10x Genomics, Inc. announced that the 10x Xenium Analyzer was used in a study recently published on bioRxiv characterizing radiation-resistance mechanisms of diffuse midline gliomas (DMGs). Led by researchers at Duke University, the study also provides a lens by which to understand clinical response in patients for current and future clinical trials using a novel kinase inhibitor as part of DMG therapeutic strategies. The study, "Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy," is among the first scientific preprints to include customer-generated data using the Xenium In Situ platform from 10x Genomics.

The high-plex, high-resolution single cell spatial mapping of Xenium was behind many critical conclusions in this study, including revealing key transcriptomic changes, the role of specific tumor compartments, key cell communication pathways and the mechanisms by which key genes function within the therapeutic response. Researchers conducting the study analyzed formalin-fixed paraffin-embedded tissue sections of a mouse brain tumor model that mimics the common human DMG genetic drivers and to examine the molecular and cellular mechanisms driving radiation efficacy or resistance in these tumors. The study put particular focus on the role that loss of Atm, which encodes a protein responsible for cellular response to double-stranded DNA damage, plays in treatment response.

The authors began by generating several DMG mouse models and identifying the conditions under which Atm loss or pharmacological inhibition with brain-penetrant ATM inhibitor AZD1390 leads tumors to exhibit increased sensitivity to radiation. After these genetic experiments implicated tumor suppressor p53 loss as the principal driver of Atm loss?mediated sensitivity to radiation, the researchers used the pre-designed Xenium Mouse Brain Gene Expression Panel to profile key cell types in the brain and designed a Custom Add-on Panel to examine DMG-specific markers. The combination of the pre-designed and custom panels allowed researchers to profile compartment-specific gene expression changes of 298 targets at single cell resolution.

Irradiation treatment was observed to cause differential expression in cell cycle regulators and cell-fate-regulating transcription factors, while the combination of irradiation and Atm loss also impacted Semaphorin genes, which have been previously implicated in glioma proliferation and expansion. The researchers next estimated the distances between tumor cells and other cell types revealing neoplastic tumor cells could be found in closer proximity to certain immune cells as a result of Atm loss or irradiation, but this effect was most pronounced in Atm-null irradiated brains. Additional analyses of the Xenium data revealed a complex interplay between p21 status, a downstream target of p53, and Atm-mediated radiosensitivity, leading the authors to emphasize the importance of considering an animal model's or patient's p21 status for clinical trials involving ATM inhibitors.