Dissecting CIC::DUX4 oncogenic circuitry through single-cell perturbation profiling and network inference

Fusion-driven sarcomas represent a unique model for studying the fundamental mechanisms of cancer initiation, as they are among the most genetically simple human cancers. These tumours are initiated by chromosomal translocations that generate potent oncogenic fusion proteins capable of reprogramming normal cells into malignant ones. One such fusion, CIC::DUX4, functions as a chimeric transcription factor that aberrantly upregulates gene expression and leads to tumour formation in children and young adults. However, the precise combinations of activated genes that kickstart malignant reprogramming remain unknown.

This PhD project aims to uncover which genes cooperate to promote malignant transformation. Using CIC::DUX4 expression in normal mesenchymal stem cells, we have established a model of CIC::DUX4-mediated tumour initiation. We have already mapped CIC::DUX4 binding sites and transcriptional signatures, identifying a set of direct transcriptional targets. Building on this foundation, the student will employ CRISPR activation (CRISPRa) to ectopically activate these target genes and use single-cell RNA sequencing to identify the gene combinations and regulatory modules that are sufficient to induce oncogenic transformation.

The project integrates cutting-edge experimental and computational training. Experimentally, the student will gain hands-on experience in cellular and molecular biology, CRISPR activation screens, and single-cell perturbation analysis. On the computational side, they will receive training in single-cell data analysis, network inference, and systems modelling. These approaches will be used to reconstruct and simulate the regulatory networks activated by CIC::DUX4 across different cellular contexts, identifying both conserved and context-specific oncogenic programs.

This interdisciplinary project is ideally suited for a student interested in functional genomics and computational systems biology, with a focus on understanding how transcriptional rewiring drives cancer.