The Pediatric Single-cell Cancer Atlas is the first public online resource of its kind dedicated to pediatric cancers.
Research team creates first publicly available single-cell atlas for childhood cancers
Researchers from Winship Cancer Institute of Emory University and the Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta have published the most comprehensive single-cell analysis of pediatric leukemia to date in Nature Communications. The study introduces the Pediatric Single-cell Cancer Atlas (PedSCAtlas), the first public online resource of its kind dedicated to pediatric cancers.
The project analyzed over 540,000 cells from 159 pediatric leukemia and healthy bone marrow samples, using cutting-edge single-cell RNA sequencing to reveal the diversity of cell types and gene expression patterns within pediatric cancers. The team identified a unique nine-gene signature that is commonly expressed in pediatric leukemia tumor cells of major leukemias with different genetic makeups. This gene signature might be associated with the malignant conversion of normal cells, providing genomic clues for early events in disease initiation and progression. The team also uncovered changes in the immune system that are strongly linked to measurable residual disease (MRD), a clinical indicator that leukemia may return after treatment. In patients who tested positive for MRD, the researchers observed a drop in key immune cells, including CD8⁺/CD4⁺ naïve T cells and M1 macrophages. These findings suggest that immune suppression at diagnosis may help explain why some pediatric patients are more likely to relapse and may offer new clues for improving treatment strategies.
Manoj Bhasin, PhD, MS
“This pediatric atlas is not just a data set, it’s a tool for the entire cancer research community to understand the contribution of cancer and immune cells in pediatric leukemias outcomes,” said Winship researcher Manoj Bhasin, PhD, MS, corresponding author of the study, director of Genomics, Proteomics, Bioinformatics and Systems Biology at Children’s, director of the Single Cell Biology Program at the Aflac Cancer and Blood Disorders Center of Children's, and professor of pediatrics at Emory University School of Medicine. “By making these resources publicly available through an interactive portal, we hope to accelerate discovery in pediatric cancer biology and support the development of more effective treatments.”
The PedSCAtlas allows researchers to visualize gene expression, cell types and clinical features across pediatric hematologic malignancies and healthy tissue. It’s designed to support the broader research community in identifying new biomarkers, therapeutic targets and insights into cancer biology at the single-cell level.
“This resource will be useful in generating detailed insights into the cellular and molecular makeup of pediatric leukemias at the single-cell level,” said Winship researcher Douglas Graham, MD, PhD, chief of the Aflac Cancer and Blood Disorders Center of Children's, and William G. Woods, MD Chair and professor of pediatrics at Emory University School of Medicine. “The study brings us one step closer to better stratification and personalized treatment for children with leukemia — by understanding their disease at the single-cell level.”
Contributing researchers from Winship Cancer Institute of Emory University and the Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta include Sunil Raikar, MD, Deborah DeRyckere, PhD; Muna Qayed, MD, MSCR; Sharon Castellino, MD, MSc; Daniel Wechsler, MD, PhD; Christopher Porter, MD, Douglas Graham, MD, PhD, and Swati Bhasin, PhD. The research also includes investigators from Bhasin's laboratory including Hope Mumme, BS, Chenbin Huang, MS, Denis Ohlstrom, MD, and Mojtaba Bakhtiari, PhD. The collaboration reflects the strength of the partnership between Emory University, Winship Cancer Institute and Children’s Healthcare of Atlanta in driving innovation across pediatric and adolescent cancer research.
This work was supported by the CURE Childhood Cancer Foundation and Emory University (DOI:10.1038/s41467-025-59362-5).