Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis

Epithelial-to-mesenchymal transition (EMT) and cancer metastasis: the status quo of methods and experimental models 2025

Epithelial-to-mesenchymal transition (EMT) is a crucial cellular process for embryogenesis, wound healing, and cancer progression. It involves a shift in cell interactions, leading to the detachment of epithelial cells and activation of gene programs promoting a mesenchymal state. EMT plays a significant role in cancer metastasis triggering tumor initiation and stemness, and activates metastatic cascades resulting in resistance to therapy. Moreover, reversal of EMT contributes to the formation of metastatic lesions. Metastasis still needs to be better understood functionally in its major but complex steps of migration, invasion, intravasation, dissemination, which contributes to the establishment of minimal residual disease (MRD), extravasation, and successful seeding and growth of metastatic lesions at microenvironmentally heterogeneous sites. Therefore, the current review article intends to present, and discuss comprehensively, the status quo of experimental models able to investigate EMT and metastasis in vitro and in vivo, for researchers planning to enter the field. We emphasize various methods to understand EMT function and the major steps of metastasis, including diverse migration, invasion and matrix degradation assays, microfluidics, 3D co-culture models, spheroids, organoids, or latest spatial and imaging methods to analyze complex compartments. In vivo models such as the chorionallantoic membrane (CAM) assay, cell line-derived and patient-derived xenografts, syngeneic, genetically modified, and humanized mice, are presented as a promising arsenal of tools to analyze intravasation, site specific metastasis, and treatment response. Furthermore, we give a brief overview on methods detecting dissemination and MRD in carcinomas, highlighting its significance in tracking the course of disease and response to treatment. Enhanced lineage tracking tools, dynamic in vivo imaging, and therapeutically useful in vivo models as powerful preclinical tools may still better reveal functional interdependencies between metastasis and EMT. Future directions are discussed in light of emerging views on the biology, diagnosis, and treatment of EMT and metastasis.

Dysregulation of the Bone Marrow Microenvironment in Pediatric Tumors: The Role of Extracellular Vesicles in Acute Leukemias and Neuroblastoma

The role of extracellular vesicles has been extensively studied in physiological and pathological conditions, and growing evidence has pinpointed them as key players in tumor progression, regulation of the metastatic niche, and modulation of anti-tumor immune responses. Indeed, a dynamic transfer of extracellular vesicles between cancer cells and immunological or non-immunological cells homing in the tumor microenvironment exists, and the balance between their release by cancer cells and by normal cells determines cancer progression. Here, we focused on the role of extracellular vesicles in the dysregulation of the bone marrow environment in pediatric tumors such as acute leukemias and neuroblastomata, whose poor prognosis is strictly related to the involvement of such anatomical site. Acute leukemias arise from bone marrow progenitors, whereas approximately 50% of neuroblastoma patients have bone marrow metastases at diagnosis. Thus, here, we discuss the mechanisms underlying the bone marrow dysregulation in pediatric acute leukemias and neuroblastomata with particular emphasis on the involvement of extracellular vesicles.

Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization

Bone is a common site for metastasis of solid cancers. The diversity of histological and molecular characteristics of bone metastases (BMs) remains poorly studied. Here, we performed single-cell RNA sequencing on 42 BMs from eight cancer types, identifying three distinct ecosystem archetypes, each characterized by an enrichment of specific immune cells: macrophages/osteoclasts, regulatory/exhausted T cells, or monocytes. We validated these archetypes by immunostaining on tissue sections and bioinformatic analysis of bulk RNA sequencing/microarray data from 158 BMs across more than 10 cancer types. Interestingly, we found only a modest correlation between the BM archetypes and the tissues of origin; BMs from the same cancer type often fell into different archetypes, while BMs from different cancer types sometimes converged on the same archetype. Additional analyses revealed parallel immunosuppression and bone remodeling mechanisms, some of which were experimentally validated. Overall, we discovered unappreciated heterogeneity of BMs across different cancers.

Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring

High-risk neuroblastoma, a leading cause of pediatric cancer mortality, exhibits substantial intratumoral heterogeneity, contributing to therapeutic resistance. To understand tumor microenvironment evolution during therapy, we longitudinally profiled 22 patients with high-risk neuroblastoma before and after induction chemotherapy using single-nucleus RNA and ATAC sequencing and whole-genome sequencing. This revealed profound shifts in tumor and immune cell subpopulations after therapy and identified enhancer-driven transcriptional regulators of neuroblastoma neoplastic states. Poor outcome correlated with proliferative and metabolically active neoplastic states, whereas more differentiated neuronal-like states predicted better prognosis. Proportions of mesenchymal neoplastic cells increased after therapy and a high proportion correlated with a poorer chemotherapy response. Macrophages significantly expanded towards pro-angiogenic, immunosuppressive and metabolic phenotypes. We identified paracrine signaling networks and validated the HB-EGF-ERBB4 axis between macrophage and neoplastic subsets, which promoted tumor growth through the induction of ERK signaling. These findings collectively reveal intrinsic and extrinsic regulators of therapy response in high-risk neuroblastoma.

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.

The mechanism of action and therapeutic potential of tumor-associated macrophages in tumor immune evasion

Tumor-associated macrophages (TAMs) play a multifaceted role in tumor progression. As specialized immune cells, macrophages are capable of phagocytosis and digesting foreign substances, as well as removing harmful substances including cellular debris and tumor cells. Under specific pathological conditions, circulating monocytes can be recruited into the tumor microenvironment and differentiate into TAMs. Macrophages are generally polarized into two distinct subpopulations: classically activated macrophages (M1) and alternatively activated macrophages (M2). TAMs constitute a significant proportion of the mononuclear leukocyte population in solid tumors, exhibiting a complex and dualistic relationship with tumor cells. Substantial evidence indicates that TAMs can interact with tumor cells, facilitating their immune evasion while promoting invasion and metastasis. This review focuses on the mechanism and regulation of macrophages in the immune response to tumor cells, as well as various macrophage-based tumor-targeted therapeutic strategies. It will provide a reference for research on macrophage-centered therapy strategies and their application in clinical practice.

Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma

INTRODUCTION

Chimeric antigen receptor (CAR) T-cell therapy is a promising and innovative cancer therapy. However, immunosuppressive tumor microenvironments (TME) limit T cell persistence and durable efficacy. Here, we aimed to identify and target immunosuppressive factors in the TME of neuroblastoma, a pediatric extracranial solid tumor, to improve CAR-T efficacy.

METHODS

Immunosuppressive factors were identified using a multi-omics approach, including single-cell RNA sequencing (scRNA-seq) of 24 neuroblastoma tumors, published bulk-RNA sequencing datasets, and mass-spectrometry of patient-derived tumoroid models. Candidate targets were validated with functional assays in vitro and in vivo. Protein degradation of the top immunosuppressive target by PROTAC technology was used to evaluate the effect on CAR T-cell activity.

RESULTS

ScRNA-seq revealed 13 immunosuppressive interactions in the TME of neuroblastoma, two effectors of which, Midkine (MDK) and Macrophage Migration Inhibitory Factor (MIF), were validated as candidate targets across multiple published datasets. Both factors were among the top 6 % of most abundantly secreted factors by patient-derived tumoroid models, substantiating their potential relevance in the TME. In vitro and in vivo functional assays confirmed MIF to be a potent inhibitor of CAR T-cell activation and killing capacity. To translate these findings into a potentially clinically applicable treatment, we explored MIF targeting by PROTAC technology, which significantly enhanced activation of CAR T-cells targeting GPC2 and B7-H3.

CONCLUSION

By defining the immunosuppressive effects of neuroblastoma's TME on CAR T-cell efficacy, revealing the pivotal role of MIF, we provide an analytic pipeline and therapeutic strategy for improving adoptive cell therapies for this pediatric malignancy and potentially other solid tumors.

Advances in tumor immunotherapy targeting macrophages

INTRODUCTION

In recent years, immunotherapy has shown significant therapeutic potential in patients with advanced tumors. However, only a small number of individuals benefit, mainly due to the tumor microenvironment (TME), which provides conditions for the development of tumors. Macrophages in TME, known as tumor-associated macrophages (TAM), are mainly divided into M1 anti-tumor and M2 pro-tumor phenotypes, which play a regulatory role in various stages of tumorigenesis, promote tumorigenesis and metastasis, and cause immunotherapy resistance.

