Advancing the genetic engineering toolbox by combining AsCas12a knock-in mice with ultra-compact screening
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PROVIDER: PRJNA1206072 | ENA |
REPOSITORIES: ENA
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Project description:Cas12a is a next-generation gene-editing tool that enables multiplexed gene targeting. Here, we present a mouse model that constitutively expresses enhanced Acidaminococcus sp. Cas12a (enAsCas12a) linked to an mCherry fluorescent reporter. We demonstrate efficient single and multiplexed gene-editing in vitro, using primary and transformed cells from enAsCas12a mice. We further demonstrate successful in vivo gene-editing, using normal and cancer-prone enAsCas12a stem cells to reconstitute the haematopoietic system of wild-type mice. We also present compact, genome-wide Cas12a knockout libraries, with four crRNAs per gene encoded across one (Scherzo) or two (Menuetto) vectors, and demonstrate the utility of these libraries across methodologies: in vitro enrichment and drop-out screening in lymphoma cells and immortalised fibroblasts, respectively, and in vivo screens to identify lymphoma-driving events. Finally, we demonstrate CRISPR multiplexing via simultaneous gene knockout (via Cas12a) and activation (via dCas9-SAM) using primary T cells and fibroblasts. Our enAsCas12a mouse and accompanying crRNA libraries enhance genome engineering capabilities and complement current CRISPR technologies.
2025-01-03 | GSE285778 | GEO
Project description:we characterized a novel compact Cas12a ortholog, EbCas12a, from the Erysipelotrichia bacterium with activities in mammalian cells. It is with the PAM sequence of 5’-TTTV-3’ (V=A, G, C) and the smallest size of ~3.47kb among reported Cas12a orthologs so far. Moreover, enhanced EbCas12a (enEbCas12a) was also developed to have comparable editing efficiency with higher specificity to AsCas12a and LbCas12a in mammalian cells. With the help of the compact enEbCas12a, all-in-one AAV delivery system with crRNA for Cas12a was developed for both in vitro and in vivo. Altogether, with the help of the novel smallest high fidelity enEbCas12a, this first case of the all-in-one AAV delivery for Cas12a could greatly boost future gene therapy and scientific research.
2023-07-10 | GSE236647 | GEO
Project description:Background : Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. Results: We have developed a toolbox allowing in vivo protein tagging by PCR-mediated homologous recombination with TAP, HA and MYC tags. The transformation cassettes were designed to accommodate a common set of integration primers. The tagged proteins can be used to perform tandem affinity purification (TAP) or chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP). Tandem affinity purification of C. albicans Nop1 revealed the high conservation of the small processome composition in yeasts. Data obtained with in vivo TAP-tagged Tbf1, Cbf1 and Mcm1 recapitulates previously published genome-wide location profiling by ChIP-CHIP. We also designed a new reporter system for in vivo analysis of transcriptional activity of gene loci in C. albicans. Conclusion: This toolbox provides a basic setup to perform purification of protein complexes and increase the number of annotated transcriptional regulators and genetic circuits in C. albicans. Two independent biological replicates of ChIP-CHIP of Mcm1-TAP in yeast and hyphal states. ChIP-CHIP of Cbf1-TAP and Tbf1-TAP.
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Project description:The loss of compact myocardial cardiomyocyte (compact CM) identity suggests that PRDM16 deficiency may dramatically alter the cellular composition in left ventricular (LV) compact myocardium. To test this hypothesis, we performed single-cell RNA-seq (scRNA-seq) to examine gene dysreulation in Prdm16cKO heart. We also performed Visium Spatial Transcriptomics (ST) to facilitate mapping CM clusters to their original locations in the heart. As a result, we were able to demonstrate gene misregulation in Prdm16cKO mouse mainly occurred in LV compact CM.
2021-12-20 | GSE179392 | GEO
Project description:The loss of compact myocardial cardiomyocyte (compact CM) identity suggests that PRDM16 deficiency may dramatically alter the cellular composition in left ventricular (LV) compact myocardium. To test this hypothesis, we performed single-cell RNA-seq (scRNA-seq) to examine gene dysreulation in Prdm16cKO heart. We also performed Visium Spatial Transcriptomics (ST) to facilitate mapping CM clusters to their original locations in the heart. As a result, we were able to demonstrate gene misregulation in Prdm16cKO mouse mainly occurred in LV compact CM.
