The landscape of genomic alterations across childhood cancers

Targeting metastasis in paediatric bone sarcomas

Paediatric bone sarcomas (e.g. Ewing sarcoma, osteosarcoma) comprise significant biological and clinical heterogeneity. This extreme heterogeneity affects response to systemic therapy, facilitates inherent and acquired drug resistance and possibly underpins the origins of metastatic disease, a key component implicit in cancer related death. Across all cancers, metastatic models have offered competing accounts on when dissemination occurs, either early or late during tumorigenesis, whether metastases at different foci arise independently and directly from the primary tumour or give rise to each other, i.e. metastases-to-metastases dissemination, and whether cell exchange occurs between synchronously growing lesions. Although it is probable that all the above mechanisms can lead to metastatic disease, clinical observations indicate that distinct modes of metastasis might predominate in different cancers. Around 70% of patients with bone sarcoma experience metastasis during their disease course but the fundamental molecular and cell mechanisms underlying spread are equivocal. Newer therapies such as tyrosine kinase inhibitors have shown promise in reducing metastatic relapse in trials, nonetheless, not all patients respond and 5-year overall survival remains at ~ 50%. Better understanding of potential bone sarcoma biological subgroups, the role of the tumour immune microenvironment, factors that promote metastasis and clinical biomarkers of prognosis and drug response are required to make progress. In this review, we provide a comprehensive overview of the approaches to manage paediatric patients with metastatic Ewing sarcoma and osteosarcoma. We describe the molecular basis of the tumour immune microenvironment, cell plasticity, circulating tumour cells and the development of the pre-metastatic niche, all required for successful distant colonisation. Finally, we discuss ongoing and upcoming patient clinical trials, biomarkers and gene regulatory networks amenable to the development of anti-metastasis medicines.

High resolution clonal architecture of hypomutated Wilms tumours

A paradigm of childhood cancers is that they have a low mutation burden, with some ostensibly bearing fewer mutations than the normal tissues from which they derive. We set out to resolve this paradox by examining paediatric renal cancers with exceptionally few mutations using high resolution, high depth sequencing approaches. We find that apparent hypomutation is the result of unusual clonal architecture due to a normal tissue-like mode of tumour evolution, raising the possibility that the mutation burden of some cancers has been systematically misjudged.

NR2F6 promotes the malignant progression of neuroblastoma as an indicator of poor prognosis

BACKGROUND

NR2F6 is an orphan nuclear receptor with dual tumorigenic activity in the immune system and tumor cells, playing an essential role in tumor differentiation and immunity. This study aimed to investigate the expression level of NR2F6 in various tumors and its effect on neuroblastoma (NB).

METHODS

We evaluated the role of NR2F6 in the genesis and development of 34 different tumors through multiple databases. In addition, we investigated the effects of NR2F6 expression levels on NB risk factors and prognosis using pathology sections and clinical data from primary retroperitoneal NB in children. The effects on cell proliferation, invasion, and migration were explored by knocking down NR2F6 expression in SK-N-BE(2) and SK-N-SH cells.

RESULTS

The findings showed that NR2F6 was significantly correlated with the prognosis of NB and was an important indicator suggesting disease regression. In addition, NR2F6 knockdown slowed down NB cells' proliferation, invasion, and migration ability in vitro.

CONCLUSION

Our results suggest that NR2F6 plays a crucial role in tumor-promoting effects and can be used as a potential prognostic marker for NB.

Influence of genetic biomarkers on cardiac diseases in childhood cancer survivors: a systematic review

Childhood cancer survivors (CCS) often suffer from cardiac disease (CD) after treatment that included anthracycline and radiotherapy involving the heart. However, the variability in CD occurrence cannot be explained solely by these treatments, suggesting the existence of genetic predisposition. We conducted a systematic review searching on Medline-PubMed and Scopus, to identify studies reporting associations between genetic factors and CD in CCS. We included studies published up to 11 April 2023, with no lower limit, and assessed the quality of genetic associations by the Q-genie tool. As a result, 20 studies were included (15 case-control and five cohorts), revealing several genes and variants associated with cardiomyopathy, among which, SLC28A3-rs7853758, RARG-rs2229774, P2RX7-rs208294 and P2RX7-rs3751143 variants gave the most consistent findings. This review highlights the necessity to establish a set of clinically useful genes and variants to identify patients most at risk of developing cardiomyopathy, and to implement monitoring and prevention strategies.

Prediction of neuroblastoma prognosis with a novel T-cell exhaustion-related gene signature

Neuroblastoma (NB) is the most common type of pediatric extra-cranial tumor that arises in the sympathetic nervous system. The heterogeneity of T-cell exhaustion (TEX) has been linked to the determination of distinct clinical outcomes and the effectiveness of immunotherapy in numerous adult malignancies. Therefore, studying the heterogeneous TEX landscape in NB as well as its impact on clinical outcomes is meaningful. The gene expression and clinical datasets of the Sequencing Quality Control (SEQC), E-MTAB-8248, and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) cohorts were downloaded from publicly available databases. Two TEX-related clusters for neuroblastoma were identified in the SEQC cohort. Patients in TEX-C1 exhibited superior overall survival (OS) and event-free survival (EFS) rates compared with those in TEX-C2. And TEX-C1 had more immune cells infiltrating, as well as higher expression of immune checkpoint genes. A total of 1984 genes were differentially expressed between these two clusters, of which 1712 were associated with OS. A gene signature consisting of ten TEX-related genes was developed, and a risk score was computed for each patient. Based on the risk score, SEQC patients were split into high- and low-risk groups with significantly different survival rates. The risk score was an independent risk factor predicting survival and showed superior prediction power for 3, 5, and 10-year survival compared to individual clinical parameters. The signature was further confirmed in the TARGET and E-MTAB-8248 cohorts. This study has successfully constructed a risk score model for NB prognosis, utilizing TEX as its foundation. The model provides risk classification and survival evaluation, which can further guide treatment.

Hepatoblastoma

Hepatoblastoma is the most common primary liver cancer in children, with an incidence of approximately 1.5 cases per million children per year. Most cases are sporadic, typically presenting at a median age of 18 months, with only 5% occurring after 4 years of age. Clinical presentation often includes an abdominal mass and, less commonly, abdominal pain, weight loss, jaundice and precocious puberty. Low birth weight is a significant risk factor, along with genetic conditions such as Beckwith-Wiedemann syndrome, Simpson-Golabi-Behmel syndrome, familial adenomatous polyposis and trisomy 18. Screening protocols for hepatoblastoma are recommended for children with predisposing conditions. Medical imaging is crucial for hepatoblastoma diagnosis and staging, with abdominal ultrasonography being the initial modality of choice, followed by abdominal contrast MRI for detailed evaluation and monitoring. Chest computer tomography is indicated to evaluate potential lung metastases. The Pretreatment Extent of Disease (PRETEXT) system is employed for hepatoblastoma staging and for guiding treatment strategies such as surgical resection and chemotherapy. Patients with advanced hepatoblastoma may require liver transplantation. Advancements in surgery and chemotherapy have improved survival rates, with 5-year survival rates exceeding 80-90% in localized disease. However, challenges remain in treating individuals with high-risk and metastatic hepatoblastoma. Ongoing research into treatment stratification, the introduction of novel therapies, including targeted and immune therapies, and the application of otoprotectants are essential to address refractory or recurrent hepatoblastoma and to increase the overall survival of patients. Long-term quality of life and the management of treatment-related sequelae are becoming increasingly important as survival rates improve.

Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors

The extent of genetic variation and its influence on gene expression across multiple tissue and cellular contexts is still being characterized, with germline Structural Variants (SVs) being historically understudied. DNA methylation also represents a component of normal germline variation across individuals. Here, we combine germline SVs (by short-read sequencing) with tumor DNA methylation across 1292 pediatric brain tumor patients. For thousands of methylation probes for CpG Islands (CGIs) or enhancers, rare and common SV breakpoints upstream or downstream associate with differential methylation in tumors spanning various histologic types, a significant subset involving genes with SV-associated differential expression. Cancer predisposition genes involving SV-associated differential methylation and expression include MSH2, RSPA, and PALB2. SV breakpoints falling within CGIs or histone marks H3K36me3 or H3K9me3 associate with differential CGI methylation. Genes with SVs and CGI methylation associated with patient survival include POLD4. Our results capture a class of normal phenotypic variation having disease implications.

