Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy

Dominantly inherited disorders are not typically considered to be therapeutic candidates for gene augmentation. Here, we utilized induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) to test the potential of gene augmentation to treat Best disease, a dominant macular dystrophy caused by over 200 missense mutations in BEST1. Gene augmentation in iPSC-RPE fully restored BEST1 calcium-activated chloride channel activity and improved rhodopsin degradation in an iPSC-RPE model of recessive bestrophinopathy as well as in two models of dominant Best disease caused by different mutations in regions encoding ion-binding domains. A third dominant Best disease iPSC-RPE model did not respond to gene augmentation, but showed normalization of BEST1 channel activity following CRISPR-Cas9 editing of the mutant allele. We then subjected all three dominant Best disease iPSC-RPE models to gene editing, which produced premature stop codons specifically within the mutant BEST1 alleles. Single-cell profiling demonstrated no adverse perturbation of retinal pigment epithelium (RPE) transcriptional programs in any model, although off-target analysis detected a silent genomic alteration in one model. These results suggest that gene augmentation is a viable first-line approach for some individuals with dominant Best disease and that non-responders are candidates for alternate approaches such as gene editing. However, testing gene editing strategies for on-target efficiency and off-target events using personalized iPSC-RPE model systems is warranted. In summary, personalized iPSC-RPE models can be used to select among a growing list of gene therapy options to maximize safety and efficacy while minimizing time and cost. Similar scenarios likely exist for other genotypically diverse channelopathies, expanding the therapeutic landscape for affected individuals.

Developing precision medicine using scarless genome editing of human pluripotent stem cells

Many avenues exist for human pluripotent stem cells (hPSCs) to impact medical care, but they may have their greatest impact on the development of precision medicine. Recent advances in genome editing and stem cell technology have enabled construction of clinically-relevant, genotype-specific "disease-in-a-dish" models. In this review, we outline the use of genome-edited hPSCs in precision disease modeling and drug screening as well as describe methodological advances in scarless genome editing. Scarless genome-editing approaches are attractive for genotype-specific disease modeling as only the intended DNA base-pair edits are incorporated without additional genomic modification. Emerging evidentiary standards for development and approval of precision therapies are likely to increase application of disease models derived from genome-edited hPSCs.

Scarless Genome Editing of Human Pluripotent Stem Cells via Transient Puromycin Selection

Genome-edited human pluripotent stem cells (hPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. We present and characterize a robust method for rapid, scarless introduction or correction of disease-associated variants in hPSCs using CRISPR/Cas9. Utilizing non-integrated plasmid vectors that express a puromycin N-acetyl-transferase (PAC) gene, whose expression and translation is linked to that of Cas9, we transiently select for cells based on their early levels of Cas9 protein. Under optimized conditions, co-delivery with single-stranded donor DNA enabled isolation of clonal cell populations containing both heterozygous and homozygous precise genome edits in as little as 2 weeks without requiring cell sorting or high-throughput sequencing. Edited cells isolated using this method did not contain any detectable off-target mutations and displayed expected functional phenotypes after directed differentiation. We apply the approach to a variety of genomic loci in five hPSC lines cultured using both feeder and feeder-free conditions.

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Stringent transient puromycin selection enriches for hPSCs with scarless genome edits

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Clonal hPSC cell populations were isolated in as little as 2 weeks

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Workflow does not require cell sorting or high-throughput sequencing

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Genome editing at three disease-associated genes in five unique hPSC lines

High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells

CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

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High-content analysis of arrayed hESC colonies increased gene-editing efficiency

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Rapid one-pot transcription of sgRNAs can be multiplexed to edit hESCs

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hESCs gene edited on ArrayEdit exhibited proper phenotypes

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ArrayEdit provides a new window into the process of gene editing human cells

High content analysis platform for optimization of lipid mediated CRISPR-Cas9 delivery strategies in human cells

Non-viral gene-editing of human cells using the CRISPR-Cas9 system requires optimized delivery of multiple components. Both the Cas9 endonuclease and a single guide RNA, that defines the genomic target, need to be present and co-localized within the nucleus for efficient gene-editing to occur. This work describes a new high-throughput screening platform for the optimization of CRISPR-Cas9 delivery strategies. By exploiting high content image analysis and microcontact printed plates, multi-parametric gene-editing outcome data from hundreds to thousands of isolated cell populations can be screened simultaneously. Employing this platform, we systematically screened four commercially available cationic lipid transfection materials with a range of RNAs encoding the CRISPR-Cas9 system. Analysis of Cas9 expression and editing of a fluorescent mCherry reporter transgene within human embryonic kidney cells was monitored over several days after transfection. Design of experiments analysis enabled rigorous evaluation of delivery materials and RNA concentration conditions. The results of this analysis indicated that the concentration and identity of transfection material have significantly greater effect on gene-editing than ratio or total amount of RNA. Cell subpopulation analysis on microcontact printed plates, further revealed that low cell number and high Cas9 expression, 24h after CRISPR-Cas9 delivery, were strong predictors of gene-editing outcomes. These results suggest design principles for the development of materials and transfection strategies with lipid-based materials. This platform could be applied to rapidly optimize materials for gene-editing in a variety of cell/tissue types in order to advance genomic medicine, regenerative biology and drug discovery.

