Rare paediatric central nervous system (CNS) tumours comprise a biologically-heterogeneous group of low-incidence diseases that present significant challenges to both therapeutic development and clinical research, limiting the availability of high-quality evidence to guide clinical care. The UK3CR Children’s Cancer Research Group (CRG) CNS Tumours Subgroup convened a multidisciplinary workshop to identify research priorities and establish a strategic framework for advancing clinical trials in this setting. Four high-priority tumour groups—craniopharyngioma, choroid plexus carcinoma (CPC), very high-risk medulloblastoma (VHR-MB), and rare embryonal and sarcomatous tumours (REST), including embryonal tumour with multilayered rosettes (ETMR)—were evaluated. Key outcomes included the feasibility of a UK-led craniopharyngioma trial, the need for enhanced national CPC data collection, and support for European early-phase platform trials in VHR-MB. REST highlighted transnational regulatory complexity requiring coordinated registries and parallel trial models. Cross-cutting barriers included regulatory discordance, contracting delays, fragmented funding, pharmacovigilance differences, data-sharing constraints, and interoperable infrastructures. The workshop emphasised innovative methodologies, including Bayesian/adaptive designs, platform trials, and external control arms, to maximise efficiency in small populations, alongside strengthened patient involvement and international collaboration. Collectively, these findings define a collaborative and internationally-aligned strategic roadmap to accelerate clinical research and improve outcomes in rare paediatric CNS tumours.

Multimodality imaging is an emerging research topic in neuro-oncology for its potential of being able to demonstrate tumours in a more comprehensive manner. Diffusion-weighted magnetic resonance imaging (dMRI) and proton magnetic resonance spectroscopy (1H-MRS) allow inferring tissue cellularity and biochemical properties, respectively. Combining dMRI and 1H-MRS may provide more accurate diagnosis for paediatric brain tumours than only one modality. This retrospective study collected 1.5-T clinical 1H-MRS and dMRI from 32 patients to assess paediatric brain tumour classification with combined dMRI and 1H-MRS. Specifically, spectral noise of 1H-MRS was suppressed before calculating metabolite concentrations. Extracted radiomic features were apparent diffusion coefficient (ADC) histogram features through dMRI and metabolite concentrations through 1H-MRS. These features were put together and then ranked according to the multiclass area under the curve (mAUC) and selected for tumour classification through machine learning. Tumours were precisely typed by combining noise-suppressed 1H-MRS and dMRI, and the cross-validated accuracy was improved to be 100% according to naïve Bayes. The finally selected radiomic biomarkers, which showed the highest diagnostic ability, were ADC fifth percentile (mAUC = 0.970), myo-inositol (mAUC = 0.952), combined glutamate and glutamine (mAUC = 0.853), total creatine (mAUC = 0.837) and glycine (mAUC = 0.815). The study indicates combining MR imaging and spectroscopy can provide better diagnostic performance than single-modal imaging.

Several treatment protocols are used for the treatment of high-risk medulloblastoma (HR-MB). In 2015, the UK Children's Cancer and Leukaemia Group issued guidance recommending treatment as per the SJMB03 protocol, whilst also recognising that the COG-99701 protocol maybe used. Patients were defined as high-risk if metastatic at presentation, large-cell/anaplastic histology, MYC amplification, significant residual disease or MYCN amplification. Recently, the latter two only define high risk if other adverse features are present. Methods: Retrospective multi-centre service evaluation of treatment of HR-MB at five UK centres. Patients were included if treated as per SJMB03 or COG-99701. Patients were excluded if initially treated for standard-risk medulloblastoma and subsequently treated with these protocols due to upstaging or disease progression. Results: 58 patients were identified: 26 treated as per SJMB03, 32 as per COG-99701. 5-year OS was 83 % (95 % CI 73-94 %) and 5-year PFS was 65 % (53-80 %). For patients treated as per SJMB03, 5-year OS and PFS were 80 % (65-97 %) and 75 % (60-95 %) respectively; for patients treated as per COG-99701, 5-year OS and PFS were 85 % (73-100 %) and 60 % (43-83 %). There was no significant difference in outcomes between protocols. There was a higher incidence of grade 3/4 ototoxicity (44 % vs 6 %, p = 0.001) and admission to paediatric intensive care (19 % vs 0 %, p = 0.014) in patients treated as per SJMB03 compared to COG-99701. Conclusion: These real-world outcomes are consistent with the published literature on HR-MB patients treated with these protocols within clinical trials, and provide important evidence to inform their use in routine practice.