Dissecting the immune landscape in pediatric high-grade glioma reveals cell state changes under therapeutic pressure

Pediatric high-grade gliomas (pHGGs) are among the most lethal childhood tumors. While therapeutic approaches were largely adapted from adult treatment regime, significant biological differences between pediatric and adult gliomas exist, which influence the immune microenvironment and may contribute to the limited response to current pHGG treatment strategies. We provide a comprehensive transcriptomic analysis of the pHGG immune landscape using single-cell RNA sequencing and spatial transcriptomics. We analyze matched malignant, myeloid, and T cells from patients with pediatric diffuse high-grade glioma (HGG) or high-grade ependymoma, examining immune microenvironment distinctions after chemo-/radiotherapy, immune checkpoint inhibition treatment, and by age. Our analysis reveals differences in the proportions of pediatric myeloid subpopulations compared to adult counterparts. Additionally, we observe significant shifts toward immune-suppressive environments following cancer therapy. Our findings offer valuable insights into potential immunotherapy targets and serve as a robust resource for understanding immune microenvironmental variations across HGG age groups and treatment regimens.

Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer

BACKGROUND

Immune checkpoint inhibition (ICI) has revolutionized oncology, offering extended survival and long-term remission in previously incurable cancers. While highly effective in tumors with high mutational burden, lowly mutated cancers, including pediatric malignancies, present low response rate and limited predictive biomarkers.

PATIENTS AND METHODS

We present a framework for the identification and validation of tumor-reactive T cells as a biomarker to quantify ICI efficacy and as candidates for a personalized TCR-T cell therapy. Therefore, we profiled a pediatric malignant rhabdoid tumor patient with complete remission after ICI therapy using deep single-cell T cell receptor (TCR) repertoire sequencing of the tumor microenvironment (TME) and the peripheral blood.

RESULTS

Tracking T cell dynamics longitudinally from the tumor to cells in circulation over a time course of 12 months revealed a systemic response and durable clonal expansion of tumor-resident and ICI-induced TCR clonotypes. We functionally validated tumor reactivity of TCRs identified from the TME and the blood by co-culturing patient-derived tumor cells with TCR-engineered autologous T cells. Here, we observed unexpectedly high frequencies of tumor-reactive TCR clonotypes in the TME and confirmed T cell dynamics in the blood post-ICI to predict tumor-reactivity.

CONCLUSION

These findings strongly support spatio-temporal tracking of T cell activity in response to ICI to inform therapy efficacy and to serve as a source of tumor-reactive TCRs for personalized TCR-T designs.

Comparative analysis of RNA expression identifies effective targeted drug in myoepithelial carcinoma

Myoepithelial carcinoma is an ultra-rare pediatric solid tumor with no targeted treatments. Clinical implementation of tumor RNA sequencing (RNA-Seq) for identifying therapeutic targets is underexplored in pediatric cancer. We previously published the Comparative Analysis of RNA Expression (CARE), a framework for incorporating RNA-Seq-derived gene expression into the clinic for difficult-to-treat pediatric cancers. Here, we discuss a 4-year-old male diagnosed with myoepithelial carcinoma who was treated at Stanford Medicine Children's Health. A metastatic lung nodule from the patient underwent standard-of-care tumor DNA profiling and CARE analysis, wherein the patient's tumor RNA-Seq profile was compared to over 11,000 uniformly analyzed tumor profiles from public data repositories. DNA profiling yielded no actionable mutations. CARE identified overexpression biomarkers and nominated a treatment that produced a durable clinical response. These findings underscore the utility of data sharing and concurrent analysis of large genomic datasets for clinical benefit, particularly for rare cancers with unknown biological drivers.

Frequency and Clinical Significance of Clonal and Subclonal Driver Mutations in High-Risk Neuroblastoma at Diagnosis: A Children's Oncology Group Study

PURPOSE

Relapsed high-risk neuroblastomas (NBLs) are enriched for targetable mutations in ALK and RAS-MAPK pathways, yet the prognostic effect of these aberrations and relevance of subclonal mutations at diagnosis remain undefined. We describe the spectrum and clinical significance of clonal and subclonal pathogenic alterations in high-risk NBL.

METHODS

We developed a focused high-risk NBL sequencing panel including ALK, NRAS, KRAS, HRAS, BRAF, PTPN11, TP53, and ATRX genes for ultra-deep sequencing and applied this assay to 242 pretherapy tumors from patients enrolled on the phase III trial Children's Oncology Group ANBL0532. We assessed the effect of clonal and subclonal mutations on event-free survival (EFS) and overall survival (OS).

RESULTS

ALK-activating mutations occurred in 21.5% of tumors (n = 52, 30 clonal, 22 subclonal), and 3.3% (n = 8) showed ALK amplification. EFS and OS for patients with any ALK-aberrant tumor were inferior to patients with wild-type (WT) ALK tumors (5-year OS 37.7% v 66.3%; hazard ratio [HR], 1.992; P = .0007). EFS and OS for patients with tumors harboring activating ALK mutations ≥5% variant allele frequency (VAF) were inferior to ALK WT (5-year OS 37.7% v 66.3%; HR, 1.966; P = .0041). The 5-year EFS and OS for patients with ALK-amplified tumors were 25.0%. RAS pathway mutations occurred in 7.9% of tumors (n = 19; four clonal, 15 subclonal), with EFS and OS for those with VAF ≥5% inferior to RAS-WT patients (5-year OS 19.1% v 60.0%; HR, 3.021; P = .0168).

CONCLUSION

Ultra-deep sequencing of high-risk NBLs demonstrates that oncogenic aberrations are more prevalent at diagnosis than previously recognized. ALK and RAS pathway aberrations confer inferior outcomes in patients treated with contemporary therapy, emphasizing the need for novel therapeutic approaches.

Targeting Hyperactive Ras Signaling in Pediatric Cancer

Somatic RAS mutations are among the most frequent drivers in pediatric and adult cancers. Somatic KRAS, NRAS, and HRAS mutations exhibit distinct tissue-specific predilections. Germline NF1 and RAS mutations in children with neurofibromatosis type 1 and other RASopathy developmental disorders have provided new insights into Ras biology. In many cases, these germline mutations are associated with increased cancer risk. Promising targeted therapeutic strategies for pediatric cancers and neoplasms with NF1 or RAS mutations include inhibition of downstream Ras effector pathways, directly inhibiting the signal output of oncogenic Ras proteins and associated pathway members, and therapeutically targeting Ras posttranslational modifications and intracellular trafficking. Acquired drug resistance to targeted drugs remains a significant challenge but, increasingly, rational drug combination approaches have shown promise in overcoming resistance. Developing predictive preclinical models of childhood cancers for drug testing is a high priority for the field of pediatric oncology.

Gain of chromosome 17 is an early genetic abnormality in neuroblastoma with PPM1D emerging as a strong candidate oncogene driving tumor progression

Segmental gain of chromosome 17q is the most common genetic aberration in high-risk neuroblastoma, but its role in disease progression is poorly understood. This study aims to address the contribution of 17q gain to neuroblastoma malignancy. We analyzed the genetic and transcriptional landscape of 417 neuroblastoma patients across various risk groups and clinical stages using multi-omic approaches. Single-cell RNA/DNA sequencing and SNP arrays were combined to characterize genomic aberrations, while evolutionary trajectories were mapped to explore the accumulation of genetic changes in patients with neuroblastoma. Additionally, DNA and RNA sequencing were used to assess mutational burden and gene expression patterns. Our findings suggest that chromosome 17 gain is an early genetic event acquired during neuroblastoma development, correlating with the accumulation of additional chromosomal aberrations and poor prognosis. Increased segmental gains of chromosome 17q were observed during clonal evolution, relapse disease and metastasis. We identified PPM1D, a p53-inducible Ser/Thr phosphatase located on chr17q22.3, as a key player activated by segmental 17q-gain, gene-fusion, or gain-of-function somatic and germline mutations, further promoting neuroblastoma development/progression. Gain of chromosome 17 is an early driver of genetic instability in neuroblastoma, with PPM1D emerging as a potential candidate gene implicated in high-risk disease progression.

