Comprehensive pediatric biobanking and model development in the Beat Childhood Cancer Research Consortium

The Pediatric Oncology Translational Research Lab (POTRL) at Penn State University (PSU) provides a critical centralized, LIMS-tracked repository of over 70,000 pediatric cancer specimens and patient-derived models, enabling validated resources for innovative translational research in precision-oncology through the Beat Childhood Cancer (BCC) Research Consortium. Background: Reliable translational research depends on high quality, well characterized patient materials. BCC operates a centralized repository managed through the POTRL at PSU. POTRL receives, processes, and stores biospecimens from multiple BCC clinical trials representing children with neuroblastoma, CNS tumors, sarcomas, and other solid malignancies. The repository includes tumor tissue, tissue slides, paraffin-embedded blocks, and blood/plasma that are processed for ctDNA, buffy coats, immune cells, cytokines, and biomarker analyses. Methods: All specimens are accessioned and tracked in Freezerworks LIMS to ensure accurate labeling and storage. Patients are consented to the BCC-BIO-001 study (NCT04715178) which collects whole exome and whole transcriptome sequencing of tumors, clinical diagnosis, pathology, treatment and outcomes of patients. Upon receipt, samples are inspected for integrity and temperature compliance. Cell lines, organoids and xenografts are generated from tumor tissue and bone cores/aspirates each of which undergo authentication at IDEXX BioAnalytics using short tandem repeat profiling with concurrent mycoplasma testing and matched patient references. Tumor line validation is performed by flow cytometric analysis using tumor-specific marker panels such as Ewings sarcoma (CD99); neuroblastoma (GD2, CD56, Synaptophysin); or medulloblastoma (CD56, Synaptophysin). Results: The repository currently houses more than 70,000 specimens from over 5,000 pediatric patients. Over 750 patient-derived cell lines and 150 patient-derived xenograft models have been established. Implementation of LIMS-based tracking has improved specimen organization and data consistency allowing for tracking of sequential patient samples. Each sample is correlated to timepoints in treatments and outcomes stored in the REDCap database. Development of patient-derived organoid models has recently begun and is ongoing across multiple tumor types, maintaining marker profiles consistent with primary tumors. Conclusions: POTRL provides an integrated platform for the collection, validation, and model generation of pediatric cancer specimens. These well characterized resources support translational research projects at Penn State and are shared throughout the BCC research centers nationally and internationally to accelerate biomarker discovery, preclinical testing, and precision-oncology studies for pediatric cancers.