Post-transcriptional dysregulation precedes morphological transformation in chemically induced liver cancer

Abstract

DNA lesions impede RNA polymerase II, yet the transcriptional consequences of that stress are less understood than the lesions themselves. We reanalysed total RNA and matched whole genomes from 438 liver lesions across four divergent mouse backgrounds, one of them the separate species M. caroli, 428 of them induced by a single dose of diethylnitrosamine (DEN) and 10 arising spontaneously, together with untreated liver and, critically, histologically normal liver from treated, tumour-bearing animals (paired normal liver). Three post-transcriptional changes accompany transformation in every background. Canonical splicing efficiency falls by 3.6 to 4.8 percentage points, and in genes that acquire them, cancer-specific junctions account for a median of 20–25% of junctions and arise at weaker splice signals. Output shifts toward circular RNA: a five-method consensus pipeline identifies 56,418 recurrent backsplice junctions, 9,718 of them detected in all four backgrounds, with ∼2-fold enrichment in circRNA abundance and an expanded repertoire of distal configurations. Adenosine-to-inosine editing sites fall 2.2-to 3.8-fold, most steeply at intronic sites. Exposure changes not only these outputs but their coordination. In untreated C57BL/6J liver, splicing efficiency, mean relative backsplice span and editing co-vary positively (pairwise ρ +0.78 to +0.87). That coordination is lost in exposed tissue, and paired normal liver shows the same loss as tumour. Pooling conditions obscures the effect because opposing estimates cancel. In C57BL/6J, paired normal liver already shows tumour-like splicing, circRNA abundance and editing roughly eight months after one exposure, while backsplice architecture has begun to reorganise. These samples carry a median of 337 callable somatic single-nucleotide variants against 78,843 in tumours and show no elevation of Mki67 or cell-cycle programmes. The post-transcriptional phenotype is therefore a durable property of damaged tissue established before morphological transformation.