Background Relapsed medulloblastoma remains a significant therapeutic challenge as it is near universally fatal. The tumor microenvironment of medulloblastoma plays a critical role in tumor progression, influencing tumor growth, immune evasion, and therapeutic resistance. We hypothesized that defining tumor-immune interactions in diagnostic and relapsed medulloblastoma may uncover mechanisms of immune evasion and identify novel therapeutic targets.Methods We analyzed paired primary and recurrent RNA-sequencing data from 140 medulloblastoma patients to profile immune cell composition and validate spatial relationships within the TME. To identify key tumor-immune interactions, we developed a novel algorithm to detect receptor-ligand pairs using single-cell RNA-sequencing data. These interactions were validated across RNA and proteomic datasets. Their functional significance was empirically demonstrated in newly developed immunocompetent models of recurrent medulloblastoma that closely recapitulate the human disease.Results We observed a shift toward a heightened immunosuppressive TME at relapse. Using our algorithm, we identified biologically significant receptor-ligand interactions, most notably MIF-CD74, constitutively expressed at RNA and protein levels across medulloblastoma subgroups, at diagnosis and relapse. Disrupting MIF-CD74 interactions led to significant alterations in the tumor microenvironment, highlighting its functional significance.Conclusions Our multifaceted approach identified key tumor-immune interactions in medulloblastoma. Among these, MIF-CD74 was validated as a targetable interaction, demonstrating the utility of our integrative approach for identifying novel therapeutic targets across multiple tumor types.

Diffuse midline gliomas (DMGs) are near-universally lethal tumours of the childhood central nervous system1,2. In animal models, DMGs form brain-wide integrated networks through neuron-to-glioma synapses3-6 and glioma-to-glioma gap junctional coupling3. This extensive connectivity robustly promotes the growth and invasion of DMG3-9 and other glial malignancies10-12 through paracrine mechanisms and direct neuron-to-glioma synapses. However, the organization and clinical implications of these connections in the living human brain remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG, defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Analyses of single-nucleus RNA sequencing data confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMGs exploit otherwise healthy brain circuits to promote tumour growth.

Tissue engineering of the esophagus has been limited by stent dependance and poor muscle regeneration. Here we report an integrated strategy to engineer a 2.5-cm esophageal segment by microinjecting autologous pericyte-like myogenic precursors and fibroblasts in a decellularized porcine scaffold to repair circumferential defects in 10-kg minipigs ( n = 8), modeling pediatric use. Bioreactor maturation induced a proangiogenic phenotype, with in vivo support from biodegradable intraluminal stents and a vascularizing pleural wrap. This coordinated approach yielded safe and effective esophageal conduits; oral feeding supported normal growth, morbidity resembled that of clinical esophageal replacement and was endoscopically manageable, and 63% (5/8) survived to the 6-month endpoint. Comprehensive multimodal analyses demonstrated progressive recapitulation of native architecture, with increasing neuromuscular regeneration and vascularization, correlating with functional recovery, absence of symptomatic stricture and the presence of secondary peristalsis by 6 months. These results demonstrate that the combination of complementary regenerative, conditioning and surgical strategies enables a functionally integrated, contractile esophageal graft with ongoing structural maturation without immunosuppression.

Medulloblastoma (MB) groups 3 and 4 arise from human-specific developmental contexts that remain experimentally inaccessible, limiting mechanistic insight into tumor initiation. We generated cerebellar organoids (CbOs) from expanded potential stem cells (EPSCs) and performed integrated single-cell transcriptomic and DNA methylation analyses, revealing discrete human rhombic lip progenitor populations whose developmental programs align with group 3- and group 4-associated lineages. Using c-MYC overexpression as an initiating oncogenic event, we demonstrated that these lineage-restricted progenitors are susceptible to neoplastic transformation, generating tumors with group 3 MB molecular features in vitro and in vivo. We further established a CbO-MB coculture system that preserves malignant and nonmalignant cellular compartments, hence enabling interrogation of tumor-microenvironment interactions and providing simultaneous readouts of antitumor efficacy and cerebellar toxicity upon drug treatment. Receptor-ligand modeling in this system identifies TGFβ paracrine signaling as a microenvironmental pathway supporting MB growth, which we validated pharmacologically. Further analyses of cocultured MB cells revealed a myogenic differentiation program enriched in MYC-driven MB and recurrent disease, which is associated with poorer prognosis. Together, this work establishes a collection of CbO models for studying group 3/4 MB initiation, growth, and microenvironmental dependencies and provides a tractable platform for further mechanistic and therapeutic investigation of these tumors.

