ID #169 A platform to interrogate tumor-neuronal relationships in genetic models of brain cancer

Abstract

Neuronal regulation of pediatric brain tumors has emerged as an important contributor to cancer progression, yet tools to interrogate tumor-neuron interactions in native, developmentally accurate models remain limited. This has constrained our ability to understand how neural circuits engage tumors across space, time, genetic context, and native cellular microenvironment; limiting identification of therapeutic vulnerabilities.

Here, we established a genetic platform to systematically investigate tumor-neuronal connectivity in pediatric brain tumors using ependymoma (EPN) as a disease model. We developed the first neuronal tracing platform in an autochthonous, in utero electroporation (IUE)-based mouse model of EPN, enabling direct interrogation of tumor-neuron interactions in the intact brain. By combining MRI-guided stereotaxic rabies viral delivery with trans-synaptic tracing, we achieved precise mapping of neuronal inputs to tumors in vivo. Integration of single-cell RNA sequencing and spatial transcriptomics generated the first transcriptomic and anatomical map of the EPN connectome, revealing how defined neuronal populations connect tumor cells across developmental stages and locations.

We demonstrate that ZFTA-RELA-driven EPNs establish structured neuronal inputs, forming a tumor-neuronal connectome composed of both glutamatergic and GABAergic neurons. These interactions are spatially organized, emerge as early as the neonatal period, and are shaped by tumor size and location, indicating that EPNs embed within developmentally programmed neural circuits. In striking contrast, YAP1-MAMLD1-driven EPN lack detectable neuronal input despite arising within the same neural environment, revealing for that neuronal integration is oncogene-specific rather than universal.

This work introduces a broadly applicable experimental platform for cancer neuroscience in other cancer types. The combination of IUE-based tumor modeling, MRI-guided circuit interrogation, and connectome-level spatial transcriptomic mapping is readily extendable to diverse developmental brain tumor models. Together, these advances expand the experimental repertoire for studying tumor-neuron crosstalk and provide a foundation for systematically defining when, where, and how neural circuits influence pediatric brain tumor biology.