Knockout Efficiencies Research Articles

An Efficient Fluorescence-Activated Protoplast Sorting (FAPS) and Regeneration Protocol for Canola (Brassica napus).

Protoplast sorting and purification methods are powerful tools enabling the enrichment of cellular subpopulations for basic and applied studies in plant sciences. Fluorescence-activated protoplast sorting (FAPS) is an efficient method to isolate specific protoplast populations based on innate features (size and autofluorescence) or expression of fluorescent proteins. FAPS-based methods have recently been deployed in single-cell purification for single-cell RNA sequencing-based transcriptional profiling studies. Protoplast sorting methods integrated with the ability to culture and recover whole plants add value to functional genomics and gene editing applications. Enriching cells expressing nucleases linked to fluorescent proteins can maximize knockout or knockin editing efficiencies and minimize toxic and off-target effects. Here, we report the protocol for protoplast preparation, sterile cell sorting, culture, and downstream regeneration of plants from canola protoplasts. This protocol can be successfully applied to all totipotent protoplast methods that can regenerate into whole plants. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Preparation of transfected canola protoplasts for sorting Basic Protocol 2: Fluorescence-activated protoplast sorting Basic Protocol 3: Bead culture of sorted protoplasts and recovery of plantlets.

Identification of Two Potential Gene Insertion Sites for Gene Editing on the Chicken Z/W Chromosomes.

The identification of accurate gene insertion sites on chicken sex chromosomes is crucial for advancing sex control breeding materials. In this study, the intergenic region NC_006127.4 on the chicken Z chromosome and the non-repetitive sequence EE0.6 on the W chromosome were selected as potential gene insertion sites. Gene knockout vectors targeting these sites were constructed and transfected into DF-1 cells. T7E1 enzyme cleavage and luciferase reporter enzyme analyses revealed knockout efficiencies of 80.00% (16/20), 75.00% (15/20), and 75.00% (15/20) for the three sgRNAs targeting the EE0.6 site. For the three sgRNAs targeting the NC_006127.4 site, knockout efficiencies were 70.00% (14/20), 60.00% (12/20), and 45.00% (9/20). Gel electrophoresis and high-throughput sequencing were performed to detect potential off-target effects, showing no significant off-target effects for the knockout vectors at the two sites. EdU and CCK-8 proliferation assays revealed no significant difference in cell proliferation activity between the knockout and control groups. These results demonstrate that the EE0.6 and NC_006127.4 sites can serve as gene insertion sites on chicken sex chromosomes for gene editing without affecting normal cell proliferation.

Genome-Wide CRISPR Screen Identifies ZNF451 Regulating Sensitivity to Topoisomerase 2 Inhibitors in Peripheral T-Cell Lymphoma Cells

Introduction: Despite the recent therapeutic developments for peripheral T-cell lymphomas (PTCLs), their prognosis remains dismal. Topoisomerase 2 inhibitors (TOP2i), which increase the amount of TOP2-DNA covalent complex and block DNA double-strand break repair, have long been used as key drugs in the treatment of PTCLs. The molecular mechanisms underlying sensitivity to TOP2i remain to be fully elucidated. Methods: To elucidate the cell-intrinsic genes affecting TOP2i sensitivity in PTCL cells, we performed whole-genome loss-of-function CRISPR screenings in adult T-cell leukemia/lymphoma (ATLL) cell lines. ST1 and KK1 cells were transduced with the Brunello CRISPR knockout pooled library targeting 19,114 genes (4 sgRNAs/gene) followed by puromycin selection. The transduced cells were then treated with etoposide (ETP), doxorubicin (DOX) or DMSO control for 8 days. The MAGeCK algorithm was used to rank the sgRNAs responsible for TOP2i sensitivity. Among the top 500 enriched genes, we further selected the those with at least 2 sgRNAs with a log2 fold change (TOP2i/DMSO) < -0.5 or >0.5 in both ST1 and KK1 cells as genes whose knockout conferred TOP2i sensitivity or resistance, respectively. Results: Using the whole genome loss-of-function CRISPR screen, we identified 3 genes and 2 genes whose knockout conferred ETP sensitivity and resistance, respectively. TOP2A, a known ETP target, was ranked as a top gene for ETP resistance, confirming the reliability of our screenings (Fig. 1). In the same way we also extracted 3 genes whose knockout conferred DOX sensitivity. Interestingly, zinc finger protein 451 (ZNF451) was identified as an overlapping gene whose knockout conferred sensitivity in both screens for ETP and DOX. ZNF451 is an E3 SUMO ligase and was previously reported to be an endogenous DNA repair factor for TOP2i-induced DNA double-strand breaks (Schellenberg et al. Science 2017). The role of ZNF451 in PTCL cells has not been previously reported, prompting us to focus on ZNF451 in further analyses. For a confirmatory experiments, we transduced sgRNAs targeting ZNF451 (sgZNF451) in ATLL cell lines. To see the knockout efficiencies of the sgZNF451, we performed immunoblot analysis by using anti-ZNF451 antibody and found three bands with different levels of reduction. To ensure whether the bands detected by the anti-ZNF451 antibody represented endogenous ZNF451 protein, we engineered the ATLL cell line with an HA-tag at the 5' UTR of the endogenous ZNF451 gene locus by CRISPR-mediated knock-in. Immunoblot analysis of sgZNF451-transduced engineered cells expressing HA-tag-ZNF451 by using anti-HA antibody showed almost the same pattern of the bands as shown in the blot by anti-ZNF451 antibody. Thus, we confirmed that sgZNF451 worked efficiently and concluded that post-transcriptional modification affected the stability of ZNF451 protein in ATLL cells. Next, we investigated the role of ZNF451 on cell viability. While sgZNF451-transduced ATLL cells did not differ from control sgRNA-transduced cells in terms of cellular proliferation under normal culture conditions, sgZNF451-transduced ATLL cells showed increased sensitivity to both ETP and DOX compared to control cells with statistical significance, confirming our screening results (Fig. 2). Importantly, sgZNF451-mediated sensitization to ETP and DOX was found not only in ATLL cells but also in other PTCL cell lines including ALK-positive and ALK-negative anaplastic large cell lymphoma (ALCL). Mechanistically, apoptosis and G2/M cell cycle arrest were induced at significantly higher frequencies by ETP treatment in ZNF451 knocked out cells compared to control cells. Given the role of ZNF451 in TOP2i sensitivity in PTCL cells, we investigated whether ZNF451 expression levels stratify the prognosis of PTCL patients treated with CHOP-like regimens. To test this, FFPE samples from 45 PTCL-NOS patients were used for Q-PCR analysis of ZNF451 mRNA but we did not find any correlation between the ZNF451 expression and prognosis. Conclusions: We performed unbiased genome-wide CRISPR/Cas9 library screens and identified ZNF451 as an important regulator of sensitivity to TOP2i in PTCL cells. Further studies are needed to determine whether measuring ZNF451 protein levels can be used as a biomarker in PTCL patients who are treated with TOP2i.