Abstract BACKGROUND Optic nerve sheath meningiomas (ONSM) are rare, comprising 1-2% of paediatric CNS meningiomas. Despite slow growth, ONSM often lead to vision loss in the affected eye. Diagnosis is challenging due to the tumour’s proximity to the optic nerve, complicating biopsy or complete removal. METHODS We searched our Neuro-Oncology MDT database for patients treated for ONSM between Jan 2018 and Dec 2023. We retrospectively reviewed clinical presentation and diagnostic workup that led to the diagnosis of ONSM. RESULTS 6 children aged 3-15years (mean 9 years) were identified over 5 years. 3 children were treated at GOSH, 2 at UCLH and 1 at BCH. 3/6 patients were male. 2/6 underwent a biopsy. Presenting symptoms included headache, acute visual loss and eye pain. 2/6 patients presented with bilateral vision deterioration. The average time between onset of symptoms and presentation was 8 months (range 3–15 months). Identified causes of delayed diagnosis included delayed presentation related to COVID-19 pandemic (2 patients) and impaired quality of imaging due to dental braces (1 patient). Whilst awaiting diagnosis, 2 patients lost vision completely in their affected eye. Diagnostic workup included: optic disc examination (6 patients), lumbar puncture (2 patients), angiotensin-converting enzyme (sACE) (2 patients), MRI brain and spine (6 patients), CT scan (6 patients), PET-DOTATE scan (3 patients), NF2 genetic testing (4 patients). Two patients completed PBT therapy while 1 is undergoing radiotherapy. One patient underwent an enucleation, while the rest are under surveillance. CONCLUSIONS Paediatric ONSM diagnosis remains challenging despite advanced imaging. Our review highlights the added value of CT and PET-DOTATATE when a biopsy is high-risk. CT reveals calcification in 20-50% ONSM while the role of PET-DOTATATE is related to the expression of somatostatin receptor 2 in meningiomas. Despite optimal treatment, vision loss maybe unavoidable. Early multidisciplinary consultations are advised for enhanced outcomes.

Background: Diffuse midline gliomas (DMGs) with histone H3K27M mutations represent a devastating paediatric brain cancer characterized by abysmal prognosis and limited treatment options. The only approved treatment is radiotherapy (RT), but most of the tumours relapse with fatal consequences. In this study, we sought to investigate whether irradiation leads to senescence induction and explore the efficacy of senolytics against DMG. Methods: We have characterised the senescent phenotype of five genetically heterogeneous H3K27M-altered human DMG cell lines, combining cellular and/or molecular approaches. The sensitivity of senescent cells to Bcl-xL inhibition has been demonstrated in dose/response curves in vitro and in a PDX model of DMG. Results: Here, we show that ionizing radiation induces senescence and SASP responses in both TP53 mutant and wild-type H3K27M-altered human DMG cell lines. We identify Navitoclax as a potent senolytic agent that selectively targets senescent DMG cells into apoptosis by inhibiting Bcl-xL. Related compounds, such as a proteolysis-targeting chimera (PROTAC)-mediated Bcl-xL degradation and a galacto-conjugated form of Navitoclax also show an effective senolytic activity in senescent cancer cells. Finally, we show that a combination therapy of irradiation and Navitoclax results in reduced tumor burden and increased mouse survival in an orthotopic xenograft DMG model. Conclusion: These results offer a rationale for further clinical development of senolytic therapies as part of multimodal treatment approaches for DMG patients ### Competing Interest Statement The authors have declared no competing interest.