Gas1-Mediated Suppression of Hepatoblastoma Tumorigenesis

Hepatoblastoma (HB), the most common pediatric liver cancer, is associated with dysregulated Wnt/β-catenin, Hippo, and/or nuclear factor erythroid 2 ligand 2/nuclear respiratory factor 2 (NFE2L2/NRF2) pathways. In mice, pairwise combinations of oncogenically active forms of the terminal transcription factors of these pathways, namely, β-catenin (B), Yes-associated protein (YAP; Y), and Nrf2 (N), generate HBs, with the triple combination (B + Y + N) being particularly potent. Each tumor group alters the expression of thousands of B-, Y-, and N-driven unique and common target genes. The identification of those most involved in transformation might reveal mechanisms and opportunities for therapy. Herein, transcription profiling of >60 murine HBs revealed a common set of 22 "BYN" genes similarly deregulated in all cases. Most were associated with multiple cancer hallmarks, and their expression often correlated with survival in HBs, hepatocellular carcinomas, and other cancers. Among the most down-regulated of these genes was Gas1, which encodes a glycosylphosphatidylinositol-linked outer membrane protein. The restoration of Gas1 expression impaired B + Y + N-driven HB tumor growth in vivo and in HB-derived immortalized BY and BYN cell lines in vitro in a manner that requires membrane anchoring of the protein via its glycosylphosphatidylinositol moiety, implicating Gas1 as a proximal mediator of HB pathogenesis and validating the BYN gene set as deserving of additional scrutiny in future studies.

Synchronous bilateral Wilms tumors are prone to develop independently and respond differently to preoperative chemotherapy

Wilms tumor (WT) is the most common kidney cancer in infants and young children. The determination of the clonality of bilateral WTs is critical to the treatment, because lineage-independent and metastatic tumors may require different treatment strategies. Here we found synchronous bilateral WT (n = 24 tumors from 12 patients) responded differently to preoperative chemotherapy. Transcriptome, whole-exome and whole-genome analysis (n = 12 tumors from 6 patients) demonstrated that each side of bilateral WT was clonally independent in terms of somatic driver mutations, copy number variations and transcriptomic profile. Molecular timing analysis revealed distinct timing and patterns of chromosomal evolution and mutational processes between the two sides of WT. Mutations in WT1, CTNNB1 and copy-neutral loss of heterozygosity of 11p15.5 provide possible genetic predisposition for the early initiation of bilateral WT. Our results provide comprehensive evidence and new insights regarding the separate initiation and early embryonic development of bilateral WT, which may benefit clinical practices in treating metastatic or refractory bilateral WT.

Integrated multi-omics characterization of neuroblastoma with bone or bone marrow metastasis

The pathogenesis of neuroblastoma with bone or bone marrow metastasis (NB-BBM) and its complex immune microenvironment remain poorly elucidated, hampering the advancement of effective risk prediction for BBM and limiting therapeutic strategies. Feature recognition of 142 paraffin-embedded hematoxylin-eosin-stained tumor section images was conducted using a Swin-Transformer for pathological histology to predict NB-BBM occurrence. Single-cell transcriptomics identified a tumor cell subpopulation (NB3) and two tumor-associated macrophage (TAM) subpopulations (SPP1+ TAMs and IGHM+ TAMs) closely associated with BBM and highlighted transketolase (TKT) as a key molecular marker for metastatic progression in NB. This extensive multi-omics investigation into NB-BBM enhances our understanding of single-cell transcriptional dynamics in NB beyond existing research, outlining the evolution from in situ carcinoma through tumorigenesis to bone marrow metastases. Furthermore, exploration of the immune microenvironment identified specific subpopulations of TAMs crucial in promoting NB-BBM, presenting new avenues for immunotherapy. These insights enhance our understanding of the metastatic process from NB to BBM and facilitate the development of more effective diagnostic and therapeutic strategies for this aggressive pediatric cancer.

Ubiquitination in lipid metabolism reprogramming: implications for pediatric solid tumors

Pediatric solid tumors represent a significant subset of childhood cancers, accounting for approximately 60% of new diagnoses. Despite advancements in therapeutic strategies, survival rates remain markedly disparate between high-income and resource-limited settings, underscoring the urgent need for novel and effective treatments. Lipid metabolic reprogramming is a fundamental hallmark of cancer, driving tumor progression, therapeutic resistance, and immune evasion through enhanced fatty acid uptake, increased de novo lipid synthesis, and activated fatty acid β-oxidation (FAO). Ubiquitination, a dynamic post-translational modification mediated by the ubiquitin-proteasome system (UPS), plays a crucial role in regulating lipid metabolism by modulating the stability and activity of key metabolic enzymes and transporters involved in cholesterol and fatty acid pathways. This review comprehensively examines the complex interplay between ubiquitination and lipid metabolic reprogramming in pediatric solid tumors. It delineates the mechanisms by which ubiquitination influences cholesterol biosynthesis, uptake, efflux, and fatty acid synthesis and oxidation, thereby facilitating tumor growth and survival. Furthermore, the review identifies potential UPS-mediated therapeutic targets and explores the feasibility of integrating ubiquitination-based strategies with existing treatments. By targeting the UPS to disrupt lipid metabolism pathways, novel therapeutic avenues may emerge to enhance treatment efficacy and overcome resistance in pediatric oncology. This synthesis of current knowledge aims to provide a foundation for the development of innovative, precision medicine approaches to improve clinical outcomes for children afflicted with solid tumors.

DNA methylation-driven genes in hepatocellular carcinoma patients: insights into immune infiltration and prognostic implications

Background

Hepatocellular carcinoma (HCC) poses a significant global burden as a highly prevalent and life-threatening malignant tumor that endangers human life and wellbeing. The purpose of this study was to examine how DNA methylation-driven genes impact the prognosis of HCC patients.

Methods

Differentially expressed genes from The Cancer Genome Atlas, GSE76427, GSE25097 and GSE14520 datasets were collected to perform differential expression analysis between HCC patients and controls. Weighted gene coexpression network analysis (WGCNA) was subsequently performed to create coexpression modules for the DEGs. Then, ssGSEA was employed to investigate the infiltration of immune cells in HCC. Enrichment analysis and methylation were carried out for the module genes. We utilized Kaplan-Meier survival analysis to assess patient prognosis.

Results

Eight coexpression modules were identified via WGCNA for 1927 upregulated and 1,231 downregulated DEGs, after which the hub genes of the modules were identified. Module 5 had high immune infiltration, and the hub gene SCAMP3 was positively associated with Tcm. Module 3 exhibited a low level of immune infiltration, and the expression of the hub gene HCLS1 was negatively correlated with T cells and dendritic cells. Furthermore, we obtained five hub genes (BOP1, BUB1B, NOTCH3, SCAMP3, and SNRPD2) as methylation-driven genes. BOP1 and BUB1B were found to be correlated with unfavorable overall survival in patients with HCC.

Conclusion

HCLS1 and SCAMP3 are associated with immunity, whereas BOP1 and BUB1B are modified by methylation and may serve as prognostic markers for HCC.

Functional screening identifies kinesin spindle protein inhibitor filanesib as a potential treatment option for hepatoblastoma

Hepatoblastoma is a rare pediatric liver malignancy usually treated with surgery and chemotherapy. To explore new treatment options for hepatoblastoma, drug screening was performed using six cell models established from aggressive hepatoblastoma tumors and healthy pediatric primary hepatocytes. Of the 527 screened compounds, 98 demonstrated cancer-selective activity in at least one hepatoblastoma model. The kinesin spindle protein (KSP) inhibitor filanesib was effective in all models and was further evaluated. Filanesib induced G2/M arrest and apoptosis in hepatoblastoma cells at concentrations tolerable to primary hepatocytes. Prominent nuclear fragmentation was observed in filanesib-treated hepatoblastoma cells. Genes participating in cell cycle regulation were noted to be differentially expressed after filanesib treatment. Filanesib reduced the rate of tumor growth in 4/5 hepatoblastoma mice models. One of these models showed complete growth arrest. Our results suggest that filanesib is a potential candidate for hepatoblastoma treatment and should be investigated in future clinical trials.