Lipid Nanoparticle-Mediated Gene Editing of Human Primary T Cells and Off-Target Analysis of the CRISPR-Cas9 Indels

Background and Aims: The CRISPR/Cas9 system has emerged as a powerful tool for gene editing of primary cells. In our previous work, we demonstrated a novel lipid nanoparticle (LNP) reagent for the multi-step engineering of gene-edited CAR T cells. We showed high cell viabilities and potent CAR-T mediated killing, even after multiple genetic manipulations. Here, we extend this work by assessing potential off-target editing effects in both LNP-treated T cells and T-cells where the CRISPR reagents were delivered by electroporation. Further, we evaluated multiple Cas9 variants and guide RNA targets. Methods: LNPs encapsulating wild type or high fidelity S.p. Cas9 mRNA and various TRAC and CD52 targeted guide RNAs (sgRNAs) were produced using our scalable NanoAssemblrTM microfluidics platform. Concurrently, electroporation was performed to deliver equivalent cargoes. Purified primary T cells were cultured, activated, and expanded in serum-free media in plates, flasks, or small bioreactors. The LNPs were added to cells by direct addition for gene editing. Gene expression and cell viability were measured using flow cytometry or colorimetric assays. Multi-target performance of CRISPR-Cas9 editing was evaluated through rhAmpSeq-based targeted next-generation sequencing (NGS) and indels analyzed for with CRISPRAltRations. Results: TCR or CD52 targeted Cas9 mRNA-LNP addition or electroporation yielded high single and double knockout efficiencies. High-throughput NGS analysis showed strong agreeance to flow cytometry for on-target analysis. We tested a range of sgRNA targets, wild-type and high-fidelity Cas9 mRNAs, and determined off-target editing for all targets and variants investigated. Similar results were obtained when comparing different LNP batch sizes (micro to milligram RNA) and cell culture vessels (0.1 to 45 million cells), demonstrating scalability of both LNP production and cell treatment. Conclusions: The results from this study further support the utility RNA-LNPs for the genetic engineering of primary T cells. The simple and gentle nature of LNP cell treatment allows for multiple genetic engineering steps for simultaneous expression and deletion of proteins for the next cell therapies. These LNPs can be easily manufactured from small-scale screening of RNA libraries to rapid scale-up for clinical translation.

