Selected Grantee Publications
Enhanced RNA-Targeting CRISPR-Cas Technology in Zebrafish
Moreno-Sánchez et al., Nature Communications. 2025.
https://pubmed.ncbi.nlm.nih.gov/40091120
CRISPR-Cas13 RNA-targeting systems, widely used in basic and applied sciences, have generated controversy because of collateral activity in mammalian cells and mouse models. In this study, researchers optimized transient formulations as ribonucleoprotein complexes or mRNA-gRNA combinations to enhance the CRISPR-RfxCas13d system in zebrafish. Researchers used chemically modified gRNAs to allow more penetrant loss-of-function phenotypes, improve nuclear RNA targeting, and compare different computational models to determine the most accurate prediction of gRNA activity in vivo. Results demonstrate that transient CRISPR-RfxCas13d can effectively deplete endogenous mRNAs in zebrafish embryos without inducing collateral effects, except when targeting extremely abundant and ectopic RNAs. Their findings contribute to CRISPR-Cas technology optimization for RNA targeting in zebrafish through transient approaches and advance in vivo applications. Supported by ORIP (R21OD034161), NICHD, and NIGMS.
Dysregulation of mTOR Signalling Is a Converging Mechanism in Lissencephaly
Zhang et al., Nature. 2025.
https://pubmed.ncbi.nlm.nih.gov/39743596
Lissencephaly (smooth brain) is a rare genetic condition, with such symptoms as epilepsy and intellectual disability and a median life expectancy of 10 years. This study reveals that reduced activity of the mTOR pathway may be a common cause of lissencephaly. Researchers used laboratory-grown brain models (organoids) and sequencing and spectrometry techniques to identify decreased mTOR activation in two types of lissencephaly disorders: p53-induced death domain protein 1 and Miller–Dieker lissencephaly syndrome. Pharmacological activation of mTOR signaling with a brain-selective mTORC1 activator molecule, NV-5138, prevented and reversed the morphological and functional defects in organoids. These findings suggest that mTOR dysregulation contributes to the development of lissencephaly spectrum disorders and highlight a potential druggable pathway for therapy. Supported by ORIP (S10OD018034, S10OD019967, S10OD030363), NCATS, NHGRI, NICHD, NIDA, NIGMS, NIMH, and NINDS.
A Collection of Split-Gal4 Drivers Targeting Conserved Signaling Ligands in Drosophila
Ewen-Campen et al., G3 (Bethesda). 2025.
https://pubmed.ncbi.nlm.nih.gov/39569452
A modest number of highly conserved signaling pathways are known to generate a broad range of responses in multicellular animals, including mammals. How this remarkable feat is achieved is not well understood. Investigators developed and characterized a collection of genetic resources, called knock-in split-Gal4 lines, that target ligands from highly conserved signaling pathways in development and biological processes, including Notch, Hedgehog, fibroblast growth factor, epidermal growth factor, and transforming growth factor β. These drosophila lines are useful in identifying tissues that co-express ligands of interest, genetically manipulating specific cell populations, and elucidating potential crosstalk among different conserved pathways. These resources are highly valuable for studying conserved intercellular signaling pathways relevant to human health and disease. Supported by ORIP (R24OD026435, R24OD031952, P40OD018537) and NIGMS.
Systematic Ocular Phenotyping of 8,707 Knockout Mouse Lines Identifies Genes Associated With Abnormal Corneal Phenotypes
Vo et al., BMC Genomics. 2025.
https://pubmed.ncbi.nlm.nih.gov/39833678
Corneal dysmorphologies (CDs) are a group of acquired but predominantly genetically inherited eye disorders that cause progressive vision loss and can be associated with systemic abnormalities. This study aimed to identify candidate CD genes in humans by looking at knockout mice with targeted deletions of orthologous genes that exhibited statistically significant corneal abnormalities. Analysis of data from 8,707 knockout mouse lines identified 213 candidate CD genes; 176 (83%) genes have not been implicated previously in CD. Bioinformatic analyses implicated candidate genes in several signaling pathways (e.g., integrin signaling pathway, cytoskeletal regulation by Rho GTPase, FAS signaling pathway), which are potential therapeutic targets. Supported by ORIP (U42OD011175, R03OD032622, UM1OD023221), NEI, and NHGRI.
Plural Molecular and Cellular Mechanisms of Pore Domain KCNQ2 Encephalopathy
Abreo et al., eLife. 2025.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11703504
This study investigates the cellular and molecular mechanisms underlying KCNQ2 encephalopathy, a severe type of early-onset epilepsy caused by mutations in the KCNQ2 gene. Researchers describe a case study of a child with a specific KCNQ2 gene mutation, G256W, and found that it disrupts normal brain activity, leading to seizures and developmental impairments. Male and female Kcnq2G256W/+ mice have reduced KCNQ2 protein levels, epilepsy, brain hyperactivity, and premature deaths. As seen in the patient study, ezogabine treatment rescued seizures in mice, suggesting a potential treatment avenue. These findings provide important insights into KCNQ2-related epilepsy and highlight possible therapeutic strategies. Supported by ORIP (U54OD020351, S10OD026804, U54OD030187), NCI, NHLBI, NICHD, NIGMS, NIMH, and NINDS.