DNA damage response deficiency enhances neuroblastoma progression and sensitivity to combination PARP and ATR inhibition

Sequencing of neuroblastoma (NB) tumors has revealed genetic alterations in genes involved in DNA damage response (DDR) pathways. However, roles for specific alterations of DDR genes in pediatric solid tumors remain poorly understood. To address this, mutations in the DDR pathway including Brca2, Atm, and Palb2 were incorporated into an established zebrafish MYCN transgenic model (Tg(dbh:EGFP-MYCN)). These mutations enhance NB formation and metastasis and result in upregulation of cell-cycle checkpoint and DNA damage repair signatures, revealing molecular vulnerabilities in DDR-deficient NB. DDR gene knockdown in zebrafish and human NB cells increases sensitivity to the poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, and this effect is enhanced by inhibition of the ataxia telangiectasia and rad3-related (ATR) kinase. This work provides in vivo evidence demonstrating that alterations in certain DDR-pathway genes promote aggressive NB and supports combination PARP + ATR inhibitor therapy for NB patients with tumors harboring specific genetic alterations in DDR.

Targeted inhibition of WIP1 and histone H3K27 demethylase activity synergistically suppresses neuroblastoma growth

High-risk neuroblastoma frequently exhibits segmental gain of chromosome 17q, including the locus of PPM1D, which encodes the phosphatase WIP1, a regulator of p53 activity, DNA repair, and apoptosis. High expression of PPM1D is correlated to poor prognosis, and genetic or pharmacologic inhibition of WIP1 suppresses neuroblastoma growth. Here, we show that combining drugs that target WIP1 and H3K27 demethylation induces synergistic cytotoxicity in neuroblastoma. We screened 527 different compounds together with inhibitors of WIP1 and identified a strong cytotoxic synergism between the WIP1 inhibitor SL-176 and GSK-J4, a specific inhibitor of the H3K27 demethylase JMJD3. Viability assays in neuroblastoma cell lines and treatment of tumor spheroids confirmed the synergistic effect of combining SL-176 with GSK-J4. Immunoblot experiments demonstrated a marked effect on WIP1 downstream targets and apoptosis markers, while qPCR showed a synergistic upregulation of p53 downstream targets PUMA and p21. RNA sequencing revealed a vast number of differentially expressed genes, suggesting a pervasive effect of this drug combination on transcription, with enrichment of pathways involved in DNA damage response. Finally, this drug combination was confirmed to reduce tumor growth in zebrafish xenograft experiments. In conclusion, the combination of the WIP1 inhibitor SL-176 and the epigenetic modifier GSK-J4 induces synergistic cytotoxicity in neuroblastoma cells by potentiating p53 downstream effects.

Association of phosphorylation status of ERK and genetic MAPK alterations in pediatric tumors

The mitogen-activated protein kinase (MAPK) pathway is one of the most frequently altered pathways in pediatric cancer. Activating genomic MAPK-alterations and phosphorylation of the MAPK downstream target ERK (pERK) were analyzed in the PTT2.0 registry to identify potential targets for MAPK-directed treatment in relapsed pediatric CNS tumors, sarcomas and other solid tumors. The present study investigates the association of ERK phosphorylation and genomic MAPK pathway alterations (mutations, fusions, amplifications) in the PTT2.0 dataset. PTT2.0 registry cases with available genomic and immunohistochemistry data (n = 235) were included. Samples with and without detected activating genomic MAPK alterations were compared regarding ERK phosphorylation, quantified by immunohistochemistry H-score. The association of pERK intensity and the presence of MAPK alteration was analyzed using a univariable binary logistic regression model.The mean pERK H-score was significantly higher in samples with activating genomic MAPK alterations. pERK H-score positively correlated with the presence of MAPK alterations. However, the pERK H-score predicted MAPK alterations only with a sensitivity of 58.3% and a specificity of 83.8%. The highest mean pERK H-scores were observed in low-grade gliomas, enriched for MAPK alterations, and in ependymoma, where MAPK alterations were absent. Although there is an association between pERK level and activating genetic MAPK alterations, the predictive power of pERK H-score for genetic MAPK alterations is low in pediatric tumors. Tumors/groups with absent genetic MAPK alterations but high pERK indicate a dissociation of the two parameters, as well as a possible MAPK pathway activation in the absence of genetic MAPK alterations.

Identification and verification of international neuroblastoma staging system (INSS) stage-related genes as potential biomarkers for neuroblastoma prognostic models

Background

Neuroblastoma (NB), one of the most common malignant extracranial solid tumors in children, is highly invasive and lethal with limited treatment efficacy. This study aimed to establish a prognostic model of advanced-stage NB.

Methods

Differentially expressed genes were screened and validated using two training datasets and one validation dataset from the Therapeutically Applicable Research to Generate Effective Treatments and Gene Expression Omnibus databases. Protein-protein interaction networks were developed using the MCode plug-in, and the top three key clusters were used to produce candidate genes. We performed gene set enrichment analysis (GSEA), gene ontology analysis (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, immune cell infiltration, and drug sensitivity analysis to further understand the functions of these candidate genes. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were used to check their prognosis value. Real-time quantitative polymerase chain reaction (qPCR), Western blot (WB), and immunohistochemistry (IHC) were employed to verify the mRNA and protein levels in clinical samples.

Results

A total of 699 differentially expressed genes were identified, including 294 upregulated and 405 downregulated genes. CNR1, PRKACB, CDKN3, and PCLAF were found to significantly affect the overall survival and event-free survival of neuroblastoma patients and were positively correlated with the INSS advanced stages. The functional analysis of these four genes revealed their cancer-promoting effects and correlations with immune-inflammatory, cell cycle, and p53 signaling pathways. After stratifying patients using the established model containing the above four genes, significantly different patterns were observed in terms of infiltrating immune cell proportion, drug sensitivity, and the expression of immune checkpoints. Finally, both the mRNA and protein expression verification assays demonstrated that the CDKN3 and PCLAF were upregulated, while the PRKACB was downregulated in advanced-stage neuroblastoma tissue samples.

Conclusion

The model containing CNR1, PRKACB, CDKN3, and PCLAF can serve as a new prognostic biomarker for predicting the prognosis of patients with neuroblastoma. Findings on immune cell infiltration and immune checkpoints provide novel insights for the immunotherapy of neuroblastoma.

LOXHD1 is an oncofusion-regulated antigen of ewing sarcoma

Ewing Sarcoma (EwS) is a rare pediatric malignancy characterized by a unique t(11:22) (q24;q12) translocation resulting in the pathognomonic EWSR1::FLI1 fusion. Recent reports indicate that the EWSR1::FLI1 oncofusion drives aberrant expression of numerous transcripts, including Lipoxygenase Homology Domains 1 (LOXHD1). Given its highly restricted protein expression pattern and role in EwS tumorigenesis and metastasis, LOXHD1 may serve as a novel immunotherapeutic target in this malignancy. LOXHD1 immunogenic epitopes restricted to HLA-A*02:01 allowed for the isolation of a high avidity αβTCR. LOXHD1-specific TCR engineered CD8+ T cells conferred cytotoxic activity against a panel of HLA-A*02:01+ EwS tumor cell lines and adoptive transfer led to tumor eradication in a mouse xenograft model of EwS. This study nominates LOXHD1 as an oncofusion regulated, non-mutated tumor associated antigen (TAA) with expression limited to inner hair cells of the cochlea, adult testis, and EwS.