Non-Viral RNA-Lipid Nanoparticles for High Efficiency Genome Editing of CD34+ Hematopoietic Stem and Progenitor Cells for Advanced Cell and Gene Therapies

Background and Aims: The application of CRISPR-Cas9 gene editing in hematopoietic stem (HSC) and progenitor cells (HSPCs) has the potential to revolutionize the treatment of genetic blood disorders by correcting disease-causing mutations. Previously, we demonstrated the utility of a novel lipid nanoparticle (LNP) reagent for the multiplexed engineering of gene-edited CAR T cells, showing high cell viabilities, rapid onset editing, and potent CAR-mediated killing. In this current work, we demonstrate the capability of LNPs for the efficient and gentle delivery of genetic material to CD34+ HSPCs. The benefits of a non-viral LNP-mediated approach paves the way for the development of next generation gene therapy products in the HSC field. Methods: LNPs encapsulating S.p. Cas9 mRNA and CD33 or CD45 targeted guide RNA (sgRNA) were produced using the scalable NanoAssemblr® NxGen™ microfluidic platform technology ( Fig. 1A). The LNP composition was optimized for the gentle and efficient cargo delivery to HSC/HSPCs. Purified human CD34+ cells were cultured, stimulated, and treated by the direct addition of the RNA-LNPs. Various commercial cell sources were tested including mobilized peripheral blood and cord blood. Gene knockout and viability were assessed using flow cytometry, cell proliferation using an automated cell counter, and differentiation capacity by colony-forming unit (CFU) assays. Results: One-step addition of LNPs to CD34+ HSPCs resulted in 84 ± 6% CD33 and 81 ± 2% CD45 knockout efficiencies (n=6 CD34+ donors, Fig. 1B). After treatment, cells maintained on average 95 ± 3% absolute cell viability, compared to 99% viability of the untreated cells, Fig. 1C. Furthermore, LNP treated HSCs maintained excellent cell proliferation, with over >90% relative cell proliferation to the untreated controls. The CFU assays showed no significant change in relative lineage formation for both the RNA-LNPs and the empty LNP vehicle control ( Fig. 1D). Finally, LNP production was successfully scaled-up using microfluidics from discovery to pre-clinical scales. Conclusions: LNP-mediated CRISPR-Cas9 mRNA delivery is a promising approach for gene editing in HSPCs. The simple and gentle nature of LNP cell treatment allows for multiple genetic engineering steps for simultaneous expression and deletion of proteins for novel gene therapies. Furthermore, LNPs can be easily manufactured using microfluidics, enabling small-scale screening of RNA libraries and rapid scale-up for clinical translation.

Platinum Talen-Mediated Knock-in of Single-Stranded DNA Templates Facilitates Manufacturing of Clinical-Scale Non-Virally Gene-Edited T Cells from Peripheral Blood

Background: During the past decade, technologies that manufacture gene-modified immune cells, such as chimeric antigen receptor T cells, have been rapidly evolved and introduced in human clinics. T cells reprogrammed to express antigen-specific T-cell receptors (TCR-T) are an up-and-coming tool to treat intractable infection or malignant neoplasm in a personalized manner. However, several caveats still exist in the production of TCR-T for clinical use, because competitive surface expression of endogenous and transduced TCRs might hamper desired expression of transduced TCR. Moreover, mispairing of TCR subunits could mediate unexpected harmful immune complications. Therefore, in this study, we aimed to develop a method to introduce any desired TCRs in human primary T cells independent of interference with endogenous TCR by way of targeted knockout of TRA and TRB gene loci using highly-efficient transcription activator-like effector nuclease (TALEN), named Platinum TALEN (Sakuma T, Sci Rep 2013). Methods: We designed and synthesized two pairs of 5'-Cap-1 Platinum TALEN mRNA targeting the gene sequences that encode constant regions of human TRA ( TRAC) and TRB ( TRBC). TCR knockout efficiencies by these TALEN pairs were assessed by flow cytometric analysis using anti-CD3/TCR antibodies. Next, we constructed single-stranded DNA (ssDNA) homology-directed repair templates for the knock-in of desired TCR transgene into the TALEN target sequence of the TRAC locus. As a model TCR, we selected a 1G4 clone that reacts with NY-ESO-1-derived peptide in an HLA-A*02-restricted manner. We delivered these TALEN mRNA pairs and 1G4-encoding ssDNA by electroporation into primary human T cells collected from healthy volunteer adult donors after 72 hours of anti-CD3/CD28 beads activation. Genome-edited T cells were subsequently cultured in Therapeak TM X-VIVO15 (Lonza) supplemented with 10% human AB serum in the presence of 2-mercaptoethanol and interleukin-2 followed by second anti-CD3/CD28 beads activation. Density of T cells were maintained approximately at 1.0-3.0 x10 6/mL and transferred to larger flasks with additional fresh media as appropriate according to cell counts throughout the culture.1G4-transduced T cells were detected and counted by HLA-A*02:01 NY-ESO-1 tetramers at 17-22 days after electroporation. Additionally, we performed optical genome mapping analysis (Bionano Genomics) of Platinum TALEN-treated cells to screen genome-editing-associated large chromosomal structural variations (SVs) including unintended translocation. Results: Platinum TALEN mRNA pairs targeting TRAC and TRBC yielded a high proportion (>70%) of CD3/TCR negative T cells without the cost of compromised cell viability. By co-electroporation of 1G4 ssDNA and these Platinum TALEN mRNA pairs, we successfully obtained an average of 10.5 (range 2.2-19.0) million (n=5)NY-ESO-1-tetramer-positive cells with high viability from 3 millionprimary T cells until 3 weeks after electroporation. By flow cytometric analysis, a proportion of 1G4-tetramer positive cells that express Vβ chains other than Vβ13 (Vβ of 1G4) was approximately 10%. The PD-1-positive fraction in the expanded 1G4-expressing T cells was less than 10%, while levels of TIM-3 expression were 40-60%. These tetramer-positive cells showed specific cytotoxicities against HLA-A*02-positive cells pulsed with cognate NY-ESO-1 peptides. In an optical genome mapping analysis of genomic DNA obtained from TALEN-treated T cells, we found unique SVs with relatively small sizes and low coverage but no large unique SVs with high coverage when compared with control genomic DNA. Additionally, no interchromosomal translocation was observed. Conclusions: We have successfully designed Platinum TALEN mRNA pairs targeting TRAC and TRBC which facilitate the production of genome-edited human primary T cells. We also developed an electroporation and expansion culture protocol that enables us to produce viable genome-edited 1G4-transduced T cells at a large cell dose equivalent to a clinical scale. Collectively, these results suggest that targeted orthotopic knock-in of antigen-specific TCR-encoding ssDNA into the TCR locus by the use of Platinum TALEN is a promising strategy that can be applied for the clinical manufacturing of therapeutic TCR-T cells.