ABSTRACT Monosomy X (45,X) is associated with Turner syndrome and pregnancy loss in humans, but the underlying mechanisms remain unclear. We therefore analyzed the transcriptomic landscape of clinically relevant human fetal 45,X tissues (including pancreas, liver, kidney, skin, placenta) with matched 46,XX and 46,XY control samples between 11-15 weeks post conception (n=78). Although most pseudoautosomal region 1 (PAR1) genes were lower in monosomy X tissues, we also found reduced expression of several key genes escaping X inactivation (e.g., KDM5C and KDM6A ), and potentially clinically important transcripts such as genes implicated in ascending aortic aneurysm. In contrast, higher expression of an autosomal, long non-coding RNA ( OVCH1-AS1 ) was seen in all 45,X tissues. In the placenta, lower expression of CSF2RA was demonstrated, likely contributing to immune dysregulation. Taken together, these findings provide novel insights into the biological consequences of a single X chromosome during early human development and potential insights in genetic mechanisms in Turner syndrome.

Pilocytic astrocytoma (PA) is the commonest low-grade tumour affecting children and is frequently experienced as a chronic disease associated with extended treatment, periods of regrowth, and long-term disability. This contrasts with the view of PA as a benign tumour with positive clinical outcomes and raises the fundamental question of biologically driven change over time within these tumours, which will impact diagnosis, stratification, and management. To investigate the molecular, cellular, and pathological stability of PA we performed RNA sequencing, methylation array profiling, immunohistochemistry, and targeted panel DNA sequencing on a cohort of 15 PA patients with matched primary/longitudinal samples at a mean sampling interval of 2.7 years. Through pairwise analysis of primary versus longitudinal tumour samples we identified changes to immune-related pathways within the expression and methylation profiles of longitudinal PA. Further interrogation of these changes revealed an enrichment over time for microglial cell populations, which was validated by immunohistochemistry against common monocyte/microglial markers. Moreover, immunohistochemical characterisation revealed concurrent increases in the expression of M2-like and anti-inflammatory markers. Microglial enrichments were consistent across the cohort and were not adequately explained by a range of potential confounders, including receipt of adjuvant therapy. Taken together, these data challenge the idea of pilocytic astrocytoma as a static entity and indicate that they consistently accumulate microglia over time, potentially co-opting the immune microenvironment towards an anti-inflammatory phenotype that may affect the natural course and treatment response of the tumours.

