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.
Suppressing APOE4-Induced Neural Pathologies by Targeting the VHL-HIF Axis
Jiang et al., PNAS. 2025.
https://pubmed.ncbi.nlm.nih.gov/39874294
The ε4 variant of human apolipoprotein E (APOE4) is a major genetic risk factor for Alzheimer’s disease and increases mortality and neurodegeneration. Using Caenorhabditis elegans and male APOE-expressing mice, researchers determined that the Von Hippel-Lindau 1 (VHL-1) protein is a key modulator of APOE4-induced neural pathologies. This study demonstrated protective effects of the VHL-1 protein; the loss of this protein reduced APOE4-associated neuronal and behavioral damage by stabilizing hypoxia-inducible factor 1 (HIF-1), a transcription factor that protects against cellular stress and injury. Genetic VHL-1 inhibition also mitigated cerebral vascular injury and synaptic damage in APOE4-expressing mice. These findings suggest that targeting the VHL–HIF axis in nonproliferative tissues could reduce APOE4-driven mortality and neurodegeneration. Supported by ORIP (R24OD010943, R21OD032463, P40OD010440), NHGRI, NIA, and NIGMS.
A Defining Member of the New Cysteine-Cradle Family Is an aECM Protein Signalling Skin Damage in C. elegans
Sonntag et al., PLoS Genetics. 2025.
https://pubmed.ncbi.nlm.nih.gov/40112269
The rigid yet flexible apical extracellular matrix (aECM), known as the cuticle, works with the underlying epidermal layer to create a protective physical barrier against injury or infection in the roundworm Caenorhabditis elegans. The aECM communicates crucial signals to the epidermis based on environmental insults, allowing it to trigger immune activation and combat potential threats. This study investigated the molecular link between aECM and immune response in C. elegans. Investigators found that a secreted protein called SPIA-1 acts as an extracellular signal activator of cuticle damage and mediates immune response. This study sheds light on how epithelial cells detect and respond to damage. Supported by ORIP (R21OD033663, P40OD010440) 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.
The Widely Used Ucp1-Cre Transgene Elicits Complex Developmental and Metabolic Phenotypes
Halurkar et al., Nature Communications. 2025.
https://pubmed.ncbi.nlm.nih.gov/39824816
Bacterial artificial chromosome technology is instrumental to mouse transgenics, including in studies of highly thermogenic brown adipose tissue and energy-storing white adipose tissue. Researchers discovered that male and female Ucp1-CreEvdr transgenic mice, which are commonly used to study fat tissue, may have unintended effects on metabolism and development. Findings revealed that these mice show changes in both brown and white fat function and disruptions in gene activity, suggesting broader physiological impacts than previously thought. This study emphasizes the need for careful validation of genetic tools in research to ensure accurate results, highlighting the potential concerns in using the Ucp1-CreEvdr model in metabolic and developmental studies. Supported by ORIP (R21OD034470, R21OD031907) NCATS, NIDCR, and NIDDK.
Elevated Inflammation Associated With Markers of Neutrophil Function and Gastrointestinal Disruption in Pilot Study of Plasmodium fragile Co-Infection of ART-Treated SIVmac239+ Rhesus Macaques
Nemphos et al., Viruses. 2024.
https://pubmed.ncbi.nlm.nih.gov/39066199/
Because of geographic overlap, a high potential exists for co-infection with HIV and malaria caused by Plasmodium fragile. Meta-analysis of data collected from 1991 to 2018 demonstrated co-incidence of these two infections to be 43%. Researchers used a male rhesus macaque (RM) model, 6–12 years of age, coinfected with P. fragile and antiretroviral (ART)-treated simian immunodeficiency virus (SIV) to mimic HIV/malaria co-infection observed in patients. ART-treated co-infected RMs demonstrated increased levels of inflammatory cytokines, shifts in neutrophil function, and gastrointestinal mucosal dysfunction. This model may be used to study molecular mechanisms of disease pathology and novel therapies, such as neutrophil-targeted interventions, for patients experiencing co-infection. Supported by ORIP (U42OD010568, U42OD024282, P51OD011104, R21OD031435) and NIGMS.
