
- Plant physiology
- Chikako Kuwabara + 11 more
Here, we report a smart genome editing system for soybean (Glycine max) using the in planta bombardment-ribonucleoprotein (iPB-RNP) method without introducing foreign DNA or requiring traditional tissue culture processes such as embryogenesis and organogenesis. Shoot apical meristem (SAM) of embryonic axes was used as the target tissue for genome editing because the SAM in soybean mature seeds has stem cells and specific cell layers that develop germ cells during the reproductive growth stage. In the iPB-RNP method, the RNP complex of the CRISPR/Cas9 system was directly delivered into SAM stem cells via particle bombardment, and genome-edited plants were generated from these SAMs. Soybean allergenic gene Gly m Bd 30K was targeted in this study. Many E0 (the first generation of genome-edited) plants in this experiment harbored mutant alleles at the targeted locus. Editing frequency of inducing mutations transmissible to the E1 generation was approximately 0.4% to 4.6% of all E0 plants utilized in various soybean varieties. Furthermore, simultaneous mutagenesis by iPB-RNP method was also successfully performed at other loci. Our results offer a practical approach for both plant regeneration and DNA-free genome editing achieved by delivering RNP into the SAM of dicotyledonous plants.
- Research Article
9
- 10.3389/fphar.2024.1454785
- Sep 20, 2024
- Frontiers in pharmacology
- Devam A Desai + 2 more
Background: In-vivo CRISPR Cas genome editing is a complex therapy involving lipid nanoparticle (LNP), messenger RNA (mRNA), and single guide RNA (sgRNA). This novel modality requires prior modeling to predict dose-exposure-response relationships due to limited information on sgRNA and mRNA biodistribution. This work presents a QSP model to characterize, predict, and translate the Pharmacokinetics/Pharmacodynamics (PK/PD) of CRISPR therapies from preclinical species (mouse, non-human primate (NHP)) to humans using two case studies: transthyretin amyloidosis and LDL-cholesterol reduction. Methods: PK/PD data were sourced from literature. The QSP model incorporates mechanisms post-IV injection: 1) LNP binding to opsonins in liver vasculature; 2) Phagocytosis into the Mononuclear Phagocytotic System (MPS); 3) LNP internalization via endocytosis and LDL receptor-mediated endocytosis in the liver; 4) Cellular internalization and transgene product release; 5) mRNA and sgRNA disposition via exocytosis and clathrin-mediated endocytosis; 6) Renal elimination of LNP and sgRNA; 7) Exonuclease degradation of sgRNA and mRNA; 8) mRNA translation into Cas9 and RNP complex formation for gene editing. Monte-Carlo simulations were performed for 1000 subjects and showed a reduction in serum TTR. Results: The rate of internalization in interstitial layer was 0.039 1/h in NHP and 0.007 1/h in humans. The rate of exocytosis was 6.84 1/h in mouse, 2690 1/h in NHP, and 775 1/h in humans. Pharmacodynamics were modeled using an indirect response model, estimating first-order degradation rate (0.493 1/d) and TTR reduction parameters in NHP. Discussion: The QSP model effectively characterized biodistribution and dose-exposure relationships, aiding the development of these novel therapies. The utility of platform QSP model can be paramount in facilitating the discovery and development of these novel agents.
- Research Article
5
- 10.1101/2023.10.04.560962
- Aug 29, 2024
- bioRxiv : the preprint server for biology
- Nicholas M Forino + 7 more
Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features thought to be required for hTERT binding. The proportion of hTR CR4/5 that is folded into the primary functional conformation does not require hTERT expression and the fraction of hTR that assumes a misfolded CR4/5 domain is not refolded by overexpression of its hTERT binding partner. This result suggests a functional role for an RNA folding cofactor other than hTERT during telomerase biogenesis. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. Moreover, the alternative CR4/5 conformation is not found in telomerase RNP complexes purified from cells via an epitope tag on hTERT, supporting the hypothesis that only the major CR4/5 conformer is active. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.
- Research Article
3
- 10.1016/j.theriogenology.2024.08.027
- Aug 22, 2024
- Theriogenology
- Meeti Punetha + 9 more
Establishment of CRISPR-Cas9 ribonucleoprotein mediated MSTN gene edited pregnancy in buffalo: Compare cells transfection and zygotes electroporation