title: Tumour-specific proline vulnerability uncovered by differential ribosome codon reading.
abstract: 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. In addition, successful therapies using L-asparaginase-induced asparagine deprivation have been developed for acute lymphoblastic leukaemia. However, a tailored detection system for measuring restrictive amino acids in each tumour is currently not available. Here we harness ribosome profiling 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, 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.
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Fabricio
authors.initials: F
authors.lastname: Loayza-Puch
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Koos
authors.initials: K
authors.lastname: Rooijers
authors.affiliation: Department of Bio-Pharmacology/ Mouse Cancer Clinic, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Levi C M
authors.initials: LC
authors.lastname: Buil
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Jelle
authors.initials: J
authors.lastname: Zijlstra
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Joachim F
authors.initials: JF
authors.lastname: Oude Vrielink
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Rui
authors.initials: R
authors.lastname: Lopes
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Alejandro Pineiro
authors.initials: AP
authors.lastname: Ugalde
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Pieter
authors.initials: P
authors.lastname: van Breugel
authors.affiliation: Core Facility Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Hofland
authors.affiliation: Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Jelle
authors.initials: J
authors.lastname: Wesseling
authors.affiliation: Department of Bio-Pharmacology/ Mouse Cancer Clinic, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Olaf
authors.initials: O
authors.lastname: van Tellingen
authors.affiliation: Division of Surgical Oncology, Department of Urology The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Axel
authors.initials: A
authors.lastname: Bex
authors.affiliation: Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.|Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
authors.forename: Reuven
authors.initials: R
authors.lastname: Agami
mesh_terms: D000818:Animals; D001215:Asparaginase / Q000378:metabolism; D001216:Asparagine / Q000235:genetics / Q000378:metabolism; D001217:Aspartate-Ammonia Ligase / Q000378:metabolism; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D003062:Codon / Q000235:genetics*; D005260:Female; D055786:Gene Knockout Techniques; D006801:Humans; D007680:Kidney Neoplasms / Q000378:metabolism* / Q000473:pathology; D051379:Mice; D011392:Proline / Q000096:biosynthesis / Q000172:deficiency / Q000378:metabolism*; D014176:Protein Biosynthesis / Q000235:genetics; D011762:Pyrroline Carboxylate Reductases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D000097502:delta-1-Pyrroline-5-Carboxylate Reductase
chemical_list: D001215:Asparaginase; D001216:Asparagine; D001217:Aspartate-Ammonia Ligase; D003062:Codon; D011392:Proline; D011762:Pyrroline Carboxylate Reductases; D000097502:delta-1-Pyrroline-5-Carboxylate Reductase