CRISPR-Cas9-Based Gene Knockout of Immune Checkpoints in Expanded NK Cells.

Natural killer (NK) cell immunotherapy has emerged as a novel treatment modality for various cancer types, including leukemia. The modulation of inhibitory signaling pathways in T cells and NK cells has been the subject of extensive investigation in both preclinical and clinical settings in recent years. Nonetheless, further research is imperative to optimize antileukemic activities, especially regarding NK-cell-based immunotherapies. The central scientific question of this study pertains to the potential for boosting cytotoxicity in expanded and activated NK cells through the inhibition of inhibitory receptors. To address this question, we employed the CRISPR-Cas9 system to target three distinct inhibitory signaling pathways in NK cells. Specifically, we examined the roles of A2AR within the metabolic purinergic signaling pathway, CBLB as an intracellular regulator in NK cells, and the surface receptors NKG2A and CD96 in enhancing the antileukemic efficacy of NK cells. Following the successful expansion of NK cells, they were transfected with Cas9+sgRNA RNP to knockout A2AR, CBLB, NKG2A, and CD96. The analysis of indel frequencies for all four targets revealed good knockout efficiencies in expanded NK cells, resulting in diminished protein expression as confirmed by flow cytometry and Western blot analysis. Our in vitro killing assays demonstrated that NKG2A and CBLB knockout led to only a marginal improvement in the cytotoxicity of NK cells against AML and B-ALL cells. Furthermore, the antileukemic activity of CD96 knockout NK cells did not yield significant enhancements, and the blockade of A2AR did not result in significant improvement in killing efficiency. In conclusion, our findings suggest that CRISPR-Cas9-based knockout strategies for immune checkpoints might not be sufficient to efficiently boost the antileukemic functions of expanded (and activated) NK cells and, at the same time, point to the need for strong cellular activating signals, as this can be achieved, for example, via transgenic chimeric antigen receptor expression.

CRISPR-Cas9 assisted non-homologous end joining genome editing system of Halomonas bluephagenesis for large DNA fragment deletion

BackgroundHalophiles possess several unique properties and have broad biotechnological applications including industrial biotechnology production. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), some proteins, small molecular compounds, organic acids, and has the potential to become a chassis cell for the next-generation of industrial biotechnology (NGIB) owing to its simple culture, fast growth, contamination-resistant, low production cost, and high production value. An efficient genome editing system is the key for its engineering and application. However, the efficiency of the established CRISPR-Cas-homologous recombination (HR) gene editing tool for large DNA fragments was still relatively low. In this study, we firstly report a CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas bluephagenesis.ResultsThree different NHEJ repair systems were selected and functionally identified in Halomonas bluephagenesis TD01. The NHEJ system from M. tuberculosis H37Rv (Mt-NHEJ) can functionally work in H. bluephagenesis TD01, resulting in base deletion of different lengths for different genes and some random base insertions. Factors affecting knockout efficiencies, such as the number and position of sgRNAs on the DNA double-strands, the Cas9 protein promoter, and the interaction between the HR and the NHEJ repair system, were further investigated. Finally, the optimized CRISPR-Cas9-NHEJ editing system was able to delete DNA fragments up to 50 kb rapidly with high efficiency of 31.3%, when three sgRNAs on the Crick/Watson/Watson DNA double-strands and the arabinose-induced promoter Para for Cas9 were used, along with the background expression of the HR repair system.ConclusionsThis was the first report of CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas spp. These results not only suggest that this editing system is a powerful genome engineering tool for constructing chassis cells in Halomonas, but also extend the application of the NHEJ repair system.

Lipofection with Lipofectamine™ 2000 in a heparin-free growth medium results in high transfection efficiency in chicken primordial germ cells.

