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Cancer-associated mutations in the ribosomal protein L5 gene dysregulate the HDM2/p53-mediated ribosome biogenesis checkpoint

Oncogene volume 39, pages 3443–3457 (2020)Cite this article

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Abstract

Perturbations in ribosome biogenesis have been associated with cancer. Such aberrations activate p53 through the RPL5/RPL11/5S rRNA complex-mediated inhibition of HDM2. Studies using animal models have suggested that this signaling pathway might constitute an important anticancer barrier. To gain a deeper insight into this issue in humans, here we analyze somatic mutations in RPL5 and RPL11 coding regions, reported in The Cancer Genome Atlas and International Cancer Genome Consortium databases. Using a combined computational and statistical approach, complemented by a range of biochemical and functional analyses in human cancer cell models, we demonstrate the existence of several mechanisms by which RPL5 mutations may impair wild-type p53 upregulation and ribosome biogenesis. Unexpectedly, the same approach provides only modest evidence for a similar role of RPL11, suggesting that RPL5 represents a preferred target during human tumorigenesis in cancers with wild-type p53. Furthermore, we find that several functional cancer-associated RPL5 somatic mutations occur as rare germline variants in general population. Our results shed light on the so-far enigmatic role of cancer-associated mutations in genes encoding ribosomal proteins, with implications for our understanding of the tumor suppressive role of the RPL5/RPL11/5S rRNA complex in human malignancies.

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Fig. 1: Assessment of positive selection of RPL5 and RPL11 missense mutations across the combined TCGA/ICGC pan-cancer cohort.
Fig. 2: Functional characterization of clustered RPL5 missense mutations.
Fig. 3: The effects of clustered RPL5 cancer-associated mutations on wt p53 protein expression.
Fig. 4: Assessment of the impact of representative cancer-associated RPL5 or RPL11 missense mutations on RPL5 or RPL11 incorporation into ribosomes.
Fig. 5: A model explaining potential functional impacts of cancer-associated RPL5 mutations.

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Acknowledgements

We are grateful to Drs George Thomas and Jonathan Ashwell for critical review of the manuscript and helpful suggestions. We would also like to thank Davor Mihalek for his expert assistance in preparing the supplementary movie as well as Miljana Uzelac and Ivana Matušić for their technical help. The authors sincerely thank Dr. Moshe Oren (Weizmann Institute of Science) for providing the pCMV-HA3-HDM1B expression plasmid. The pCHDM1A-HDM2 expression plasmid was kindly provided by Dr. Karen Vousden (Francis Crick Institute). SV laboratory was supported with grants from the Croatian Science Foundation (09.01/220 and 2079 to SV), the Scientific Center of Excellence for Reproductive and Regenerative Medicine (KK.01.1.1.01.0008 to SV), the University of Rijeka (uniri-biomed-18-206 to SV). JB laboratory is funded by grants from the Swedish Cancer Society (grant number: 170176) and the Swedish Research Council (VR-MH 2014-46602-117891-30), the Novo Nordisk Foundation (no. 16854), the Danish National Research Foundation (project CARD: no. DNRF125), the Danish Cancer Society (R204-A12617), and the Lundbeck Foundation.

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  1. Department of Molecular Medicine and Biotechnology, University of Rijeka, Faculty of Medicine, Rijeka, 51000, Croatia

    Ines Oršolić, Slađana Bursać, Deana Jurada, Ivana Mihalek & Siniša Volarević

  2. Department of Medical Chemistry and Biochemistry, University of Split, School of Medicine, Split, 21000, Croatia

    Irena Drmić Hofman

  3. Institute for Oral Biology, Faculty of Dentistry, University of Oslo, PB 1052 Blindern, Oslo, N0316, Norway

    Zlatko Dembić

  4. Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, 17176, Stockholm, Sweden

    Jiri Bartek

  5. The Danish Cancer Society Research Center, DK-2100, Copenhagen, Denmark

    Jiri Bartek

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  1. Ines Oršolić
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Oršolić, I., Bursać, S., Jurada, D. et al. Cancer-associated mutations in the ribosomal protein L5 gene dysregulate the HDM2/p53-mediated ribosome biogenesis checkpoint. Oncogene 39, 3443–3457 (2020). https://doi.org/10.1038/s41388-020-1231-6

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