Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation

Abstract

BackgroundActivating mutations in KRAS frequently occur in colorectal cancer (CRC) patients, leading to resistance to EGFR-targeted therapies.MethodsTo better understand the cellular reprogramming which occurs in mutant KRAS cells, we have undertaken a systems-level analysis of four CRC cell lines which express either wild type (wt) KRAS or the oncogenic KRASG13D allele (mtKRAS).ResultsRNAseq revealed that genes involved in ribosome biogenesis, mRNA translation and metabolism were significantly upregulated in mtKRAS cells. Consistent with the transcriptional data, protein synthesis and cell proliferation were significantly higher in the mtKRAS cells. Targeted metabolomics analysis also confirmed the metabolic reprogramming in mtKRAS cells. Interestingly, mtKRAS cells were highly transcriptionally responsive to EGFR activation by TGFα stimulation, which was associated with an unexpected downregulation of genes involved in a range of anabolic processes. While TGFα treatment strongly activated protein synthesis in wtKRAS cells, protein synthesis was not activated above basal levels in the TGFα-treated mtKRAS cells. This was likely due to the defective activation of the mTORC1 and other pathways by TGFα in mtKRAS cells, which was associated with impaired activation of PKB signalling and a transient induction of AMPK signalling.ConclusionsWe have found that mtKRAS cells are substantially rewired at the transcriptional, translational and metabolic levels and that this rewiring may reveal new vulnerabilities in oncogenic KRAS CRC cells that could be exploited in future.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

“…Likewise, our results that phosphorylation changes contribute to PPIN rewiring may "repurpose" kinase inhibitors as PPIN rewiring agents. We recently showed that mtKRAS also profoundly changes the metabolic and transcriptional landscapes of CRC cells 53 confirming that mtKRAS widely affects cellular regulation on different levels. Surprisingly, our analysis shows that a low-level expression of mtKRAS is compatible with normal (i.e., untransformed) biochemical and biological behavior.…”

Ribosome Biogenesis Alterations in Colorectal Cancer

“…Although it is well documented that ribosome biogenesis can be controlled by growth factor receptors through MAPK/RAS/signaling [52,91] and that constitutive activation of KRAS represents a major determinant of some CRC subtypes, only few studies have explored the contribution of the oncogenic RAS pathway in ribosome biogenesis-mediated colorectal tumorigenesis. Human colorectal cancer cell lines with constitutive KRAS activation display a gene signature enriched in ribosome biogenesis and translation factors [92]. A recent report showed that the cysteine protease calpain-2 is involved in the inhibition of 47S pre-rRNA biogenesis as well as in the disruption of nucleolar integrity in human CRC DLD-1 cells [93].…”

Targeting Protein Synthesis in Colorectal Cancer

“…The second-most common mutation in CRC is found in KRAS, leading to constitutively active MAPK signaling, which is also implicated in the regulation of rDNA synthesis [67]. Additionally, CRC cells with mutant KRAS show increased expression of genes involved in ribosome biogenesis and mRNA translation; this is associated with enhanced protein synthesis in CRC cells as compared to cells with wild-type KRAS [68]. Finally, the mTOR signaling pathway is a master regulator of ribosome biogenesis and is highly deregulated in CRC [69].…”