Selected Grantee Publications
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.
The Power of the Heterogeneous Stock Rat Founder Strains in Modeling Metabolic Disease
Wagner et al., Endocrinology. 2023.
https://pubmed.ncbi.nlm.nih.gov/37882530/
Metabolic diseases are a host of complex conditions, including obesity, diabetes mellitus, and metabolic syndrome. Endocrine control systems (e.g., adrenals, thyroid, gonads) are causally linked to metabolic health outcomes. In this study, investigators determined novel metabolic and endocrine health characteristics in both sexes of six available substrains similar to the N/NIH Heterogeneous Stock (HS) rat founders. This deep-phenotyping protocol provides new insight into the exceptional potential of the HS rat population to model complex metabolic health states. The following hypothesis was tested: The genetic diversity in the HS rat founder strains represents a range of endocrine health conditions contributing to the diversity of cardiometabolic disease risks exhibited in the HS rat population. Supported by ORIP (R24OD024617), NHLBI, NIGMS and NIDDK.
Allelic Strengths of Encephalopathy-Associated UBA5 Variants Correlate Between In Vivo and In Vitro Assays
Pan et al., eLife. 2023.
https://pubmed.ncbi.nlm.nih.gov/37502976/
The UBA5 gene is associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder, in humans. The link between UBA5 variants and severity of DEE44, however, is not established. Investigators developed humanized fly models carrying a series of patient UBA5 variants. These flies showed differences in survival rates, developmental progress, life span, and neurological well-being. The severity of these defects correlated strongly with functional defects of UBA5 variants, allowing the classification of UBA5 loss-of-function variants into mild, intermediate, and severe allelic strengths in patients. This study provides resources for systematic investigation of the mechanistic link between UBA5 variants and DEE44 and for developing diagnostic approaches. Supported by ORIP (R24OD022005, R24OD031447, U54OD035865) and NCATS.
A Comprehensive Drosophila Resource to Identify Key Functional Interactions Between SARS-CoV-2 Factors and Host Proteins
Guichard et al., Cell Reports. 2023.
https://pubmed.ncbi.nlm.nih.gov/37480566/
To address how interactions between SARS-CoV-2 factors and host proteins affect COVID-19 symptoms, including long COVID, and facilitate developing effective therapies against SARS-CoV-2 infections, researchers reported the generation of a comprehensive set of resources, mainly genetic stocks and a human cDNA library, for studying viral–host interactions in Drosophila. Researchers further demonstrated the utility of these resources and showed that the interaction between NSP8, a SARS-CoV-2 factor, and ATE1 arginyltransferase, a host factor, causes actin arginylation and cytoskeleton disorganization, which may be relevant to several pathogenesis processes (e.g., coagulation, cardiac inflammation, fibrosis, neural damage). Supported by ORIP (R24OD028242, R24OD022005, R24OD031447), NIAID, NICHD, NIGMS, and NINDS.
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.
Resolution of Structural Variation in Diverse Mouse Genomes Reveals Chromatin Remodeling due to Transposable Elements
Ferraj et al., Cell Genomics. 2023.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203049/
Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. Here, investigators used long-read whole genome sequencing to assemble the genomes of 20 diverse inbred laboratory strains of mice. From whole-genome comparisons, they generated a sequence-resolved callset of 413,758 structural variants. These data are presented as a comprehensive resource that can be used for future genomic studies, aid in modeling and studying the effects of genetic variation, and enhance genotype-to-phenotype research. Supported by ORIP (R24OD021325), NCI, NIGMS, and NHGRI.
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).
Human Hematopoietic Stem Cell Engrafted IL-15 Transgenic NSG Mice Support Robust NK Cell Responses and Sustained HIV-1 Infection
Abeynaike et al., Viruses. 2023.
https://www.mdpi.com/1999-4915/15/2/365
A major obstacle to human natural killer (NK) cell reconstitution is the lack of human interleukin‑15 (IL-15) signaling, as murine IL-15 is a poor stimulator of the human IL-15 receptor. Researchers show that immunodeficient NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice expressing a transgene encoding human IL-15 (NSG-Tg(IL-15)) have physiological levels of human IL-15 and support long-term engraftment of human NK cells when transplanted with human umbilical cord blood–derived hematopoietic stem cells (HSCs). These mice demonstrate robust and long-term reconstitution with human immune cells but do not develop graft-versus-host disease, allowing long-term studies of human NK cells. The HSC-engrafted mice can sustain HIV-1 infection, resulting in human NK cell responses. This work provides a robust novel model to study NK cell responses to HIV-1. Supported by ORIP (R24OD026440), NIAID, NCI, and NIDDK.