Tumour hypoxia promotes increased proliferation, migration, and invasion of cancer cells. Expression of the hypoxia-induced enzyme carbonic anhydrase IX is associated with an unfavourable prognosis in breast cancer patients, highlighting the need for novel chemotherapeutic strategies to enhance the sensitivity of hypoxic tumour cells to chemoradiotherapy. Notably, combinations of triterpenes with carbonic anhydrase inhibitors (CAIs) have been shown to induce high cytotoxicity, apoptosis, and radiosensitization in breast cancer cells.

Here, we perform RNA-seq experiments to investigate the transcriptional response of the triple-negative breast cancer cell line MDA-MB-231 to a novel betulinic-acid-based sulfamate (CAI3) in a quantitative, fold-change-specific manner. We find that CAI3 simultaneously orchestrates a broad spectrum of biological pathways, including mitosis, DNA replication and repair, and chromatin regulation. The coordination principles underlying this complex orchestration remain poorly understood, but we observe that (i) genes associated with the same pathway respond to CAI3 with remarkably similar fold changes and that (ii) these fold changes differ systematically between pathways.

These findings suggest the existence of a transcriptional logic that governs the coordinated, pathway-specific regulation of gene expression in a fold-change-dependent manner. To gain initial insight into this coordinated response, we developed a novel pathway-enrichment approach that identifies pathways shared by groups of genes exhibiting similar response magnitudes, e.g., pathways associated with weakly, moderately, or strongly differentially expressed genes. Applying this method to CAI3-treated MDA-MB-231 cells, we identify numerous pathways enriched in a fold-change-specific manner, several of which remain undetected by conventional pathway enrichment approaches.

Co-authors: Matthias Bache, Jan Grau, Antje Güttler, Marina Petrenko, Dirk Vordermark, Ivo Grosse