Biology subjects

Silvius, K. M.

Publications and source records attributed to Silvius, K. M..

7 recordsLinked to original sources

bioRxiv2026

Structure-Function Analysis of an Infantile Rhabdomyosarcoma Fusion-Oncogene Reveals Domain Requirements for Tumorigenesis

Rhabdomyosarcoma is a pediatric soft-tissue sarcoma that reflects impaired skeletal muscle differentiation. Spindle cell/sclerosing rhabdomyosarcoma is a histological subtype found in children and adults. In children under two, spindle cell rhabdomyosarcoma is genetically driven by fusion-oncogenes of transcription factors or co-activators important for skeletal muscle lineage commitment and development. The most common fusion-oncogene in this group is VGLL2::NCOA2, a fusion between vestigial-like family member 2 (VGLL2) and nuclear receptor coactivator 2 (NCOA2). Children with fusion-driven rhabdomyosarcoma are treated with general chemotherapy, surgery, and radiation, which are not specific to the molecular underpinnings, and increase risk of secondary malignancies and premature death. Previously, we showed that VGLL2::NCOA2 is transforming in mouse myoblasts and transgenic zebrafish tumor models. Here, we build on this work by detailing the structure-function relationship of the retained VGLL2::NCOA2 protein domains to define domain requirements and their molecular interactions for tumorigenesis. We created deletion mutants of the VGLL2 vestigial/Tondu (TDU) domain and the NCOA2 activating domains 1 and 2 (AD1 and AD2), and a double mutant lacking the TDU+AD1 domains and assessed their function in a mouse myoblast model. We find that the TDU and AD1 domains support nuclear fusion-oncogene localization, transformation in vitro, and tumorigenesis in a mouse allograft model. Furthermore, transcriptomic analysis demonstrates that the TDU or AD1 mutant VGLL2::NCOA2 drives an upregulation of myogenesis gene sets and supports terminal differentiation. Overall, our results indicate that VGLL2::NCOA2 requires the TDU and AD1 domains for optimal transformation, and that targeting these domains, or their interacting protein partners, represents a therapeutic opportunity.

cancer biology↗

bioRxiv2026

HES3-dependent regulatory functions in development and fusion-positive rhabdomyosarcoma

HES3/Her3 is a transcription factor that functions in non-canonical STAT3 signaling to promote the renewal of neural stem cells and has roles in multiple cancer contexts. To study its role in development and disease, we previously generated a CRISPR/Cas9 zebrafish knockout of her3, the ortholog to human HES3. HES3 is also a cooperating gene in fusion-positive rhabdomyosarcoma, an aggressive pediatric cancer, where HES3 prevents terminal myogenic differentiation, and high expression correlates with worse patient outcomes. Here, we utilize our her3/HES3 knockout model with chromatin and transcriptional profiling techniques to assess its role during early zebrafish gastrulation with the goal of understanding the function of this transcription factor and how these activities are co-opted in cancer. We found that the Her3/HES3 preferential binding motif is distinct from other HES-family members, including a CG-rich E-box motif, that it leverages to modulate the expression of genes involved in neurogenesis and WNT signaling. We also determined that motif preferences of Her3/HES3 altered its interactions with DNA, allowing it to function canonically as a transcriptional repressor with additional duality as an activator. In the context of PAX3::FOXO1, a monogenic driver of fusion-positive rhabdomyosarcoma, we find that Her3/HES3 plays an influential role in modulating the initial activities of this core oncogenic transcription factor. Upon expressing PAX3::FOXO1 in early developing zebrafish embryos, her3 knockout allowed for enhanced activation of neural programs, which are observed in the human disease, along with alterations to cell adhesion programs. Patient tumor samples could be clustered and stratified based on HES3 expression alone. We saw that patient PAX3::FOXO1-positive tumors with high levels of HES3 contained a more neural identity than those with low levels of HES3, altogether suggesting HES3 plays a critical role in regulating this neural signature during both the initial functions of PAX3::FOXO1 and in established tumors.

cancer biology↗

bioRxiv2026

Ungulate conservation: Lessons from experimental white-lipped peccary management in agricultural-natural landscape mosaics of the Brazilian Cerrado