PURPOSE:High-grade gliomas (HGG) occur in any central nervous system location and at any age. HGGs in teenagers/young adults (TYA) are understudied. This project aimed to characterize these tumors to support accurate stratification of patients. EXPERIMENTAL DESIGN:207 histone/IDH wild-type tumors from patients aged 13 to 30 years were collected. DNA methylation profiling [Illumina EPIC BeadArrays, brain tumor classifier (MNPv12.8 R package)] classified cases against reference cohorts of HGG. Calibrated scores guided characterization workflows [RNA-based ArcherDx fusion panel (n = 92), whole-exome sequencing (n = 107), and histology review). RESULTS:53.4% (n = 86) matched as pediatric-type subgroups [pedHGG_RTK1A/B/C (31.7%, n = 51, PDGFRA, CDKN2A/B, SETD2, and NF1 alterations), pedHGG_MYCN (8.1%, n = 13, MYCN/ID2 amplifications), and pedHGG_RTK2A/B (7.5%, n = 12, TP53, BCOR, ATRX, and EGFR alterations)]. Eighteen percent (n = 29) classified as adult-type subgroups [GBM_MES (15.5%, n = 25, enriched for RB1, PTEN, and NF1 alterations) and GBM_RTK1/2 (2.5%, n = 4, CDK4 amplifications)]. Twenty-three cases (14.7%) classified as novel, poorly characterized subgroups with distinct methylation profiles and molecular features [pedHGG_A/B (n = 10 6.2%), HGG_E (n = 6 3.7%), HGG_B (n = 2 1.0%), and GBM_CBM (n = 5 3.1%)] with variable histologic morphology. Eight cases (5.1%) showed hypermutator phenotypes, enriched in HGG_E, one of which was associated with constitutional mismatch repair deficiency, and their sibling, who was diagnosed with the same syndrome, was diagnosed with a tumor that classified as a pedHGG_RTK1B. HGGs that have developed on a background of previous treatment for a childhood cancer are detected in the TYA population, classifying most frequently as pedHGG_RTK1 and contributing to the poor prognosis of this subgroup. Age distribution/molecular profile comparisons using publicly available methylation/sequencing data (and from local diagnostic cohorts) for HGG_B (n = 19), GBM_CBM (n = 35), and GBM_MES_ATYP (n = 102), irrespective of age, show that HGG_B is a TYA-specific subgroup (median age 29 years) and that GBM_CBM and GBM_MES_ATYP show a peak of distribution in the TYA population but also have a wider age distribution (median age 35.7 and 50.5 years, respectively), with the latter showing distinct differences in copy-number profiles compared with older adults in the same subgroup and containing fewer chr7 gains, chr10 losses, more CDKN2A/B deletions and MET amplifications, and a worse survival compared with adult-specific GBM_MES_TYP. CONCLUSIONS:TYA HGGs comprise novel methylation subgroups with distinct methylation and molecular profiles. Accurate stratification of these patients will open opportunities to more effective treatments, including immune checkpoint, MAPK pathway, and PDGFRA inhibitors. See related commentary by Ritzmann et al., p. 3110.

Supplementary Table 3 Copy number analysis. Gene deletions derived from methylation array analysis for the TYA cohort with associated frequencies.

ATRX is one of the most frequently mutated genes in high-risk neuroblastoma. ATRX mutations are mutually exclusive with MYCN amplification and mark a recognizable patient subgroup, presenting in older children with chemotherapy-resistant, slowly progressive disease. The mechanisms underlying how ATRX mutations drive high-risk and difficult-to-treat neuroblastoma are still largely elusive.To unravel the role of ATRX in neuroblastoma, we generated isogenic neuroblastoma cell line models with ATRX loss-of-function and ATRX in-frame multi-exon deletions, representing different types of alterations found in patients. RNA-sequencing analysis consistently showed significant upregulation of inflammatory response pathways in the ATRX-altered cell lines. In vivo, ATRX alterations are consistently associated with macrophage infiltration across multiple xenograft models. Furthermore, ATRX alterations also result in upregulation of epithelial-to-mesenchymal transition pathways and a reduction in expression of adrenergic core-regulatory circuit genes.Consistent with this, bioinformatic analysis of previously published neuroblastoma patient data sets revealed that ATRX-altered neuroblastomas display an immunogenic phenotype and higher score of macrophages (with no distinction between M1 and M2 macrophage populations) and dendritic cells, but not lymphocytes. Histopathological assessment of diagnostic samples from patients with ATRX mutant disease confirmed these findings with significantly more macrophage infiltration compared to MYCN-amplified tumors. In conclusion, we show that gene-expression and cell-state changes as a result of ATRX alterations associate with a characteristic immune cell infiltration in both in vivo models and patient samples. Together, this provides novel insight into mechanisms underlying the distinct clinical phenotype seen in this group of patients.

Adenosine deaminase type 2 deficiency (DADA2) is caused by bi-allelic loss-of-function mutations in ADA2. While anti-TNF therapy is effective for the autoinflamatory and vasculitic components of the disease it does not correct marrow failure or immunodeficiency. Allogeneic stem cell transplantation (HSCT) offers a potential cure but is limited by challenges such as graft-versus-host-disease and donor availability. We previously demonstrated that lentiviral-mediated ADA2 gene therapy could restore ADA2 enzyme activity in patient-derived cells, correct macrophage inflammatory activation and reduce endothelial activation in vitro. Here, we evaluated the biodistribution and engraftment potential of lentivirally transduced healthy donor and patient-derived haematopoietic stem cells (HSC) in vivo using a humanised NBSGW mouse model. Transduced healthy HSC retained multilineage differentiation and engraftment capacity, without functional impairment. PCR analysis confirmed the absence of viral integration in non-haematopoietic organs, and histology showed no abnormal tissue changes, underscoring the safety and precision of this approach. In DADA2 patient-derived HSC, ADA2 transduction restored protein expression and enzyme activity, supporting improved cellular function and enhanced engraftment potential. These findings provide a strong foundation for advancing ADA2 gene therapy as a therapeutic strategy for DADA2, bringing it closer to clinical application.

