Beckwith-Wiedemann syndrome multiomic analysis of hepatoblastoma uncovers unique tumour heterogeneity and cellular landscapes, including transition cells leading to tumour formation

www.nature.com/bjcreports ARTICLE OPEN Beckwith-Wiedemann syndrome multiomic analysis of hepatoblastoma uncovers unique tumour heterogeneity and cellular landscapes, including transition cells leading to tumour formation Snehal Nirgude1,8, Elisia D. Tichy1,8, Yuanchao Zhang2, Khanh B. Trang3, Rose D. Pradieu1, Michael Xie2, Kathrin M. Bernt4,5,6, ✉ Suzanne P. MacFarland4,5,6 and Jennifer M. Kalish1,4,6,7 1234567890();,: © The Author(s) 2026 BACKGROUND: Beckwith-Wiedemann syndrome (BWS) is an overgrowth and cancer predisposition syndrome caused by epigenetic alterations on chromosome 11p15 that predisposes children to multiple cancer types, including hepatoblastoma. Hepatoblastoma is heterogenous in nature, and the 11p15 changes that cause BWS can also be found as a somatic alteration in nonBWS hepatoblastomas, further adding complexity to this disease. METHODS: To understand the impact of the predisposition molecular cues in BWS hepatoblastoma, we interrogated BWS and nonBWS hepatoblastomas, as well as adjacent normal liver, using a multiomic approach [single nuclei RNA-sequencing (snRNA-seq) + single nuclei assay for transposable-accessible chromatin sequencing (snATAC-seq)]. RESULTS: Our approach identified an enrichment of the WNT signaling pathway in BWS hepatoblastoma. Despite similar histology, we found greater tumour heterogeneity and embryonic transcriptional signatures in BWS hepatoblastoma. Furthermore, using pseudotime analysis, we identified a population of transition cells in BWS, with unique molecular profiles, which likely promote the precancer to cancer neoplastic transition in BWS. CONCLUSIONS: This study highlights key signaling pathways, particularly WNT, and identifies a unique population of intermediate/ transition cells that may drive neoplastic transformation in BWS hepatoblastoma. These findings provide new insights into the molecular events leading to cancer in BWS and suggest potential targets for early intervention and prevention strategies. BJC Reports; https://doi.org/10.1038/s44276-026-00215-z INTRODUCTION Hepatoblastoma accounts for 60% of pediatric hepatic malignancies, with an incidence rate of 1.7 cases per million per year [1]. This rate has increased steadily over the past several decades. Hepatoblastoma is typically diagnosed within the first five years of life [2] and is associated with multiple cancer predisposition syndromes, including Beckwith–Wiedemann syndrome (BWS) [3, 4]. In patients with BWS, hepatoblastoma tends to be diagnosed earlier, often before 30 months of age [5]. BWS is an overgrowth syndrome caused by epigenetic and structural alterations on chromosome 11p15 [6]. Allele-specific differential methylation of two imprinting centers (IC1 and IC2) within the 11p15 region regulates the expression of a cluster of growthrelated genes, including Cyclin dependent kinase inhibitor 1C (CDKN1C) and Insulin-like growth factor 2 (IGF2). Specific BWS subtypes are defined by the methylation status of these imprinting centers. However, BWS patients with IC2 loss of methylation (IC2 LOM, reduced CDKN1C expression) or paternal uniparental isodisomy of chromosome 11 (pUPD11, reduced CDKN1C expression and increased IGF2 expression) are more likely to develop hepatoblastoma [6]. Hepatoblastoma is a histologically and molecularly heterogeneous tumour, which is broadly classified into two main categories: epithelial and mixed epithelial–mesenchymal subtypes, according to the International Pediatric Liver Tumours Consensus Classification [7]. Epithelial hepatoblastomas, which constitute more than half of cases [8], include both fetal embryonal and small cell undifferentiated components, each of which is associated with distinct clinical behavior and prognosis [7, 9]. Well-differentiated fetal histology is associated with favorable outcomes, whereas the presence of small cell undifferentiated elements is linked to high-risk disease and reduced survival [9, 10]. Mixed epithelial-mesenchymal tumours exhibit mesenchymal and teratoid features, suggesting a multidirectional trajectory of hepatoblastoma development [11]. 1 Division of Genetic and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 2Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 3Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 4Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. 5Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, USA. 6Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 7Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. 8These authors contributed equally: Snehal Nirgude, Elisia D. Tichy. ✉email: Received: 3 October 2025 Revised: 9 February 2026 Accepted: 17 February 2026 S. Nirgude et al. 2 In current Children’s Oncology Group (COG) and Société Internationale d’Oncologie Pédiatrique - Epithelial Liver Tumour Study Group (SIOPEL) treatment protocols, risk stratification and therapeutic decisions are based on an integrated assessment of histology, serum alpha-fetoprotein (AFP) levels, metastatic status, and radiographic staging using the PRETEXT (PRE-Treatment EXTent of disease) system, with further refinement by annotation factors and POSTTEXT staging following neoadjuvant therapy [9, 12–14]. Although patients with well-differentiated fetal histology and low-risk disease generally have excellent outcomes, long-term survival depends on multiple clinical and surgical factors, including tumour resectability, PRETEXT stage, vascular involvement, margin status, and treatment response; accordingly, some patients still require neoadjuvant or adjuvant chemotherapy despite favorable histology [10, 15–17]. In contrast, tumours with more aggressive histologic features, such as mixed epithelial–mesenchymal subtypes, are typically associated with higher-risk disease and often require intensive multimodal therapy, which can lead to significant short- and long-term toxicities, as illustrated by reported cases of BWS-associated hepatoblastoma [18]. Together, these observations underscore the clinical relevance of hepatoblastoma tumour heterogeneity in predicting outcomes and guiding therapy. While numerous groups have defined hepatoblastoma tumour heterogeneity transcriptomically, using diverse criteria [11, 19–27], BWS-driven hepatoblastoma tumour heterogeneity has never been examined at single-nucleus resolution. At the genomic level, hepatoblastoma is driven by a constellation of molecular alterations, including increased CTNNB1 (βcatenin) expression and/or mutation, 11p15 abnormalities, and other oncogenic drivers [22]. However, the chronological order and functional interdependence of these events remain poorly defined. Pilet et al. [28] provided evide (...truncated)