Epigenomic reprogramming of repetitive noncoding RNAs and IFN-stimulated genes by mutant KRAS

Abstract

RAS genes are the most frequently mutated oncogenes in cancer. However, the effects of oncogenic RAS signaling on the noncoding transcriptome are unclear. We analyzed the transcriptomes of human airway epithelial cells transformed with mutant KRAS to define the landscape of KRAS-regulated noncoding RNAs. We found that oncogenic KRAS upregulates noncoding transcripts throughout the genome, many of which arise from transposable elements. These repetitive noncoding RNAs exhibit differential RNA editing in single cells, are released in extracellular vesicles, and are known targets of KRAB zinc-finger proteins, which are broadly down-regulated in mutant KRAS cells and lung adenocarcinomas. Moreover, mutant KRAS induces IFN-stimulated genes through both epigenetic and RNA-based mechanisms. Our results reveal that mutant KRAS remodels the noncoding transcriptome through epigenomic reprogramming, expanding the scope of genomic elements regulated by this fundamental signaling pathway and revealing how mutant KRAS induces an intrinsic IFN-stimulated gene signature often seen in ADAR-dependent cancers.

Extracellular RNA signatures of mutant KRAS(G12C) lung adenocarcinoma cells

“…Consistent with our previous work 8 , noncoding RNAs are strongly enriched in EVs. We also observed a pronounced increase in library complexity upon the inclusion of TE annotations, with a significant amount of TE RNAs present in the secreted exRNA population.…”

“…TE RNAs are among the most abundantly expressed transcripts in the human genome 26 , and TE dysregulation has been observed in numerous cancers 27,28 . Moreover, oncogenic KRAS signaling specifically leads to TE RNA dysregulation through epigenomic reprogramming 8 . To determine the dynamics of TE RNA secretion in the context of KRAS(G12C) signaling, we included TE annotations in our RNA-seq analysis.…”

“…These noncoding RNAs include long noncoding RNAs (lncRNAs), transposable element RNAs (TE RNAs), microRNAs, and other classes of RNAs that are involved in a diverse array of biological processes [2][3][4][5][6] . A subset of lncRNAs and TE RNAs are regulated by fundamental signaling pathways that are dysregulated during cancer formation, such as the RAS signaling pathway 7,8 . Moreover, these noncoding RNAs are preferentially secreted in extracellular vesicles (EVs) 8 , which are membrane-bound, nanometer-sized vesicles that protect extracellular RNAs (exRNAs) from degradation 9 .…”

“…A subset of lncRNAs and TE RNAs are regulated by fundamental signaling pathways that are dysregulated during cancer formation, such as the RAS signaling pathway 7,8 . Moreover, these noncoding RNAs are preferentially secreted in extracellular vesicles (EVs) 8 , which are membrane-bound, nanometer-sized vesicles that protect extracellular RNAs (exRNAs) from degradation 9 . Many studies have described the biomarker potential of exRNAs for cancer diagnosis 10 , but the clinical utility of mutation-specific exRNA signatures remains unclear.…”

Transposable element RNA dysregulation in mutant KRAS(G12C) 3D lung cancer spheroids

“…Transposable element (TE) RNAs are recurrently dysregulated in the context of cancer 1 . In mutant KRAS lung cancer cells, KRAB zinc-finger (KZNF) genes are broadly downregulated, leading to the aberrant upregulation of TE RNAs derived from LINE, SINE, and LTR elements 2,3 . In addition to TE RNAs, long noncoding RNAs (lncRNAs) are also coordinately regulated with RAS signaling genes 4 , and their expression patterns are similarly altered in many cancers 5-8 .…”