H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability

The oncomutation lysine 27-to-methionine in histone H3 (H3K27M) is frequently identified in tumors of patients with diffuse midline glioma-H3K27 altered (DMG-H3K27a). H3K27M inhibits the deposition of the histone mark H3K27me3, which affects the maintenance of transcriptional programs and cell identity. Cells expressing H3K27M are also characterized by defects in genome integrity, but the mechanisms linking expression of the oncohistone to DNA damage remain mostly unknown. In this study, we demonstrate that expression of H3.1K27M in the model plant Arabidopsis thaliana interferes with post-replicative chromatin maturation mediated by the H3.1K27 methyltransferases ATXR5 and ATXR6. As a result, H3.1 variants on nascent chromatin remain unmethylated at K27 (H3.1K27me0), leading to ectopic activity of TONSOKU (TSK/TONSL), which induces DNA damage and genomic alterations. Elimination of TSK activity suppresses the genome stability defects associated with H3.1K27M expression, while inactivation of specific DNA repair pathways prevents survival of H3.1K27M-expressing plants. Overall, our results suggest that H3.1K27M disrupts the chromatin-based mechanisms regulating TSK activity, which causes genomic instability and may contribute to the etiology of DMG-H3K27a.

LGALS3BP antibody-drug conjugate enhances tumor-infiltrating lymphocytes and synergizes with immunotherapy to restrain neuroblastoma growth

BACKGROUND

LGALS3BP, also referred as Gal-3BP, Mac2-BP, or 90 K, is a heavily glycosylated, secreted protein prominently localized at the surface of cancer-derived extracellular vesicles (EVs). Its levels are significantly elevated in various types of cancer, including neuroblastoma, and are generally associated with advanced disease and tumor progression. Our previous research has shown that LGALS3BP is an effective target for ravtansine (DM4)-based Antibody-Drug Conjugate (ADC) therapy in multiple preclinical models.

METHODS

We assessed total and extracellular vesicles (EVs)-associated LGALS3BP through ELISA assay in serum of a pseudometastatic neuroblastoma model to evaluate the correlation of LGALS3BP levels with tumor dissemination. We employed a syngeneic neuroblastoma mouse model using murine neuroblastoma NXS2 cells overexpressing human LGALS3BP in order to evaluate immunogenic cell death (ICD) induced by anti-LGALS3BP ADC therapy and investigated the nature of the tumor immune infiltrate by cytofluorimetry. Furthermore, we designed a six-arm in vivo experiment to evaluate the efficacy of ADC in combination with an immune check-point inhibitor (ICI) anti-PD-1. Finally, a rechallenge assay was conducted on cured mice to assess the presence of immunological memory.

RESULTS

Here, we report that circulating and EVs-associated LGALS3BP levels significantly correlate with neuroblastoma progression and dissemination. Moreover, we show that in the syngeneic NXS2 neuroblastoma model, DM4 treatment induces cell surface expression of ICD markers calreticulin, HSP70, and HSP90, and an increased PD-L1 expression in vitro, followed by enhanced tumor-infiltrating lymphocytes in vivo. Notably, the combination therapy of anti-LGALS3BP-targeting ADC with anti-PD-1 results in a higher inhibition of tumor growth and prolonged survival compared with either agent given alone. Rechallenge assay reveals that mice previously treated and cured with the ADC retain immune memory, suggesting the therapy's ability to induce a durable and protective antitumor immune response.

CONCLUSIONS

Our findings establish that circulating LGALS3BP is a potential biomarker for liquid biopsy and uncover this protein as a suitable target for therapeutic strategies combining 1959-sss/DM4 ADC with an anti-PD-1 ICI for the treatment of LGALS3BP expressing neuroblastoma.

Multimodal cell maps as a foundation for structural and functional genomics

Human cells consist of a complex hierarchy of components, many of which remain unexplored1,2. Here we construct a global map of human subcellular architecture through joint measurement of biophysical interactions and immunofluorescence images for over 5,100 proteins in U2OS osteosarcoma cells. Self-supervised multimodal data integration resolves 275 molecular assemblies spanning the range of 10-8 to 10-5 m, which we validate systematically using whole-cell size-exclusion chromatography and annotate using large language models3. We explore key applications in structural biology, yielding structures for 111 heterodimeric complexes and an expanded Rag-Ragulator assembly. The map assigns unexpected functions to 975 proteins, including roles for C18orf21 in RNA processing and DPP9 in interferon signalling, and identifies assemblies with multiple localizations or cell type specificity. It decodes paediatric cancer genomes4, identifying 21 recurrently mutated assemblies and implicating 102 validated new cancer proteins. The associated Cell Visualization Portal and Mapping Toolkit provide a reference platform for structural and functional cell biology.

Progressive chromatin rewiring by ETO2::GLIS2 revealed in a genome-edited human iPSC model of pediatric leukemia initiation

ABSTRACT

Pediatric acute myeloid leukemia frequently harbors fusion oncogenes associated with poor prognosis, including KMT2A, NUP98, and GLIS2 rearrangements. Although murine models have demonstrated their leukemogenic activities, the steps from a normal human cell to leukemic blasts remain unclear. Here, we precisely reproduced the inversion of chromosome 16 resulting in the ETO2::GLIS2 fusion in human induced pluripotent stem cells (iPSCs). iPSC-derived ETO2::GLIS2-expressing hematopoietic cells showed differentiation alterations in vitro and efficiently induced in vivo development of leukemia that closely phenocopied human acute megakaryoblastic leukemia (AMKL), reflected by flow cytometry and single-cell transcriptomes. Comparison of iPS-derived cells with patient-derived cells revealed altered chromatin accessibility at early and later bona fide leukemia stages, with aberrantly higher accessibility and expression of the osteogenic homeobox factor DLX3 that preceded increased accessibility to ETS factors. DLX3 overexpression in normal CD34+ cells increased accessibility to ETS motifs and reduced accessibility to GATA motifs. A DLX3 transcriptional module was globally enriched in both ETO2::GLIS2 AMKL and some aggressive pediatric osteosarcoma. Importantly, DLX3 knockout abrogated leukemia initiation in this ETO2::GLIS2 iPSC model. Collectively, the characterization of a novel human iPSC-derived AMKL model revealed that hijacking of the osteogenic homeobox transcription factor DLX3 is an essential early step in chromatin changes and leukemogenesis driven by the ETO2::GLIS2 fusion oncogene.

Machine learning-predicted chromatin organization landscape across pediatric tumors

Structural variants (SVs) are increasingly recognized as important contributors to oncogenesis through their effects on 3D genome folding. Recent advances in whole-genome sequencing have enabled large-scale profiling of SVs across diverse tumors, yet experimental characterization of their individual impact on genome folding remains infeasible. Here, we leveraged a convolutional neural network, Akita, to predict disruptions in genome folding caused by somatic SVs identified in 61 tumor types from the Children's Brain Tumor Network dataset. Our analysis reveals significant variability in SV-induced disruptions across tumor types, with the most disruptive SVs coming from lymphomas and sarcomas, metastatic tumors, and germline cell tumors. Dimensionality reduction of disruption scores identified five recurrently disrupted regions enriched for high-impact SVs across multiple tumors. Some of these regions are highly disrupted despite not being highly mutated, and harbor tumor-associated genes and transcriptional regulators. To further interpret the functional relevance of high-scoring SVs, we integrated epigenetic data and developed a modified Activity-by-Contact scoring approach to prioritize SVs with disrupted genome contacts at active enhancers. This method highlighted highly disruptive SVs near key oncogenes, as well as novel candidate loci potentially implicated in tumorigenesis. These findings highlight the utility of machine learning for identifying novel SVs, loci, and genetic mechanisms contributing to pediatric cancers. This framework provides a foundation for future studies linking SV-driven regulatory changes to cancer pathogenesis.

Stratified Medicine Pediatrics: Cell-Free DNA and Serial Tumor Sequencing Identifies Subtype-Specific Cancer Evolution and Epigenetic States

SIGNIFICANCE

In tumors of childhood, we identify mutations in epigenetic genes as drivers of relapse, with matched cfDNA sequencing showing significant intratumor genetic heterogeneity and cell-state specific patterns of chromatin accessibility. This highlights the power of cfDNA analysis to identify both genetic and epigenetic drivers of aggressive disease in pediatric cancers.

