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Updated: Jan 7, 2026
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
Published on: August 25, 2020
Single-cell and spatial transcriptome sequencing analysis reveals characteristics of a unique subpopulation in
Wei Chen1, Min Zheng2, Jia-Yin An1,3
1Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
Introduction:
(Isocitrate dehydrogenase) IDH-mutant astrocytoma is classified as World Health Organization (WHO) grade 2-4 and is second only to IDH wild-type glioblastoma in the incidence of adult glioma. However, few studies use single-cell and spatial transcriptome sequencing to analyze its malignant progression.
Methods:
Intraoperative navigation and yellow fluorescence visualization were utilized to accurately isolate high-grade (WHO grade 3-4) and low-grade (WHO grade 2) samples of IDH-mutant astrocytoma for single-cell and spatial transcriptome sequencing. By combining single-cell, spatial transcriptome, The Cancer Genome Atlas (TCGA), and The Chinese Glioma Genome Atlas (CGGA) data, analyses of survival, enriched pathways, transcription factors, intercellular communication, differentiation trajectories, and immune response were performed to identify the characteristics of a unique subpopulation of high-grade IDH-mutant astrocytoma.
Results:
Our single-cell RNA sequencing analysis identified a distinct subpopulation (Cluster 7) present in high-grade IDH-mutant astrocytoma, which was localized to the terminus of the pseudotime trajectory. Importantly, this cluster not only exhibited an immunosuppressive phenotype correlated with poor clinical prognosis, but also demonstrated significant enrichment in Developmental Biology and Calcium Signaling pathways. Furthermore, this subpopulation engaged in prominent ligand-receptor interactions, particularly through PTN_PTPRZ1 and MIF_CD74 pairs. Notably, comparative analysis revealed that high-grade astrocytoma displayed both quantitatively and qualitatively enhanced communication networks when compared to their low-grade counterparts.
Conclusions:
Our single-cell RNA sequencing analysis identifies a distinct tumor cell subpopulation present in high-grade (WHO grade 3-4) adult IDH-mutant astrocytoma. This cluster, which likely arises from malignant progression in adult astrocytoma, may provide new insights for developing therapeutic strategies against this clinically challenging disease.