Abstract BACKGROUND Current European standard-of-care for localised intracranial germinoma is multi-agent chemotherapy (carboPEI: carboplatin/etoposide/ifosfamide) followed by definitive radiotherapy, with excellent survival. MonoGerm is a de-escalation, non-inferiority trial aiming to reduce toxicity. Twelve-week carboplatin (PMID:8039122) AUC10 or vinblastine (PMIDs:32642701/34520101) induction will be evaluated to test if as effective as carboPEI from SIOP-CNS-GCT-II. A novel trial design was required to answer this question pragmatically/safely. METHODS Clinical trials in rare diseases recruit slowly, allowing continuous monitoring of efficacy outcomes. Efficacy-transition-pathways (ETP) are innovative visual tools to aid determination of trial design parameters, and an extension of the dose-transition-pathways concept introduced for dose-finding trials (PMID:28733440). RESULTS MonoGerm includes two monotherapies, with each single arm recruiting six cohorts of three patients, with interim assessment after each recruited cohort and final analysis at 18 patients (total n=36). Insufficient tumour volume response (<30%) at 6-week safety MRI results in 12-weeks carboPEI. Primary outcome is radiological complete response (CR) by 12-weeks of induction monotherapy. A beta-binomial conjugate analysis will generate posterior probability distributions, combining observed trial data as realisations from a binomial distribution with a minimally informative Beta (1,1) prior. Decision criteria to allow early stopping at interim analyses and go/no-go decisions at final analysis are based on probabilities from these posterior distributions. ETP visually maps out parameters used to assert decisions after each interim assessment as a pyramid decision tree. For each recruited cohort and every CR outcome, estimates of the true CR rate and probabilities with associated decisions are mapped out. ETP allows clear communication between statisticians, clinicians, and patient-public-involvement (PPI) teams, facilitating informed decisions in an efficient/realistic trial design. CONCLUSION MonoGerm, a novel Bayesian de-escalation trial, funded by Little Princess Trust (https://www.littleprincesses.org.uk/), uses ETP and continuous monitoring with built-in stopping rules to ensure patient safety in this treatment de-escalation trial.

Childhood cancers are increasingly recognised as disorders of tissue growth and development, through early life into adulthood. A rising proportion are currently considered to be related to a familial predisposition or associated with identified genetic mutations in predisposition genes. Their threat to life and risk of associated serious disability at diagnosis and need for complex life saving therapies makes them a research priority. Inadequate progress has been made in diagnosing childhood cancers earlier within global health systems, which means that their clinical presentations are either missed altogether or constitute high risk emergencies. Whilst knowledge of tumour biology has improved dramatically over the last decade due to the expansion in research technologies directed at innovative approaches to prognostication and treatment. A concerted research initiative to apply this knowledge to making the diagnosis of childhood cancers at earlier points in tumourgenesis has not developed. The risk for a child getting a cancer by the age of 5 is equivalent to the risks of the conditions selected as part of newborn population screening for rare inherited health conditions and is nearly 3 times that at age 18 years. We are proposing that research directed at accelerating cancer diagnosis for children by focussing upon feasibility and acceptability of linking targeted surveillance with population screening for all childhood cancers. This would be supported by enhanced public and professional awareness of a child’s risks of cancer and the range of clinical presentations. We suggest this must now be a top priority for research because of the potential for improving outcomes for treatment of all types of cancer and reducing the burden of disability and late effects of therapy.

