Selected Grantee Publications
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- Aquatic Vertebrate Models
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- Genetics
Stat3 Mediates Fyn Kinase-Driven Dopaminergic Neurodegeneration and Microglia Activation
Siddiqui et al., Disease Models & Mechanisms. 2024.
https://pubmed.ncbi.nlm.nih.gov/39641161
The FYN gene is a risk locus for Alzheimer’s disease and several other neurodegenerative disorders. FYN encodes Fyn kinase, and previous studies have shown that Fyn signaling in dopaminergic neurons and microglia plays a role during neurodegeneration. This study investigated Fyn signaling using zebrafish that express a constitutively active Fyn Y531F mutant in neural cells. Activated neural Fyn signaling in the mutant animals resulted in dopaminergic neuron loss and induced inflammatory cytokine expression when compared with controls. Transcriptomic and chemical inhibition analyses revealed that Fyn-driven changes were dependent on the Stat3 and NF-κB signaling pathways, which work synergistically to activate neuronal inflammation and degeneration. This study provides insight into the mechanisms underlying neurodegeneration, identifying Stat3 as a novel effector of Fyn signaling and a potential translational target. Supported by ORIP (R24OD020166).
Temperature-Dependent Alterations in the Proteome of the Emergent Fish Pathogen Edwardsiella piscicida
Jacobsen et al., Journal of Fish Diseases. 2024.
https://pubmed.ncbi.nlm.nih.gov/39304982
Reported outbreaks of Edwardsiella piscicida, a bacterial pathogen among cultured and wild fish, have been steadily increasing over the past decade in tandem with climate change–mediated increases in water temperatures. The capacity for this increasingly prevalent fish pathogen to infect and cause disease in mammals is important to understand. Researchers examined the role of temperature on the virulence of E. piscicida to understand its pathogenesis in the context of climate warming trends and better understand its zoonotic potential. Findings revealed downregulation of virulence-related proteins, such as flagellar and Type VI secretion system proteins, at colder temperatures. These findings highlight the potential environmental factors influencing the pathogen’s threat to aquaculture and public health. Supported by ORIP (S10OD026918, T32OD011147).
A New Atlas to Study Embryonic Cell Types in Xenopus
Petrova et al., Developmental Biology. 2024.
https://pubmed.ncbi.nlm.nih.gov/38614285
Petrova et al. have designed a new single-cell atlas for developmental stages in Xenopus tropicalis that encompasses gastrulation, neurulation, and early tail bud. Compared to its predecessors, the new atlas enhances gene mapping, read counts, and gene/cell-type nomenclature. The atlas also leverages the latest X. tropicalis genome version to maintain consistency with previous cell-type annotations while rectifying prior nomenclature issues. The new resource emphasizes previously unexplored germ-cell populations in which novel transcription onset features have been uncovered. Finally, the new atlas offers interactive exploration through a user-friendly web portal and allows users to download complete data sets. Supported by ORIP (R24OD031956).
Age-Associated DNA Methylation Changes in Xenopus Frogs
Morselli et al., Epigenetics. 2023.
https://www.tandfonline.com/doi/full/10.1080/15592294.2023.2201517
Age-associated changes in DNA methylation have not been characterized yet in amphibians, which include widely studied model organisms. Here the authors present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. Whole-genome bisulfite sequencing profiles from skin samples of frogs representing young, mature, and old adults demonstrated that many of the methylation features and changes they observed are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. The results of this study will allow researchers to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of aging. Supported by ORIP (P40OD010997, R24OD031956, R24OD030008) and NICHD.
Photoreceptor Disc Incisures Form as an Adaptive Mechanism Ensuring the Completion of Disc Enclosure
Lewis et al., eLife. 2023.
https://elifesciences.org/articles/89160
The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or discs, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called incisures. This presence of incisures has been documented in several species, yet their role remains elusive. This study demonstrated that incisures are formed only after discs become completely enclosed. At the earliest stage of their formation, discs are not round but rather are highly irregular in shape and resemble expanding lamellipodia. In genetically modified mice and frogs, researchers measuring outer segment protein abundances found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. High perpherin-2-to-rhodopsin ratio causes an increase in incisure size and structural complexity; low ratio precludes incisure formation. They propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure. Supported by ORIP (P40OD010997, R24OD030008).
Early Detection of Pseudocapillaria tomentosa by qPCR in Four Lines of Zebrafish, Danio rerio (Hamilton 1882)
Schuster et al., Journal of Fish Diseases. 2023.
https://onlinelibrary.wiley.com/doi/10.1111/jfd.13773
The intestinal nematode Pseudocapillaria tomentosa in zebrafish (Danio rerio) causes profound intestinal lesions, emaciation, and death and is a promoter of a common intestinal cancer in zebrafish. This nematode has been detected in an estimated 15% of zebrafish laboratories. Adult worms are readily detected about 3 weeks after exposure by either histology or wet mount preparations of the intestine, and larval worms are inconsistently observed in fish before this time. A quantitative PCR (qPCR) test was recently developed to detect the worm in fish and water, and here the authors determined that the test on zebrafish intestines was effective for earlier detection. Supported by ORIP (R24OD010998, P40OD011021).
