Differential Ribosome Codon Reading Reveals Limiting Amino Acids

The shortage of certain amino acids can restrict tumor growth, with different tumor types depending on specific amino acids for growth and survival. Asparagine deprivation therapy with L-asparaginase has been utilized to treat patients with acute lymphoblastic leukemia, serving as a proof of concept for therapies targeting amino acid vulnerabilities. To determine which amino acids are limiting in specific tumors, Loayza-Puch, Rooijers, and colleagues developed a differential ribosome codon reading method (termed diricore) using ribosome profiling measurements to detect the availability of amino acids for protein synthesis. This approach used global ribosome occupancy to identify limiting amino acids. In cancer cells, L-asparaginase treatment resulted in a specific diricore signal at asparagine codons, an increase in the enzyme responsible for synthesizing asparagine, and a reduction in aminoacylated asparagine-tRNAs. Diricore identified robust signals at methionine and proline codons in clear cell renal cell carcinomas (ccRCC) compared to normal tissues. The methionine signal was due to ribosomes at the ATG start codon, indicating a global increase in the rate of translation initiation, whereas the proline signal suggested a limited availability of proline in the tumors. Consistent with this idea, ccRCCs had high levels of non-aminoacylated proline-tRNAs and high expression of pyrroline-5-carboxylate reductase 1 (PYCR1), an enzyme involved in proline synthesis. PYCR1 upregulation serves as a compensatory mechanism to maintain tumor growth. Knockdown of PYCR1 increased the level of non-aminoacylated proline-tRNAs and reduced ccRCC cell proliferation under conditions of limited proline availability, which were reversed by the addition of proline. Further, in xenografts of breast cancer cells with high PYCR1 expression, diricore signals were strong at proline codons, and PYCR1 knockdown suppressed cell growth in vivo. Taken together, these findings indicate that diricore is able to identify limiting amino acids that are required for tumor growth, and suggest that this method may detect amino acid vulnerabilities that may be rationally targeted in cancer therapy.

Loayza-Puch F, Rooijers K, Buil LCM, Zijlstra J, Oude Vrielink JF, Lopes R, et al. Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. Nature 2016;530:490–4.

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