BACKGROUND:Cellular senescence can have positive and negative effects on the body, including aiding in damage repair and facilitating tumor growth. Adamantinomatous craniopharyngioma (ACP), the most common pediatric sellar/suprasellar brain tumor, poses significant treatment challenges. Recent studies suggest that senescent cells in ACP tumors may contribute to tumor growth and invasion by releasing a senesecence-associated secretory phenotype. However, a detailed analysis of these characteristics has yet to be completed. METHODS:We analyzed primary tissue samples from ACP patients using single-cell, single-nuclei, and spatial RNA sequencing. We performed various analyses, including gene expression clustering, inferred senescence cells from gene expression, and conducted cytokine signaling inference. We utilized LASSO to select essential gene expression pathways associated with senescence. Finally, we validated our findings through immunostaining. RESULTS:We observed significant diversity in gene expression and tissue structure. Key factors such as NFKB, RELA, and SP1 are essential in regulating gene expression, while senescence markers are present throughout the tissue. SPP1 is the most significant cytokine signaling network among ACP cells, while the Wnt signaling pathway predominantly occurs between epithelial and glial cells. Our research has identified links between senescence-associated features and pathways, such as PI3K/Akt/mTOR, MYC, FZD, and Hedgehog, with increased P53 expression associated with senescence in these cells. CONCLUSIONS:A complex interplay between cellular senescence, cytokine signaling, and gene expression pathways underlies ACP development. Further research is crucial to understand how these elements interact to create novel therapeutic approaches for patients with ACP.

Abstract Adamantinomatous Craniopharyngioma (ACP) is a rare pituitary tumor of the sellar region, with a bimodal presentation pattern in children and middle-aged adults. ACPs are primarily driven by a mutation in CTNNB1 that prevents beta-catenin from degrading properly, resulting in accumulation in the nuclei of epithelial whorl-like structures sometimes referred to as cluster cells. Clinical management is challenging due to the location of the tumor, such that complete surgical resection is often not possible so radiation therapy, which can lead to high morbidity, is also used. Greater insight into these tumors can help develop less damaging treatment strategies. In this analysis we have employed single-cell RNA sequencing technology to examine seven pediatric human ACPs (28594 cells). Using consensus non-negative matrix factorization, and traditional marker genes, we have partitioned our dataset into several cell types including cluster cells, palisading epithelial cells, microglia, T-cells, B-cells, plasma cells, and fibroblasts. Though cluster cells themselves do not actively proliferate, we believe the complex inter-cellular signaling is responsible for tumor formation. We propose a model in which malignant fibroblasts form from the existing epithelium and remodel the extracellular matrix (ECM) creating a stiffened tumor microenvironment. To support this claim we show activation markers suggesting myofibroblast differentiation, the expression of EMT signatures indicating a transformation from epithelial to fibroblast, and RNA velocity analysis that demonstrates lineage tracing. We believe that the remodeling of the ECM is a wound healing response influenced by TGF-beta, SPP1, and other signaling pathways. Our analysis of ACPs reveals the role of the tumor microenvironment in the formation of these tumors.

The two types of craniopharyngioma, adamantinomatous (ACP) and papillary (PCP), are clinically relevant tumours in children and adults. Although the biology of primary craniopharyngioma is starting to be unravelled, little is known about the biology of recurrence. To fill this gap in knowledge, we have analysed through methylation array, RNA sequencing and pERK1/2 immunohistochemistry a cohort of paired primary and recurrent samples (32 samples from 14 cases of ACP and 4 cases of PCP). We show the presence of copy number alterations and clonal evolution across recurrence in 6 cases of ACP, and analysis of additional whole genome sequencing data from the Children's Brain Tumour Network confirms chromosomal arm copy number changes in at least 7/67 ACP cases. The activation of the MAPK/ERK pathway, a feature previously shown in primary ACP, is observed in all but one recurrent cases of ACP. The only ACP without MAPK activation is an aggressive case of recurrent malignant human craniopharyngioma harbouring a CTNNB1 mutation and loss of TP53. Providing support for a functional role of this TP53 mutation, we show that Trp53 loss in a murine model of ACP results in aggressive tumours and reduced mouse survival. Finally, we characterise the tumour immune infiltrate showing differences in the cellular composition and spatial distribution between ACP and PCP. Together, these analyses have revealed novel insights into recurrent craniopharyngioma and provided preclinical evidence supporting the evaluation of MAPK pathway inhibitors and immunomodulatory approaches in clinical trials in against recurrent ACP.