Primordial germ cells (PGCs) that can differentiate into gametes are used to produce genome-edited chickens. However, the transfection efficiency into PGCs is low in chickens; therefore, the yield efficiency of PGCs modified via genome editing is problematic. In this study, we improved transfection efficiency and achieved highly efficient genome editing in chicken PGCs. For transfection, we used lipofection, which is convenient for gene transfer. Chicken PGC cultures require adding heparin to support growth; however, heparin significantly reduces lipofection efficiency (p<0.01). Heparin-induced lipofection efficiency was restored by adding protamine. Based on these results, we optimized gene transfer into chicken PGCs. Lipofectamine™ 2000 and our PGC medium was the most efficient transfection reagent and medium, respectively. Finally, based on established conditions, we compared the gene knock-out efficiencies of ovomucoid, a major egg allergen, and gene knock-in efficiencies at the ACTB locus. These results indicate that optimized lipofection is useful for CRISPR/Cas9-mediated knock-out and knock-in. Our findings may contribute to the generation of genome-edited chickens and stimulate research in various applications involving them. This article is protected by copyright. All rights reserved.

Establishment of a CRISPR/Cas9-Mediated Efficient Knockout System of Trichoderma hamatum T21 and Pigment Synthesis PKS Gene Knockout

Trichoderma hamatum is a filamentous fungus that serves as a biological control agent for multiple phytopathogens and as an important resource promising for fungicides. However, the lack of adequate knockout technologies has hindered gene function and biocontrol mechanism research of this species. This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. Based on genomic information, we established a CRISPR/Cas9 system with dual sgRNAs targets and dual screening markers. CRISPR/Cas9 plasmid and donor DNA recombinant plasmid were constructed for disruption of the Thpyr4 and Thpks1 genes. The result indicates the consistency between phenotypic characterization and molecular identification of the knockout strains. The knockout efficiencies of Thpyr4 and Thpks1 were 100% and 89.1%, respectively. Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi.

Abstract 1785: Multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles

Abstract Autologous chimeric antigen receptor (CAR) T therapies utilize patient cells and can be limited by cell quality, and the high manufacturing burden of viral vectors. As such, there is a need for allogeneic, “off-the-shelf” CAR T cells to make these transformative treatments widely available. However, allogeneic therapies require multiple genetic engineering steps to express CAR and to delete proteins responsible for graft-versus-host disease. Messenger RNA (mRNA) is a promising approach for expression of therapeutic proteins and gene editing nucleases. In this work, we demonstrate a new method for multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles (LNPs). LNPs encapsulating Spy-Cas9 mRNA, TCR and CD52 guide RNA (sgRNA), and CAR mRNA were produced using microfluidics. The CAR construct contained an anti-CD19 scFv binding domain and CD3ζ/4-1BB co-stimulatory domains. Microgram quantities of RNA LNPs were produced to optimize LNP packaging, cargo ratios, and sgRNA combinations. Lead candidates were scaled to milligrams. Purified human primary T cells were cultured, activated, and expanded in serum-free media in plates, flasks and bioreactors. CAR+, TCR− or CD52− cells were generated by addition of the corresponding LNP to activated cells. Cytotoxic killing was determined by co-culture assays with leukemia cells. Gene knockout, CAR expression, viability and cell killing were measured using flow-cytometry. CD19 CAR was selected as a relevant protein for expression, with TCR and CD52 proteins as gene knockout targets. Single-step addition of CAR LNPs to T cells resulted in transfection efficiencies of 95.0 ± 2.1% and high protein expression. Upon TCR or CD52 LNP addition to T cells, the onset of gene editing was within 48 hours, reaching single target knockout efficiencies of 92.3 ± 3.0% (TCR−), and double knockouts (TCR−/CD52−) of 74.5 ± 6.1%. Similar results were obtained when comparing different LNP batch sizes (microgram to milligram RNA) and cell culture vessels (125,000 to 45 million cells), demonstrating scalability of both the LNP production and cell treatment. Cell viabilities above 90% were maintained at all steps and for all RNA LNPs. Finally, as proof-of-concept for multi-step engineering, sequential addition of TCR LNPs and CAR LNPs resulted in simultaneous CAR expression and TCR gene knockout. These “off-the-shelf” gene-edited CAR T cells were functionally equivalent to non-edited cells in a B cell killing assay, efficiently clearing over 80% of leukemia target cells at a 1:1 ratio. Our findings demonstrate the advantages of LNPs for RNA delivery to T cells. The simple and gentle nature of LNP cell treatment allows for multiple genetic engineering steps for simultaneous expression and deletion of proteins. Furthermore, LNPs can be easily manufactured using microfluidics, enabling small-scale screening of RNA libraries and rapid scale-up of lead candidates for clinical translation. Citation Format: Samuel Clarke, R Geczy, A Balgi, S Park, R Zhao, M Swaminathan, R Tieu, N Hoang, C Webb, E Watt, M Wong, M Fujisawa, N Jain, Angela Zhang, Anitha Thomas. Multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1785.

A simple, rapid, and efficient method for generating multigene-knockout culture cells by the CRISPR/Cas9 system.

