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.
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.
Genetic Basis For an Evolutionary Shift From Ancestral Preaxial to Postaxial Limb Polarity in Non-urodele Vertebrates
Trofka et al., Current Biology. 2021.
https://www.sciencedirect.com/science/article/pii/S0960982221012501
In most tetrapod vertebrates, limb skeletal progenitors condense with postaxial dominance. Posterior elements (ulna and fibula) appear prior to their anterior counterparts (radius and tibia), followed by digit-appearance order with continuing postaxial polarity. Recent fossil evidence suggests that preaxial polarity represents an ancestral rather than derived state. These authors report that 5'Hoxd (Hoxd11-d13) gene deletion in mouse is atavistic and uncovers an underlying preaxial polarity in mammalian limb formation. Evolutionary changes in Gli3R activity level, key in the fin-to-limb transition, appear to be fundamental to the shift from preaxial to postaxial polarity in formation of the tetrapod limb skeleton. Supported by ORIP (P40OD01979) and NCI.
Multiplexed Drug-Based Selection and Counterselection Genetic Manipulations in Drosophila
Matinyan et al., Cell Reports. 2021.
https://www.cell.com/cell-reports/pdf/S2211-1247(21)01147-5.pdf
Many highly efficient methods exist which enable transgenic flies to contribute to diagnostics and therapeutics for human diseases. In this study, researchers describe a drug-based genetic platform with four selection and two counterselection markers, increasing transgenic efficiency by more than 10-fold compared to established methods in flies. Researchers also developed a plasmid library to adapt this technology to other model organisms. This highly efficient transgenic approach significantly increases the power of not only Drosophila melanogaster but many other model organisms for biomedical research. Supported by ORIP (P40OD018537, P40OD010949, R21OD022981), NCI, NHGRI, NIGMS, and NIMH.
TGF-β1 Signaling Is Essential for Tissue Regeneration in the Xenopus Tadpole Tail
Nakamura et al., Biochemical and Biophysical Research Communications. 2021.
https://www.sciencedirect.com/science/article/pii/S0006291X21008731
Amphibians, such as Xenopus tropicalis, exhibit a remarkable capacity for tissue regeneration after traumatic injury. Nakamura et al. show that inhibition of TGF-β1 function prevents tail regeneration in Xenopus tropicalis tadpoles. CRISPR-mediated knock-out (KO) of tgfb1 retards tail regeneration; the phenotype of tgfb1 KO tadpoles can be rescued by injection of tgfb1 mRNA. Cell proliferation, critical for tissue regeneration, is downregulated in tgfb1 KO tadpoles; tgfb1 KO reduces the expression of phosphorylated Smad2/3 (pSmad2/3). These results show that TGF-β1 regulates cell proliferation through the activation of Smad2/3. They propose that TGF-β1 plays a critical role in TGF-β receptor-dependent tadpole tail regeneration in Xenopus. Supported by ORIP (P40OD010997, R24OD030008).
Innate Immunity Stimulation via CpG Oligodeoxynucleotides Ameliorates Alzheimer’s Disease Pathology in Aged Squirrel Monkeys
Patel et al., Brain: A Journal of Neurology. 2021.
https://pubmed.ncbi.nlm.nih.gov/34128045/
Alzheimer's disease is the only illness among the top 10 causes of death for which there is no disease-modifying therapy. The authors have shown in transgenic Alzheimer's disease mouse models that harnessing innate immunity via TLR9 agonist CpG oligodeoxynucleotides (ODNs) modulates age-related defects associated with immune cells and safely reduces amyloid plaques, oligomeric amyloid-β, tau pathology, and cerebral amyloid angiopathy (CAA). They used a nonhuman primate model for sporadic Alzheimer's disease pathology that develops extensive CAA-elderly squirrel monkeys. They demonstrate that long-term use of Class B CpG ODN 2006 induces a favorable degree of innate immunity stimulation. CpG ODN 2006 has been well established in numerous human trials for a variety of diseases. This evidence together with their earlier research validates the beneficial therapeutic outcomes and safety of this innovative immunomodulatory approach. Supported by ORIP (P40OD010938), NINDS, NIA, and NCI.
A Symphony of Destruction: Dynamic Differential Fibrinogenolytic Toxicity by Rattlesnake (Crotalus and Sistrurus) Venoms
Seneci et al., Comparative Biochemistry and Physiology Part C. 2021.
https://pubmed.ncbi.nlm.nih.gov/33766656/
This study adopts rattlesnakes as a model group to investigate the evolutionary history of venom coagulotoxicity in the context of phylogenetics, natural history, and biology. Venom-induced clotting of human plasma and fibrinogen was determined and mapped onto the rattlesnake phylogenetic tree to reconstruct the evolution of coagulotoxicity across the group. Results indicate that venom phenotype is often independent of phylogenetic relationships in rattlesnakes, suggesting the importance of diet and/or other environmental variables. This study is the most comprehensive effort to date to characterize the evolutionary and biological aspects of coagulotoxins in rattlesnake venom. Further research at finer taxonomic levels is recommended. Supported by ORIP (P40OD010960).
Antibody-Based CCR5 Blockade Protects Macaques From Mucosal SHIV Transmission
Chang et al., Nature Communications. 2021.
https://doi.org/10.1038/s41467-021-23697-6
The efficacy of antiretroviral therapy (ART) as pre-exposure prophylaxis against HIV is hindered by incomplete patient adherence and ART-resistant variants. Researchers found that competitive inhibition of HIV Env-CCR5 binding via the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges with a CCR5-tropic simian-human immunodeficiency virus (SHIVSF162P3). Biweekly injection of Leronlimab at 50 mg/kg provided complete protection from SHIV infection. Tissue biopsies from protected macaques post-challenge revealed complete CCR5 receptor occupancy and an absence of viral DNA. After Leronlimab washout, transfer of hematologic cells into naïve monkeys did not transmit infection, supporting the initiation of clinical trials. Supported by ORIP (P51OD011092, K01OD026561, P40OD028116) and NIAID.
Characterization of Axolotl Lampbrush Chromosomes by Fluorescence In Situ Hybridization and Immunostaining
Keinath et al., Experimental Cell Research. 2021.
https://pubmed.ncbi.nlm.nih.gov/33675804/
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified by their relative lengths and predicted centromeres; they have never been associated completely with the mitotic karyotype, linkage maps, or genome assembly. The authors identified 9 of the axolotl LBCs using RNA sequencing to identify actively transcribed genes and 13 bacterial artificial clone probes containing pieces of active genes. This study presents a simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences to the LBCs by immunostaining and fluorescence in situ hybridization. This data will facilitate a more detailed analysis of LBC loops. Supported by ORIP (P40OD019794, R24OD010435) and NIGMS.
The Giant Axolotl Genome Uncovers the Evolution, Scaling, and Transcriptional Control of Complex Gene Loci
Schloissnig et al., PNAS. 2021.
https://pubmed.ncbi.nlm.nih.gov/33827918/
Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, Schloissnig et al. describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the major histocompatibility complex (MHC) and the functional regulatory landscape of the fibroblast growth factor 8 (Axfgf8) region. The axolotl serves as a primary model for studying successful regeneration. Supported by ORIP (R24OD010435, P40OD019794).