AREAS COVERED

This review focuses on research strategies and preclinical/clinical research progress in translating TAM into antitumor phenotype by referring to the PubMed database for five years. These include small molecule chemotherapy drug development, metabolic regulation, gene editing, physical stimulation, nanotechnology-mediated combination therapy strategies, and chimeric antigen receptor-based immunotherapy.

EXPERT OPINION

It is necessary to explore the surface-specific receptors and cell signaling pathways of TAM further to improve the specificity and targeting of drugs and to strengthen research in the field of probes that can monitor changes in TAM in real time. In addition, the physical stimulation polarization strategy has the advantages of being noninvasive, economical, and stable and will have excellent clinical transformation value in the future.

Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid

Retinoic acid (RA) is a standard-of-care neuroblastoma drug thought to be effective by inducing differentiation. Curiously, RA has little effect on primary human tumors during upfront treatment but can eliminate neuroblastoma cells from the bone marrow during post-chemo maintenance therapy-a discrepancy that has never been explained. To investigate this, we treat a large cohort of neuroblastoma cell lines with RA and observe that the most RA-sensitive cells predominantly undergo apoptosis or senescence, rather than differentiation. We conduct genome-wide CRISPR knockout screens under RA treatment, which identify bone morphogenic protein (BMP) signaling as controlling the apoptosis/senescence vs differentiation cell fate decision and determining RA's overall potency. We then discover that BMP signaling activity is markedly higher in neuroblastoma patient samples at bone marrow metastatic sites, providing a plausible explanation for RA's ability to clear neuroblastoma cells specifically from the bone marrow, by seemingly mimicking interactions between BMP and RA during normal development.

CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data

Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and have many arbitrary parameter choices. Methods that can model scRNA-seq data as non-discrete "gene expression programs" (GEPs) can better preserve the data's structure, but currently, they are often not scalable, not consistent across repeated runs, and lack an established method for choosing key parameters. Here, we developed a GPU-based unsupervised learning approach, "consensus and scalable inference of gene expression programs" (CSI-GEP). We show that CSI-GEP can recover ground truth GEPs in real and simulated atlas-scale scRNA-seq datasets, significantly outperforming cutting-edge methods, including GPT-based neural networks. We applied CSI-GEP to a whole mouse brain atlas of 2.2 million cells, disentangling endothelial cell types missed by other methods, and to an integrated scRNA-seq atlas of human tumors and cell lines, discovering mesenchymal-like GEPs unique to cancer cells growing in culture.

Detection of circulating tumor cells using a microfluidic chip for diagnostics and therapeutic prediction in mediastinal neuroblastoma

Circulating tumor cells (CTCs) have served as noninvasive tumor biomarkers in many types of cancer. Here, we detected CTCs in mediastinal neuroblastoma (mNB) patients for use as diagnostic and treatment response predictive biomarkers. We employed a cascaded filter deterministic lateral displacement microfluidic chip (CFD-Chip) to enrich CTCs in peripheral blood from 32 mNB patients and 7 healthy children. CTCs were identified by immunofluorescence staining and integrated neoplastic cell morphology. In total, 66.67% of newly diagnosed mNB patients were positive for CTCs while no CTCs were detected in healthy children. Moreover, CTC count differed significantly across different International Neuroblastoma Staging System, International Neuroblastoma Risk Group staging system, and risk stratifications. CTC count was also significantly higher in children with metastasis than those without metastasis. Additionally, CTC demonstrated a significant difference among patients with different clinical responses to therapy. CTC count decreased or fluctuated at low levels in patients with complete and partial response, compared to considerably increased in patients with stable and progressive diseases.Conclusion: CTCs may serve as non-invasive indicators for mNB diagnosis, staging, and metastasis prediction, and demonstrate promising potential as a liquid biopsy biomarker for the dynamic monitoring of therapeutic efficacy.

