KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells

TL;DR

KRAS silencing in colorectal cancer cells leads to chromatin reorganization and transcriptional changes, enabling drug tolerance.

Contribution

The study reveals a novel mechanism of drug tolerance through global chromatin reorganization, not specific gene mutations.

Findings

KRAS-dependent cells undergo G0/G1 arrest and show a quiescent transcriptomic signature after KRAS silencing.

Chromatin reorganization includes changes in euchromatin/heterochromatin states and topologically associating domains.

Transcriptional alterations over time link chromatin changes to increased transcriptional reprogramming capacity.

Abstract

Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity

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