Up-regulated transcriptional regulators in mutant RAS gene signatures: a time-resolved multi-omics study in generic epithelial cell models

Kasack, K.; Metzger, P.; Koch, H.; Klinger, B.; Malek, A.; Tchernitsa, O.; Gross, A.; Wruck, W.; Györffy, B.; Küster, B.; Sers, C.; Börries, M.; Schäfer, R.

doi:10.1101/2024.06.04.597297

bioRxiv · 10.1101/2024.06.04.597297

Up-regulated transcriptional regulators in mutant RAS gene signatures: a time-resolved multi-omics study in generic epithelial cell models

Kasack, K.·Metzger, P.·Koch, H.·Klinger, B.·Malek, A.·Tchernitsa, O.·Gross, A.·Wruck, W.·Györffy, B.·Küster, B.·Sers, C.·Börries, M.·Schäfer, R.

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Abstract

The expression of mutated RAS genes drives extensive transcriptome alterations. Perturbation experiments have shown that the transcriptional responses to downstream effector pathways are partially unique and non-overlapping, suggesting a modular organization of the RAS-driven expression program. However, the relationship between individual deregulated transcription factors and the entire cancer cell-specific genetic program is poorly understood. To identify potential regulators of the RAS/MAPK-dependent fraction of the genetic program, we monitored transcriptome and proteome changes following conditional, time-resolved expression of mutant HRASG12V in human epithelial cells during neoplastic conversion. High mobility group AT hook2 (HMGA2), an architectural chromatin modulating protein and oncofetal tumour marker, was recovered as the earliest upregulated transcription factor. Knock-down of HMGA2 reverted anchorage-independent growth and epithelial-mesenchymal transition not only in HRAS-transformed cells but also in an independent, KRASG12V-driven rat epithelial model. Moreover, HMGA2 silencing reverted the deregulated expression of 60% of RAS-responsive target genes. These features qualify HMGA2 as a master regulator of mutant RAS-driven expression patterns. The delayed deregulation of FOSL1, ZEB1 and other transcription factors with known oncogenic activity suggests that HMGA2 acts in concert with a network of regulatory factors to trigger full neoplastic conversion. Although transcription factors are considered difficult to drug, the central role of HMGA2 in the transcription factor network as well as its relevance for cancer prognosis has motivated attempts to block its function using small molecular weight compounds. The further development of direct HMGA2 antagonists may prove useful in cancer cells that have developed resistance to signalling chain inhibition.

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Kasack, K., Metzger, P., Koch, H., Klinger, B., Malek, A., Tchernitsa, O., Gross, A., Wruck, W., Györffy, B., Küster, B., Sers, C., Börries, M., Schäfer, R.. 2024-06-06. Up-regulated transcriptional regulators in mutant RAS gene signatures: a time-resolved multi-omics study in generic epithelial cell models. https://doi.org/10.1101/2024.06.04.597297

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