High-Resolution Genomes of Multiple Xiphophorus Species Provide New Insights into Microevolution, Hybrid Incompatibility, and Epistasis
Lu et al., Genome Research. 2023.
https://pubmed.ncbi.nlm.nih.gov/37147111/
Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, hindering advancement of evolutionary, comparative, and translational biomedical studies. Investigators assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species. They found that expanded gene families and positively selected genes associated with live bearing. Positively selected gene families were enriched in nonpolymorphic transposable elements, suggesting that dispersal has accompanied the evolution of the genes, possibly by incorporating new regulatory elements. The investigators also characterized interspecific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans. Supported by ORIP (R24OD011120, R24OD031467, R24OD011198) and NCI.
Leukocyte Tyrosine Kinase (Ltk) Is the Mendelian Determinant of the Axolotl Melanoid Color Variant
Kabangu et al., Genes. 2023.
https://www.mdpi.com/2073-4425/14/4/904
The diversity of color patterns among amphibians is largely explained by the differentiation of a few pigment cell types during development. Mexican axolotls have a variety of color phenotypes, from leucistic to highly melanistic. The melanoid axolotl is a Mendelian variant characterized by large numbers of melanophores, fewer xanthophores, and no iridophores. Studies of melanoid were influential in developing the single-origin hypothesis of pigment cell development, proposing that all three pigment cell types derive from a common progenitor cell, with pigment metabolites playing potential roles in directing the development of organelles that define different pigment cell types. Xanthine dehydrogenase (XDH) activity was identified as a mechanism for the permissive differentiation of melanophores at the expense of xanthophores and iridophores. The authors used bulked segregant RNA-Seq (including a region on chromosome 14q) to screen the axolotl genome for melanoid candidate genes and identify the associated locus. The region 14q contains gephyrin (Gphn), an enzyme that catalyzes the synthesis of the molybdenum cofactor that is required for XDH activity, and Ltk, a cell surface signaling receptor required for iridophore differentiation in zebrafish. Wild-type Ltk crispants present similar pigment phenotypes to melanoid, strongly implicating Ltk as the melanoid locus. The results support the idea of direct fate specification of pigment cells, as well as the single-origin hypothesis of pigment cell development. Supported by ORIP (P40OD019794, R24OD010435, R24OD021479).
Genome Structures Resolve the Early Diversification of Teleost Fishes
Parey et al., Science. 2023.
https://pubmed.ncbi.nlm.nih.gov/36758078/
The early evolution of teleost fishes remains an unanswered question among evolutionary biologists. The three earliest branching clades of crown teleosts are Elopomorpha (e.g., tarpons, eels), Osteoglossomorpha (e.g., arapaima, elephantnose fish), and Clupeocephala (e.g., zebrafish, medaka). Building on recently described genome assemblies in Elopomorpha, the authors explored teleost phylogeny using independent gene sequencing and chromosomal rearrangement phylogenomic approaches. They found that Elopomorpha and Osteoglossomorpha comprise a monophyletic sister group to all other teleosts. This report highlights the value of combining different levels of genome-wide information to solve complex phylogenies and will serve as a basis for new investigations into the genomic and functional evolution of teleosts. Supported by ORIP (R01OD011116).
Rbbp4 Loss Disrupts Neural Progenitor Cell Cycle Regulation Independent of Rb and Leads to Tp53 Acetylation and Apoptosis
Schultz-Rogers et al., Developmental Dynamics. 2022.
https://www.doi.org/10.1002/dvdy.467
Retinoblastoma binding protein 4 (Rbbp4) is a component of transcription regulatory complexes that control cell cycle gene expression by cooperating with the Rb tumor suppressor to block cell cycle entry. The authors used genetic analysis to examine the interactions of Rbbp4, Rb, and Tp53 in zebrafish neural progenitor cell cycle regulation and survival. Rbbp4 is upregulated across the spectrum of human embryonal and glial brain cancers, and it is essential for zebrafish neurogenesis. Rbbp4 loss leads to apoptosis and γ-H2AX in the developing brain that is suppressed by tp53 knockdown or maternal zygotic deletion. Mutant retinal neural precursors accumulate in M phase and fail to initiate G0 gene expression. Rbbp4; Rb1 double mutants show an additive effect on the number of M phase cells. The study demonstrates that Rbbp4 is necessary for neural progenitor cell cycle progression and initiation of G0, independent of Rb, and suggests that Rbbp4 is required for cell cycle exit and contributes to neural progenitor survival. Supported by ORIP (R24OD020166) and NIGMS.