Natural killer cells in neuroblastoma: immunological insights and therapeutic perspectives

Natural killer (NK) cells have multifaceted roles within the complex tumor milieu. They are pivotal components of innate immunity and shape the dynamic landscape of tumor-immune cell interactions, and thus can be leveraged for use in therapeutic interventions. NK-based immunotherapies have had remarkable success in hematological malignancies, but these therapies are met with many challenges in solid tumors, including neuroblastoma (NB), a childhood tumor arising from the sympathetic nervous system. With a focus on NB, this review outlines the mechanisms employed by NK cells to recognize and eliminate malignant cells, delving into the dynamic relationship between ligand-receptor interactions, cytokines, and other molecules that facilitate the cross talk between NK and NB cells. We discuss the immunomodulatory functions of NK cells and the mechanisms that contribute to loss of this immunosurveillance in NB, with a focus on how this dynamic has been utilized in recent immunotherapy advancements for NB.

Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway

Neuroblastoma (NB) is the most prevalent extracranial solid tumor in pediatric patients, and its treatment failure often associated with metastasis. In this study, LASSO, SVM-RFE, and random forest tree algorithms, was used to identify the pivotal gene involved in NB metastasis. NB cell lines (SK-N-AS and SK-N-BE2), in conjunction with NB tissue were used for further study. ABLIM3 was identified as the hub gene and can be an independent prognostic factor for patients with NB. The immunohistochemical analysis revealed that ABLIM3 is negatively correlated with the metastasis of NB. Patients with low expression of ABLIM3 had a poor prognosis. High ABLIM3 expression correlated with APC co-stimulation and Type1 IFN response, and TIDE analysis indicated that patients with low ABLIM3 expression exhibited enhanced responses to immunotherapy. Downregulation of ABLIM3 by shRNA transfection increased the migration and invasion ability of NB cells. Gene Set Enrichment Analysis (GSEA) revealed that genes associated with ABLIM3 were primarily enriched in the cell adhesion molecules (CAMs) pathway. RT-qPCR and western blot analyses demonstrated that downregulation of ABLIM3 led to decreased expression of ITGA3, ITGA8, and KRT19, the key components of CAMs. This study indicated that ABLIM3 can be an independent prognostic factor for NB patients, and CAMs may mediate the effect of ABLIM3 on the metastasis of NB, suggesting that ABLIM3 is a potential therapeutic target for NB metastasis, which provides a novel strategy for future research and treatment strategies for NB patients.

Neuroblastoma plasticity during metastatic progression stems from the dynamics of an early sympathetic transcriptomic trajectory

Despite their indisputable importance in neuroblastoma (NB) pathology, knowledge of the bases of NB plasticity and heterogeneity remains incomplete. They may be rooted in developmental trajectories of their lineage of origin, the sympatho-adrenal neural crest. We find that implanting human NB cells in the neural crest of the avian embryo allows recapitulating the metastatic sequence until bone marrow involvement. Using deep single cell RNA sequencing, we characterize transcriptome states of NB cells and their dynamics over time and space, and compare them to those of fetal sympatho-adrenal tissues and patient tumors and bone marrow samples. Here we report remarkable transcriptomic proximities restricted to an early sympathetic neuroblast branch that co-exist with phenotypical adaptations over disease progression and recapitulate intratumor and interpatient heterogeneity. Combining avian and patient datasets, we identify a list of genes upregulated during bone marrow involvement and associated with growth dependency, validating the relevance of our multimodal approach.

Macrophage diversity in cancer dissemination and metastasis

Invasion and metastasis are hallmarks of cancer. In addition to the well-recognized hematogenous and lymphatic pathways of metastasis, cancer cell dissemination can occur via the transcoelomic and perineural routes, which are typical of ovarian and pancreatic cancer, respectively. Macrophages are a universal major component of the tumor microenvironment and, in established tumors, promote growth and dissemination to secondary sites. Here, we review the role of tumor-associated macrophages (TAMs) in cancer cell dissemination and metastasis, emphasizing the diversity of myeloid cells in different tissue contexts (lungs, liver, brain, bone, peritoneal cavity, nerves). The generally used models of lung metastasis fail to capture the diversity of pathways and tissue microenvironments. A better understanding of TAM diversity in different tissue contexts may pave the way for tailored diagnostic and therapeutic approaches.

NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell of origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus datasets into a harmonized cell atlas covering 362,991 cells across 61 patients. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution, revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune-cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with additional data and using it as a reference for data-driven cell-type annotation.

