Astrocyte and Microglial Transcriptional Programs in the Atypical Teratoid/Rhabdoid Tumor Microenvironment

Background/Objectives: The original GSE283839 study characterized malignant-cell heterogeneity in atypical teratoid/rhabdoid tumor (ATRT). Building on this resource, we investigated the less-characterized glial microenvironment, focusing on astrocyte and microglial transcriptional programs and expression-supported candidate interactions with tumor cells. Methods: We reanalyzed single-nucleus RNA-sequencing data from 12 ATRT tumors using published annotations, program scoring, paired astrocyte–tumor comparisons, and conservative annotation sensitivities. CellChat analyses used 10,000 permutations and within-model Benjamini–Hochberg (BH) correction. An independent cohort comprised eight specimens from four patients. Results: The discovery dataset included 47 annotated astrocytes and 288 annotated microglia. Astrocytes expressed SLC1A2, SLC1A3, and GLUL, with higher glutamate/glutamine-module scores than matched tumor cells in two of three evaluable tumors. This difference persisted in the single tumor evaluable under conservative annotation. Microglia exhibited overlapping inflammatory, immunoregulatory, phagocytic/lipid-processing, and antigen-presentation programs. Across 12 tumors, microglial CD74 expression correlated with the antigen-presentation module score. Candidate interactions included astrocyte-to-tumor NCAM1–FGFR1 and PTN–PTPRZ1 and microglia-to-tumor SPP1-related pairs. Tumor-to-microglia APP–CD74 passed within-model BH correction in 7/10 eligible discovery tumors. External analyses supported tumor-to-myeloid APP–CD74 in at least one myeloid population in each of five evaluable specimens from four patients. Conclusions: This exploratory study highlights astrocyte metabolic expression programs and immune-related microglial programs in ATRT, prioritizing APP–CD74 and additional expression-supported glia–tumor interaction candidates for future spatial and functional investigation.