Single-Cell and Spatial Transcriptomics Study of Meningeal Solitary Fibrous Tumors

Academic Background

Meningeal Solitary Fibrous Tumors (SFTs) are rare mesenchymal tumors originating from the meninges of the central nervous system (CNS). Although SFTs are histologically similar to other meningeal tumors (such as meningiomas), their unique clinical behavior, particularly their tendency for local recurrence and hematogenous metastasis, has drawn significant attention to their biological mechanisms and treatment strategies. Currently, treatment options for SFTs are limited, primarily relying on surgery and radiotherapy, and there are no effective drug therapies for metastatic or treatment-resistant SFTs. Therefore, a deeper understanding of the cellular states and spatial transcriptomic architecture of SFTs is crucial for developing new therapeutic targets.

In recent years, the rapid development of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics has provided new tools for studying tumor heterogeneity and the tumor microenvironment. However, research on SFTs using single-cell and spatial transcriptomics is still in its infancy, particularly regarding their differences from other CNS tumors such as meningiomas. This study aims to integrate single-cell, spatial, and bulk RNA sequencing data to reveal the cellular states, gene expression programs, and differences between SFTs and meningiomas, offering new insights into the biological mechanisms and treatment strategies for SFTs.

Source of the Paper

This paper was co-authored by Kanish Mirchia, Abrar Choudhury, Tara Joseph, Janeth Ochoa Birrueta, Joanna J. Phillips, Aparna Bhaduri, Elizabeth E. Crouch, Arie Perry, and David R. Raleigh. The authors are affiliated with multiple departments at the University of California San Francisco (UCSF), including Radiation Oncology, Neurological Surgery, and Pathology. The paper was published online ahead of print on August 29, 2024, in the journal Neuro-Oncology, with the DOI 10.1093/neuonc/noae172.

Research Process and Results

1. Single-Cell RNA Sequencing Reveals Cellular States of SFTs

The study began with single-cell RNA sequencing of 4 SFT samples, analyzing a total of 40,022 cells. Through UMAP dimensionality reduction analysis, researchers identified 12 cell clusters, including tumor cells and microenvironment cells (such as macrophages, immature neurons, T cells, and endothelial cells). The tumor cell states of SFTs were distinguished by the expression of NAB2 and STAT6 and exhibited gene expression features related to vascular development and homeostasis. For example, some tumor cells highly expressed NCAM2 (neural cell adhesion molecule) and VCAM1 (vascular cell adhesion molecule), while others showed high expression of cell stress genes (e.g., EGR1, HSPA1A) and extracellular matrix (ECM) remodeling genes (e.g., ADAMTS6, PLCG2).

RNA velocity and pseudotime trajectory analysis revealed that the cellular states of SFTs are dynamically plastic, indicating that tumor cell fate decisions are interchangeable. Additionally, cell-cell communication analysis uncovered abundant receptor-ligand interactions within the SFT microenvironment, particularly between SFT cells and endothelial cells or immature neurons.

2. Comparison of Cellular States Between SFTs and Meningiomas

To further distinguish SFTs from meningiomas, researchers integrated single-cell RNA sequencing data from SFTs and 6 meningioma samples, analyzing a total of 70,956 cells. The results showed that SFT cells highly expressed endothelial markers (e.g., CD34), while meningioma cells highly expressed mural cell markers (e.g., NOTCH3). This finding was validated through immunofluorescence and immunohistochemistry experiments, demonstrating significant differences in cellular states between SFTs and meningiomas.

3. Spatial Transcriptomics Reveals Regional Heterogeneity in SFTs

The study also performed spatial transcriptomics on 8 SFT samples, combined with DNA methylation profiling and targeted next-generation sequencing to validate the SFT characteristics of the samples. Spatial transcriptomics data revealed regional heterogeneity in cellular states and gene expression programs across different WHO histological grades and patient-matched primary/recurrent or intracranial/metastatic samples. For instance, WHO grade 3 SFTs showed significantly higher expression of genes related to protein synthesis and ECM remodeling compared to WHO grade 1 SFTs.

4. Bulk RNA Sequencing Validates Gene Expression Features of SFTs

The study further conducted bulk RNA sequencing on 22 SFT samples to validate the findings from single-cell and spatial transcriptomics. The results showed that WHO grade 3 and recurrent SFTs exhibited significant upregulation of genes such as HOXA13 and TNNT1, which are closely associated with tumor progression and metastasis. Additionally, the aberrant expression of VCAM1 in SFTs may provide a new therapeutic target.

Conclusions and Significance

By integrating single-cell, spatial, and bulk RNA sequencing data, this study comprehensively revealed the cellular states, gene expression programs, and differences between SFTs and meningiomas for the first time. The findings indicate that the cellular states of SFTs resemble cerebral vascular development and homeostasis, exhibiting high regional heterogeneity and cellular plasticity. These discoveries not only provide new insights into the biological mechanisms of SFTs but also lay the foundation for developing novel treatment strategies (e.g., targeting VCAM1 or the HOXA13-IGF1R signaling pathway) for SFTs.

Research Highlights

1. Single-Cell RNA Sequencing Reveals SFT Cellular States Resembling Cerebral Vascular Development: The study found that SFT cells highly express endothelial markers and exhibit gene expression features related to cerebral vascular development and homeostasis.
2. Spatial Transcriptomics Reveals Regional Heterogeneity in SFTs: SFTs exhibit regional heterogeneity in cellular states and gene expression programs across different WHO histological grades and patient-matched primary/recurrent or intracranial/metastatic samples.
3. Comparison of Cellular States Between SFTs and Meningiomas: SFT cells highly express endothelial markers, while meningioma cells highly express mural cell markers, providing new molecular markers for differential diagnosis.
4. Bulk RNA Sequencing Validates Gene Expression Features of SFTs: WHO grade 3 and recurrent SFTs show significant upregulation of genes such as HOXA13 and TNNT1, which may serve as potential therapeutic targets for SFTs.

Additional Valuable Information

The single-cell RNA sequencing, spatial RNA sequencing, and targeted next-generation DNA sequencing data from this study have been uploaded to the NCBI Sequence Read Archive (Bioproject ID: PRJNA986661) and Gene Expression Omnibus (Accession: GSE235922), providing valuable data resources for future research.

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Through this study, researchers have not only uncovered the cellular states and gene expression features of SFTs but also provided important scientific evidence for developing novel treatment strategies for this rare tumor. In the future, clinical trials based on these findings may bring new hope to SFT patients.