Gene Editing of Pigs to Control Influenza A Virus Infections
Kwon et al., Emerging Microbes & Infections. 2024.
https://pubmed.ncbi.nlm.nih.gov/39083026/
A reduction in the efficacy of vaccines and antiviral drugs for combating infectious diseases in agricultural animals has been observed. Generating genetically modified livestock species to minimize susceptibility to infectious diseases is of interest as an alternative approach. The researchers developed a homozygous transmembrane serine protease 2 (TMPRSS2) knockout (KO) porcine model to investigate resistance to two influenza A virus (IAV) subtypes, H1N1 and H3N2. TMPRSS2 KO pigs demonstrated diminished nasal cavity viral shedding, lower viral burden, and reduced microscopic lung pathology compared with wild-type (WT) pigs. In vitro culturing of primary bronchial epithelial cells (PBECs) demonstrated delayed viral replication in TMPRSS2 KO pigs compared with WT pigs. This study demonstrates the potential use of genetically modified pigs to mitigate IAV infections in pigs and limit transmission to humans. Supported by ORIP (U42OD011140), NHLBI, NIAID, and NIGMS.
Amphiphilic Shuttle Peptide Delivers Base Editor Ribonucleoprotein to Correct the CFTR R553X Mutation in Well-Differentiated Airway Epithelial Cells
Kulhankova et al., Nucleic Acids Research. 2024.
https://academic.oup.com/nar/article/52/19/11911/7771564?login=true
Effective translational delivery strategies for base editing applications in pulmonary diseases remain a challenge because of epithelial cells lining the intrapulmonary airways. The researchers demonstrated that the endosomal leakage domain (ELD) plays a crucial role in gene editing ribonucleoprotein (RNP) delivery activity. A novel shuttle peptide, S237, was created by flanking the ELD with poly glycine-serine stretches. Primary airway epithelia with the cystic fibrosis transmembrane conductance regulator (CFTR) R533X mutation demonstrated restored CFTR function when treated with S237-dependent ABE8e-Cas9-NG RNP. S237 outperformed the S10 shuttle peptide at Cas9 RNP delivery in vitro and in vivo using primary human bronchial epithelial cells and transgenic green fluorescent protein neonatal pigs. This study highlights the efficacy of S237 peptide–mediated RNP delivery and its potential as a therapeutic tool for the treatment of cystic fibrosis. Supported by ORIP (U42OD027090, U42OD026635), NCATS, NHGRI, NHLBI, NIAID, NIDDK, and NIGMS.
Murine MHC-Deficient Nonobese Diabetic Mice Carrying Human HLA-DQ8 Develop Severe Myocarditis and Myositis in Response to Anti-PD-1 Immune Checkpoint Inhibitor Cancer Therapy
Racine et al., Journal of Immunology. 2024.
Myocarditis has emerged as a relatively rare but often lethal autoimmune complication of checkpoint inhibitor (ICI) cancer therapy, and significant mortality is associated with this phenomenon. Investigators developed a new mouse model system that spontaneously develops myocarditis. These mice are highly susceptible to myocarditis and acute heart failure following anti-PD-1 ICI-induced treatment. Additionally, the treatment accelerates skeletal muscle myositis. The team performed characterization of cardiac and skeletal muscle T cells using histology, flow cytometry, adoptive transfers, and RNA sequencing analyses. This study sheds light on underlying immunological mechanisms in ICI myocarditis and provides the basis for further detailed analyses of diagnostic and therapeutic strategies. Supported by ORIP (U54OD020351, U54OD030187), NCI, NIA, NIDDK, and NIGMS.
Macrophages Derived From Human Induced Pluripotent Stem Cells (iPSCs) Serve As a High-Fidelity Cellular Model for Investigating HIV-1, Dengue, and Influenza viruses
Yang et al., Journal of Virology. 2024.
https://pubmed.ncbi.nlm.nih.gov/38323811/
Macrophages can be weaponized by viruses to host viral reproduction and support long-term persistence. The most common way of studying these cells is by isolating their precursors from donor blood and differentiating the isolated cells into macrophages. This method is costly and technically challenging, and it produces varying results. In this study, researchers confirmed that macrophages derived from iPSC cell lines—a model that is inexpensive, consistent, and modifiable by genome editing—are a suitable model for experiments involving HIV and other viruses. Macrophages derived from iPSCs are as susceptible to infection as macrophages derived from blood, with similar infection kinetics and phenotypes. This new model offers researchers an unlimited source of cells for studying viral biology. Supported by ORIP (R01OD034046, S10OD021601), NIAID, NIDA, NIGMS, and NHLBI.
Identification of a Heterogeneous and Dynamic Ciliome during Embryonic Development and Cell Differentiation
Elliott et al., Development. 2023.
Ciliopathies are a class of diseases that arise when the structure or function of the cilium is compromised. To definitively determine the extent of heterogeneity within the ciliome, investigators compared the ciliomes of six distinct embryonic domains. The data comprehensively revealed that about 30% of the ciliome is differentially expressed across analyzed tissues in the developing embryo. Furthermore, upregulation of numerous ciliary genes correlated with osteogenic cell-fate decisions, suggesting that changes in the ciliome contribute to distinct functions of cell types in vertebrate species. Supported by ORIP (UM1OD023222), NIDCR, and NIGMS.