Animal population control is widely used to mitigate conflicts between wildlife and agriculture worldwide. Structured, monitored removals are rare in South America, however, and their consequences for wildlife populations as well as their effectiveness in reducing crop damage are little understood. Using eight years of data from an experimental white-lipped peccary management program in an agricultural mosaic in the Brazilian Cerrado biome, we assess how structured, non-lethal removals affect both peccary demography and second-crop corn damage. Leslie removal models based on 6,619 captured individuals indicated that cumulative removals to approximately 85% of the initial population strongly reduced peccary abundance, with limited demographic compensation despite fluctuations in reproductive output. Corn crop damage, quantified with satellite imagery, declined over time and was correlated with peccary population size. Interannual variation in population growth and juvenile recruitment was poorly explained by climate, fire, or landscape composition. Source-sink dynamics likely play a role in maintaining healthy populations at the regional scale. Together, these results demonstrate that sustained and monitored ungulate removals can reliably reduce population size and agricultural damage, supporting coexistence between wildlife and food crop production in human-dominated tropical landscapes.

ecology↗

bioRxiv2024

Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo

Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, functions as a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1s in vivo epigenetic mechanisms has hindered therapeutic development. Here, we establish a PAX3::FOXO1 zebrafish injection model and semi-automated ChIP-seq normalization strategy to evaluate how PAX3::FOXO1 initially interfaces with chromatin in a developmental context. We investigated PAX3::FOXO1s recognition of chromatin and subsequent transcriptional consequences. We find that PAX3::FOXO1 interacts with inaccessible chromatin through partial/homeobox motif recognition consistent with pioneering activity. However, PAX3::FOXO1-genome binding through a composite paired-box/homeobox motif alters chromatin accessibility and redistributes H3K27ac to activate neural transcriptional programs. We uncover neural signatures that are highly representative of clinical rhabdomyosarcoma gene expression programs that are enriched following chemotherapy. Overall, we identify partial/homeobox motif recognition as a new mode for PAX3::FOXO1 pioneer function and identify neural signatures as a potentially critical PAX3::FOXO1 tumor initiation event.

cancer biology↗

bioRxiv2023

A robust closed-tube method for resolving tp53M214K genotypes

The tp53M214K zebrafish mutant developed by Berghmans et al 20051 is a versatile platform with which to model a diverse spectrum of human diseases. However, currently available genotyping methods for this mutant require lengthy processes such as restriction digests and outsourced Sanger sequencing. To address this deficiency, we leveraged high-resolution melting analysis (HRMA) technology in conjunction with a parallel, in-tandem wildtype spike-in approach to develop a robust genotyping protocol capable of discriminating tp53M214K zygosity. Here, we describe our method in detail. We anticipate that our genotyping protocol will benefit researchers utilizing the tp53M214K zebrafish mutant by offering reliable results with a faster turnaround time than conventional approaches.

cancer biology↗

bioRxiv2022

Zebrafish her3 knockout impacts developmental and cancer-related gene signatures

HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3s role in neurogenesis. To investigate HES3s function during development, we generated a zebrafish CRISPR/Cas9 knockout of her3, the zebrafish ortholog of HES3. Loss of her3 is not embryonic lethal and adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants are significantly smaller than wildtype and a subset present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 knockout embryos are enriched for HOX and SOX10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts. Summary StatementHere, we generate and characterize a zebrafish her3/HES3 knockout to elucidate the functional role of her3/HES3, a transcriptional repressor, in neural development and tumorigenic processes.

developmental biology↗

bioRxiv2020

Mysterious disappearances of a large mammal in Neotropical forests

The drivers of periodic population cycling by some animal species in northern systems remain unresolved1. Mysterious disappearances of populations of the Neotropical, herdforming white-lipped peccary (Tayassu pecari, henceforth "WLP") have been anecdotally documented and explained as local events resulting from migratory movements or overhunting2,3,4, or as disease outbreaks5,6, and have not been considered in the context of large-scale species-specific population dynamics. Here we present evidence that WLP disappearances represent troughs in population cycles that occur with regular periodicity and are synchronized at regional and perhaps continent-wide spatial scales. Analysis of 43 disappearance events and 88 years of commercial and subsistence harvesting data reveals boom - bust population cycles lasting from 20 to 30 years, in which a rapid population crash occurring over 1 to 5 years is followed by a period of absence of 7 to12 years and then a slow growth phase. Overhunting alone cannot explain the crashes, but as in northern systems dispersal during the growth phase appears to play a key role. This is the first documentation of population cycling in a tropical vertebrate.

ecology↗