CAR T-cell-mediated delivery of bispecific innate immune cell engagers for neuroblastoma

Novel chimeric antigen receptor (CAR) T-cell approaches are needed to improve therapeutic efficacy in solid tumors. High-risk neuroblastoma is an aggressive pediatric solid tumor that expresses cell-surface GPC2 and GD2 with a tumor microenvironment infiltrated by CD16a-expressing innate immune cells. Here we engineer T-cells to express a GPC2-directed CAR and simultaneously secrete a bispecific innate immune cell engager (BiCE) targeting both GD2 and CD16a. In vitro, GPC2.CAR-GD2.BiCE T-cells induce GPC2-dependent cytotoxicity and secrete GD2.BiCE that promotes GD2-dependent activation of antitumor innate immunity. In vivo, GPC2.CAR-GD2.BiCE T-cells locally deliver GD2.BiCE and increase intratumor retention of NK-cells. In mice bearing neuroblastoma patient-derived xenografts and reconstituted with human CD16a-expressing immune cells, GD2.BiCEs enhance GPC2.CAR antitumor efficacy. A CAR.BiCE strategy should be considered for tumor histologies where antigen escape limits CAR efficacy, especially for solid tumors like neuroblastoma that are infiltrated by innate immune cells.

Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma

Neuroblastoma (NB) is one of the most common childhood malignancies. Sixty percent of patients present with widely disseminated clinical signs at diagnosis and exhibit poor outcomes. However, the molecular mechanisms triggering NB metastasis remain largely uncharacterized. In this study, we generated a transcriptomic atlas of 15 447 NB cells from eight NB samples, including paired samples of primary tumors and bone marrow metastases. We used time-resolved analysis to chart the evolutionary trajectory of NB cells from the primary tumor to the metastases in the same patient and identified a common 'starter' subpopulation that initiates tumor development and metastasis. The 'starter' population exhibited high expression levels of multiple cell cycle-related genes, indicating the important role of cell cycle upregulation in NB tumor progression. In addition, our evolutionary trajectory analysis demonstrated the involvement of partial epithelial-to-mesenchymal transition (p-EMT) along the metastatic route from the primary site to the bone marrow. Our study provides insights into the program driving NB metastasis and presents a signature of metastasis-initiating cells as an independent prognostic indicator and potential therapeutic target to inhibit the initiation of NB metastasis.

The neuroblastoma tumor microenvironment: From an in-depth characterization towards novel therapies

Neuroblastoma is a cancer of the sympathetic nervous system that develops in young children, either as low-risk or high-risk disease. The tumor microenvironment (TME) is now recognized as an important player of the tumor ecosystem that may promote drug resistance and immune escape. Targeting the TME in combination with therapies directly targeting tumor cells therefore represents an interesting strategy to prevent the emergence of resistance in cancer and improve patient's outcome. The development of such strategies however requires an in-depth understanding of the TME landscape, due to its high complexity and intra and inter-tumoral heterogeneity. Various approaches have been used in the last years to characterize the immune and non-immune cell populations present in tumors of neuroblastoma patients, both quantitatively and qualitatively, in particular with the use of single-cell transcriptomics. It is anticipated that in the near future, both genomic and TME information in tumors will contribute to a precise approach to therapy in neuroblastoma. Deciphering the mechanisms of interaction between neuroblastoma cells and stromal or immune cells in the TME is key to identify novel therapeutic combinations. Over the last decade, numerous in vitro studies and in vivo pre-clinical experiments in immune-competent and immune-deficient models have identified therapeutic approaches to circumvent drug resistance and immune escape. Some of these studies have formed the basis for early phase I and II clinical trials in children with recurrent and refractory high-risk neuroblastoma. This review summarizes recently published data on the characterization of the TME landscape in neuroblastoma and novel strategies targeting various TME cellular components, molecules and pathways activated as a result of the tumor-host interactions.

