Selected Grantee Publications
HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration
Voss et al., Frontiers in Cell and Development Biology. 2021.
https://pubmed.ncbi.nlm.nih.gov/35036404/
New patterns of gene expression are enacted and regulated during tissue regeneration. Romidepsin, an FDA-approved HDAC inhibitor, potently blocks axolotl embryo tail regeneration by altering initial transcriptional responses to injury. Regeneration inhibitory concentrations of romidepsin increased and decreased the expression of key genes. Single-nuclei RNA sequencing at 6 HPA illustrated that key genes were altered by romidepsin in the same direction across multiple cell types. These results implicate HDAC activity as a transcriptional mechanism that operates across cell types to regulate the alternative expression of genes that associate with regenerative success versus failure outcomes. Supported by ORIP (P40OD019794, R24OD010435, R24OD021479), NICHD, and NIGMS.
AAV Capsid Variants with Brain-Wide Transgene Expression and Decreased Liver Targeting After Intravenous Delivery in Mouse and Marmoset
Goertsen et al., Nature Neuroscience. 2021.
https://www.nature.com/articles/s41593-021-00969-4
Genetic intervention is increasingly being explored as a therapeutic option for debilitating disorders of the central nervous system (CNS). This project focused on organ-specific targeting of adeno-associated virus (AAV) capsids after intravenous delivery. These results constitute an important step forward toward achieving the goal of engineered AAV vectors that can be used to broadly deliver gene therapies to the CNS in humans. Supported by ORIP (U24OD026638), NIMH, and NINDS.
Dynamics and Origin of Rebound Viremia in SHIV-Infected Infant Macaques Following Interruption of Long-Term ART
Obregon-Perko et al., JCI Insight. 2021.
https://pubmed.ncbi.nlm.nih.gov/34699383/
Animal models that recapitulate human COVID-19 disease are critical for understanding SARS-CoV-2 viral and immune dynamics, mechanisms of disease, and testing of vaccines and therapeutics. A group of male pigtail macaques (PTMs) were euthanized either 6- or 21-days after SARS-CoV-2 viral challenge and demonstrated mild-to-moderate COVID-19 disease. Pulmonary infiltrates were dominated by T cells, virus-targeting T cells were predominantly CD4+, increases in circulating inflammatory and coagulation markers, pulmonary pathologic lesions, and the development of neutralizing antibodies were observed. Collectively, the data suggests PTMs are a valuable model to study COVID-19 pathogenesis and may be useful for testing vaccines and therapeutics. Supported by ORIP (P51OD011104) and NIAID.
An NR2F1-Specific Agonist Suppresses Metastasis by Inducing Cancer Cell Dormancy
Khalil et al., The Journal of Experimental Medicine. 2021.
Researchers described the discovery of a nuclear receptor NR2F1 antagonist that specifically activates dormancy programs in malignant cells. Agonist treatment resulted in a self-regulated increase in NR2F1 mRNA and protein and downstream transcription of a novel dormancy program. This program led to growth arrest in multiple human cell lines, as well as patient-derived organoids. This effect was lost when NR2F1 was knocked out. In mice, agonist treatment resulted in inhibition of lung metastasis of head and neck squamous cell carcinomas, even after cessation of the treatment. This work provides proof of principle supporting the use of NR2F1 agonists to induce dormancy as a therapeutic strategy to prevent metastasis. Supported by ORIP (S10OD018522 and S10OD026880) and others.
Deep Learning Is Widely Applicable to Phenotyping Embryonic Development and Disease
Naert et al., Development. 2021.
https://pubmed.ncbi.nlm.nih.gov/34739029/
Genome editing simplifies the generation of new animal models for congenital disorders. The authors illustrate how deep learning (U-Net) automates segmentation tasks in various imaging modalities. They demonstrate this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). They provide a library of pre-trained networks and detailed instructions for applying deep learning to datasets and demonstrate the versatility, precision, and scalability of deep neural network phenotyping on embryonic disease models. Supported by ORIP (P40OD010997, R24OD030008), NICHD, NIDDK, and NIMH.
Challenges and Considerations During In Vitro Production of Porcine Embryos
Chen et al., Cells. 2021.
https://pubmed.ncbi.nlm.nih.gov/34685749/
Genetically modified pigs have become valuable tools for generating advances in animal agriculture and human medicine. Importantly, in vitro production and manipulation of embryos is an essential step in the process of creating porcine models. As the in vitro environment is still suboptimal, it is imperative to examine the porcine embryo culture system from several angles to identify methods for improvement. Understanding metabolic characteristics of porcine embryos and considering comparisons with other mammalian species is useful for optimizing culture media formulations. Furthermore, stressors arising from the environment and maternal or paternal factors must be taken into consideration to produce healthy embryos in vitro. In this review, Chen et al progress stepwise through in vitro oocyte maturation, fertilization, and embryo culture in pigs to assess the status of current culture systems and address points where improvements can be made. Supported by ORIP (U42OD011140).
Integrated Spatial Multiomics Reveals Fibroblast Fate During Tissue Repair
Foster et al., PNAS. 2021.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8521719/
The function of regenerative medicine in wound healing remains elusive, partially because of how fibroblasts program and respond to injury remains unclear. Investigators presented a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which allowed characterization of cells involved in wound healing across time and space. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, fibroblast epigenomes were imputed with temporospatial resolution. This allowed revelation of potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and reexamination of the canonical phases of wound healing. Supported by ORIP (S10OD018220) and others.
Collective Behavior Emerges from Genetically Controlled Simple Behavioral Motifs in Zebrafish
Harpaz et al., Science Advances. 2021.
https://www.science.org/doi/10.1126/sciadv.abi7460
Harpaz et al. report that zebrafish regulate their proximity and alignment with each other at early larval stages. Two visual responses (one measuring relative visual field occupancy and one accounting for global visual motion), account for emerging group behavior. Mutations in genes known to affect social behavior in humans perturb these reflexes in individual larval zebrafish and change their emergent collective behaviors. Model simulations show that changes in these two responses in individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence, group behaviors reflect in part genetically defined primitive sensorimotor “motifs” evident in young larvae. Supported by ORIP (R43OD024879, R44OD024879) and NINDS.
Limited Expansion of Human Hepatocytes in FAH/RAG2-Deficient Swine
Nelson et al., Tissue Engineering – Part A. 2021.
https://pubmed.ncbi.nlm.nih.gov/34309416/
The mammalian liver's regenerative ability has led researchers to engineer animals as incubators for expansion of human hepatocytes. Nelson et al. engineered immunodeficient swine to support expansion of human hepatocytes and identify barriers to their clinical application. Immunodeficient swine were engineered by knockout of the recombinase-activating gene 2 (RAG2) and fumarylacetoacetate hydrolase (FAH). Immature human hepatocytes (ihHCs) were injected into fetal swine by intrauterine cell transplantation (IUCT) at day 40 of gestation. They identified the mechanism of the eventual graft rejection by the intact NK cell population. They confirmed the presence of residual adaptive immunity in this model of immunodeficiency. Supported by ORIP (U42OD011140).
Comparative Cellular Analysis of Motor Cortex in Human, Marmoset and Mouse
Bakken et al., Nature. 2021.
https://pubmed.ncbi.nlm.nih.gov/34616062/
Investigators used high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmosets, and mice, to characterize the cellular makeup of the primary motor cortex (M1), which exhibits similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. Despite the overall conservation, many species-dependent specializations are apparent. These results demonstrate the robust molecular foundations of cell-type diversity in M1 across mammals and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations. Supported by ORIP (P51OD010425), NIMH, NCATS, NINDS, and NIDA.