Exploiting tumor-specific amino acid vulnerabilities to improve aggressive breast cancer treatment

• Applicant: Fabricio Loayza-Puch, Ph.D.
• Subject Area: Cell Biology ; General Genetics and Functional Genome Biology ; Biochemistry
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 504774163

The demand for amino acids for protein synthesis, nucleotide, and energy production, is very high in the growing tumor. The metabolic changes a tumor undergoes to adapt to deregulated growth represent vulnerabilities that can be exploited for therapy. This was successfully demonstrated in past years for the amino acid asparagine, resulting in a very effective combined treatment of chemotherapy and L-asparaginase in acute lymphoblastic leukemia (ALL). To exploit metabolic vulnerabilities related to amino acids one needs to overcome the major obstacle of identifying which amino acid is restrictive to the tumor. It is important to realize that amino acid demand depends on many genetic and environmental factors of the growing tumor in the organism – such as extracellular amino acid, amino acid uptake, production and catabolism, protein synthesis rate, the divergent use of amino acid for energy, and tRNA levels and their accessibility for protein synthesis. It is therefore insufficient to measure free amino acid levels in tumors or body fluids in order to identify such vulnerabilities in a given cancer. We recently developed a novel measurement approach that senses restrictive amino acid in cells. We named it diricore (differential ribosome codon reading), and it is based on ribosome profiling technology. Using diricore we already uncovered shortage in proline in breast cancer cell lines expanded in vivo, and in human kidney tumors. Intriguingly, proline shortage was linked to high levels of PYCR1, a key enzyme in proline production, and its knockout compromised tumor growth in vivo, demonstrating the importance of identifying amino acid shortages in growing tumors. In preliminary work, using the diricore technology, we found that in response to conventional therapy cancer cells experience a limitation in arginine, an amino acid that is tightly linked to polyamine metabolism. Here, we propose to uncover novel deficiencies in amino acid availabilities in response to mitotic inhibition using the diricore technology platform and exploit them for better cancer killing. Following diricore analysis, we will setup experiments to elucidate relevant metabolic pathways using genetic and biochemical tools, such as CRISPR-Cas9 knockouts, RNAi knockdowns, and overexpression vectors. If appropriate, also inhibitors of metabolic pathways will be employed. The identified amino acid shortages and their links to changes in metabolic genes will serve as signatures for diagnosis and guideline for therapy. Moreover, our findings here will offer ways to make the treatment of aggressive tumors more effective.

• DFG Programme: Research Grants