Mgp High-Expressing MSCs Orchestrate the Osteoimmune Microenvironment of Collagen/Nanohydroxyapatite-Mediated Bone Regeneration

Activating autologous stem cells after the implantation of biomaterials is an important process to initiate bone regeneration. Although several studies have demonstrated the mechanism of biomaterial-mediated bone regeneration, a comprehensive single-cell level transcriptomic map revealing the influence of biomaterials on regulating the temporal and spatial expression patterns of mesenchymal stem cells (MSCs) is still lacking. Herein, the osteoimmune microenvironment is depicted around the classical collagen/nanohydroxyapatite-based bone repair materials via combining analysis of single-cell RNA sequencing and spatial transcriptomics. A group of functional MSCs with high expression of matrix Gla protein (Mgp) is identified, which may serve as a pioneer subpopulation involved in bone repair. Remarkably, these Mgp high-expressing MSCs (MgphiMSCs) exhibit efficient osteogenic differentiation potential and orchestrate the osteoimmune microenvironment around implanted biomaterials, rewiring the polarization and osteoclastic differentiation of macrophages through the Mdk/Lrp1 ligand-receptor pair. The inhibition of Mdk/Lrp1 activates the pro-inflammatory programs of macrophages and osteoclastogenesis. Meanwhile, multiple immune-cell subsets also exhibit close crosstalk between MgphiMSCs via the secreted phosphoprotein 1 (SPP1) signaling pathway. These cellular profiles and interactions characterized in this study can broaden the understanding of the functional MSC subpopulations at the early stage of biomaterial-mediated bone regeneration and provide the basis for materials-designed strategies that target osteoimmune modulation.

Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid

Retinoic acid (RA) is a standard-of-care neuroblastoma drug thought to be effective by inducing differentiation. Curiously, RA has little effect on primary human tumors during upfront treatment but can eliminate neuroblastoma cells from the bone marrow during post-chemo consolidation therapy-a discrepancy that has never been explained. To investigate this, we treated a large cohort of neuroblastoma cell lines with RA and observed that the most RA-sensitive cells predominantly undergo apoptosis or senescence, rather than differentiation. We conducted genome-wide CRISPR knockout screens under RA treatment, which identified BMP signaling as controlling the apoptosis/senescence vs differentiation cell fate decision and determining RA's overall potency. We then discovered that BMP signaling activity is markedly higher in neuroblastoma patient samples at bone marrow metastatic sites, providing a plausible explanation for RA's ability to clear neuroblastoma cells specifically from the bone marrow, seemingly mimicking interactions between BMP and RA during normal development.

A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.

Management of High-Risk Neuroblastoma with Soft-Tissue-Only Disease in the Era of Anti-GD2 Immunotherapy

Neuroblastoma presents with two patterns of disease: locoregional or systemic. The poor prognostic risk factors of locoregional neuroblastoma (LR-NB) include age, MYCN or MDM2-CDK4 amplification, 11q, histology, diploidy with ALK or TERT mutations, and ATRX aberrations. Anti-GD2 immunotherapy has significantly improved the outcome of high-risk (HR) NB and is mostly effective against osteomedullary minimal residual disease (MRD), but less so against soft tissue disease. The question is whether adding anti-GD2 monoclonal antibodies (mAbs) benefits patients with HR-NB compounded by only soft tissue. We reviewed 31 patients treated at SJD for HR-NB with no osteomedullary involvement at diagnosis. All tumors had molecular genetic features of HR-NB. The outcome after first-line treatment showed 25 (80.6%) patients achieving CR. Thirteen patients remain in continued CR, median follow-up 3.9 years. We analyzed whether adding anti-GD2 immunotherapy to first-line treatment had any prognostic significance. The EFS analysis using Cox models showed a HR of 0.20, p = 0.0054, and an 80% decrease in the risk of relapse in patients treated with anti-GD2 immunotherapy in the first line. Neither EFS nor OS were significantly different by CR status after first-line treatment. In conclusion, adding treatment with anti-GD2 mAbs at the stage of MRD helps prevent relapse that unequivocally portends poor survival.

Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation

Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defense. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized, which limits their applicability to studying human disease. Here we show, by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages, a high-resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors, including C/ebp-β, which is important for late neutrophil maturation. Cross-species comparison of zebrafish, mouse, and human samples confirms high molecular similarity of immature stages and discriminates zebrafish-specific from pan-species gene signatures. Applying the pan-species neutrophil maturation signature to RNA-sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease.