Oncohistone-sculpted epigenetic mechanisms in pediatric brain cancer

Chromatin dynamics, involving reversible changes in chromatin structure, shape key cellular processes and genomic integrity during development and proliferation, with disruptions leading to cancer. Histones, core components of chromatin and substrates for chromatin-modifying enzymes, play crucial roles in oncogenesis when misregulated or mutated. This is particularly pronounced in pediatric hind brain cancers, some of which are driven primarily by the oncohistone H3K27M and the recently identified oncohistone-mimic protein CXorf67/EZHIP. Notably, H3K27M and EZHIP-driven cancers exhibit low mutation burdens, highlighting the enigmatic role of non-mutational epigenetic reprogramming in oncogenesis beyond traditional paradigms of oncogene activation and tumor suppressor loss. Here, we review the impact of H3K27M and EZHIP-driven cancer mechanisms on chromatin and transcriptional dysregulation leading to aberrant cell fate determination, and their potential influence beyond gene activity, affecting broader cellular pathways. Illuminating these mechanisms is crucial for advancing treatment options for pediatric brain cancers, where therapeutic regimens are poorly defined.

Environmental health disparities in pediatric cancer: a report from the Fourth Symposium on Childhood Cancer Health Disparities

The 4th Symposium on Childhood Cancer Health Disparities was held at Texas Children's Hospital in Houston, Texas, on September 26, 2023. The symposium registered 94 attendees from different backgrounds (e.g. clinicians, epidemiologists, exposure assessment scientists, geospatial experts) with an interest in environmental health disparities of pediatric cancer susceptibility and treatment outcomes. The focus of the symposium was to provide an overview of the role of environmental risk factors in studies of pediatric cancer, introduce novel exposure assessment tools that can be applied to the field, and highlight opportunities to study the impact of environmental health disparities in pediatric cancer susceptibility and outcomes. This report summarizes the scientific content of the symposium and highlights priorities to advance the field.

Childhood, adolescent, and young adulthood cancer risk in BRCA1 or BRCA2 pathogenic variant carriers

BACKGROUND

Whether carriers of BRCA1 or BRCA2 pathogenic variants have increased risks of childhood, adolescent, and young adult cancers is controversial. We aimed to evaluate this risk and to inform clinical care of young BRCA1 and BRCA2 pathogenic variant carriers and genetic testing for childhood, adolescent, and young adult cancer patients.

METHODS

Using data from 47 117 individuals from 3086 BRCA1 or BRCA2 families, we conducted pedigree analysis to estimate relative risks (RRs) for cancers diagnosed before age 30 years.

RESULTS

Our data included 274 cancers diagnosed before age 30 years: 139 breast cancers, 10 ovarian cancers, and 125 nonbreast nonovarian cancers. Associations for breast cancer in young adulthood (aged 20-29 years) were found with relative risks of 11.4 (95% confidence interval [CI] = 5.5 to 23.7) and 5.2 (95% CI = 1.6 to 17.7) for BRCA1 and BRCA2 pathogenic variant carriers, respectively. No association was found for any other investigated childhood, adolescent, and young adult cancer or for all nonbreast nonovarian cancers combined; the relative risks were 0.4 (95% CI = 0.1 to 1.4) and 1.4 (95% CI = 0.7 to 3.0) in BRCA1 and BRCA2 pathogenic variant carriers, respectively.

CONCLUSION

We found no evidence that BRCA1 and BRCA2 pathogenic variant carriers have an increased childhood, adolescent, and young adult cancer risk aside from breast cancer in women aged between 20 and 30 years. Our results, along with a critical evaluation of previous germline sequencing studies, suggest that the childhood and adolescent cancer risk conferred by BRCA1 and BRCA2 pathogenic variant would be low (ie, RR < 2) if it existed. Our findings do not support pathogenic variant testing for offspring of BRCA1 and BRCA2 pathogenic variant carriers at ages younger than 18 years or for conducting BRCA1 and BRCA2 pathogenic variant testing for childhood and adolescent cancer patients.

Narrative review on ethical and psychological issues raised by genetic and genomic testing in pediatric oncology care

In pediatric oncology, genetic and genomic tests are proposed throughout the care pathway for many reasons (e.g., cancer characterization, identification of the most appropriate treatment, patient selection for clinical trials, identification of tissue/organ donors, or risk of relapse prediction). Despite the many different approaches (somatic or germline testing, targeted gene or genome sequencing), the implicated individuals are confronted with situations that may intersect and that are interesting to compare. No study has identified and analyzed the available works on these new practices in pediatric oncology. The aim of this narrative literature review was to describe the ethical and psychological perspectives of children with cancer, parents, and healthcare professionals when genetic or genomic testing is proposed as part of the cancer management. Eighteen articles met the inclusion criteria and were comprehensively coded using MAXQDA. Their analysis showed that concerning the subjective implications of genetic and genomic testing, the areas of ambivalence (desire of treatment, desire for knowledge, uncertainty, and guilt) reported by patients and their parents seem to mirror the healthcare professionals' concerns. The ethical and psychological issues about predisposition testing, long discussed in the context of hereditary retinoblastoma and Li-Fraumeni syndrome, represent a useful starting point for a wider discussion of a genetic and genomic testing pathway in pediatric oncology more broadly.

New models for the development of and access to CAR T-cell therapies for children and adolescents with cancer: an ACCELERATE multistakeholder analysis

Realising the potentially substantial benefits of chimeric antigen receptor (CAR) T-cell therapy for children with cancer is hindered by non-scientific barriers that are also relevant for other rare diseases. A solely commercial development model will not deliver optimally due to insufficient return on investment for pharmaceutical companies. Access to therapies is restricted for patients who might benefit and advancing innovation in the academic research setting is difficult. Challenges relating to CAR T-cell therapies in paediatric malignancies and how they might be addressed were discussed in a meeting convened by ACCELERATE-an international multistakeholder organisation aiming to advance the timely investigation of new anticancer drugs. New academic and biopharma hybrid development models could benefit rare populations and coordination of early development can promote synergy and avoid duplicative efforts. Following promising first-in-child trials, new models are needed to support pivotal trials, decentralised manufacturing, registration, and reduced costs. The European Medicines Agency and the US Food and Drug Administration encourage academic development and early discussions. A biotech company funded via a pooled investment vehicle could provide access to safe and effective products for children and adolescents with cancer through registration and reimbursement.

Advances in Hodgkin lymphoma research

Hodgkin lymphoma (HL) has been and still is the most enigmatic lymphoid malignancy in humans. Since the first molecular analysis of isolated Hodgkin and Reed-Sternberg (HRS) tumor cells of classic HL 30 years ago, substantial advances in our understanding of HL have been made. This review describes the cellular origin of HL, summarizes the current knowledge about the genetic lesions in HRS cells, and highlights the role of Epstein-Barr virus (EBV) in HL pathogenesis. Moreover, the pathobiological roles of altered gene expression and deregulated signaling pathways are discussed and key aspects of the HL microenvironment are presented.

Risk of carcinomas among children and adolescents with birth defects

BACKGROUND

Birth defects are associated with childhood cancer, but little is known regarding pediatric carcinomas, a group of especially rare tumors.

METHODS

We used Cox proportional hazards regression to estimate the hazard ratio (HR) and 95 % confidence interval (CI) for any carcinoma, as well as thyroid, hepatocellular, and renal carcinoma specifically, up to 18 years of age among children with major, non-syndromic anomalies or chromosomal/genetic syndromes, relative to unaffected children.

RESULTS

Our registry-linkage study included nine states and 21,933,476 children between 1990 and 2018: 641,827 with non-syndromic anomalies, and 49,619 with syndromes. Carcinomas were diagnosed in 833 children, including 35 with non-syndromic anomalies and eight with syndromes. The hazard of carcinoma was increased both among children with non-syndromic anomalies (HR: 1.7, CI: 1.2-2.4; N = 35) and syndromes (HR: 4.7, CI: 2.3-9.5; N = 7). Hepatocellular carcinoma was associated with non-syndromic anomalies (HR: 4.6, CI: 2.2-9.7; N = 8) and syndromes (HR: 8.0, CI: 1.1-58.1; N < 5). The hazard of renal carcinoma was markedly increased in children with tuberous sclerosis (HR 59.6, CI: 23.7-149.5; N = 5), a known cause of renal cancer. Thyroid carcinoma was not associated with non-syndromic anomalies or syndromes.

CONCLUSION

Birth defects are associated with hepatocellular and renal carcinoma in children.