Abstract BACKGROUND Several treatment protocols are used in the treatment of patients with high risk medulloblastoma (HRMB). In 2015 the UK Children’s Cancer and Leukaemia Group issued interim guidance recommending treatment as per the SJMB03 protocol, whilst also recognising that the COG99701 protocol may be used. Patients were defined as high risk, if metastatic at presentation, large cell anaplastic histology, MYC amplification, significant residual disease or MYCN amplification, the latter two, more recently only if other adverse features present. METHODS We present a retrospective multi-centre service evaluation of treatment of patients with HRMB at 5 tertiary paediatric oncology centres in the UK. Patients were included if treated for HRMB with SJMB03, COG-99701. Patients were excluded if treated for HRMB on other protocols, including the SIOP HRMB trial, or if initially treated for standard risk medulloblastoma and subsequently treated with these protocols due to upstaging or disease progression. Event free, and overall (EFS and OS) survival analyses were calculated from date of primary resection. RESULTS 59 patients were included (median age 8 years, range 3-19): 26 treated as per SJMB03, 33 as per COG-99701. 5-year OS was 83% (95% Confidence Interval, 73-94%) and 5-year EFS was 66% (54-80%). For patients treated as per SJMB03 5-year OS and EFS was 79% (65-97%) and 70% (55-92%)respectively. and for patients treated as per COG99701, 5-year OS and EFS was 86% (73-99%) and 60% (44-83%). There was a higher incidence of grade 3 & 4 ototoxicity (44% vs 6%) and a higher rate of admission to paediatric intensive care (36% vs 6%) in patients treated as per SJMB03 compared to those treated with COG97701 (p<0.05). CONCLUSIONS These real-world outcomes of patients treated in the UK for HRMB are consistent with the published literature for their outcomes for high risk medulloblastoma.

Abstract BACKGROUND Craniopharyngiomas are rare challenging tumours, with around 25% of cases recurring despite surgery and/or radiotherapy. Relatively little is known about the biology of recurrence and there is an urgent need to develop new therapies. Our previous studies have suggested preclinical efficacy of MEKinhition with trametinib in human and murine adamantinomatous craniopharyngoioma (ACP) tissue. At ISPNO2022 we reported methylation and expression profiling results from a cohort of relapsed craniopharyngioma, identifying acquisition of chromosomal abnormalities across recurrence, the persistent activation of MAPK pathway at recurrence, the presence of myeloid cells and a rare case of malignant transformation associated with TP53 loss. METHODS Here we present an update from this study through exploring additional datasets, preclinical drug testing, and genetic manipulation of genetic engineered mouse models of ACP RESULTS Exploration of whole genome sequencing data from 67 cases of ACP from Children’s Brain Tumour Network has confirmed the presence of chromosomal arm changes in 7 (10%) of cases, including at diagnosis, confirming that the genomic landscape of ACP is more complex than previously thought. To further explore the potential of MAPK pathway inhibiton we have demonstrated efficacy of a further two clinically available MEK inbhiibtors, Selumetinib and Binimetinib, in reducing proliferation and inducing cell death in ex vivo explants of murine ACP. To explore the role of TP53 loss in aggressive craniopharyngioma, we show that Trp53 loss in a murine ACP model results in very aggressive tumours and reduced mouse survival. Finally, we have further characterised the tumour immune infiltrate showing differences in the cellular composition between ACP and Papillary CP, and revealing a diverse phenotype of macrophages in ACP. CONCLUSIONS Together, this research provides further preclinical support for the ongoing evaluation of MAPK pathway inhibitors and immunomodulatory approaches in clinical trials in patients with craniopharyngioma.

