Abstract
Simple SummaryTranslation occurs in the cell both through cytoplasmic and mitochondrial ribosomes, respectively translating mRNAs encoded by the nuclear and the mitochondrial genome. Here we found that the silencing of DHX30, an RNA-binding protein that we previously studied for its role in p53-dependent apoptosis, enhances the translation of mRNAs coding for cytoplasmic ribosomal proteins while reducing that of the mRNAs encoding for mitoribosomal proteins. This coordination of the cytoplasmic and mitochondrial translation machineries affected both cell proliferation and energy metabolism, suggesting an important role for this mechanism in determining the fitness of cancer cells. By integrating multiple datasets, we identified a gene signature that will represent a starting point to assess the prognostic value of this mechanism in cancer. We thus propose DHX30 as a potential vulnerability in cancer cells that could be exploited to develop novel therapeutic strategies.DHX30 was recently implicated in the translation control of mRNAs involved in p53-dependent apoptosis. Here, we show that DHX30 exhibits a more general function by integrating the activities of its cytoplasmic isoform and of the more abundant mitochondrial one. The depletion of both DHX30 isoforms in HCT116 cells leads to constitutive changes in polysome-associated mRNAs, enhancing the translation of mRNAs coding for cytoplasmic ribosomal proteins while reducing the translational efficiency of the nuclear-encoded mitoribosome mRNAs. Furthermore, the depletion of both DHX30 isoforms leads to higher global translation but slower proliferation and lower mitochondrial energy metabolism. Isoform-specific silencing supports a role for cytoplasmic DHX30 in modulating global translation. The impact on translation and proliferation was confirmed in U2OS and MCF7 cells. Exploiting RIP, eCLIP, and gene expression data, we identified fourteen mitoribosome transcripts we propose as direct DHX30 targets that can be used to explore the prognostic value of this mechanism in cancer. We propose that DHX30 contributes to cell homeostasis by coordinating ribosome biogenesis, global translation, and mitochondrial metabolism. Targeting DHX30 could, thus, expose a vulnerability in cancer cells.
Highlights
The DHX30 RNA binding protein (RBP) is an ATP-dependent RNA helicase highly expressed in neural cells and somites during embryogenesis in mice
We previously identified DHX30 as a negative modulator of p53-dependent apoptosis, performing polysomal profiling followed by RNA-seq of HCT116 cells clones stably depleted for DHX30 and treated with the MDM2 inhibitor Nutlin [8]
We reanalyzed that dataset (GSE95024), complementing it by performing a total-cytoplasmic RNA profiling of the same cells by RNA-seq (GSE154065) and focusing on the comparison between DHX30-depleted cells and control HCT116 cells in the untreated condition. shRNAs led to about 80% reduction in DHX30 protein levels (Figure S1B,C,H)
Summary
The DHX30 RNA binding protein (RBP) is an ATP-dependent RNA helicase highly expressed in neural cells and somites during embryogenesis in mice It plays an important role in development and its homozygous deletion is embryonic lethal [1]. De novo missense mutations were identified in DHX30 in twelve unrelated patients affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment, and gait abnormalities [3,4] Those mutations caused amino acid changes in the highly conserved helicase motif, impairing the protein’s ATPase activity or RNA recognition. The depletion of DHX30 in HCT116 by stable shRNA increased the translation potential of mRNAs containing the CGPD motif, resulting in higher levels of apoptosis after p53 activation by Nutlin treatment, mimicking in part the apoptotic phenotype of SJSA1 cells [7]. Depleting DHX30 in HCT116 cells enhanced global translation but reduced cell proliferation, as confirmed in two other cancer cell line models
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