Browsing by Author "Zheng, Yanjiang"

Now showing 1 - 7 of 7
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    Author Correction: Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
    (Springer Nature, 2021-08-19) VanDusen, Nathan J.; Lee, Julianna Y.; Gu, Weiliang; Butler, Catalina E.; Sethi, Isha; Zheng, Yanjiang; King, Justin S.; Zhou, Pingzhu; Suo, Shengbao; Guo, Yuxuan; Ma, Qing; Yuan, Guo-Cheng; Pu, William T.; Medical and Molecular Genetics, School of Medicine
    Correction to: Nature Communications 10.1038/s41467-021-24743-z, published online 21 July 2021. The original version of this Article contained an error in the spelling of the author William T. Pu, which was incorrectly given as William William Pu. This has now been corrected in both the PDF and HTML versions of the Article.
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    Cardiac Applications of CRISPR/AAV-Mediated Precise Genome Editing
    (bioRxiv, 2024-12-04) Zheng, Yanjiang; Mayourian, Joshua; King, Justin S.; Li, Yifei; Bezzerides, Vassilios J.; Pu, William T.; VanDusen, Nathan J.; Pediatrics, School of Medicine
    The ability to efficiently make precise genome edits in somatic tissues will have profound implications for gene therapy and basic science. CRISPR/Cas9 mediated homology-directed repair (HDR) is one approach that is commonly used to achieve precise and efficient editing in cultured cells. Previously, we developed a platform capable of delivering CRISPR/Cas9 gRNAs and donor templates via adeno-associated virus to induce HDR (CASAAV-HDR). We demonstrated that CASAAV-HDR is capable of creating precise genome edits in vivo within mouse cardiomyocytes at the neonatal and adult stages. Here, we report several applications of CASAAV-HDR in cardiomyocytes. First, we show the utility of CASAAV-HDR for disease modeling applications by using CASAAV-HDR to create and precisely tag two pathological variants of the titin gene observed in cardiomyopathy patients. We used this approach to monitor the cellular localization of the variants, resulting in mechanistic insights into their pathological functions. Next, we utilized CASAAV-HDR to create another mutation associated with human cardiomyopathy, arginine 14 deletion (R14Del) within the N-terminus of Phospholamban (PLN). We assessed the localization of PLN-R14Del and quantified cardiomyocyte phenotypes associated with cardiomyopathy, including cell morphology, activation of PLN via phosphorylation, and calcium handling. After demonstrating CASAAV-HDR utility for disease modeling we next tested its utility for functional genomics, by targeted genomic insertion of a library of enhancers for a massively parallel reporter assay (MPRA). We show that MPRAs with genomically integrated enhancers are feasible, and can yield superior assay sensitivity compared to tests of the same enhancers in an AAV/episomal context. Collectively, our study showcases multiple applications for in vivo precise editing of cardiomyocyte genomes via CASAAV-HDR.
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    CRISPR-Cas9-mediated homology-directed repair for precise gene editing
    (Elsevier, 2024-09-26) Liao, Hongyu; Wu, Jiahao; VanDusen, Nathan J.; Li, Yifei; Zheng, Yanjiang; Pediatrics, School of Medicine
    CRISPR-Cas9-mediated homology-directed repair (HDR) is a versatile platform for creating precise site-specific DNA insertions, deletions, and substitutions. These precise edits are made possible through the use of exogenous donor templates that carry the desired sequence. CRISPR-Cas9-mediated HDR can be widely used to study protein functions, disease modeling, and gene therapy. However, HDR is limited by its low efficiency, especially in postmitotic cells. Here, we review CRISPR-Cas9-mediated HDR, with a focus on methodologies for boosting HDR efficiency, and applications of precise editing via HDR. First, we describe two common mechanisms of DNA repair, non-homologous end joining (NHEJ), and HDR, and discuss their impact on CRISPR-Cas9-mediated precise genome editing. Second, we discuss approaches for improving HDR efficiency through inhibition of the NHEJ pathway, activation of the HDR pathway, modification of donor templates, and delivery of Cas9/sgRNA reagents. Third, we summarize the applications of HDR for protein labeling in functional studies, disease modeling, and ex vivo and in vivo gene therapies. Finally, we discuss alternative precise editing platforms and their limitations, and describe potential avenues to improving CRISPR-Cas9-mediated HDR efficiency and fidelity in future research.
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    Efficient In Vivo Homology-Directed Repair Within Cardiomyocytes
    (American Heart Association, 2022) Zheng, Yanjiang; VanDusen, Nathan J.; Butler, Catalina E.; Ma, Qing; King, Justin S.; Pu, William T.; Pediatrics, School of Medicine
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    Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
    (Springer Nature, 2021-07-21) VanDusen, Nathan J.; Lee, Julianna Y.; Gu, Weiliang; Butler, Catalina E.; Sethi, Isha; Zheng, Yanjiang; King, Justin S.; Zhou, Pingzhu; Suo, Shengbao; Guo, Yuxuan; Ma, Qing; Yuan, Guo-Cheng; Pu, William T.; Medical and Molecular Genetics, School of Medicine
    The forward genetic screen is a powerful, unbiased method to gain insights into biological processes, yet this approach has infrequently been used in vivo in mammals because of high resource demands. Here, we use in vivo somatic Cas9 mutagenesis to perform an in vivo forward genetic screen in mice to identify regulators of cardiomyocyte (CM) maturation, the coordinated changes in phenotype and gene expression that occur in neonatal CMs. We discover and validate a number of transcriptional regulators of this process. Among these are RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicate that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.
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    Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
    (MDPI, 2023-03-29) Zheng, Yanjiang; VanDusen, Nathan J.; Pediatrics, School of Medicine
    The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic cis-regulatory elements, generation of mice featuring transgenic reporters or cis-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research.
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    Precise genome-editing in human diseases: mechanisms, strategies and applications
    (Springer Nature, 2024-02-26) Zheng, Yanjiang; Li, Yifei; Zhou, Kaiyu; Li, Tiange; VanDusen, Nathan J.; Hua, Yimin; Pediatrics, School of Medicine
    Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.