Cancer is often characterized with the accumulation of mutations and deregulated signaling pathways or metabolic processes, which in turn facilitates uncontrolled proliferative ability to the cell with high dependency on nucleotide metabolisms. Notably, aberrant expression levels in the rate-limiting enzymes of pyrimidine metabolism (PyMet) attributes 80% of cancer types, and the understanding of the intricate signaling pathways or metabolic processes behind PyMet is quite limited. Therefore, a comprehensive portrait of the signaling pathways and metabolisms connections with PyMet is essential to exploit therapeutic strategies for cancer.

A pan-cancer analysis of PyMet’s interaction with signaling pathways and metabolic processes was performed using a pathway-based approach in around 10,000 gene expression profiles of 32 cancer types utilizing a large collection of gene-sets representing signaling pathways and metabolic processes. The identified interactions were further validated in vitro using pyrimidine metabolic inhibitor (brequinar) treatments and genetic knockdowns. In addition, PyMet inhibition was explored for the synergistic activity with commonly used chemotherapeutic drugs such as cisplatin and doxorubicin using cell lines and mouse derived KrasG12D p53Δ/Δ lung tumor organoids to improve chemosensitivity of the drugs.

Pan-cancer analysis with pathway-based approach has identified a strong inter-dependency of regulatory connections of PyMet including TERT, MTOR, DAX1, HOXA1, TP53 and TNC which in turn was tightly linked to chemoresistance. These PyMet-signaling interactions were further validated in vitro by inhibiting thymidylate synthase activity using knockdown approach and with brequinar treatment. Strikingly, chemoresistance gene signatures of widely used clinical drugs such as doxorubicin and cisplatin showed an inverse association pattern with brequinar treatment profile. In fact, brequinar treatment in cell lines and mouse-derived lung tumor organoids displayed a synergistic sensitization of cells to chemotherapeutic drugs implying targeting PyMet can overcome chemoresistance in cancer.

The study highlights the complex signaling and metabolic cascades governing pyrimidine metabolism and its role in chemoresistance, and thereby providing an effective tool for advancing PyMet targeting strategy in cancer. The analysis as an accessible resource is available at: www.pype.compbio.sdu.dk