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Single-cell transcriptomics of neuroblastoma tumors

ABSTRACT: Single-cell transcriptomics of neuroblastoma tumors

PROVIDER: PRJNA1067585 | ENA |

REPOSITORIES: ENA

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Single-cell transcriptomics of neuroblastoma tumors

Project description:Neuroblastoma is a rare embryonic tumor arising from neural crest development and is responsible for 15% of pediatric cancer-related deaths. Over the past years, several single-cell transcriptome studies were performed to investigate the cell-of-origin and tumor heterogeneity. These individual studies typically involved a limited number of neuroblastoma tumors. To overcome this limitation, we integrated seven single-cell or single-nucleus data sets into a harmonized cell atlas covering 362,991 cells across 68 patient samples. We use this integrated atlas to decipher the transcriptional tumoral landscape of neuroblastoma at single-cell resolution. Notably, within the tumor compartment, we find associations between transcriptomic profiles and clinical outcomes. In addition, we characterize the complex immune cell landscape of neuroblastoma and uncover considerable heterogeneity amongst tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with new data and using it as a reference for data-driven cell type prediction.

2024-08-29 | GSE253865 | GEO

Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics

Project description:The bone marrow (BM) is the third most frequent site of metastasis for solid tumors, creating an unfavorable clinical outcome. It provides a unique microenvironment that promotes growth of tumors, however, the role of different BM cells, their molecular features, and their interactions with tumor cells, are poorly defined. Here, we investigate the BM niche in neuroblastoma (NB), a pediatric cancer of the sympathetic nervous system. NB has been molecularly defined at the primary cancer site, yet, the metastatic site is poorly characterized. We performed single-cell transcriptomics (scRNA-seq) and epigenomic profiling (scATAC-seq) of BM aspirates from 11 subjects spanning three major NB subtypes: patients with MYCN amplification (MNA), ATRX mutations (ATRXmut), and cases that lack these alterations (sporadic): NB cases were then compared to five age-matched and metastasis-free BM (controls), followed by in-depth single cell analyses of tissue diversity and cell-cell interactions. We present the first map of the epigenetic and transcriptomic effects of bone marrow metastases. Our analyses demonstrate that tumor cells in the metastatic niche display plasticity that differs among NB subtypes. NB cells via cell-cell interaction signal to the bone marrow microenvironment, rewiring specifically monocytes, which exhibit M1 and M2 features, marked by activation of pro- and anti-inflammatory programs, and express tumor-promoting factors, reminiscent of tumor-associated macrophages. Our study may provide the basis for a therapeutic approach, targeting tumor-to-microenvironment interactions.

2023-07-20 | PXD036979 | Pride

Gene expression profile at single cell level of neuroblastoma tumors

Project description:Gene expression profile at single cell level of neuroblastoma tumors

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Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity

Project description:Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity

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Project description:Xenograft tumors of neuroblastoma cell lines

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Gene expression profile at single cell level of neuroblastoma tumors and their tumor microenvironment

Project description:Neuroblastoma (NBL) tumors are considered heterogeneous tumors. So far, little detailed information available on their immune environment. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenvironment of neuroblastoma.

2023-12-22 | GSE218003 | GEO

Primary neuroblastoma tumors

Project description:Primary neuroblastoma tumors

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Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics [Spatial Transcriptomics]

Project description:Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage and cell lines derived from neuroblastoma patients have features of either adrenergic neurons (ADRN) or mesenchymal cells (MES). However, identification of MES neuroblastoma cells in patient tumors has been challenging and controversial. This may be due to inter- or intra-patient tumor heterogeneity or discrepancies between the established neuroblastoma cell lines and patient tumors. To characterize the intra- and inter-patient cellular heterogeneity, we analyzed 54 neuroblastoma tumors, spanning a broad range of clinical, genetic, and histologic features. We combined single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, spatial transcriptomics, and spatial proteomics. We discovered that the tumor cells are in distinct cellular neighborhoods from the non-malignant immune and stromal cells, but we could not identify MES neuroblastoma cells using the established gene expression signatures developed from cell lines. However, using ADRN/MES gene expression signatures developed from early passage orthotopic patient-derived xenografts, we were able to identify MES neuroblastoma tumor cells. We validated our results using RNA-seq, RNA in situ hybridization, immunostaining, chromatin profiling, spatial transcriptomics, functional studies in organoids, and electron microscopy. MES neuroblastoma tumor cells were more likely to be found in high-risk, MYCN amplified post-treatment samples. Taken together, our results demonstrate that MES neuroblastoma tumor cells are present in patient tumors and may correlate with response to therapy and outcome.

2026-08-20 | GSE332618 | GEO

Single cell RNAseq of human neuroblastoma

Project description:Single cell RNAseq of human neuroblastoma

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Gene expression profile at single cell level of Mycn-nGEMM mouse neuroblastoma tumors and their tumor microenvironment

Project description:Neuroblastomas are highly heterogeneous tumors originating from neural crest-derived cells destined to form the sympathetic nervous system. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenvironment of Mycn-nGEMM mouse neuroblastoma.

2025-06-30 | GSE299403 | GEO

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