Predicting Bone Marrow Metastasis in Neuroblastoma: An Explainable Machine Learning Approach Using Contrast-Enhanced Computed Tomography Radiomics Features

PURPOSE

To predict bone marrow metastasis in neuroblastoma using contrast-enhanced computed tomography (CECT) radiomics features and explainable machine learning.

METHODS

This cohort study retrospectively included a total of 345 neuroblastoma patients who underwent testing for bone marrow metastatic status. Tumor lesions on CECT images were delineated by two radiologists, and 1409 radiomics features were extracted. Correlation analysis, Least Absolute Shrinkage and Selection Operator regression, and one-way analysis of variance were used to identify radiomics features associated with bone marrow metastasis. A predictive model for bone marrow metastasis was then developed using the support vector machine algorithm based on the selected radiomics features. The performance of the radiomics model was evaluated using the area under the curve (AUC), 95% confidence interval (CI), accuracy, sensitivity, and specificity.

RESULTS

The radiomics model included 16 features, with a predominant focus on texture features (12/16, 75%). In the training set, the model demonstrated an AUC of 0.891 (95% CI: 0.848-0.933), an accuracy of 0.831 (95% CI: 0.829-0.832), a sensitivity of 0.893 (95% CI: 0.840-0.946), and a specificity of 0.757 (95% CI: 0.677-0.837). In the test set, the AUC, accuracy, sensitivity, and specificity were 0.807 (95% CI: 0.720-0.893), 0.767 (95% CI: 0.764-0.770), 0.696 (95% CI: 0.576-0.817), and 0.851 (95% CI: 0.749-0.953), respectively.

CONCLUSION

Radiomics features extracted from CECT images are associated with the presence of bone marrow metastasis in neuroblastoma, providing potential new imaging biomarkers for predicting bone marrow metastasis in this disease.

Targeting the myeloid microenvironment in neuroblastoma

Myeloid cells (granulocytes and monocytes/macrophages) play an important role in neuroblastoma. By inducing a complex immunosuppressive network, myeloid cells pose a challenge for the adaptive immune system to eliminate tumor cells, especially in high-risk neuroblastoma. This review first summarizes the pro- and anti-tumorigenic functions of myeloid cells, including granulocytes, monocytes, macrophages, and myeloid-derived suppressor cells (MDSC) during the development and progression of neuroblastoma. Secondly, we discuss how myeloid cells are engaged in the current treatment regimen and explore novel strategies to target these cells in neuroblastoma. These strategies include: (1) engaging myeloid cells as effector cells, (2) ablating myeloid cells or blocking the recruitment of myeloid cells to the tumor microenvironment and (3) reprogramming myeloid cells. Here we describe that despite their immunosuppressive traits, tumor-associated myeloid cells can still be engaged as effector cells, which is clear in anti-GD2 immunotherapy. However, their full potential is not yet reached, and myeloid cell engagement can be enhanced, for example by targeting the CD47/SIRPα axis. Though depletion of myeloid cells or blocking myeloid cell infiltration has been proven effective, this strategy also depletes possible effector cells for immunotherapy from the tumor microenvironment. Therefore, reprogramming of suppressive myeloid cells might be the optimal strategy, which reverses immunosuppressive traits, preserves myeloid cells as effectors of immunotherapy, and subsequently reactivates tumor-infiltrating T cells.

The molecular basis of tumor metastasis and current approaches to decode targeted migration-promoting events in pediatric neuroblastoma

Cell motility is a crucial biological process that plays a critical role in the development of multicellular organisms and is essential for tissue formation and regeneration. However, uncontrolled cell motility can lead to the development of various diseases, including neoplasms. In this review, we discuss recent advances in the discovery of regulatory mechanisms underlying the metastatic spread of neuroblastoma, a solid pediatric tumor that originates in the embryonic migratory cells of the neural crest. The highly motile phenotype of metastatic neuroblastoma cells requires targeting of intracellular and extracellular processes, that, if affected, would be helpful for the treatment of high-risk patients with neuroblastoma, for whom current therapies remain inadequate. Development of new potentially migration-inhibiting compounds and standardized preclinical approaches for the selection of anti-metastatic drugs in neuroblastoma will also be discussed.