Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

• Published in: Nature (London) Vol. 530; no. 7591; pp. 490 - 494
• Main Authors: Loayza-Puch, Fabricio, Rooijers, Koos, Buil, Levi C. M., Zijlstra, Jelle, F. Oude Vrielink, Joachim, Lopes, Rui, Ugalde, Alejandro Pineiro, van Breugel, Pieter, Hofland, Ingrid, Wesseling, Jelle, van Tellingen, Olaf, Bex, Axel, Agami, Reuven
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.02.2016; Nature Publishing Group
• Subjects: 631/1647/514/1949; 631/337/574; 631/67/2327; Amino acids; Animals; Asparaginase - metabolism; Asparagine - genetics; Asparagine - metabolism; Aspartate-Ammonia Ligase - metabolism; Breast cancer; Breast Neoplasms - metabolism; Breast Neoplasms - pathology; Carcinoma, Ductal, Breast - metabolism; Carcinoma, Ductal, Breast - pathology; Cell growth; Cell Line, Tumor; Cell Proliferation; Codon; Codon - genetics; delta-1-Pyrroline-5-Carboxylate Reductase; Enzymes; Female; Gene expression; Gene Knockout Techniques; Genetic aspects; Humanities and Social Sciences; Humans; Kidney cancer; Kidney Neoplasms - metabolism; Kidney Neoplasms - pathology; Kidneys; letter; Leukemia; Metabolism; Mice; multidisciplinary; Physiological aspects; Proline; Proline - biosynthesis; Proline - deficiency; Proline - metabolism; Protein biosynthesis; Protein Biosynthesis - genetics; Protein synthesis; Pyrroline Carboxylate Reductases - deficiency; Pyrroline Carboxylate Reductases - genetics; Pyrroline Carboxylate Reductases - metabolism; Ribonucleic acid; Ribosomes; Ribosomes - metabolism; RNA; Science; Tumors; Netherlands
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature16982

Tumours can require certain amino acids for their proliferation, and the diricore method described here helps to identify such restrictive amino acids; using this method in kidney cancer tissue and breast carcinoma cells, the authors observe an association between proline deficiency and upregulation of PYCR1, an enzyme required for proline synthesis. Amino acid deprivation as an antitumour weapon Tumours can require certain amino acids for their proliferation. To identify such restrictive amino acids, Reuven Agami and colleagues have developed a ribosome profiling-based method — termed diricore — to assess the availability of specific amino acids for protein synthesis. Using this method in kidney cancer tissue, the authors observe an association between proline deficiency and upregulation of PYRC1, an enzyme required for proline synthesis. Application of diricore to breast carcinoma cells also revealed proline deficiency. In growth-limiting conditions, PYRC1 was required to maintain tumorigenic growth. These results illustrate an approach to identifying critical amino acid vulnerabilities that can be used therapeutically to target key metabolic pathways. Tumour growth and metabolic adaptation may restrict the availability of certain amino acids for protein synthesis. It has recently been shown that certain types of cancer cells depend on glycine, glutamine, leucine and serine metabolism to proliferate and survive 1 , 2 , 3 , 4 . In addition, successful therapies using L -asparaginase-induced asparagine deprivation have been developed for acute lymphoblastic leukaemia 5 . However, a tailored detection system for measuring restrictive amino acids in each tumour is currently not available. Here we harness ribosome profiling 6 for sensing restrictive amino acids, and develop diricore, a procedure for differential ribosome measurements of codon reading. We first demonstrate the functionality and constraints of diricore using metabolic inhibitors and nutrient deprivation assays. Notably, treatment with L -asparaginase elicited both specific diricore signals at asparagine codons and high levels of asparagine synthetase (ASNS). We then applied diricore to kidney cancer and discover signals indicating restrictive proline. As for asparagine, this observation was linked to high levels of PYCR1, a key enzyme in proline production 7 , suggesting a compensatory mechanism allowing tumour expansion. Indeed, PYCR1 is induced by shortage of proline precursors, and its suppression attenuated kidney cancer cell proliferation when proline was limiting. High PYCR1 is frequently observed in invasive breast carcinoma. In an in vivo model system of this tumour, we also uncover signals indicating restrictive proline. We further show that CRISPR-mediated knockout of PYCR1 impedes tumorigenic growth in this system. Thus, diricore has the potential to reveal unknown amino acid deficiencies, vulnerabilities that can be used to target key metabolic pathways for cancer treatment.