Macrophage-Tumor Cell Interaction Promotes ATRT Progression and Chemoresistance (NODSCID)

Atypical teratoid/rhabdoid tumors (ATRT) are known for their heterogeneity concerning pathophysiology and outcome. However, predictive factors within distinct subgroups still need to be uncovered. Using multiplex immunofluorescent staining and singe-cell RNA sequencing we unraveled distinct compositions of the immunological tumor microenvironment (TME) across ATRT subgroups. CD68+ cells predominantly infiltrate ATRT-SHH and ATRT-MYC and are a negative prognostic factor for patients’ survival. Within the murine ATRT-MYC and ATRT-SHH TME, Cd68+ macrophages are core to intercellular communication with tumor cells. In ATRT-MYC distinct tumor cell phenotypes express macrophage marker genes. These cells are involved in the acquisition of chemotherapy resistance in our relapse xenograft mouse model. In conclusion, the tumor cell-macrophage interaction contributes to ATRT-MYC heterogeneity and tumor recurrence. We used 7-9 weeks old immune-compromised NOD/SCID mice (Jackson Laboratory, www.jax.org) for xenograft experiments. Ten thousand single sphere-forming cells of the BT-16 cell line (ATRT-MYC) were diluted in 5 µl sterile PBS and injected into the striatum (anteroposterior: 0 mm; lateral: 2.5 mm; dorso-ventral: 3 mm). Orthotopically transplanted NOD/SCID mice were monitored regularly for signs of tumor formation and examined by small animal Magnetic Resonance Imaging (MRI) for the assessment of tumor engraftment and growth. After detection of tumor presence, mice were treated in adaptation to the European Rhabdoid Registry (EU-RHAB) to assess potential therapy-resistant ATRT. Tumors from chemotreated and untreated mice were isolated, dispersed into single cells and further processed for scRNA-seq. Quality-filtered sequence data were merged and subjected to dimensionality reduction and cell cycle regression to mitigate the effects of cell cycle heterogeneity. This resulted in a total of 9,637 cells, which represent tumor cells as well as tumor-associated non-tumor cells including immune cells.