(COLUMBUS, Ohio) – Researchers from the Center for Childhood Cancer Research at Nationwide Children’s Hospital offer a new platform technology and proof of concept that illuminates the role of PAX3::FOXO1, a known gene fusion driving rhabdomyosarcoma.
In two new publications, Genevieve Kendall, PhD, and Benjamin Stanton, PhD, both principal investigators in the Center for Childhood Cancer Research, have developed new collaborative studies increasing the capacity for quantitative comparisons of protein-genome binding built on chromatin immunoprecipitation sequencing (ChIP-seq) – one of the foundational methologies at the interface of epigenetics and genomics – with spike-in cells amenable to in vivo models of cancer, enabling quantitative in vivo epigenomics in preclinical models.
In a paper published in Cell Reports, the research team used their new PerCell ChIP-seq spike-in approach to identify binding sites and changes to the two-dimensional chromatin landscape in a preclinical cancer model. The study found that PAX3::FOXO1, a known fusion and driver of rhabdomyosarcoma, reorchestrates the chromatin landscape to promote distinct neuronal transcriptional signatures – including a neural cluster observed in fusion-positive rhabdomyosarcoma, identifying a potential targetable tumor cell population for additional research.
“Importantly, what we’ve done here is broadly implementable and can be used to define the oncogenic and pioneering activities of known fusions with the addition of comparative and quantitative analysis,” says Dr. Kendall. “This is an important step for taking what we learn in preclinical models and beginning to translate it into impactful changes to care and outcomes for children with cancer.”
The PerCell ChIP-seq approach is published in Cell Reports Methods. The approach takes advantage of “orthologous” genomes (genes in different species that evolved from a common ancestral gene) that can be resolved through next-generation sequencing, even when indexed the same way, within the same experimental sample. The spike-in used in this approach supports efficient, cost-effective, non-commercial and reproducible strategies for epigenomic sequencing.
“Building a modular, intuitive, integration of wet lab and dry lab workflows, the approach we developed enables direct quantitative comparisons, even for complex animal systems,” says Dr. Stanton. “This creates an opportunity for more collaboration, more analysis and a more rigorous comparative understanding of chromatin landscapes in cancer and other diseases.”
References:
Tallan A, Kucinski J, Sunkel B, Taslim C, LaHaye S, Liu Q, Qi J, Wang M, Kendall GC, Stanton BZ. Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing. Cell Rep Methods. 2025 Jun 16;5(6):101052.
 Kucinski J. Tallan A, Taslim C, Vontell AM, Silvius KM, Wang M, Cannon MV, Stanton BZ, Kendall GC. Rhabdomyosarcoma fusion oncoprotein initially pioneers neural signature in vivo. Cell Reports. 22 July 2025;44(7):115923. [Epub ahead of print]
About The Abigail Wexner Research Institute at Nationwide Children's Hospital
Named to the Top 10 Honor Roll on U.S. News & World Report’s 2024-25 list of “Best Children’s Hospitals,” Nationwide Children’s Hospital is one of America’s largest not-for-profit free-standing pediatric health care systems providing unique expertise in pediatric population health, behavioral health, genomics and health equity as the next frontiers in pediatric medicine, leading to best outcomes for the health of the whole child. Integrated clinical and research programs are part of what allows Nationwide Children’s to advance its unique model of care. As home to the Department of Pediatrics of The Ohio State University College of Medicine, Nationwide Children’s faculty train the next generation of pediatricians, scientists and pediatric specialists. The Abigail Wexner Research Institute at Nationwide Children’s Hospital is one of the Top 10 National Institutes of Health-funded free-standing pediatric research facilities in the U.S., supporting basic, clinical, translational, behavioral and population health research. The AWRI is comprised of multidisciplinary Centers of Emphasis paired with advanced infrastructure supporting capabilities such as technology commercialization for discoveries; gene- and cell-based therapies; and genome sequencing and analysis. More information is available at NationwideChildrens.org/Research.