Craniopharyngiomas (CPs) are clinically aggressive tumors because of their invasive behavior and recalcitrant tendency to recur after therapy. There are 2 types based on their distinct histology and molecular features: the papillary craniopharyngioma (PCP), which is associated with BRAF-V600E mutations and the adamantinomatous craniopharyngioma (ACP), characterized by mutations in CTNNB1 (encoding β-catenin). Patients with craniopharyngioma show symptoms linked to the location of the tumor close to the optic pathways, hypothalamus, and pituitary gland, such as increased intracranial pressure, endocrine deficiencies, and visual defects. Treatment is not specific and mostly noncurative, and frequently includes surgery, which may achieve gross total or partial resection, followed by radiotherapy. In cystic tumors, frequent drainage is often required and intracystic instillation of drugs has been used to help manage cyst refilling. More recently targeted therapies have been used, particularly in PCP, but also now in ACP and clinical trials are underway or in development. Although patient survival is high, the consequences of the tumor and its treatment can lead to severe comorbidities resulting in poor quality of life, in particular for those patients who bear tumors with hypothalamic involvement. Accordingly, in these patients at risk for the development of a hypothalamic syndrome, hypothalamus-sparing treatment strategies such as limited resection followed by irradiation are recommended. In this review, we provide an update on various aspects of CP, with emphasis on recent advances in the understanding of tumor pathogenesis, clinical consequences, management, and therapies.

Journal Article A promising future for hypothalamic dysfunction in craniopharyngioma Get access John Richard Apps, John Richard Apps Institute of Cancer and Genomics Sciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UKDevelopmental Biology and Cancer, Birth Defects Research Centre, GOS Institute of Child Health, University College London, WC1N 1EH, London, UKBirmingham Women's and Children's NHS Foundation Trust, Birmingham, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Juan Pedro Martinez-Barbera Juan Pedro Martinez-Barbera Developmental Biology and Cancer, Birth Defects Research Centre, GOS Institute of Child Health, University College London, WC1N 1EH, London, UK Corresponding Author: Juan Pedro Martinez-Barbera, PhD, University College London, London, UK (j.martinez-barbera@ucl.ac.uk). https://orcid.org/0000-0002-5292-7276 Search for other works by this author on: Oxford Academic PubMed Google Scholar Neuro-Oncology, Volume 25, Issue 4, April 2023, Pages 733–734, https://doi.org/10.1093/neuonc/noac284 Published: 27 December 2022 Article history Published: 27 December 2022 Corrected and typeset: 13 January 2023

Background Relapsed ependymoma has a dismal prognosis, and the role of chemotherapy at relapse remains unclear. This study prospectively evaluated the efficacy of intensive intravenous (IV) etoposide in patients less than 21 years of age with relapsed intracranial ependymoma (NCT00278252). Methods This was a single-arm, open-label, phase II trial using Gehan’s two-stage design. Patients received IV etoposide 100 mg/m2 on days 1-3, 8-10, and 15-17 of each 28-day cycle, up to maximum of 6 cycles. Primary outcome was radiological response after 3 cycles. Pharmacokinetic analysis was performed in 10 patients. Results Twenty-five patients were enrolled and included in the intention-to-treat (ITT) analysis. Three patients were excluded in per-protocol (PP) analysis. After 3 cycles of etoposide, 5 patients (ITT 20%/PP 23%) had a complete response (CR), partial response (PR), or objective response (OR). Nine patients (ITT 36%/PP 41%,) had a best overall response of CR, PR, or OR. 1-year PFS was 24% in ITT and 23% in PP populations. 1-year OS was 56% and 59%, 5-year OS was 20% and 18%, respectively, in ITT and PP populations. Toxicity was predominantly hematological, with 20/25 patients experiencing a grade 3 or higher hematological adverse event. Conclusions This study confirms the activity of IV etoposide against relapsed ependymoma, however, this is modest, not sustained, and similar to that with oral etoposide, albeit with increased toxicity. These results confirm the dismal prognosis of this disease, provide a rationale to include etoposide within drug combinations, and highlight the need to develop novel treatments for recurrent ependymoma.