Proinflammatory Cytokines Suppress Stemness-Related Properties and Expression of Tight Junction in Canine Intestinal Organoids
Nakazawa et al., In Vitro Cellular & Developmental Biology—Animal. 2024.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11419940
Cells in the gastrointestinal tract are exposed to numerous stressors that can promote excessive inflammation, including environmental chemicals and dietary substances. Researchers studied how canine intestinal epithelial cell (IEC)–derived organoids responded to exposure to one of three proinflammatory cytokines; interferon-γ (IFN-γ), tumor necrosis factor-α (TNFα), or interleukin-1β (IL1β). Exposure to IFN-γ resulted in downregulation of the stem cell marker Lgr5. Only IFN-γ exposure resulted in increased production of caspase 3 and caspase 8. Exposure to either IFN-γ or IL1β resulted in suppressed cell proliferation. The pro-inflammatory cytokines caused reduced tight junction protein expression and compromised membrane integrity. These findings are important to understanding IEC response to different inflammatory stimuli and to broadening knowledge of gut physiology. Supported by ORIP (K01OD030515, R21OD031903).
Fetal Bone Engraftment Reconstitutes the Immune System in Pigs With Severe Combined Immunodeficiency
Monarch et al., Lab Animal. 2024.
https://pubmed.ncbi.nlm.nih.gov/39289566/
A valuable preclinical model for studying immune-related pathologies is the severe combined immunodeficiency (SCID) pig through modification of recombination activating gene 2 (RAG2) and interleukin-2 receptor-γ (IL2RG). RAG2/IL2RG double knockout SCID pigs are hard to maintain for breeding and long-term studies because their life span is 8 weeks or less. The researchers investigated fetal allograft transplantation derived from immunocompetent pigs as a strategy for reconstituting the immune system of SCID pigs and promoting survival. Following fetal allograft, SCID pigs demonstrated increased levels of lymphocytes. SCID pigs that received the fetal allograft demonstrated improved body condition and extended life span compared with nonrecipient SCID littermates. This study demonstrates the potential use of fetal allograft transplantation to extend the life span of SCID pigs to breeding age to reduce the resources used to maintain this model for biomedical research. Supported by ORIP (U42OD011140, R21OD027062).
Large Animal Models Enhance the Study of Crypt-Mediated Epithelial Recovery From Prolonged Intestinal Ischemia Reperfusion Injury
McKinney-Aguirre et al., American Journal of Physiology-Gastrointestinal and Liver Physiology. 2024.
https://pubmed.ncbi.nlm.nih.gov/39404771/
Intestinal ischemia and reperfusion injury (IRI) is a severe pathological alteration that compromises the intestinal epithelial barrier, causing bacterial translocation, shock, sepsis, and potentially death. Preclinical research for IRI has focused on utilizing murine models, but mice demonstrate key anatomical and physiological intestinal differences from humans, such as tissue enzymes, intestinal permeability, and hypoxic response pathways. The researchers compared a 3-hour IRI porcine model to a 3-hour IRI murine model to reveal which demonstrated a stronger translational capacity. Both models demonstrated crypt damage, but only the porcine model showed recovery-associated crypt death expansion and re-epithelialization. At 72 hours post-IRI, mouse mortality was 84.6%, whereas porcine mortality was 0%. A porcine model would be more reliable for future translational studies focused on understanding IRI mechanisms for diagnosis and therapy advancements. Supported by ORIP (T32OD011130, K01OD010199, R03OD026598) and NIDDK.
Enterohemorrhagic Escherichia coli (EHEC) Disrupts Intestinal Barrier Integrity in Translational Canine Stem Cell-Derived Monolayers
Nagao et al., Microbiology Spectrum. 2024.
https://pubmed.ncbi.nlm.nih.gov/39162490/
EHEC produces Shiga toxin, which causes acute colitis with symptoms such as hemolytic uremic syndrome and bloody diarrhea. The researchers developed a colonoid-derived monolayer model to understand EHEC’s impact on canine gut health. Colonoid-derived monolayers co-cultured with EHEC demonstrated key differences compared with the control and nonpathogenic E. coli co-cultures. Scanning electron microscopy displayed EHEC aggregated and attached to the microvilli. EHEC-infected monolayers demonstrated significantly weakened membrane integrity and increased inflammatory cytokine production, specifically TNFα. The researchers developed a novel in vitro model that offers an additional platform for understanding the mechanisms of EHEC pathogenicity, developing therapeutics for EHEC, and studying additional enteric pathogens. Supported by ORIP (K01OD030515, R21OD031903).