We evaluated the efficacy of simultaneous multiple-gene knockout in human culture cells. By simple co-transfection of HeLa cells with a mixture of pX330-based targeting plasmids together with a puromycin resistance plasmid, followed by transient selection of puromycin-resistant cells, Cas9/single-guide RNA (sgRNA)-transduced polyclonal cell populations were selected and grown. Western blot analyses revealed co-transfection of up to seven targeting plasmids for p38α, p38β, JNK1, JNK2, Mnk1, ERK1, and mLST8 genes, drastically reduced protein expression of these genes in the polyclonal population. Analyses of a randomly isolated group of 25 clones revealed knockout efficiencies for the seven targeted genes ranging between 68% and 100%, and in six clones (24%), all targeted genes were disrupted. Deep sequencing analyses of the individual target sites revealed that, in most cases, Cas9/sgRNA-induced nonhomologous end joining resulted in deletion or insertion of only a few base pairs at the break points. These results demonstrate that simple co-transfection-based simultaneous targeting offers an easy, rapid, and efficient method to generate multiplex gene-knockout cell lines.

An Optimized CRISPR/Cas9 Adenovirus Vector (AdZ-CRISPR) for High-Throughput Cloning of sgRNA, Using Enhanced sgRNA and Cas9 Variants.

Recombinant adenovirus vectors enable highly efficient gene delivery in vitro and in vivo. As a result, they are widely used in gene therapy, vaccination, and anticancer applications. We have previously developed the AdZ vector system, which uses recombineering to permit high-throughput cloning of transgenes into Adenovirus vectors, simplifies alteration of the vector backbone, and enables rapid recovery of infectious virus, even if a transgene is incompatible with vector replication. In this study, we adapt this vector system to enable high-throughput cloning of sequences for CRISPR/Cas9 editing. Vectors were optimized to ensure efficient cloning, and high editing efficiency using spCas9 and single guide RNA (sgRNA) sequences in a single vector. Using a multiplicity of infection of 50, knockout efficiencies of up to 80% could be achieved with a single sgRNA. Vectors were further enhanced by altering the spCas9 sequence to match that of SniperCas9, which has reduced off-target activity, but maintains on-target efficiency, and by applying modifications to the sgRNA sequence that significantly enhance editing efficiency. Thus, the AdZ-CRISPR vectors offer highly efficient knockout, even in hard to transfect cells, and enables large-scale CRISPR/Cas9 projects to be undertaken easily and quickly.

Impact of Formulation Conditions on Lipid Nanoparticle Characteristics and Functional Delivery of CRISPR RNP for Gene Knock-Out and Correction.

The CRISPR-Cas9 system is an emerging therapeutic tool with the potential to correct diverse genetic disorders. However, for gene therapy applications, an efficient delivery vehicle is required, capable of delivering the CRISPR-Cas9 components into the cytosol of the intended target cell population. In this study, we optimized the formulation conditions of lipid nanoparticles (LNP) for delivery of ready-made CRISPR-Cas9 ribonucleic protein (RNP). The buffer composition during complexation and relative DOTAP concentrations were varied for LNP encapsulating in-house produced Cas9 RNP alone or Cas9 RNP with additional template DNA for gene correction. The LNP were characterized for size, surface charge, and plasma interaction through asymmetric flow field flow fractionation (AF4). Particles were functionally screened on fluorescent reporter cell lines for gene knock-out and gene correction. This revealed incompatibility of RNP with citrate buffer and PBS. We demonstrated that LNP for gene knock-out did not necessarily require DOTAP, while LNP for gene correction were only active with a low concentration of DOTAP. The AF4 studies additionally revealed that LNP interact with plasma, however, remain stable, whereby HDR template seems to favor stability of LNP. Under optimal formulation conditions, we achieved gene knock-out and gene correction efficiencies as high as 80% and 20%, respectively, at nanomolar concentrations of the CRISPR-Cas9 RNP.

Preclinical Results of an Allogeneic, Universal CD19/CD7-Targeting CAR-T Cell Therapy (GC502) for B Cell Malignancies