Utility of genomic testing in children, adolescents, and young adults with cancer

Genomic testing can inform the diagnosis and personalize management of cancers in children, adolescents, and young adults (CAYA). This scoping review explored the clinical utility and impact of genomic testing in general CAYA cancer cohorts. Relevant records published in English between 2017 and 2024 were identified by searching PubMed. 36 studies (32 original articles; 4 reviews) were identified on genomic testing in CAYA cancers, most of which were advanced cancers. Studies internationally reported that approximately 16%-18% of CAYAs with cancer carry an associated pathogenic germline variant where 40% are de novo, and can guide treatment (eg, DNA repair gene variants). Somatic variants, predominantly copy number or structural rearrangements, inform diagnosis in up to 95% of primary cancers. Between 18% and 69% of patients have a somatic variant with a matched therapy, but only one third receive the genomic-guided recommendation, predominantly due to declining patient condition. Few studies evaluated the impact of matched therapies on response and survival. Combining comprehensive DNA and RNA sequencing maximises sensitivity. Circulating tumour DNA was detected in most primary cancers and shows high concordance with tumour tissue. In conclusion, genomic testing of CAYA cancers is feasible, informs diagnoses and guides personalised care. Further research is needed on response to genomic-guided treatments.

The origin and polarization of Macrophages and their role in the formation of the Pre-Metastatic niche in osteosarcoma

Osteosarcoma, a primary malignant bone tumor commonly found in adolescents, is highly aggressive, with a high rate of disability and mortality. It has a profound negative impact on both the physical and psychological well-being of patients. The standard treatment approach, comprising surgery and chemotherapy, has seen little improvement in patient outcomes over the past several decades. Once relapse or metastasis occurs, prognosis worsens significantly. Therefore, there is an urgent need to explore new therapeutic approaches. In recent years, the successful application of immunotherapy in certain cancers has demonstrated its potential in the field of cancer treatment. Macrophages are the predominant components of the immune microenvironment in osteosarcoma and represent critical targets for immunotherapy. Macrophages exhibit dual characteristics; while they play a key role in maintaining tumor-promoting properties within the microenvironment, such as inflammation, angiogenesis, and immune suppression, they also possess antitumor potential as part of the innate immune system. A deeper understanding of macrophages and their relationship with osteosarcoma is essential for the development of novel therapeutic strategies.

Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution

Over 80% of children with acute lymphoblastic leukemia (pALL) can be cured by treating them with multiple chemotherapeutic agents administered over several years, whereas pALL is incurable with 1-3 medications, suggesting significant variation in drug susceptibility across clonal populations. While bulk sequencing studies indicate that pALL cells contain relatively few genetic variants compared to other cancers, the true extent of genetic diversity at the single-cell level remains unknown. Here, we used three complementary approaches to investigate pALL genetic heterogeneity: error-corrected bulk sequencing, single-cell exome sequencing, and primary template-directed amplification (PTA)-enabled single-cell genome sequencing. We discovered that some ETV6-RUNX1 samples harbor multiple independent ras clones and that individual pALL cells harbor substantially more mutations (mean 3,553 per cell) than detected in bulk samples (mean 965 mutations), with variant signatures suggesting both early and late APOBEC-driven mutagenesis in ETV6-RUNX1 patients. Using PTA-based phylogenetic analysis of over 150 single-cell genomes from four pALL patients, we identified heritable phenotypes associated with specific genetic alterations, including some low-frequency clones that are preferentially selected for during chemotherapy treatment. Our findings reveal previously undetected genetic diversity in pALL and suggest that pre-existing mutations influence treatment response, with implications for future therapeutic strategies. This study provides a high-resolution framework for understanding cancer clonal evolution during treatment, yielding important new insights for developing more effective therapeutic approaches for pALL.

Exploring high-throughput drug sensitivity testing in neuroblastoma cell lines and patient-derived tumor organoids in the era of precision medicine

INTRODUCTION

Despite druggable events to be present in 80 % of neuroblastomapatients within the Princess Máxima Center precision medicine program 'iTHER', clinical uptake of treatment recommendations has been low, and the clinical impact for individual patients remains hard to predict. This stresses the need for a method integrating genomics and transcriptomics with functional approaches into therapeutic decision making.

METHODS

We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fifteen neuroblastoma patient-derived organoids (NBL-PDOs). Cell lines, NBL-PDOs and their parental tumors were characterized utilizing (lc)WGS, WES and RNAseq. Cells were exposed to ∼200 compounds. Results were transferred to the R2 visualization platform.

RESULTS

A powerful reference set of cell lines is available, reflecting distinct known pharmacologic vulnerabilities. HTS identified additional therapeutic vulnerabilities, such as a striking correlation between a positive mesenchymal signature and sensitivity to BCL2-inhibitor venetoclax. Finally, we explored personalized drug sensitivities within iTHER, demonstrating HTS can support genomic and transcriptomic results, thereby strengthening the rationale for clinical uptake.

CONCLUSION

We established a dynamic publicly available dataset with detailed genomic, transcriptomic, and pharmacological annotation of classical neuroblastoma cell lines as well as novel sharable NBL-PDOs, representing the heterogeneous landscape of neuroblastoma. We anticipate that in vitro drug screening will be complementary to genomic-guided precision medicine by supporting clinical decision making, thereby improving prognosis for all neuroblastoma patients in the future.

Alternative lengthening of telomere-based immortalization renders H3G34R-mutant diffuse hemispheric glioma hypersensitive to PARP inhibitor combination regimens

BACKGROUND

Diffuse hemispheric glioma, H3 G34R/V-mutant (DHG-H3G34) is characterized by poor prognosis and lack of effective treatment options. DHG-H3G34R further harbor deactivation of alpha-thalassemia/mental retardation syndrome X-linked protein (ATRX; DHG-H3G34R_ATRX) suggesting a unique interaction of these 2 oncogenic alterations. In this study, we dissect their cell biological interplay, investigate the impact on telomere stabilization, and consequently validate a targeted therapy approach.

METHODS

We characterized patient-derived primary pediatric high-grade glioma (pHGG) models for telomere-maintenance mechanisms, DNA damage stress (including protein expression, pH2AX/Rad51 foci, cell-cycle arrest) and their sensitivity towards poly-ADP ribose polymerase inhibitor (PARPi) combinations. Human induced pluripotent stem cells (iPSCs) were used for modeling the disease. The anticancer activity of PARPi combinations in vivo was studied in Chorioallantoic Membrane (CAM) and orthotopic in vivo experiments. Finally, we treated a DHG-H3G34R_ATRX patient with PARPi combination therapy.

RESULTS

We elaborate that alternative lengthening of telomeres (ALT) is a key characteristic of DHG-H3G34R_ATRX. A dominant cooperative effect between H3G34R and ATRX loss in ALT activation also became apparent in iPSCs, which endogenously exert telomerase activity. In both, patient-derived DHG-H3G34R_ATRX models and H3G34R+/ATRX- iPSCs, the ALT-phenotype was associated with increased basal DNA damage stress, mediating synergistic susceptibility towards PARPi (talazoparib, niraparib) combinations with topoisomerase-I inhibitors (topotecan, irinotecan). In a first-of-its-kind case, treatment of a DHG-H3G34R_ATRX patient with the brain-penetrant PARP inhibitor niraparib and topotecan resulted in significant tumor reduction.

CONCLUSIONS

Our preclinical and clinical data strongly support the further development of PARPi together with DNA damage stress-inducing treatment regimens for DHG-H3G34R_ATRX.

Systems-level immunomonitoring in children with solid tumors to enable precision medicine

Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic T cell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded T cell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded T cells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.

Access Program for Unapproved and Off-Label Drug Use in Pediatric BRAF V600E-Mutated Brain Tumors in Japan

Programs allowing access to investigational drugs and off-label drug use for serious diseases have often been applied to pediatric cancers. A clinical study conducted under the Japanese "Patient-Proposed Healthcare Services" evaluated the efficacy and safety of dabrafenib plus trametinib in children with BRAF V600 mutant glioma (jRCTs071210071). This study successfully provided unapproved and off-label medications to four enrolled patients, two with low-grade glioma and two with high-grade glioma (median age: 10.5 years), until regulatory approval. The timeframe and data collection from such access programs need to be optimized for pediatric patients in accordance with the healthcare system of each nation.