STATEMENT OF SIGNIFICANCE

CRISPR-Cas9 is a new gene-editing technology for "genome surgery" that is anticipated to treat genetic diseases. This technology uses multiple components of the Cas9 system to cut out disease-causing mutations in the human genome and precisely suture in therapeutic sequences. Biomaterials based delivery strategies could help transition these technologies to the clinic. The design space for materials based delivery strategies is vast and optimization is essential to ensuring the safety and efficacy of these treatments. Therefore, new methods are required to rapidly and systematically screen gene-editing efficacy in human cells. This work utilizes an innovative platform to generate and screen many formulations of synthetic biomaterials and components of the CRISPR-Cas9 system in parallel. On this platform, we watch genome surgery in action using high content image analysis. These capabilities enabled us to identify formulation parameters for Cas9-material complexes that can optimize gene-editing in a specific human cell type.

Drug-loaded nanoparticles induce gene expression in human pluripotent stem cell derivatives

Tissue engineering and advanced manufacturing of human stem cells requires a suite of tools to control gene expression spatiotemporally in culture. Inducible gene expression systems offer cell-extrinsic control, typically through addition of small molecules, but small molecule inducers typically contain few functional groups for further chemical modification. Doxycycline (DXC), a potent small molecule inducer of tetracycline (Tet) transgene systems, was conjugated to a hyperbranched dendritic polymer (Boltorn H40) and subsequently reacted with polyethylene glycol (PEG). The resulting PEG-H40-DXC nanoparticle exhibited pH-sensitive drug release behavior and successfully controlled gene expression in stem-cell-derived fibroblasts with a Tet-On system. While free DXC inhibited fibroblast proliferation and matrix metalloproteinase (MMP) activity, PEG-H40-DXC nanoparticles maintained higher fibroblast proliferation levels and MMP activity. The results demonstrate that the PEG-H40-DXC nanoparticle system provides an effective tool to controlling gene expression in human stem cell derivatives.

[Assessment of the use of electronic portal imaging]

Improvement in the accuracy of the positioning of the patient during external irradiation is one of the most important issues of the last decades, due to the detrimental impact of the misplacements on treatment outcome. Since 1990, the evolution of the technologic environment has led to a full integration of the portal imaging devices into linac technology. It offers a real on-line verification tool for "high-dose, high-accuracy" treatments. This overview based upon data from the literature describes the different types of imaging devices, the strategies of use and the results obtained. It also considers the use of imaging devices as an in vivo dosimeter.

[Evolution of the use of the portal imaging device: prospective study over three years]

PURPOSE

To describe the evolution of the use of the electronic portal imaging device (EPID) over three periods.

MATERIAL AND METHODS

From 1990, as part of the quality assurance research programs, the radiotherapy department of the G.-F. Leclerc Centre of Dijon used EPID systems in a prospective fashion. During the first of the three periods (PER 1:1990-1993), the study consisted of analysis criteria determination, software efficiency improvement and a selection of patients who could benefit from the method. Eight hundred and forty-five images of 40 patients were analysed qualitatively and quantitatively. Two verifications per week were planned, and the action level for correction was 10 mm. Head and neck images were also displayed in 'cinema' presentation for internal movements analysis. From 1994 to 1995 (PER 2), off-line procedure (OLP) based upon early correction of the systematic error and the rules calculated from our previous experience were tested for checking the brain, head and neck (LOC 1: 396 images) and many of the pelvic irradiations (LOC 2: 260 images). A double-exposure procedure and/or movie loop presentation was reserved for other patients. During the last period (PER 3: 1996-1997), the OLP procedure was routinely performed in 54 patients (images: 321 LOC 1, 680 LOC 2).

RESULTS

LOC 1: deviations of < 3 mm increased from 75.5% during PER 1 to 81% during PER 2 to 83% during PER3. Conversely, deviations of 3-5 mm dropped from 19.5 to 13%, while deviations of more than 5 mm remained stable, around 5%. The actual standard error of the mean deviation observed was 2 mm. LOC 2: deviations of < 5 mm were observed in 81% of the cases during PER 1 and in 91% during PER 3 (89.5% in PER 2). These good results led to a decrease in deviation of 5 to 7 mm (11 to 6%) and also to a significant drop in deviations of more than 7 mm, 8 to 3% respectively. The actual precision obtained was 2.5 mm +/- 3 mm SD.

CONCLUSIONS

The OLP based upon the early correction of the systematic error led to a significant increase of setup accuracy of patients irradiated for the brain, head and neck, and especially for pelvic lesions.

[The dose response relations in geotropic and phototropic stimulation: Comparison of mono-with dicotyledonous plants]

The increase in the geotropic curvatures of Avena coleoptiles and Lens epicotyls is linear and proportional to the time of stimulation. With low stimulation the sensitivities of both objects are equal; with longer stimulation the curvature of Avena coleoptiles is somewhat greater.To increased phototropic irradiance Lens epicotyls react with a first and a second positive curvature. Between the two ranges of curvature (from about 10,000 up to 1,000,000 lx · sec) they are phototropically insensitive; negative curvatures never occur. The same reaction is shown by 12 other dicotyledonous plants (Brassica napus, Brassica oleracea subsp. capitata, Brassica oleracea subsp. bullata, Lepidium sativum, Vicia villosa, Sinapis alba, Cucumis sativus, Linum usitatissimum, Helianthus annuus, Agrostemma githago, Raphanus sativus, Convolvulus tricolor) and by 3 other monocotyledonous plants (Hordeum distichon, Secale cereale, Triticum aestivum). In the first positive reaction the phototropic sensitivities of Avena coleoptiles and Lens epicotyls are equal, in the second positive reaction Avena coleoptiles are more sensitive. For Lens epicotyls (for Avena coleoptiles, too) the reciprocity law is valid in the first positive reaction, but not in the second positive reaction.