BackgroundAutologous CD19 CAR-T therapies show very promising clinical efficacy, but are limited in their applicability by several factors including cost, time to manufacture, and other factors involving patients own T-cell qualities. GC027, a CD7 targeting allogeneic, universal CAR-T (UCAR-T) currently in development for the treatment of T-cell acute lymphoblastic leukemia (T-ALL) has demonstrated robust expansion and anti-leukemia efficacy with a manageable safety profile in an investigator-initiated trial in China. These data suggest that, a single CD7 targeting CAR-T therapy is able to generate a therapeutic window by suppressing host vs graft (HvG) rejection of UCAR-T cells by patients' own NK and T cells, and achieve efficacy in patients with T-ALL. Based on these findings we developed GC502, a CD19/CD7 dual-targeting, allogeneic CAR-T therapy for B-cell malignancies, in which the CD19 CAR moiety targets malignant cells while CD7 CAR moiety suppresses HvG in variety of preclinical models.MethodsGC502 was manufactured using leukopaks from HLA-unmatched healthy donors. It contains a 4-1BB based 2 nd-generation dual targeting CAR comprising an anti-CD19 and an anti-CD7 single-chain variable fragments (scFvs). TRAC and CD7 loci were disrupted to avoid graft vs host disease and fratricide, respectively. To select the leading CAR candidate, CAR expression and functionalities of CAR constructs with different heavy-light (H-L) chain orientations of the dual CAR were analyzed via in vitro assays and mouse xenograft models, in comparing to single CD19 CAR and CD7 CAR products. To achieve optimal anti-tumor efficacy, a T-cell enhancer was included in the CAR construct.ResultGene editing and dual CAR orientation selectionTRAC and CD7 double knockout efficiencies were constantly above 97% across multiple donor pan T cells. Although CD19/CD7 CAR expression levels in different H-L chain orientations were similar, in the final CAR-T product as measured by flow cytometry (FCM) analysis, significant difference was observed in their cytotoxicity and in vitro expansion under repeated antigen stimulations by CD19+ B-cell acute lymphoblastic leukemia (B-ALL) cell line Nalm6 and CD7+ T-cell line CCRF-CEM. CAR candidates mediated the strongest cytotoxicity and most durable response were selected for further optimizations.CAR construct optimizationsFor the leading candidates, we first assessed the dual CAR efficacy after incorporation of an enhancer. While the IL-2, TNFα and IFNγ secretion levels were comparable, enhancer addition significantly improved tumor killing and CAR-T cell expansion under repeated stimulations by either CD19+ or CD7+ target cells. Anti-leukemia response under sub-optimal CAR-T cell dosages were also greatly enhanced as assessed by both B-ALL and T-ALL mouse xenograft models.GC502 CAR functionality comparison to single CAR products with proven clinical efficaciesGC502 and GC027 were compared for their CD7 CAR function to assess their anti-HvG activities. GC502 and GC027 exhibited comparable toxicities towards pan T cells and similar efficacies in a highly malignant T-ALL mouse model. The CD19 CAR functionality of GC502 were evaluated and compared to a 2 nd generation CD19 CAR product comprising a FMC63 scFv and a 4-1BB-CD3ȥ signaling domain. In a Raji based B-ALL mouse xenograft model, both products rapidly eliminated cancer cells. While CD19 CAR treated mice showed signs of relapse at 2 weeks post CAR-T infusion, GC502 treatment group maintained “leukemia free” status till the end of study (Day28).ConclusionGC502 was optimized for CD19/CD7 dual CAR functionality and in vivo durability. It demonstrated robust anti-tumor efficacy and promising potentials to suppress HvG. This report presents an example that the dual CAR design of GC502 may serve as a novel “off-the-shelf” CAR-T technology. DisclosuresGe: GracellBiotechnologies Ltd: Current Employment, Current equity holder in publicly-traded company. Yang: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Sun: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Chen: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Qiu: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Yin: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Shen: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Sersch: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Cao: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company. Wang: GracellBiotechnologies Inc: Current Employment, Current equity holder in publicly-traded company.

Chronic HBV Infection Using CRISPR/Cas9 Delivered by Novel pH-Sensitive Cationic Liposomes

Background: Current research focuses on reducing the level of HBV virus. We designed CRISPR/Cas9s that target the HBV genome. Methods: To prevent the emergence of escape mutant viruses, we mixed HBV-CRISPR/Cas9s (HBV-CRISPR/Cas9 complex). These HBV-CRISPR/Cas9s complexes were encapsulated in a nano-liposome complex, which is a hepatocyte-specific drug delivery system. CRISPR/Cas9 was used to assess delivery and knockout efficiencies of nano-liposome-gRNA-HBV complexes in the treatment of mice. The potency of the nano-liposome-gRNA-HBV complexes was evaluated in HepG2.2.15 cells and in HBV-Tg mice. Findings: Effective knockout of targets, efficient delivery of CRISPR/Cas9, and liver-specific delivery were observed with nano-liposome-gRNA-HBV complex treatment. Nano-liposome-gRNA-HBV complexes efficiently reduced HBsAg in vitro and in vivo. However, ETV treatment did not efficiently reduce HBsAg when compared with nano-liposome-gRNA-HBV complex treatment. In addition, the suppressive effects of nano-liposome-gRNA-HBV complexes persisted for 21 days in vitro and in vivo. We indicated that treatment with nano-liposome-gRNA-HBV complexes controlled HBV infection more efficiently than ETV treatment did. Furthermore, the effect of a single dose of nano-liposome-gRNA-HBV complexes persisted for a long time. Interpretation: The results demonstrate that nano-liposome-gRNA-HBV complex may be a promising novel HBV treatment that is more effective than reverse transcriptase inhibitors. Funding Statement: This study was supported by grants from the National Natural Science Foundation of China (Grant nos. 81602295 to Shuai Zhen). This study was supported by grants from Special Talent Training Program in Northwest Women and Children Hospital (2020ZD02) Declaration of Interests: The other authors declare that they have no competing interests. Ethics Approval Statement: All mouse experiments were conducted according to the National Institutes of Health Guidelines for Animal Care. All animal procedures were performed according to the guidelines developed by the China Council on Animal Care and the protocol was approved by the Xi’an jiaotong university.