The relative contributions of genetic and non-genetic factors to the risk of neuroblastoma

Previous literature has well-established genetic factors as being associated with neuroblastoma (NB). About 1%-2% of NB cases are familial, with 85% of these cases predisposed to mutations in the PHOX2B and ALK genes. The genetic basis of sporadic NB has been studied through genome-wide association studies and next-generation sequencing approaches. Particularly, germline variants, as well as copy number variations, confer increased risks of NB, often with effect estimates ≥1.5, underscoring the strong genetic contributions to NB. However, the strength of the association varied in non-genetic factors. Some risk factors, such as birth defects, maternal illicit drug use, and early infections, had relatively stronger associations (effect estimates ≥1.5 or ≤0.67), while some other factors remain inconclusive. This suggests that certain non-genetic factors may play a more prominent role in NB risk, while further research is needed to clarify the impact of others. We synthesized and critically evaluated existing literature on the risk factors of NB to provide an overview, analyze the current state of knowledge, and outline a research path to address the relative contributions of genetic and non-genetic factors in NB. Future epidemiologic studies should incorporate novel methods for measuring genetic and non-genetic factors to comprehensively assess the full extent of factors contributing to NB. Furthermore, the utilization of dried blood spots holds promise to overcome technical and recruitment challenges for future studies. These strategies will contribute to a more holistic understanding of NB etiology and potentially lead to improved prevention strategies.

T cells in the microenvironment of solid pediatric tumors: the case of neuroblastoma

Neuroblastoma (NB) is an immunologically "cold" tumor with poor or no inflamed substrates as most of solid pediatric tumors (SPT). Consistent data indicate that NB tumor microenvironment (TME) is dominated by myeloid cells, with little (but variable) T cell infiltration. The obstacles to lymphocyte infiltration and to their anti-tumor activity are due to different tumor immune evasion strategies, including loss of HLA Class I molecules, high expression of immune checkpoint molecular ligands leading to exhaustion of T effector (and NK) cells, induction of T regulatory, myeloid and stromal cells and secretion of immunosuppressive mediators. In odds with adult solid tumors, NB displays weak immunogenicity caused by intrinsic low mutational burden and scant expression of neoepitopes in the context of MHC-class I antigens which, in turn, are particularly poorly expressed on NB cells, thus inducing low anti-tumor T cell responses. In addition, NB is generated from embryonal cells and is the result of transcriptional abnormalities and not of the accumulation of genetic mutations over time, thus further explaining the low immunogenicity. The poor expression of immunogenic molecules on tumor cells is associated with the high production of immunosuppressive factors which further downregulate lymphocyte infiltration and activity, thus explaining the limited efficacy of new drugs in NB, as immune checkpoint inhibitors. This review is focused on examining the role of T effector and regulatory cells infiltrating TME of NB, taking into account their repertoire, phenotype, function, plasticity and, importantly, predictive value for defining novel targets for therapy.

Characterization of RNF144B and PPP2R2A identified by a novel approach using TCGA data in ovarian cancer

TCGA has identified predominant somatic copy number alterations (SCNA) affecting numerous genes in HGSOC. To identify cancer-driver genes from the regions of SCNA, we have devised a scoring system that integrates information from different genetic alterations. Applying this scoring system to the TCGA-HGSOC dataset (n = 316) we have identified several well-known and novel putative cancer genes in HGSOC. We functionally validated the roles of two previously unknown genes, RNF144B and PPP2R2A. RNF144B, an E3 ubiquitin-ligase is amplified and overexpressed in 16% of HGSOC (TCGA). Overexpression of RNF144B in ovarian cancer cells increased cell proliferation, colony formation, and migration. RNF144B was significantly overexpressed in 50% of primary tumors from patients with HGSOC compared to the ovary. Further, it had significantly reduced expression in tumors after chemotherapy. PPP2R2A, the regulatory subunit of PP2A is deleted and downregulated in 38% of HGSOCs (TCGA). Overexpression of PPP2R2A inhibited cell proliferation, colony-formation, migration, and invasion in ovarian cancer cells. In OVCAR-5, which expresses low levels of PPP2R2A, Niraparib inhibited cell proliferation. PPP2R2A was not expressed in 72% of HGSOCs. This report demonstrates this approach to identifying genes from the TCGA data. Further experiments are required to conclusively prove the role of these genes in the pathogenesis of ovarian cancer.

Family-Level Impact of Germline Genetic Testing in Childhood Cancer: A Multi Family Member Interview Analysis

Objectives: Germline genetic testing is increasingly being integrated into pediatric oncology and a large number of families are interested. Current research on the psychological impact of germline genetic testing is limited by a main focus on individual outcomes in parents or children and little is known about its impact at the family level. Our study addresses that limitation by exploring parents' lived experiences of how their family-as a whole-is affected by germline genetic testing for cancer predisposition. Methods: In six families who opted for germline genetic testing in the context of cancer predisposition, both parents of six ill children (five boys) with an average age of 9.67 years (SD = 3.77 years) were interviewed individually (N = 12). Germline genetic testing was performed by exome sequencing followed by analysis of a panel of childhood cancer predisposition genes in pediatric cancer patients and their parents. Their experiences were elicited through semi-structured interviews and the data were analyzed using Multi Family Member Interview Analysis. This qualitative study was conducted at Ghent University Hospital in Belgium. Results: The findings demonstrated that while germline genetic testing was generally viewed as a valuable and straightforward step in the child's oncology trajectory, parents found it difficult to distinguish its impact from the overwhelming stressors of their child's cancer diagnosis and treatment. However, parents recognized that the testing also significantly affected various family-level processes. Five main themes were identified: talking about germline genetic testing, being together matters (more), differences in coping with germline genetic testing between partners, feelings of guilt and mutual forgiveness, and concerns about the future health of the family. Conclusions: Given the expanded use of germline genetic testing in pediatric oncology, it is critical for clinicians to address the family-level impacts of germline genetic testing. Although families are affected by these issues, they often do not raise them due to the overwhelming challenges posed by the cancer diagnosis and treatment. Proactively addressing these themes could improve the support provided to families undergoing germline genetic testing for cancer predisposition.

MSH2, MSH6, MLH1, and PMS2 immunohistochemistry as highly sensitive screening method for DNA mismatch repair deficiency syndromes in pediatric high-grade glioma

Pediatric high-grade glioma (pedHGG) can occur as first manifestation of cancer predisposition syndromes resulting from pathogenic germline variants in the DNA mismatch repair (MMR) genes MSH2, MSH6, MLH1, and PMS2. The aim of this study was to establish a generalized screening for Lynch syndrome and constitutional MMR deficiency (CMMRD) in pedHGG patients, as the detection of MMR deficiencies (MMRD) may enable the upfront therapeutic use of checkpoint inhibitors and identification of variant carriers in the patients' families. We prospectively enrolled 155 centrally reviewed primary pedHGG patients for MMR-immunohistochemistry (IHC) as part of the HIT-HGG-2013 trial protocol. MMR-IHC results were subsequently compared to independently collected germline sequencing data (whole exome sequencing or pan-cancer DNA panel next-generation sequencing) available in the HIT-HGG-2013, INFORM, and MNP2.0 trials. MMR-IHC could be successfully performed in 127/155 tumor tissues. The screening identified all present cases with Lynch syndrome or CMMRD (5.5%). In addition, MMR-IHC also detected cases with exclusive somatic MMR gene alterations (2.3%), including MSH2 hypermethylation as an alternative epigenetic silencing mechanism. Most of the identified pedHGG MMRD patients had no family history of MMRD, and thus, they represented index patients in their families. Cases with regular protein expression in MMR-IHC never showed evidence for MMRD in DNA sequencing. In conclusion, MMR-IHC presents a cost-effective, relatively widely available, and fast screening method for germline MMRD in pedHGG with high sensitivity (100%) and specificity (96%). Given the relatively high prevalence of previously undetected MMRD cases among pedHGG patients, we strongly recommend incorporating MMR-IHC into routine diagnostics.