Abstract Background The thymus, responsible for T cell-mediated adaptive immune system, has a structural and functional complexity that is not yet fully understood. Until now, thymic anatomy has been studied using histological thin sections or confocal microscopy 3D reconstruction, necessarily for limited volumes. Methods We used Phase Contrast X-Ray Computed Tomography to address the lack of whole-organ volumetric information on the microarchitecture of its structural components. We scanned 15 human thymi (9 foetal and 6 postnatal) with synchrotron radiation, and repeated scans using a conventional laboratory x-ray system. We used histology, immunofluorescence and flow cytometry to validate the x-ray findings. Results Application to human thymi at pre- and post-natal stages allowed reliable tracking and quantification of the evolution of parameters such as size and distribution of Hassall’s Bodies and medulla-to-cortex ratio, whose changes reflect adaptation of thymic activity. We show that Hassall’s bodies can occupy 25% of the medulla volume, indicating they should be considered a third thymic compartment with possible implications on their role. Moreover, we demonstrate compatible results can be obtained with standard laboratory-based x-ray equipment, making this research tool accessible to a wider community. Conclusions Our study allows overcoming the resolution and/or volumetric limitations of existing approaches for the study of thymic disfunction in congenital and acquired disorders affecting the adaptive immune system.

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.

Stem cell gene therapy and hematopoietic stem cell transplantation (SCT) require conditioning to ablate the recipient's hematopoietic stem cells (HSCs) and create a niche for gene-corrected/donor HSCs. Conventional conditioning agents are non-specific, leading to off-target toxicities and resulting in significant morbidity and mortality. We developed tissue-specific anti-human CD45 antibody-drug conjugates (ADCs), using rat IgG2b anti-human CD45 antibody clones YTH24.5 and YTH54.12, conjugated to cytotoxic pyrrolobenzodiazepine (PBD) dimer payloads with cleavable (SG3249) or non-cleavable (SG3376) linkers. In vitro, these ADCs internalized to lysosomes for drug release, resulting in potent and specific killing of human CD45+ cells. In humanized NSG mice, the ADCs completely ablated human HSCs without toxicity to non-hematopoietic tissues, enabling successful engraftment of gene-modified autologous and allogeneic human HSCs. The ADCs also delayed leukemia onset and improved survival in CD45+ tumor models. These data provide proof of concept that conditioning with anti-human CD45-PBD ADCs allows engraftment of donor/gene-corrected HSCs with minimal toxicity to non-hematopoietic tissues. Our anti-CD45-PBDs or similar agents could potentially shift the paradigm in transplantation medicine that intensive chemo/radiotherapy is required for HSC engraftment after gene therapy and allogeneic SCT. Targeted conditioning both improve the safety and minimize late effects of these procedures, which would greatly increase their applicability.

Faithful genetically engineered in vivo models of medulloblastoma (MB) are currently available only for some molecular subgroups, in keeping with recent studies showing the unique role of human-specific progenitors in the development of G3 and G4 MB subgroups. We generated human cerebellar organoids (CbO) from expanded potential stem cells (EPSC) and characterised in depth their epigenetic and transcriptomic profile. We show the presence of sub compartment-specific cerebellar lineages linked to MB formation, including populations expressing signature genes of G3 and G4 MB cells-of-origin in a 1 month-old CbO. Moreover, we demonstrate that CbO sustains MB cells proliferation and invasion in a 3D co-culture model (CbO-MB) while preserving their molecular identity, and that treatment of CbO-MB with anti-tumour compounds recapitulate the efficacy of in vivo drug testing in PDX models. ### Competing Interest Statement The authors have declared no competing interest.

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.