Highly Efficient Knockout of a Squid Pigmentation Gene

Seminal studies using squid as a model led to breakthroughs in neurobiology. The squid giant axon and synapse, for example, laid the foundation for our current understanding of the action potential [1], ionic gradients across cells [2], voltage-dependent ion channels [3], molecular motors [4-7], and synaptic transmission [8-11]. Despite their anatomical advantages, the use of squid as a model receded over the past several decades as investigators turned to genetically tractable systems. Recently, however, two key advances have made it possible to develop techniques for the genetic manipulation of squid. The first is the CRISPR-Cas9 system for targeted gene disruption, a largely species-agnostic method [12, 13]. The second is the sequencing of genomes for several cephalopod species [14-16]. If made genetically tractable, squid and other cephalopods offer a wealth of biological novelties that could spur discovery. Within invertebrates, not only do they possess by far the largest brains, they also express the most sophisticated behaviors [17]. In this paper, we demonstrate efficient gene knockout in the squid Doryteuthis pealeii using CRISPR-Cas9. Ommochromes, the pigments found in squid retinas and chromatophores, are derivatives of tryptophan, and the first committed step in their synthesis is normally catalyzed by Tryptophan 2,3 Dioxygenase (TDO [18-20]). Knocking out TDO in squid embryos efficiently eliminated pigmentation. By precisely timingCRISPR-Cas9 delivery during early development, the degree of pigmentation could be finely controlled. Genotyping revealed knockout efficiencies routinely greater than 90%. This study represents a critical advancement toward making squid genetically tractable.

Generation of Gene-Knockout Mongolian Gerbils via CRISPR/Cas9 System.

The Mongolian gerbil (Meriones unguiculatus), a well-known “multifunctional” experimental animal, plays a crucial role in the research of hearing, cerebrovascular diseases and Helicobacter pylori infection. Although the whole-genome sequencing of Mongolian gerbils has been recently completed, lack of valid gene-editing systems for gerbils largely limited the further usage of Mongolian gerbils in biomedical research. Here, efficient targeted mutagenesis in Mongolian gerbils was successfully conducted by pronuclear injection with Cas9 protein and single-guide RNAs (sgRNAs) targeting Cystatin C (Cst3) or Apolipoprotein A-II (Apoa2). We found that 22 h after human chorionic gonadotropin (hCG) injection, zygote microinjection was conducted, and the injected zygotes were transferred into the pseudopregnant gerbils, which were induced by injecting equine chorionic gonadotropin (eCG) and hCG at a 70 h interval and being caged with ligated male gerbils. We successfully obtained Cst3 and Apoa2 gene knockout gerbils with the knockout efficiencies of 55 and 30.9%, respectively. No off-target effects were detected in all knockout gerbils and the mutations can be germline-transmitted. The absence of CST3 protein was observed in the tissues of homozygous Cst3 knockout (Cst3-KO) gerbils. Interestingly, we found that disruption of the Cst3 gene led to more severe brain damage and neurological deficits after unilateral carotid artery ligation, thereby indicating that the gene modifications happened at both genetic and functional levels. In conclusion, we successfully generated a CRISPR/Cas9 system based genome editing platform for Mongolian gerbils, which provided a foundation for obtaining other genetically modified gerbil models for biomedical research.

CRISPR-Cas9 Ribonucleoprotein-Mediated Genomic Editing in Mature Primary Innate Immune Cells

CRISPR genome engineering has become a powerful tool to functionally investigate the complex mechanisms of immune system regulation. While decades of work have aimed to genetically reprogram innate immunity, the utility of current approaches is restricted by poor knockout efficiencies or limited specificity for mature cell lineages invivo. Here, we describe an optimized strategy for non-viral CRISPR-Cas9 ribonucleoprotein (cRNP) genomic editing of mature primary mouse innate lymphocyte cells (ILCs) and myeloid lineage cells that results in an almost complete loss of single or double target gene expression from a single electroporation. Furthermore, we describe invivo adoptive transfer mouse models that can be utilized to screen for gene function during viral infection using cRNP-edited naive natural killer (NK) cells and bone-marrow-derived conventional dendritic cell precursors (cDCPs). This resource will enhance target gene discovery and offer a specific and simplified approach to gene editing in the mouse innate immune system.

Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes.

Homing based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent disease transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate genes has not been thoroughly explored. To test this approach, we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host-encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of disruption of both genes during super-Mendelian propagation of split-HGD. Furthermore, both genes were knocked out one generation earlier than expected indicating the robust somatic expression of Cas9 driven by Drosophila germline-limited promoters. We also assess the efficiency of ‘shadow drive’ generated by maternally deposited Cas9 protein and accumulation of drive-induced resistance alleles along multiple generations, and discuss design principles of HGD that could mitigate the accumulation of resistance alleles while incorporating a GME.