The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity

PLoS Biol. 2017 Dec 7;15(12):e2002940. doi: 10.1371/journal.pbio.2002940. eCollection 2017 Dec.

Abstract

The mammalian circadian clock and the cell cycle are two major biological oscillators whose coupling influences cell fate decisions. In the present study, we use a model-driven experimental approach to investigate the interplay between clock and cell cycle components and the dysregulatory effects of RAS on this coupled system. In particular, we focus on the Ink4a/Arf locus as one of the bridging clock-cell cycle elements. Upon perturbations by the rat sarcoma viral oncogene (RAS), differential effects on the circadian phenotype were observed in wild-type and Ink4a/Arf knock-out mouse embryonic fibroblasts (MEFs), which could be reproduced by our modelling simulations and correlated with opposing cell cycle fate decisions. Interestingly, the observed changes can be attributed to in silico phase shifts in the expression of core-clock elements. A genome-wide analysis revealed a set of differentially expressed genes that form an intricate network with the circadian system with enriched pathways involved in opposing cell cycle phenotypes. In addition, a machine learning approach complemented by cell cycle analysis classified the observed cell cycle fate decisions as dependent on Ink4a/Arf and the oncogene RAS and highlighted a putative fine-tuning role of Bmal1 as an elicitor of such processes, ultimately resulting in increased cell proliferation in the Ink4a/Arf knock-out scenario. This indicates that the dysregulation of the core-clock might work as an enhancer of RAS-mediated regulation of the cell cycle. Our combined in silico and in vitro approach highlights the important role of the circadian clock as an Ink4a/Arf-dependent modulator of oncogene-induced cell fate decisions, reinforcing its function as a tumour-suppressor and the close interplay between the clock and the cell cycle network.

MeSH terms

  • Animals
  • Cell Cycle / genetics
  • Cell Differentiation / genetics
  • Cells, Cultured
  • Circadian Clocks / genetics*
  • Cyclin-Dependent Kinase Inhibitor p16 / genetics*
  • Embryo, Mammalian
  • Gene Expression Regulation, Developmental
  • Genetic Loci / physiology*
  • Mice
  • Mice, Knockout
  • ras Proteins / metabolism
  • ras Proteins / physiology*

Substances

  • Cdkn2a protein, mouse
  • Cyclin-Dependent Kinase Inhibitor p16
  • ras Proteins

Grant support

Deutsche Krebshilfe https://www.krebshilfe.de/ (grant number 110678) funded the work in CS’s laboratory. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. German Federal Ministry of Education and Research (BMBF) https://www.bmbf.de/ (grant number eBio-CIRSPLICE - FKZ031A316) funded the work in AR’s laboratory as well as RE, NG, JM, LF, YL and MA. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Berlin School of Integrative Oncology (BSIO) of the Charité – Universitätsmedizin Berlin http://www.bsio-cancerschool.de/ provided additional funding to NG and LF. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Jinan Huaiyin Hospital of Shandong Province http://www.jnhyyy.com/ provided additional funding to YL. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutsche Forschungsgemeinschaft http://www.dfg.de/ (grant number TRR186/A17) funded the work in AK’s laboratory. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.