Abstract MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression of target mRNAs and can control whole gene networks. ACPs are benign pituitary tumours that can result in significant morbidity and premature mortality. ACPs harbour mutations in CTNNB1 and are driven by the activation of the WNT/beta-catenin pathway. We sought to explore the expression of miRNAS in adamantinomatous craniopharyngioma (ACP) in a cohort of samples previously subjected to RNA-Seq analysis (Apps et al, Acta Neuropathologica, 2018, May;135(5):757-777). Total RNA ACP samples (n=18), non-functioning pituitary adenomas (n=3) and normal foetal pituitaries (n=3) underwent miRNA sequencing using the Qiagen miRNA library prep kit on a NextSeq 500 to a depth of 16 million reads. Differential expression was performed using DESeq2 and functional analysis with mirPath v.3. Expression of miRNAs was correlated with previously published mRNA expression We found that 210 miRNA were upregulated and 275 down regulated in ACP compared with controls (adjusted p-value <0.1). MIR-205-5p was the most upregulated miRNA (619 fold) and its expression correlated with genes expressed within the tumour epithelium (e.g. TP63). miR-375 an inhibitor of the WNT pathway was the most down regulated miRNA (361 fold). KEGG Pathway analysis identified Glycosphingolipid synthesis as the most enriched pathway targeted by upregulated miRNAs. Pathways that were enriched by down regulated miRNAs included: ECM-receptor interaction, fatty acid biosynthesis, Hippo, TGF-beta, WNT, and ErbB pathways. Down regulation of miR-132 has previously been suggested as a marker of aggressiveness in ACP, and was 16 fold down regulated (adjusted p-value<0.001) in this cohort and expression was inversely correlated with genes relating to epithelial development. This data confirms previous studies indicating that miRNA expression is altered in ACP. In silico analysis suggest that the dysregulation of miRNA affects the expression of genes involved in pathogenic pathways in ACP.

Chordomas are rare malignant bone tumours that develop from the ectopic remnants of the embryonic notochord. In contrast to adults, the majority in children under 16 present intra-cranially (63%). In 2006, we reported the youngest case of a large clival chordoma, a 15-week old baby, the second case to present without skull base involvement and the fourth case of chordoma in a patient with tuberous sclerosis (TS) Kombogiorgas (Childs Nerv Syst 22(10):1369–1374, 2006 ). In this report, we provide an update on this patient’s journey through a range of therapeutic options and summarize an update of the literature, since 2006, for this patient group.

Abstract INTRODUCTION: Adamantinomatous craniopharyngiomas (ACPs) are rare brain tumors that primarily occur in children and impact long-term morbidity and mortality. The canonical driver mutation for ACP growth occurs in CTNNB1 and leads to constitutive activation of the Wnt/β-catenin signaling pathway. In this study, we outline the genomic, transcriptomic, and structural variant (SV) landscape in a cohort of 41 ACP samples. METHODS: We performed whole-genome sequencing (WGS) and RNA-sequencing of 41 ACP samples. Matched normal samples were also characterized by WGS. Mutect2 was used to detect single nucleotide variants (SNVs) and indels, and copy number data was generated using the GATK pipeline. SvABA was used to perform SV analysis and to identify significantly recurrent breakpoints and juxtapositions. DESeq2 was used to perform differential gene expression analysis based on clinical and molecular annotation data. RESULTS: 29/41 (70%) of the ACP samples harbored missense mutations in exon 3 of CTNNB1, all of which have previously been reported in ACP tumors. SV analysis identified a median of 11.5 events per tumor. Overall, 9.7% of events were interchromosomal. Of the remainder, the majority (78.6%) were deletions. No SVs occurred within CTNNB1. A positive correlation (r = 0.533) was observed between the frequency of SVs and SNVs within samples. Analysis of significantly recurring breakpoints (SRBs) did not identify recurrent breakpoint events. Differential gene expression analysis comparing samples with and without CTNNB1 variants identified 2,143 differentially expressed genes with q-value < 0.05. CONCLUSION: This study identifies activating mutations in exon 3 of CTNNB1 in a large cohort of ACP samples. We also integrate SV and transcriptomic data to comprehensively investigate ACP tumor genomes and identify putative novel tumorigenic mechanisms that advance our understanding of ACP biology.