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Project description:The innovation of combined chemical tools, such as small molecule inhibitors, activity-based probes (ABPs), and proteolysis targeting chimeras (PROTACs) for a specific target, not only advances clinical drug discovery but also provides a chemical toolbox to study the diverse biological perspective of targeted proteins. Here we report the development of such a chemical toolbox for the multifunctional human Parkinson disease protein 7 (PARK7/DJ-1) that has drawn attention as a candidate for drug discovery due to its involvement with Parkinson's disease and cancers. By combining structure-guided design, small library synthesis and high-throughput screening, we identified two compounds, JYQ-164 and JYQ-173, inhibiting PARK7 with high potency in vitro and in cell. These compounds covalently and selectively target its highly conserved and functionally essential residue, Cys106. Based on these compounds, we further developed two cell-permeable fluorescent probes, JYQ-192 and JYQ-196, with a SulfoCy5 dye to visualize PARK7 activity in living cells and a first-in-class PARK7 degrader JYQ-194 that selectively targets PARK7 to proteasomal degradation in human cells. Together, our study provides a valuable toolbox to advance the biology research of PARK7 in a cellular context and opens new opportunities for potential therapeutic application.
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Project description:Application of microfluidics offers numerous advantages in the field of radiochemistry and could enable dramatic reductions in the cost of producing radiotracers for positron emission tomography (PET). Droplet-based microfluidics, in particular, requires only microgram quantities of expensive precursors and reagents (compared to milligram used in conventional radiochemistry systems), and occupies a more compact footprint (potentially eliminating the need for specialized shielding facilities, i.e. hot cells). However, the reported platforms for droplet radiosynthesis have several drawbacks, including high cost/complexity of microfluidic reactors, requirement for manual intervention (e.g. for adding reagents), or difficulty in precise control of droplet processes. We describe here a platform based on a particularly simple chip, where reactions take place atop a hydrophobic substrate patterned with a circular hydrophilic liquid trap. The overall supporting hardware (heater, rotating carousel of reagent dispensers, etc.) is very simple and the whole system could be packaged into a very compact format (about the size of a coffee cup). We demonstrate the consistent synthesis of [18F]fallypride with high yield, and show that protocols optimized using a high-throughput optimization platform we have developed can be readily translated to this device with no changes or re-optimization. We are currently exploring the use of this platform for routine production of a variety of 18F-labeled tracers for preclinical imaging and for production of tracers in clinically-relevant amounts by integrating the system with an upstream radionuclide concentrator.
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Project description:Point-of-care medical diagnosis demands immediate feedback on tissue pathology. Confocal endomicroscopy can provide real-time in vivo images with histology-like features. The working channel in medical endoscopes are becoming smaller in dimension. Microsystems methods can produce tiny mechanical scanners. We demonstrate a flexible fiber instrument for in vivo imaging as an endoscope accessory. The optical path is folded on-axis to reduce length while allowing the beam to expand and achieve a numerical aperture of 0.41. A high-speed parametric resonance mirror produces large deflection angles > 13°, and is mounted on a 2 mm diameter chip designed with clamp structures for reduced space. A compact lens assembly provides diffraction-limited lateral and axial resolution of 1.5 and [Formula: see text], respectively. A working distance of [Formula: see text] and field-of-view of [Formula: see text] m are achieved. Miniature apparatus is fabricated to assemble and align the scanhead components. The optics and scanner are packaged in a distal tip with 2.4 mm diameter and 10 mm rigid length. These dimensions allow the endomicroscope to pass forward easily through the 2.8 mm diameter working channel in medical endoscopes commonly used in clinical practice. Fluorescence images are collected in vivo at 10 frames per second in the colon of genetically-engineered mice that spontaneously develop adenomas. A FITC-labeled peptide heterodimer is administered intravenously to provide specific contrast. Sub-cellular structures are visualized to distinguish pre-malignant from normal mucosa. These results demonstrate use of microsystems methods to produce an ultra-compact instrument with sufficiently small dimensions for broad use.
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